diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 0718b7848..421d9b59f 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -12,6 +12,8 @@ jobs: if: github.event.pull_request.head.repo.fork == false steps: - uses: actions/checkout@v2 + with: + fetch-depth: 0 - uses: actions/setup-python@v2 with: python-version: 3.x diff --git a/.github/workflows/test-suite.yml b/.github/workflows/test-suite.yml index 062440244..5a0390dc4 100644 --- a/.github/workflows/test-suite.yml +++ b/.github/workflows/test-suite.yml @@ -17,15 +17,6 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: webfactory/ssh-agent@v0.4.1 - with: - ssh-private-key: ${{ secrets.FORCED_PHOT_DEPLOY_KEY }} - - - name: Use ssh instead of https when cloning from github - run: | - git config --global url.ssh://git@github.com/.insteadOf https://github.com/; - git config --global core.sshCommand 'ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no' - - name: Create dev database uses: ./.github/actions/create-dev-database with: @@ -68,7 +59,7 @@ jobs: vast vastpsw vastdb - name: Make relevant directories - run: mkdir pipeline-runs && mkdir reference-surveys + run: mkdir pipeline-runs - name: Download regression test data run: bash -e ./download.sh diff --git a/.gitignore b/.gitignore index 2046cb28b..aa7139680 100644 --- a/.gitignore +++ b/.gitignore @@ -108,3 +108,4 @@ celerybeat-schedule docker/ .dockerignore .idea/ +mypy.ini diff --git a/CHANGELOG.md b/CHANGELOG.md index 676324360..7cb633e90 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,13 +1,38 @@ -# Change Log +# Changelog All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), with an added `List of PRs` section and links to the relevant PRs on the individal updates. This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased](https://github.com/askap-vast/vast-pipeline/compare/0.2.0...HEAD) +## [Unreleased](https://github.com/askap-vast/vast-pipeline/compare/v1.0.0...HEAD) #### Added +#### Changed + +#### Fixed + +#### Removed + +#### List of PRs + +## [1.0.0](https://github.com/askap-vast/vast-pipeline/releases/v1.0.0) (2021-05-21) + +#### Added + +- When searching by source names, any "VAST" prefix on the name will be silently removed to make searching for published VAST sources easier [#536](https://github.com/askap-vast/vast-pipeline/pull/536). +- Added acknowledgements and help section to docs [#535](https://github.com/askap-vast/vast-pipeline/pull/535). +- Added `vast_pipeline/_version.py` to store the current software version and updated release documentation [#532](https://github.com/askap-vast/vast-pipeline/pull/532). +- Added created and last updated dates to doc pages using mkdocs-git-revision-date-localized-plugin [#514](https://github.com/askap-vast/vast-pipeline/pull/514). +- Added support for glob expressions when specifying input files in the run config file [#504](https://github.com/askap-vast/vast-pipeline/pull/504) +- Added `DEFAULT_AUTO_FIELD` to `settings.py` to silence Django 3.2 warnings [#507](https://github.com/askap-vast/vast-pipeline/pull/507) +- Added lightgallery support for all images in the documentation [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Added new entries in the documentation contributing section [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Added new entries in the documentation FAQ section [#491](https://github.com/askap-vast/vast-pipeline/pull/491). +- Added new home page for documentation [#491](https://github.com/askap-vast/vast-pipeline/pull/491). +- Added dark mode switch on documentation [#487](https://github.com/askap-vast/vast-pipeline/pull/487). +- Added .env file information to documentation [#487](https://github.com/askap-vast/vast-pipeline/pull/487). +- Added further epoch based association information to documentation page [#487](https://github.com/askap-vast/vast-pipeline/pull/487). - Added script to auto-generate code reference documentation pages [#480](https://github.com/askap-vast/vast-pipeline/pull/480). - Added code reference section to documentation [#480](https://github.com/askap-vast/vast-pipeline/pull/480). - Added new pages and sections to documentation [#471](https://github.com/askap-vast/vast-pipeline/pull/471) @@ -24,6 +49,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Changed +- Changed source naming convention to `Jhhmmss.s(+/-)ddmmss` to match VAST-P1 paper (Murphy, et al. 2021) convention [#536](https://github.com/askap-vast/vast-pipeline/pull/536) +- Updated npm packages to resolve dependabot security alert [#533](https://github.com/askap-vast/vast-pipeline/pull/533). +- Updated homepage text to reflect new features and documentation [#534](https://github.com/askap-vast/vast-pipeline/pull/534). +- Changed layout of source detail page [#526](https://github.com/askap-vast/vast-pipeline/pull/526). +- Updated mkdocs-material to 7.1.4 for native creation date support [#518](https://github.com/askap-vast/vast-pipeline/pull/518). +- Updated developing docs to specify the main development branch as dev instead of master [#521](https://github.com/askap-vast/vast-pipeline/pull/521). +- Updated tests to account for relation fix [#510](https://github.com/askap-vast/vast-pipeline/pull/510). +- All file examples in docs are now enclosed in an example admonition [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Further changes to layout of documentation [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Changed arrow file generation from `vaex` to `pyarrow` [#503](https://github.com/askap-vast/vast-pipeline/pull/503). +- Changed layout of documentation to use tabs [#491](https://github.com/askap-vast/vast-pipeline/pull/491). +- Dependabot: Bump y18n from 3.2.1 to 3.2.2 [#482](https://github.com/askap-vast/vast-pipeline/pull/482). +- Replaced run config .py format with .yaml [#483](https://github.com/askap-vast/vast-pipeline/pull/483). +- Changed docs VAST logo to icon format to avoid stretched appearence [#487](https://github.com/askap-vast/vast-pipeline/pull/487). - Bumped Browsersync from 2.26.13 to 2.26.14 [#481](https://github.com/askap-vast/vast-pipeline/pull/481). - Dependabot: Bump prismjs from 1.22.0 to 1.23.0 [#469](https://github.com/askap-vast/vast-pipeline/pull/469). - Changed non-google format docstrings to google format [#480](https://github.com/askap-vast/vast-pipeline/pull/480). @@ -42,6 +81,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Fixed +- Fixed the broken link to the image detail page on measurement detail pages [#528](https://github.com/askap-vast/vast-pipeline/pull/528). +- Fixed simbad and ned external search results table nan values [#523](https://github.com/askap-vast/vast-pipeline/pull/523). +- Fixed inaccurate total results reported by some paginators [#517](https://github.com/askap-vast/vast-pipeline/pull/517). +- Removed excess whitespace from coordinates that get copied to the clipboard [#515](https://github.com/askap-vast/vast-pipeline/pull/515) +- Fixed rogue relations being created during one-to-many functions [#510](https://github.com/askap-vast/vast-pipeline/pull/510). +- Fixed JS9 regions so that the selected source components are always on top [#508](https://github.com/askap-vast/vast-pipeline/pull/508) +- Fixed docstring in config.py [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Fixed arrow files being generated via the website [#503](https://github.com/askap-vast/vast-pipeline/pull/503). +- Fixed a bug that returned all sources when performing a cone search where one of the coords = 0 [#501](https://github.com/askap-vast/vast-pipeline/pull/501) +- Fixed the missing hover tool for lightcurve plots of non-variable sources [#493](https://github.com/askap-vast/vast-pipeline/pull/493) - Fixed the default Dask multiprocessing context to "fork" [#472](https://github.com/askap-vast/vast-pipeline/pull/472). - Fixed Selavy catalogue ingest to discard the unit row before reading the data [#473](https://github.com/askap-vast/vast-pipeline/pull/473). - Fixed initial job processing from the UI [#466](https://github.com/askap-vast/vast-pipeline/pull/466). @@ -56,6 +105,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### Removed +- Removed `SURVEYS_WORKING_DIR` from settings and env file [#538](https://github.com/askap-vast/vast-pipeline/pull/538). +- Removed `default_survey` from run configuration file [#538](https://github.com/askap-vast/vast-pipeline/pull/538). +- Removed importsurvey command and catalogue.py [#538](https://github.com/askap-vast/vast-pipeline/pull/538). +- Removed SurveySource, Survey and SurveySourceQuerySet models [#538](https://github.com/askap-vast/vast-pipeline/pull/538). +- Removed email and Slack links from docs footer [#535](https://github.com/askap-vast/vast-pipeline/pull/535). +- Removed bootstrap as the required version is bundled with startbootstrap-sb-admin-2 [#533](https://github.com/askap-vast/vast-pipeline/pull/533). +- Removed `docs/readme.md` softlink as it is no longer used [#494](https://github.com/askap-vast/vast-pipeline/pull/494). +- Removed `vaex-arrow` from the dependancies [#503](https://github.com/askap-vast/vast-pipeline/pull/503). - Removed `requirements/*.txt` files. Development dependency management moved to Poetry [#472](https://github.com/askap-vast/vast-pipeline/pull/472). - Removed `init-tools/init-db.sh` [#472](https://github.com/askap-vast/vast-pipeline/pull/472). - Removed `INSTALL.md`, `PROFILE.md` and `static/README.md` [#433](https://github.com/askap-vast/vast-pipeline/pull/433) @@ -63,6 +120,32 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), #### List of PRs +- [#538](https://github.com/askap-vast/vast-pipeline/pull/538) feat: Removed survey source models, commands and references. +- [#536](https://github.com/askap-vast/vast-pipeline/pull/536) feat: changed source naming convention. +- [#535](https://github.com/askap-vast/vast-pipeline/pull/535) doc: added help and acknowledgement doc page. +- [#534](https://github.com/askap-vast/vast-pipeline/pull/534) feat: Update homepage text. +- [#532](https://github.com/askap-vast/vast-pipeline/pull/532) feat, doc: Versioning. +- [#533](https://github.com/askap-vast/vast-pipeline/pull/533) dep: updated npm deps; removed bootstrap. +- [#528](https://github.com/askap-vast/vast-pipeline/pull/528) fix: fixed broken image detail link. +- [#526](https://github.com/askap-vast/vast-pipeline/pull/526) feat: Updated source detail page layout. +- [#518](https://github.com/askap-vast/vast-pipeline/pull/518) dep: Updated mkdocs-material for native creation date support. +- [#523](https://github.com/askap-vast/vast-pipeline/pull/523) fix: Fixed external search results table nan values. +- [#521](https://github.com/askap-vast/vast-pipeline/pull/521) doc: update doc related to default dev branch. +- [#517](https://github.com/askap-vast/vast-pipeline/pull/517) fix: pin djangorestframework-datatables to 0.5.1. +- [#515](https://github.com/askap-vast/vast-pipeline/pull/515) fix: remove linebreaks from coordinates. +- [#514](https://github.com/askap-vast/vast-pipeline/pull/514) dep: Added created and updated dates to doc pages. +- [#510](https://github.com/askap-vast/vast-pipeline/pull/510) fix: Fix rogue relations. +- [#508](https://github.com/askap-vast/vast-pipeline/pull/508) fix: Draw selected source components on top in JS9. +- [#504](https://github.com/askap-vast/vast-pipeline/pull/504) feat: Add glob expression support to yaml run config. +- [#507](https://github.com/askap-vast/vast-pipeline/pull/507) fix: set default auto field model. +- [#494](https://github.com/askap-vast/vast-pipeline/pull/494) doc, dep: Docs: Added lightgallery support, layout update, minor fixes and additions. +- [#503](https://github.com/askap-vast/vast-pipeline/pull/503) fix, dep: Change arrow file generation from vaex to pyarrow. +- [#501](https://github.com/askap-vast/vast-pipeline/pull/501) fix: fix broken cone search when coord = 0 +- [#491](https://github.com/askap-vast/vast-pipeline/pull/491) doc: Updated the docs layout, home page and FAQs. +- [#493](https://github.com/askap-vast/vast-pipeline/pull/493) fix: Fix bokeh hover tool for lightcurve plots. +- [#482](https://github.com/askap-vast/vast-pipeline/pull/482) dep: Bump y18n from 3.2.1 to 3.2.2. +- [#483](https://github.com/askap-vast/vast-pipeline/pull/483) feat: replace run config .py files with .yaml. +- [#487](https://github.com/askap-vast/vast-pipeline/pull/487) doc: Minor documentation improvements. - [#481](https://github.com/askap-vast/vast-pipeline/pull/481) dep: Bump Browsersync from 2.26.13 to 2.26.14. - [#469](https://github.com/askap-vast/vast-pipeline/pull/469) dep: Bump prismjs from 1.22.0 to 1.23.0. - [#480](https://github.com/askap-vast/vast-pipeline/pull/480) feat: Code reference documentation update. @@ -82,7 +165,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - [#429](https://github.com/askap-vast/vast-pipeline/pull/429) fix: Fixed sources table on measurement detail page. - [#427](https://github.com/askap-vast/vast-pipeline/pull/427) fix: Fixed missing meta columns in parallel association. -## [0.2.0](https://github.com/askap-vast/vast-pipeline/releases/0.2.0) (2020-11-30) +## [0.2.0](https://github.com/askap-vast/vast-pipeline/releases/v0.2.0) (2020-11-30) #### Added @@ -242,7 +325,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - [#305](https://github.com/askap-vast/vast-pipeline/pull/305) feat: 2 epoch metrics - [#345](https://github.com/askap-vast/vast-pipeline/pull/345) feat, fix: Website improvements. -## [0.1.0](https://github.com/askap-vast/vast-pipeline/releases/0.1.0) (2020-09-27) +## [0.1.0](https://github.com/askap-vast/vast-pipeline/releases/v0.1.0) (2020-09-27) First release of the Vast Pipeline. This was able to process 707 images (EPOCH01 to EPOCH11x) on a machine with 64 GB of RAM. diff --git a/README.md b/README.md index 6c5b4ebb7..8e366ef63 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,12 @@ -This repository holds the code of the Radio Transient detection pipeline for the VAST project. - -[![VAST Pipeline Login](https://github.com/askap-vast/vast-pipeline/blob/master/docs/img/login.png)](https://github.com/askap-vast/vast-pipeline/blob/master/docs/img/login.png) +This repository holds the code of the VAST Pipeline, a radio transient detection pipeline for the ASKAP survey science project, VAST. Please read the [Installation Instructions](https://vast-survey.org/vast-pipeline/quickstart/installation/). If you have any questions or feedback, we welcome you to open an [issue](https://github.com/askap-vast/vast-pipeline/issues). If you are interested in contributing to the code, please read and follow the [Contributing and Developing Guidelines](https://vast-survey.org/vast-pipeline/developing/intro/). +If using this tool in your research, please cite Murphy, et al. (2021). + ## Features * Code base in `Python 3.7+` @@ -30,24 +30,24 @@ Please read the [Installation Instructions](https://vast-survey.org/vast-pipelin [![VAST Pipeline Overview](https://github.com/askap-vast/vast-pipeline/blob/master/docs/img/vast_pipeline_overview1.gif)](https://github.com/askap-vast/vast-pipeline/blob/master/docs/img/vast_pipeline_overview1.gif) -## Credits & Acknowledgements +## Contributors -This tool was developed by Sergio Pintaldi from the [Sydney Informatics Hub](https://informatics.sydney.edu.au) – a core research facility of [The University of Sydney](https://www.sydney.edu.au/) – together with Adam Stewart from the [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/), Andrew O'Brien and David Kaplan from the [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/). Substantial contributions have been made by the [ADACS team](https://adacs.org.au/who-we-are/our-team/) Shibli Saleheen, David Liptai, Ella Xi Wang. +* Sergio Pintaldi – [Sydney Informatics Hub](https://informatics.sydney.edu.au) +* Adam Stewart – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) +* Andrew O'Brien – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/) +* Tara Murphy – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) +* David Kaplan – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/) +* Shibli Saleheen – [ADACS](https://adacs.org.au/who-we-are/our-team/) +* David Liptai – [ADACS](https://adacs.org.au/who-we-are/our-team/) +* Ella Xi Wang – [ADACS](https://adacs.org.au/who-we-are/our-team/) -The developers thank the creators of [SB Admin 2](https://github.com/StartBootstrap/startbootstrap-sb-admin-2) to make the dashboard template freely available. +## Acknowledgements -If using this tool in your research, please acknowledge the [Sydney Informatics Hub](https://informatics.sydney.edu.au) in publications. - -```console - - / /\ ___ /__/\ - / /:/_ / /\ \ \:\ - / /:/ /\ / /:/ \__\:\ - / /:/ /::\ /__/::\ ___ / /::\ - /__/:/ /:/\:\ \__\/\:\__ /__/\ /:/\:\ - \ \:\/:/~/:/ \ \:\/\ \ \:\/:/__\/ - \ \::/ /:/ \__\::/ \ \::/ - \__\/ /:/ /__/:/ \ \:\ - /__/:/ please \__\/ \ \:\ - \__\/ acknowledge your use\__\/ -``` +The VAST Pipeline development was supported by: + +* The Australian Research Council through grants FT150100099 and DP190100561. +* The Sydney Informatics Hub (SIH), a core research facility at the University of Sydney. +* Software support resources awarded under the Astronomy Data and Computing Services (ADACS) Merit Allocation Program. ADACS is funded from the Astronomy National Collaborative Research Infrastructure Strategy (NCRIS) allocation provided by the Australian Government and managed by Astronomy Australia Limited (AAL). +* NSF grant AST-1816492. + +The developers thank the creators of [SB Admin 2](https://github.com/StartBootstrap/startbootstrap-sb-admin-2) to make the dashboard template freely available. diff --git a/docs/README.md b/docs/README.md deleted file mode 120000 index 32d46ee88..000000000 --- a/docs/README.md +++ /dev/null @@ -1 +0,0 @@ -../README.md \ No newline at end of file diff --git a/docs/adminusage/app.md b/docs/adminusage/app.md index 31f9c6553..08f30217f 100644 --- a/docs/adminusage/app.md +++ b/docs/adminusage/app.md @@ -4,7 +4,7 @@ This section describes how to run the pipeline Django web app/server. ## Starting the Pipeline Web App -Make sure you installed and compiled correctly the frontend assets see [guide](../quickstart/installation.md#front-end-assets-quickstart) +Make sure you installed and compiled correctly the frontend assets see [guide](../gettingstarted/installation.md#front-end-assets-quickstart) 1. Start the Django development web server: diff --git a/docs/adminusage/cli.md b/docs/adminusage/cli.md index 67a6cb7c3..14d7143dc 100644 --- a/docs/adminusage/cli.md +++ b/docs/adminusage/cli.md @@ -3,22 +3,22 @@ This section describes the commands available to the administrators of the pipelines. ## Pipeline Usage + All the pipeline commands are run using the Django global `./manage.py ` interface. Therefore you need to activate the `Python` environment. You can have a look at the available commands for the pipeline app: -```bash +```terminal (pipeline_env)$ ./manage.py help ``` Output: -```bash +```terminal ... [vast_pipeline] clearpiperun createmeasarrow debugrun - importsurvey initpiperun restorepiperun runpipeline @@ -26,21 +26,60 @@ Output: ... ``` -There are 7 commands, described in detail below. +There are 6 commands, described in detail below. ### clearpiperun -Detailed commands for resetting the database can be found in [Contributing and Developing Guidelines](../developing/localdevenv.md#reset-the-database). - Resetting a pipeline run can be done using the `clearpiperun` command. This will delete all images and related objects such as sources associated with that pipeline run. Images that have been used in other pipeline runs will not be deleted. -```bash +```terminal +./manage.py clearpiperun --help +usage: manage.py clearpiperun [-h] [--keep-parquet] [--remove-all] [--version] + [-v {0,1,2,3}] [--settings SETTINGS] + [--pythonpath PYTHONPATH] [--traceback] + [--no-color] [--force-color] [--skip-checks] + piperuns [piperuns ...] + +Delete a pipeline run and all related images, sources, etc. Will not delete +objects if they are also related to another pipeline run. + +positional arguments: + piperuns Name or path of pipeline run(s) to delete. Pass + "clearall" to delete all the runs. + +optional arguments: + -h, --help show this help message and exit + --keep-parquet Flag to keep the pipeline run(s) parquet files. Will + also apply to arrow files if present. + --remove-all Flag to remove all the content of the pipeline run(s) + folder. + --version show program's version number and exit + -v {0,1,2,3}, --verbosity {0,1,2,3} + Verbosity level; 0=minimal output, 1=normal output, + 2=verbose output, 3=very verbose output + --settings SETTINGS The Python path to a settings module, e.g. + "myproject.settings.main". If this isn't provided, the + DJANGO_SETTINGS_MODULE environment variable will be + used. + --pythonpath PYTHONPATH + A directory to add to the Python path, e.g. + "/home/djangoprojects/myproject". + --traceback Raise on CommandError exceptions + --no-color Don't colorize the command output. + --force-color Force colorization of the command output. + --skip-checks Skip system checks. +``` + +Example usage: + +```terminal (pipeline_env)$ ./manage.py clearpiperun path/to/my_pipe_run # or (pipeline_env)$ ./manage.py clearpiperun my_pipe_run ``` -More details on the `clearpiperun` command can be found in the [Contributing and Developing Guidelines](../developing/localdevenv.md#clearing-run-data). +!!!tip + Further information on clearing a specific run, or resetting the database, can be found in the [Contributing and Developing](../developing/localdevenv.md#removingclearing-data) section. ### createmeasarrow @@ -80,6 +119,7 @@ optional arguments: ``` Example usage: + ```terminal ./manage.py createmeasarrow docs_example_run 2021-03-30 10:48:40,952 createmeasarrow INFO Creating measurements arrow file for 'docs_example_run'. @@ -89,6 +129,7 @@ Example usage: ``` ### debugrun + The `debugrun` command is used to print out a summary of the pipeline run to the terminal. A single pipeline run can be entered as an argument or `all` can be entered to print the statistics of all the pipeline runs in the database. @@ -126,6 +167,7 @@ optional arguments: ``` Example usage: + ```terminal ./manage.py debugrun docs_example_run * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * @@ -138,22 +180,19 @@ Nr of association: 3276 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ``` -### importsurvey - -This functionality is not yet available. - ### initpiperun + In order to process the images in the pipeline, you must create/initialise a pipeline run first. The pipeline run creation is done using the `initpiperun` django command, which requires a pipeline run folder. The command creates a folder with the pipeline run name under the settings `PROJECT_WORKING_DIR` defined in [settings](https://github.com/askap-vast/vast-pipeline/blob/master/webinterface/settings.template.py){:target="_blank"}. -```bash +```terminal (pipeline_env)$ ./manage.py initpiperun --help ``` Output: -```bash +```terminal usage: manage.py initpiperun [-h] [--version] [-v {0,1,2,3}] [--settings SETTINGS] [--pythonpath PYTHONPATH] [--traceback] [--no-color] [--force-color] @@ -184,16 +223,16 @@ optional arguments: The command yields the following folder structure: -```bash +```terminal (pipeline_env)$ ./manage.py initpiperun my_pipe_run ``` Output: -```bash +```terminal 2020-02-27 23:04:33,344 initpiperun INFO creating pipeline run folder 2020-02-27 23:04:33,344 initpiperun INFO copying default config in pipeline run folder -2020-02-27 23:04:33,344 initpiperun INFO pipeline run initialisation successful! Please modify the "config.py" +2020-02-27 23:04:33,344 initpiperun INFO pipeline run initialisation successful! Please modify the "config.yaml" ``` ### restorepiperun @@ -202,7 +241,7 @@ Details on the add images feature can be found [here](../using/addtorun.md). It allows for a pipeline run that has had an image added to the run to be restored to the state it was in before the image addition was made. By default the command will ask for confirmation that the run is to be restored (the option `--no-confirm` skips this). -```bash +```terminal ./manage.py restorepiperun --help usage: manage.py restorepiperun [-h] [--no-confirm] [--version] [-v {0,1,2,3}] [--settings SETTINGS] @@ -237,65 +276,115 @@ optional arguments: --skip-checks Skip system checks. ``` -```bash +```terminal (pipeline_env)$ ./manage.py restorepiperun path/to/my_pipe_run # or (pipeline_env)$ ./manage.py restorepiperun my_pipe_run ``` Example usage: -```bash -./manage.py restorepiperun docs_example_run -2021-01-31 12:45:31,039 restorepiperun INFO Will restore the run to the following config: -PIPE_RUN_PATH...................................../Users/adam/GitHub/vast-pipeline/pipeline-runs/docs_example_run -IMAGE_FILES.......................................['/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout.fits'] -SELAVY_FILES......................................['/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout.components.txt', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout.components.txt'] -BACKGROUND_FILES..................................['/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout_bkg.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout_bkg.fits'] -NOISE_FILES.......................................['/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout_rms.fits', '/Users/adam/askap/pipeline-test-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout_rms.fits'] -SOURCE_FINDER.....................................selavy -MONITOR...........................................True -MONITOR_MIN_SIGMA.................................3.0 -MONITOR_EDGE_BUFFER_SCALE.........................1.2 -MONITOR_CLUSTER_THRESHOLD.........................3.0 -MONITOR_ALLOW_NAN.................................False -ASTROMETRIC_UNCERTAINTY_RA........................1 -ASTROMETRIC_UNCERTAINTY_DEC.......................1 -ASSOCIATION_PARALLEL..............................True -ASSOCIATION_EPOCH_DUPLICATE_RADIUS................2.5 -ASSOCIATION_METHOD................................basic -ASSOCIATION_RADIUS................................15.0 -ASSOCIATION_DE_RUITER_RADIUS......................5.68 -ASSOCIATION_BEAMWIDTH_LIMIT.......................1.5 -NEW_SOURCE_MIN_SIGMA..............................5.0 -DEFAULT_SURVEY....................................None -FLUX_PERC_ERROR...................................0 -USE_CONDON_ERRORS.................................True -SELAVY_LOCAL_RMS_ZERO_FILL_VALUE..................0.2 -CREATE_MEASUREMENTS_ARROW_FILES...................False -SUPPRESS_ASTROPY_WARNINGS.........................True -SOURCE_AGGREGATE_PAIR_METRICS_MIN_ABS_VS..........4.3 + +```console +(pipeline_env)$ ./manage.py restorepiperun docs_example_run +2021-04-02 21:24:20,497 restorepiperun INFO Will restore the run to the following config: +run: + path: /Users/obrienan/sandbox/vast-pipeline-dirs/pipeline-runs/docs_example_run + suppress_astropy_warnings: yes +inputs: + image: + 1: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout.fits + 2: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout.fits + 3: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout.fits + 4: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout.fits + 5: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout.fits + 6: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout.fits + 7: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout.fits + selavy: + 1: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout.components.txt + 2: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout.components.txt + 3: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout.components.txt + 4: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout.components.txt + 5: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout.components.txt + 6: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout.components.txt + 7: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout.components.txt + noise: + 1: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_0127-73A.EPOCH01.I.cutout_rms.fits + 2: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118+00A.EPOCH01.I.cutout_rms.fits + 3: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH01/VAST_2118-06A.EPOCH01.I.cutout_rms.fits + 4: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118+00A.EPOCH02.I.cutout_rms.fits + 5: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH02/VAST_2118-06A.EPOCH02.I.cutout_rms.fits + 6: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118+00A.EPOCH03x.I.cutout_rms.fits + 7: + - /Users/obrienan/sandbox/vast-pipeline-dirs/raw-images/regression-data/EPOCH03x/VAST_2118-06A.EPOCH03x.I.cutout_rms.fits +source_monitoring: + monitor: no + min_sigma: 3.0 + edge_buffer_scale: 1.2 + cluster_threshold: 3.0 + allow_nan: no +source_association: + method: basic + radius: 10.0 + deruiter_radius: 5.68 + deruiter_beamwidth_limit: 1.5 + parallel: no + epoch_duplicate_radius: 2.5 +new_sources: + min_sigma: 5.0 +measurements: + source_finder: selavy + flux_fractional_error: 0.0 + condon_errors: yes + selavy_local_rms_fill_value: 0.2 + write_arrow_files: no + ra_uncertainty: 1.0 + dec_uncertainty: 1.0 +variability: + source_aggregate_pair_metrics_min_abs_vs: 4.3 + Would you like to restore the run ? (y/n): y -2021-01-31 12:45:38,567 restorepiperun INFO Restoring 'docs_example_run' from backup parquet files. -2021-01-31 12:45:39,216 restorepiperun INFO Deleting new sources and associated objects to restore run Total objects deleted: 2475 -2021-01-31 12:45:39,532 restorepiperun INFO Deleting forced measurement and associated objects to restore run. Total objects deleted: 3769 -2021-01-31 12:45:39,576 restorepiperun INFO Restoring metrics for 459 sources. -2021-01-31 12:45:39,631 restorepiperun INFO Removing 7 images from the run. -2021-01-31 12:45:39,826 restorepiperun INFO Deleting associations to restore run. Total objects deleted: 3239 -2021-01-31 12:45:40,651 restorepiperun INFO Deleting measurement pairs to restore run. Total objects deleted: 14692 -2021-01-31 12:45:40,653 restorepiperun INFO Restoring run metrics. -2021-01-31 12:45:40,662 restorepiperun INFO Restoring parquet files and removing .bak files. -2021-01-31 12:45:40,669 restorepiperun INFO Restore complete. +2021-04-02 21:24:28,685 restorepiperun INFO Restoring 'docs_example_run' from backup parquet files. +2021-04-02 21:24:29,602 restorepiperun INFO Deleting new sources and associated objects to restore run Total objects deleted: 433 +2021-04-02 21:24:29,624 restorepiperun INFO Restoring metrics for 461 sources. +2021-04-02 21:24:29,663 restorepiperun INFO Removing 7 images from the run. +2021-04-02 21:24:29,754 restorepiperun INFO Deleting associations to restore run. Total objects deleted: 846 +2021-04-02 21:24:29,979 restorepiperun INFO Deleting measurement pairs to restore run. Total objects deleted: 4212 +2021-04-02 21:24:29,981 restorepiperun INFO Restoring run metrics. +2021-04-02 21:24:29,990 restorepiperun INFO Restoring parquet files and removing .bak files. +2021-04-02 21:24:29,995 restorepiperun INFO Restore complete. ``` ### runpipeline + The pipeline is run using `runpipeline` django command. -```bash +```terminal (pipeline_env)$ ./manage.py runpipeline --help ``` Output: -```bash + +```terminal usage: manage.py runpipeline [-h] [--version] [-v {0,1,2,3}] [--settings SETTINGS] [--pythonpath PYTHONPATH] [--traceback] [--no-color] [--force-color] @@ -327,6 +416,7 @@ optional arguments: ``` General usage: -```bash + +```terminal (pipeline_env)$ ./manage.py runpipeline path/to/my_pipe_run -``` \ No newline at end of file +``` diff --git a/docs/architecture/database.md b/docs/architecture/database.md index 6f8e1a56f..81a2529e7 100644 --- a/docs/architecture/database.md +++ b/docs/architecture/database.md @@ -6,14 +6,14 @@ This section describes the relationships between the objects/tables stored in th The following figure shows a detailed schematics of the schema and relationships as well as tables parameters of the Django App. -[![VAST Pipeline Schema](../img/schema.png){: loading=lazy }](../img/schema.png) +![!VAST Pipeline database schema.](../img/schema.png){: loading=lazy } ## Pipeline Detailed Schema -A details to the pipeline schema is shown below: +A focussed view of the pipeline schema is shown below: -[![VAST Pipeline Schema Detail](../img/schema_pipeline.png){: loading=lazy }](../img/schema_pipeline.png) +![!VAST Pipeline focussed database schema.](../img/schema_pipeline.png){: loading=lazy } ### Important points diff --git a/docs/architecture/intro.md b/docs/architecture/intro.md index 2d2a32537..76c4fe9e0 100644 --- a/docs/architecture/intro.md +++ b/docs/architecture/intro.md @@ -2,7 +2,7 @@ The pipeline is essentially a [Django app](https://www.djangoproject.com/){:target="_blank"} in which the pipeline is run as a Django admin command. The main structure of the pipeline is described in this schematics: -[![VAST Pipeline Stack](../img/vast_pipeline_architecture.png){: loading=lazy }](../img/vast_pipeline_architecture.png) +![!VAST Pipeline Stack](../img/vast_pipeline_architecture.png){: loading=lazy } ## Design Philosophy diff --git a/docs/design/association.md b/docs/design/association.md index ca800249e..5b5ece04a 100644 --- a/docs/design/association.md +++ b/docs/design/association.md @@ -13,7 +13,6 @@ There are three association methods available which are summarised in the table | [Advanced](#advanced) | Yes | `search_around_sky` | many-to-many, many-to-one, one-to-many | | [de Ruiter (TraP)](#de-ruiter) | No | `search_around_sky` | many-to-many, many-to-one, one-to-many | - ## General Association Notes ### Terminology @@ -39,6 +38,7 @@ Sources positions are reported using the weighted averages. For a better understanding on the underlying process, see [this page](https://docs.astropy.org/en/stable/coordinates/matchsep.html#matching-catalogs){:target="_blank"} in the astropy documentation for examples on matching catalogues. ### Basic + The most basic association method uses the astropy [`match_coordinates_sky`](https://docs.astropy.org/en/stable/api/astropy.coordinates.match_coordinates_sky.html){:target="_blank"} function which: * Associates measurements using only the nearest neighbour for each source when comparing catalogues. @@ -46,6 +46,7 @@ The most basic association method uses the astropy [`match_coordinates_sky`](htt * Only one-to-many [relations](#relations) are possible. ### Advanced + This method uses the same process as `Basic`, however the astropy function [`search_around_sky`](https://docs.astropy.org/en/stable/api/astropy.coordinates.search_around_sky.html){:target="_blank"} is used instead. This means: * All possible matches between the two catalogues are found, rather than only the nearest neighbour. @@ -53,9 +54,10 @@ This method uses the same process as `Basic`, however the astropy function [`sea * All types of [relations](#relations) are possible. ### de Ruiter -The de Ruiter method is a translation of the association method used by the [LOFAR Transients Pipeline (TraP)](https://tkp.readthedocs.io/en/latest/){:target="_blank"}, which uses the `de Ruiter radius` in order to define associations. -The `search_around_sky` astropy method is still used, but the threshold for a potential match is first limited by a `beamwidth limit` value which is defined in the pipeline run configuration file (`ASSOCIATION_BEAMWIDTH_LIMIT`), such that the initial threshold separation distance is set to +The de Ruiter method is a translation of the association method used by the [LOFAR Transients Pipeline (TraP)](https://tkp.readthedocs.io/en/latest/){:target="_blank"}, which uses the `de Ruiter radius` in order to define associations. + +The `search_around_sky` astropy method is still used, but the threshold for a potential match is first limited by a `beamwidth limit` value which is defined in the pipeline run configuration file (`source_association.deruiter_beamwidth_limit`), such that the initial threshold separation distance is set to $$ \text{beamwidth limit} \times \frac{\theta_{\text{bmaj,img}}}{2}, @@ -66,15 +68,19 @@ where $\theta_{\text{bmaj,img}}$ is the major axis of the restoring beam of the $$ r_{i,j} = \sqrt{ \frac{ (\alpha_{i} - \alpha_{j})^{2}((\delta_{i} + \delta_{j})/2)}{\sigma^{2}_{\alpha_{i}} + \sigma^{2}_{\alpha_{j}}} - + \frac{(\delta_{i} + \delta_{j})^{2}}{\sigma^{2}_{\delta_{i}} + \sigma^{2}_{\delta_{j}}} + \\+ \frac{(\delta_{i} + \delta_{j})^{2}}{\sigma^{2}_{\delta_{i}} + \sigma^{2}_{\delta_{j}}} } $$ -where $\alpha_{n}$ is the right ascension of source n, $\delta_{n}$ is its declination, and $\sigma_{y}$ represents the error on the quantity y. Matches are then identified by applying a threshold maximum value to the de Ruiter radius which is defined by the user in the pipeline run configuration file (`ASSOCIATION_DE_RUITER_RADIUS`). +where $\alpha_{n}$ is the right ascension of source n, $\delta_{n}$ is its declination, and $\sigma_{y}$ represents the error on the quantity y. Matches are then identified by applying a threshold maximum value to the de Ruiter radius which is defined by the user in the pipeline run configuration file (`source_association.deruiter_radius`). All relation types are possible using this method. +!!!note "Epoch Based Association Note" + When the de Ruiter association method is used with epoch based assocation, the `beamwidth limit` is applied to the maximum `bmaj` value out of all the images included in the epoch. See the [de Ruiter and Epoch Based Association](#de-ruiter-and-epoch-based-association) section below for further details. + ## Relations + Situations can arise where a source is associated with more than one source in the catalogue being cross-matched (or vice versa). Internally these types of associations are called: * `many-to-many` @@ -90,28 +96,69 @@ The VAST Pipeline reports the `one-to-many` and `many-to-one` associations by `r A read-through of the [TraP documentation](https://tkp.readthedocs.io/en/latest/devref/database/assoc.html#database-assoc){:target="_blank"} is highly encouraged on this point as it contains an excellent description. +### Relations False Variability + +The VAST Pipeline builds associations only using the component information. What this means is that, while the island information from the selavy source finder is stored, it is not considered during the association stage. +Because of this, the relation process detailed above has the potential to cause sources to appear variable, when in reality it is not the case. + +For an example consider the source below: + +![!An example of a source that changes from one component to two between epochs.](../img/association_false_variability_stamps.png){: loading=lazy } +![!The lightcurve of the example source that changes from one component to two between epochs.](../img/association_false_variability_lc.png){: loading=lazy } + +In the 3rd, 7th, and 8th measurement (EPOCH02, EPOCH09, and EPOCH12), the source is detected as an island with two Gaussian components, as opposed to the one component in all other epochs. +The source lightcurve shows how the flux has reduced by approximately 50% in these three epochs, which makes the source appear variable. +The pipeline provides information for each source that allows for these kind of situations to be swiftly identified: + +* the number number of measurements that contain siblings, and +* the number of relations. + +These are the columns `n_sibl` and `n_rel`, respectively, in the pipeline sources output file (refer to the [Column Descriptions](../outputs/coldesc.md#sources) section). +If these values are not 0 for a source then care must be taken when analysing variability. + +For the example source above, the values are `n_sibl = 3` and `n_rel = 1`. The missing flux can be seen in the lightcurve of the related source: + +![!The lightcurve of the related source of the example source that changes from one component to two between epochs.](../img/association_false_variability_lc_relation.png){: loading=lazy } + ## Epoch Based Association -The pipeline is able to associate inputs on an epoch basis. What this means is that, for example, all VAST Pilot Epoch 1 measurements are grouped together and are associated with grouped together Epoch 2 measurements, and so on. In doing this, duplicate measurements from within the same epoch are cut with the measurement kept being that which is closest to the centre of its respective image. The separation distance that defines a duplicate is defined in the pipeline run configuration file (`ASSOCIATION_EPOCH_DUPLICATE_RADIUS`). -The mode is activated by entering the images to be processed as `dictionary` objects, using an orderable string as the key and lists of images as the values, as demonstrated below. +The pipeline is able to associate inputs on an epoch basis. What this means is that, for example, all VAST Pilot Epoch 1 measurements are grouped together and are associated with grouped together Epoch 2 measurements, and so on. In doing this, duplicate measurements from within the same epoch are cut with the measurement kept being that which is closest to the centre of its respective image. The separation distance that defines a duplicate is defined in the pipeline run configuration file (`source_association.epoch_duplicate_radius`). -```python -IMAGE_FILES = { - "epoch01": ["/full/path/to/image1.fits", "/full/path/to/image2.fits"], - "epoch02": ["/full/path/to/image3.fits"], -} -``` +The mode is activated by entering the images to be processed under an extra heading in the `.yaml` configuration file as demonstrated below. The heading acts as the epoch 'key', hence be sure to use a string that can be ordered as the heading to maintain the correct epoch order. + +!!! example "config.yaml" + ```yaml + inputs: + image: + epoch01: + - /full/path/to/image1.fits + - /full/path/to/image2.fits + epoch02: + - /full/path/to/image3.fits + ``` The lightcurves below show the difference between 'regular' association (top) and 'epoch based' association (lower) for a source. -[![Regular Association](../img/regular_association.png){: loading=lazy }](../img/regular_association.png) -[![Epoch Based Association](../img/epoch_based_association.png){: loading=lazy }](../img/epoch_based_association.png) +![!Regular association light curve of source.](../img/regular_association.png){: loading=lazy } +![!Epoch based association light curve of source.](../img/epoch_based_association.png){: loading=lazy } For large surveys where transient and variablity searches on the epoch timescale is required, using this mode can greatly speed up the association stage. !!! warning Epoch based association does eliminate the full time resolution of your data! The base time resolution will be between the defined epochs. +### de Ruiter and Epoch Based Association + +During the standard [de Ruiter assoication](#de-ruiter), an initial on sky separation cut is made of $\text{beamwidth limit} \times \frac{\theta_{\text{bmaj,img}}}{2}$, where `beamwidth limit` is a value entered by the user and $\theta_{\text{bmaj,img}}$ is the major component size of the restoring beam of the image being associated. + +When using epoch based association, an epoch that contains more than one image will have multiple values of $\theta_{\text{bmaj,img}}$ to apply to the combined measurements. +In this case, the maximum major axis value of all the images, $\theta_{\text{bmaj,max}}$, is used. +Hence, the initial de Ruiter association step threshold becomes + +$$ +\text{beamwidth limit} \times \frac{\theta_{\text{bmaj,max}}}{2}. +$$ + ## Parallel Association -When parallel association is used, the images to process are analysed and grouped into distinct patches of the sky that do not overlap. These distinct regions are then processed through the source association in parallel. It is recommended to use parallel association when your dataset covers three or more distinct patches of sky. +When parallel association is used, the images to process are analysed and grouped into distinct patches of the sky that do not overlap. These distinct regions are then processed through the source association in parallel. It is recommended to use parallel association when your dataset covers three or more distinct patches of sky. diff --git a/docs/design/imageingest.md b/docs/design/imageingest.md index e350ec0ad..5b7af5be9 100644 --- a/docs/design/imageingest.md +++ b/docs/design/imageingest.md @@ -2,29 +2,31 @@ This page details the stage of the pipeline that ingests the images to be processed. -When the pipeline encounters an image for the first time (in any pipeline run), the image and accompanying selavy catalogue are uploaded to the pipeline database. The portion of a pipeline log file below shows the messages for the ingestion of three images. +When the pipeline encounters an image for the first time (in any pipeline run), the image and accompanying selavy catalogue are uploaded to the pipeline database. +The portion of a pipeline log file below shows the messages for the ingestion of three images. !!! note Once an image is uploaded then that image is available for all other runs to use without having to re-upload. -```console -2021-03-11 12:59:49,751 loading INFO Reading image VAST_0127-73A.EPOCH01.I.cutout.fits ... -2021-03-11 12:59:49,756 utils INFO Adding new frequency band: 887 -2021-03-11 12:59:49,771 utils INFO Created sky region 21.838, -73.121 -2021-03-11 12:59:49,775 utils INFO Adding new-test-data to sky region 21.838, -73.121 -2021-03-11 12:59:50,100 loading INFO Processed measurements dataframe of shape: (203, 40) -2021-03-11 12:59:50,273 loading INFO Bulk created #203 Measurement -2021-03-11 12:59:50,334 loading INFO Reading image VAST_2118+00A.EPOCH01.I.cutout.fits ... -2021-03-11 12:59:50,345 utils INFO Created sky region 322.439, -3.987 -2021-03-11 12:59:50,347 utils INFO Adding new-test-data to sky region 322.439, -3.987 -2021-03-11 12:59:50,577 loading INFO Processed measurements dataframe of shape: (148, 40) -2021-03-11 12:59:50,708 loading INFO Bulk created #148 Measurement -2021-03-11 12:59:50,736 loading INFO Reading image VAST_2118-06A.EPOCH01.I.cutout.fits ... -2021-03-11 12:59:50,749 utils INFO Created sky region 322.439, -4.487 -2021-03-11 12:59:50,752 utils INFO Adding new-test-data to sky region 322.439, -4.487 -2021-03-11 12:59:50,977 loading INFO Processed measurements dataframe of shape: (159, 40) -2021-03-11 12:59:51,111 loading INFO Bulk created #159 Measurement -``` +!!! example "log.txt" + ```console + 2021-03-11 12:59:49,751 loading INFO Reading image VAST_0127-73A.EPOCH01.I.cutout.fits ... + 2021-03-11 12:59:49,756 utils INFO Adding new frequency band: 887 + 2021-03-11 12:59:49,771 utils INFO Created sky region 21.838, -73.121 + 2021-03-11 12:59:49,775 utils INFO Adding new-test-data to sky region 21.838, -73.121 + 2021-03-11 12:59:50,100 loading INFO Processed measurements dataframe of shape: (203, 40) + 2021-03-11 12:59:50,273 loading INFO Bulk created #203 Measurement + 2021-03-11 12:59:50,334 loading INFO Reading image VAST_2118+00A.EPOCH01.I.cutout.fits ... + 2021-03-11 12:59:50,345 utils INFO Created sky region 322.439, -3.987 + 2021-03-11 12:59:50,347 utils INFO Adding new-test-data to sky region 322.439, -3.987 + 2021-03-11 12:59:50,577 loading INFO Processed measurements dataframe of shape: (148, 40) + 2021-03-11 12:59:50,708 loading INFO Bulk created #148 Measurement + 2021-03-11 12:59:50,736 loading INFO Reading image VAST_2118-06A.EPOCH01.I.cutout.fits ... + 2021-03-11 12:59:50,749 utils INFO Created sky region 322.439, -4.487 + 2021-03-11 12:59:50,752 utils INFO Adding new-test-data to sky region 322.439, -4.487 + 2021-03-11 12:59:50,977 loading INFO Processed measurements dataframe of shape: (159, 40) + 2021-03-11 12:59:51,111 loading INFO Bulk created #159 Measurement + ``` ## Ingest Steps Summary @@ -55,17 +57,17 @@ The selavy measurements are checked for erroneous values that could cause issues In addition, components are also checked for zero values that can be corrected, where the correction values to apply are defined in either the user or overall pipeline configuration files. The field names of these zero checks are defined in the table below. -| Field Name | Correct with | Location | -| ------------------- | ------------------------------------- | ------------- | -| `flux_int_err` | `FLUX_DEFAULT_MIN_ERROR` | `settings.py` | -| `flux_peak_err` | `FLUX_DEFAULT_MIN_ERROR` | `settings.py` | -| `ra_err` | `POS_DEFAULT_MIN_ERROR` | `settings.py` | -| `dec_err` | `POS_DEFAULT_MIN_ERROR` | `settings.py` | -| `local_rms` | `SELAVY_LOCAL_RMS_ZERO_FILL_VALUE` | `config.py` | +| Field Name | Correct with | Location | +| ------------------- | ------------------------------------------ | ------------- | +| `flux_int_err` | `FLUX_DEFAULT_MIN_ERROR` | `settings.py` | +| `flux_peak_err` | `FLUX_DEFAULT_MIN_ERROR` | `settings.py` | +| `ra_err` | `POS_DEFAULT_MIN_ERROR` | `settings.py` | +| `dec_err` | `POS_DEFAULT_MIN_ERROR` | `settings.py` | +| `local_rms` | `measurements.selavy_local_rms_fill_value` | `config.yaml` | !!! note `settings.py` refers to the pipeline configuration file `webinterface/settings.py` which is configured by the system administrator and cannot be modified by regular users. - `config.py` refers to a pipeline run configuration file which is set by the user. + `config.yaml` refers to a pipeline run configuration file which is set by the user. #### Condon (1997) Flux & Positional Errors @@ -81,12 +83,12 @@ If selected in the pipeline run configuration file, the flux and positional erro #### Positional Errors (de Ruiter method) -Firstly, the systematic astrometry error from the user pipeline run configuration file (`ASTROMETRIC_UNCERTAINTY_RA` and `ASTROMETRIC_UNCERTAINTY_DEC`) are applied to the measurement. These values are saved as `ew_sys_err` and `ns_sys_err`. +Firstly, the systematic astrometry error from the user pipeline run configuration file (`measurements.ra_uncertainty` and `measurements.dec_uncertainty`) are applied to the measurement. These values are saved as `ew_sys_err` and `ns_sys_err`. !!! warning Currently the systematic errors applied at the pipeline run stage are then permanently fixed to the measurements, meaning that all subsequent runs using these measurements will use the fixed astrometic error. - It is recommended to leave the values to the default value of 1.0. + It is recommended to leave the values to the default value of 1.0. In order to apply the `TraP` de Ruiter association method, some extra positional error values are calculated. Firstly the `ra_err` and `dec_err` are used to estimate the largest angular uncertainty of the measurement which is recorded as the `error_radius`. It is estimated by finding the largest angular separation between the measurement coordinate and every coordinate combination of $ra \pm \delta ra$ and $dec \pm \delta dec$. diff --git a/docs/design/monitor.md b/docs/design/monitor.md index a6535d428..257fc53a4 100644 --- a/docs/design/monitor.md +++ b/docs/design/monitor.md @@ -4,7 +4,7 @@ This page details the forced measurements obtained by the pipeline. ## Definition -When `MONITOR = True` is set in the pipeline run configuration file, any sources that have non-detections in their lightcurve will have these measurements 'filled in' by performing `forced measurements`. This means that the flux at the source's current average position in the non-detection image is forcefully measured by fitting a Gaussian with the same shape as the respective image restoring beam. +When `source_monitoring.monitor: true` is set in the pipeline run configuration file, any sources that have non-detections in their lightcurve will have these measurements 'filled in' by performing `forced measurements`. This means that the flux at the source's current average position in the non-detection image is forcefully measured by fitting a Gaussian with the same shape as the respective image restoring beam. Forced measurements are labelled in the measurements table and parquet files by the column `forced`. @@ -21,32 +21,36 @@ Before forced measurements are processed, a minimum sigma check is made to make The check is performed like that which is made in the [New Sources](newsources.md) process where the signal-to-noise ratio is calculated using the rms$_{min}$ of the image it is to be extracted from. Hence, for a forced measurement to take place the following condition must be met: $$ -\frac{f_{peak,det}}{\text{rms}_{min,i}} > \text{MONITOR_MIN_SIGMA}, -$$ +\frac{f_{peak,det}}{\text{rms}_{min,i}} > \text{source_monitoring.min_sigma}, +$$ where $i$ is the image for which the measurement is to be forcefully measured. -`MONITOR_MIN_SIGMA` is able to be controlled by the user in the pipeline run configuration file. By default the value is set to 3.0. +`source_monitoring.min_sigma` is able to be controlled by the user in the pipeline run configuration file. By default the value is set to 3.0. !!! tip - Setting `MONITOR_MIN_SIGMA = 0.0` will ensure that all forced measurements are performed regardless of signal-to-noise. + Setting `source_monitoring.min_sigma: 0.0` will ensure that all forced measurements are performed regardless of signal-to-noise. ## Configuration File Options -The following options are present in the pipeline run configuration file to users along with their defaults: -```python -MONITOR = False -MONITOR_MIN_SIGMA = 3.0 -MONITOR_EDGE_BUFFER_SCALE = 1.2 -MONITOR_CLUSTER_THRESHOLD = 3.0 -MONITOR_ALLOW_NAN = False -``` +The following options are present in the pipeline run configuration file to users along with their defaults: -* `MONITOR` turns forced measurements on (`True`) or off (`False`). -* `MONITOR_MIN_SIGMA` controls the the minimum sigma check threshold as explained in [Minimum Sigma Filter](#minimum-sigma-filter). -* `MONITOR_EDGE_BUFFER_SCALE` controls the size of the buffer from the image edge where forced measurements are not performed (`MONITOR_EDGE_BUFFER_SCALE` $\times 3\theta_{beam}$). An error can sometimes occur that increasing this value can solve. -* `MONITOR_CLUSTER_THRESHOLD` is directly passed to the [forced photometry package](#software-forced_phot) used by the pipeline. It defines the multiple of `major_axes` to use for identifying clusters. -* `MONITOR_ALLOW_NAN` is directly passed to the [forced photometry package](#software-forced_phot) used by the pipeline. It defines whether `NaN` values are allowed to be present in the extraction area in the rms or background maps. `True` would mean that `NaN` values are allowed. +!!! example "config.yaml" + ```yaml + source_monitoring: + monitor: false + min_sigma: 3.0 + edge_buffer_scale: 1.2 + cluster_threshold: 3.0 + allow_nan: false + ``` + +* `source_monitoring.monitor` turns forced measurements on (`true`) or off (`false`). +* `source_monitoring.min_sigma` controls the the minimum sigma check threshold as explained in [Minimum Sigma Filter](#minimum-sigma-filter). +* `source_monitoring.edge_buffer_scale` controls the size of the buffer from the image edge where forced measurements are not performed (`source_monitoring.edge_buffer_scale` $\times 3\theta_{beam}$). An error can sometimes occur that increasing this value can solve. +* `source_monitoring.cluster_threshold` is directly passed to the [forced photometry package](#software-forced_phot) used by the pipeline. It defines the multiple of `major_axes` to use for identifying clusters. +* `source_monitoring.allow_nan` is directly passed to the [forced photometry package](#software-forced_phot) used by the pipeline. It defines whether `NaN` values are allowed to be present in the extraction area in the rms or background maps, i.e. `true` would mean that `NaN` values are allowed. ## Software - forced_phot + The software used to perform the forced measurements, `forced_phot`, was written by David Kaplan and can be found on the VAST GitHub [here](https://github.com/askap-vast/forced_phot). diff --git a/docs/design/newsources.md b/docs/design/newsources.md index c50c7d622..6748e5367 100644 --- a/docs/design/newsources.md +++ b/docs/design/newsources.md @@ -3,6 +3,7 @@ This page details the new source analysis performed by the pipeline. ## Definition + A `new source` is defined as a source that is detected during the pipeline run that was **not detected** in any previous epoch of the location of the source, and has a peak flux such that it should have been detected. !!! note @@ -12,22 +13,22 @@ A `new source` is defined as a source that is detected during the pipeline run t The pipeline identifies new sources by using the following steps: -1. Sources are found that have 'incomplete' light curves, i.e. there are epochs in the pipeline run of the source location where the source is not detected. +1. Sources are found that have 'incomplete' light curves, i.e. there are epochs in the pipeline run of the source location where the source is not detected. The would-be 'ideal' coverage is then calculated to determine which images contain the source location but have a non-detection. 2. Remove sources where the epoch of the first detection is also the earliest possible detection epoch. 3. For the remaining sources a general rms check is made to answer the question of should this source be expected to be detected at all in the previous epochs. This is done by taking the minimum $\text{rms}_{min}$ of all the non-detection images and making sure that $$ - \frac{f_{peak,det}}{\text{minimum rms}_{min}} > \text{NEW_SOURCE_MIN_SIGMA}, - $$ + \frac{f_{peak,det}}{\text{minimum rms}_{min}} > \text{new_sources.min_sigma}, + $$ - where $f_{peak,det}$ is the peak flux density of the first detection of the source. The default value of `NEW_SOURCE_MIN_SIGMA` is 5.0, but the parameter can be controlled by the user in the pipeline run configuration file. + where $f_{peak,det}$ is the peak flux density of the first detection of the source. The default value of `new_sources.min_sigma` is 5.0, but the parameter can be controlled by the user in the pipeline run configuration file. 4. The sources that meet the above criteria are marked as a `new source`. 5. The `new source high sigma` value is calculated for all new sources. - ## New Source High Sigma + In the process detailed above, the rms check is made against the minimum rms of the previous non-detection images. This might not be an accurate representation of the rms at the source's actual location in the image, for example, the rms might be high at the source location such that a detection of the source wouldn't be expected at the $5\sigma$ level. To account for this the `new source high sigma` value is calculated for all new sources. For each non-detection image for a source, the true signal-to-noise ratio the source would have in the non-detection image is calculated, i.e. diff --git a/docs/design/overview.md b/docs/design/overview.md index ee622f100..7dce57fa4 100644 --- a/docs/design/overview.md +++ b/docs/design/overview.md @@ -1,6 +1,6 @@ # Pipeline Steps Overview -This page gives an overview of the processing steps of a pipeline run. Each section contains a link to feature page that contains more details. +This page gives an overview of the processing steps of a pipeline run. Each section contains a link to a feature page that contains more details. ## Terminology @@ -59,12 +59,13 @@ All the results from the pipeline run are uploaded to the database. Specifically For large runs this can be a substantional component of the pipeline run time. `Bulk upload` statements will be seen in the pipeline run log file such as these shown below: -```console -2021-03-11 13:00:04,893 loading INFO Bulk created #557 Source -2021-03-11 13:00:04,910 loading INFO Populate "related" field of sources... -2021-03-11 13:00:04,919 loading INFO Bulk created #29 RelatedSource -2021-03-11 13:00:04,943 loading INFO Upload associations... -2021-03-11 13:00:05,650 loading INFO Bulk created #3276 Association -2021-03-11 13:00:08,374 loading INFO Bulk created #10000 MeasurementPair -2021-03-11 13:00:08,663 loading INFO Bulk created #1150 MeasurementPair -``` +!!! example "log.txt" + ```console + 2021-03-11 13:00:04,893 loading INFO Bulk created #557 Source + 2021-03-11 13:00:04,910 loading INFO Populate "related" field of sources... + 2021-03-11 13:00:04,919 loading INFO Bulk created #29 RelatedSource + 2021-03-11 13:00:04,943 loading INFO Upload associations... + 2021-03-11 13:00:05,650 loading INFO Bulk created #3276 Association + 2021-03-11 13:00:08,374 loading INFO Bulk created #10000 MeasurementPair + 2021-03-11 13:00:08,663 loading INFO Bulk created #1150 MeasurementPair + ``` diff --git a/docs/design/sourcestats.md b/docs/design/sourcestats.md index 1b9ff2934..e35fbd977 100644 --- a/docs/design/sourcestats.md +++ b/docs/design/sourcestats.md @@ -1,3 +1,4 @@ + # Source Statistics This page details the source statistics that are calculated by the pipeline. @@ -9,7 +10,7 @@ The table below provides a summary of all the statistic and counts provided by t !!! note Remember that all source statistics and counts are calculated from the individual measurements that are associated with the source. -| Parameter | Includes Forced Meas. | Description | +| Parameter | Includes Forced Meas. | Description | | ------------------------------ | ------------------------ | ----------------- | | `wavg_ra` | No | The weighted average of the Right Ascension, degrees. | | `wavg_dec` | No | The weighted average of the Declination, degrees. | @@ -36,9 +37,9 @@ The table below provides a summary of all the statistic and counts provided by t ## Variability Statistics -Below is a table describing the variability metrics of the source. See the following sections for further explanation of these metrics. +Below is a table describing the variability metrics of the source. See the following sections for further explanation of these metrics. -| Parameter | Includes Forced Meas. | Description | +| Parameter | Includes Forced Meas. | Description | | ------------------------------- | ------------------------ | ----------------- | | `v_int` | Yes | The $V$ metric for the integrated flux. | | `v_peak` | Yes | The $V$ metric for the peak flux. | @@ -49,7 +50,6 @@ Below is a table describing the variability metrics of the source. See the follo | `vs_abs_significant_max_peak` | Yes | The $\mid V_s \mid$ value of the most significant two-epoch pair using the peak fluxes. Will be `0` if no significant pair.| | `m_abs_significant_max_peak` | Yes | The $\mid m \mid$ value of the most significant two-epoch pair using the peak fluxes. Will be `0` if no significant pair.| - ### _V_ and _η_ Metrics The $V$ and $\eta$ metrics are the same as those used by the [LOFAR Transients Pipeline (TraP)](https://tkp.readthedocs.io/en/latest/){:target="_blank"}, for a complete description please refer to [Swinbank et al. (2015)](https://ui.adsabs.harvard.edu/abs/2015A%26C....11...25S/abstract){:target="_blank"}. In the VAST Pipeline, the metrics are calculated twice, for both the integrated and peak fluxes. @@ -70,7 +70,7 @@ where $w$ is the uncertainty ($e$) in $I$ of a measurement, and is given by $w=\ ### Two-Epoch Metrics -Alternative variability metrics, $V_s$ and $m$, are also calculated which we refer to as the 'two-epoch metrics'. +Alternative variability metrics, $V_s$ and $m$, are also calculated which we refer to as the 'two-epoch metrics'. They are calculated for each unique pair of measurements assoicated with the source, with the most significant pair of values attached to the source (see section below). Please refer to [Mooley et al. (2016)](https://ui.adsabs.harvard.edu/abs/2016ApJ...818..105M/abstract){:target="_blank"} for further details. !!! note @@ -104,8 +104,17 @@ which equates to a variability of 30%. However the user is free to set their own #### Significant Source Values -The $V_s$ and $m$ metrics of the 'maximum signficant pair' is attached to the source. -The maximum significant pair is determind by selecting the most significant $\mid m \mid$ value given a minimum $V_s$ threshold which is defined in the pipeline configuration file `SOURCE_AGGREGATE_PAIR_METRICS_MIN_ABS_VS`. +The $V_s$ and $m$ metrics of the 'maximum signficant pair' is attached to the source. +The maximum significant pair is determind by selecting the most significant $\mid m \mid$ value given a minimum $V_s$ threshold which is defined in the pipeline configuration file `variability.source_aggregate_pair_metrics_min_abs_vs`: + +!!! example "config.yaml" + ```yaml + variability: + # Only measurement pairs where the Vs metric exceeds this value are selected for the + # aggregate pair metrics that are stored in Source objects. + source_aggregate_pair_metrics_min_abs_vs: 4.3 + ``` + By default this value is set to 4.3. For example, if a source with three associatied measurements gave the following pair metrics: | Pair | $\mid V_s \mid$ | $\mid m \mid$ | @@ -114,5 +123,5 @@ By default this value is set to 4.3. For example, if a source with three associa | B-C | 2.5 | 0.05 | | A-C | 4.3 | 0.4 | -then the `A-C` pair metrics are attached to the source as the most significant. This can be used to quickly determine significant two-epoch variability for a source. +then the `A-C` pair metrics are attached to the source as the most significant. This can be used to quickly determine significant two-epoch variability for a source. If there are no pair values above the minimum $V_s$ threshold then these values attached to the source will be 0. The `measurement_pairs.parquet` file can be used to manually explore the measurement pairs if one wishes to lower the threshold. diff --git a/docs/developing/docsdev.md b/docs/developing/docsdev.md index 0509345b7..81eda98a8 100644 --- a/docs/developing/docsdev.md +++ b/docs/developing/docsdev.md @@ -4,42 +4,212 @@ The pipeline documentation has been developed using the python package `mkdocs`a ## Documentation development server +!!! note + Remember to install the [development dependencies](localdevenv.md) which include the modules required for the documentation. + This section describes how to set up a development server to live reload your changes to the pipeline documentation. -The main code of the documentation is under the `docs` folder, with fews hacks: in order to keep the repository `README.md`, `CHANGELOG.md`, `LICENSE.txt` and `CODE_OF_CONDUCT.md` on the root path, relative soft links have been created under the docs folder: +The main code of the documentation is located in the `docs` directory. In order to keep the repository, `CHANGELOG.md`, `LICENSE.txt` and `CODE_OF_CONDUCT.md` on the root path, relative soft links have been created under the docs folder: -```bash +```console +adminusage architecture changelog.md -> ../CHANGELOG.md code_of_conduct.md -> ../CODE_OF_CONDUCT.md +design developing +exploringwebsite +faqs.md +gen_doc_stubs.py +gettingstarted img +index.md license.md -> ../LICENSE.txt -quickstart -README.md -> ../README.md +outputs +reference theme -usage +using ``` Start the development server: -```bash +```console (pipeline_env)$ mkdocs serve ``` -And start to modify/add the documentation by changing the markdown files under the `docs` folder. +Files in the docs directory are then 'watched' such that any changes will cause the mkdocs server to reload the new content. The structure of the site (see `nav` section) and the settings are in the `mkdocs.yml` in the root of the repository. -`mkdocs` and the material theme have a lot of customizations and plugins, so please refer to their documentation. +## Plugins and Customisations + +`mkdocs` and the material theme have a lot of customisations and plugins available. The more involved plugins or customisations that are in use for this documentation are detailed in the following sections. + +### Custom `theme` directory + +The `theme` directory contains various overrides to the standard material template. This is enabled by the following line in the `mkdocs.yml` file: + +!!! example "mkdocs.yml" + ```yaml + theme: + custom_dir: docs/theme + ``` + +Custom javascript and css files are also stored in this directory and are enabled in the following `mkdocs.yml` file: + +!!! example "mkdocs.yml" + ```yaml + extra_css: + - theme/css/extra.css + extra_javascript: + - theme/js/extra.js + - https://polyfill.io/v3/polyfill.min.js?features=es6 + - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js + ``` + +The contents of the `theme` directory are shown below: + +```console +docs/theme +├── assets +│   └── stylesheets +│   └── overrides.css +├── css +│   ├── extra.css +│   └── lightgallery.min.css +├── fonts +│   ├── lg.svg +│   ├── lg.ttf +│   └── lg.woff +├── home.html +├── img +│   └── loading.gif +├── js +│   ├── extra.js +│   ├── lg-zoom.js +│   └── lightgallery.min.js +└── main.html +``` + +Full documentation on customising the `mkdocs-material` theme can be found in the [documentation](https://squidfunk.github.io/mkdocs-material/customization/){:target="_blank"}. + +`main.html` contains edits to the `main.html` as described in the documentation linked to above. The other files shown are used for the custom homepage and the Lightgallery. -Python docstrings and source code can be rendered using the `mkdocstrings` plugin: for example rendering `models.py` functions docstrings can be done with: +### Custom Homepage -```md -::: vast_pipeline.models +The homepage is overwritten by a custom stylised HTML page. This is achieved using the following files: + +```console +docs +├── index.md +├── theme +│   ├── assets +│   │   └── stylesheets +│   │   └── overrides.css +│   ├── home.html +│   └── main.html ``` -More details on how to display the source code and additional tweaks can be found in [mkdocstrings documentation](https://pawamoy.github.io/mkdocstrings/usage/){:target="_blank"}. +The `index.md` file in the main `docs` directory should only contain the following. + +!!! example "index.md" + ```md + --- + title: VAST Pipeline + template: home.html + --- + + ``` + +### Creation and Last Updated Dates + +Each page displays a date of creation and also a "last updated" date. +This is done by using the plugin [mkdocs-git-revision-date-localized-plugin](https://github.com/timvink/mkdocs-git-revision-date-localized-plugin){:target="_blank"}. +The following options are used: + +!!! example "mkdocs.yml" + ```yaml + plugins: + - git-revision-date-localized: + fallback_to_build_date: true + enable_creation_date: true + ``` + +!!! warning "Dates and Code Reference Pages" + The option `fallback_to_build_date: true` is required for the code reference pages that are auto generated by the [`mkdocs-gen-files`](https://oprypin.github.io/mkdocs-gen-files/){:target="_blank"} plugin (see the [Python Docstrings and Source Code](#python-docstrings-and-source-code) section below). + These pages will show the build date rather than the "last updated" date. During the build process the following warning will be seen, which is expected and ok to ignore: + ```console + WARNING - [git-revision-date-localized-plugin] Unable to find a git directory and/or git is not installed. Option 'fallback_to_build_date' set to 'true': Falling back to build date + ``` + +### Lightgallery + +Images are displayed in the documentation using the [`lightgallery-markdown`](https://github.com/g-provost/lightgallery-markdown){:target="_blank"} plugin. +As described in the repository linked to above, certain assets from [`lightgallery.js`](https://github.com/sachinchoolur/lightgallery.js){:target="_blank"} are copied over to make the extension work, the files that apply here are: + +```console +docs/theme +├── css +│   └── lightgallery.min.css +├── fonts +│   ├── lg.svg +│   ├── lg.ttf +│   └── lg.woff +├── img +│   └── loading.gif +├── js +│   ├── extra.js +│   ├── lg-zoom.js +│   └── lightgallery.min.js +└── main.html +``` + +`lg-zoom.js` is also copied over to activate the zoom feature on the gallery images. + +!!! note + The javascript to select the lightgallery class objects and run them through the lightgallery function is placed in + `theme/js/extra.js` such that the plugin works with [instant navigation](https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#instant-loading){:target="_blank"}. + +### MathJax + +`MathJax` is enabled as described in the [`mkdocs-material` documentation](https://squidfunk.github.io/mkdocs-material/reference/mathjax/){:target="_blank"}. + +### Python Docstrings and Source Code + +Python docstrings and source code are rendered using the [`mkdocstrings`](https://mkdocstrings.github.io){:target="_blank"} plugin. + +!!! warning "Docstrings Format" + All docstrings must be done using the [Google format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html){target="_blank"}. + +The markdown files for the docstrings are automatically generated using [`mkdocs-gen-files`](https://oprypin.github.io/mkdocs-gen-files/){:target="_blank"} in the file `docs/gen_doc_stubs.py`. +It is activated by the following lines in the `mkdocs.yml` file: + +!!! example "mkdocs.yml" + ```yaml hl_lines="3 4 5" + plugins: + - search + - gen-files: + scripts: + - docs/gen_doc_stubs.py + ``` + +The markdown files are programmatically generated, this means that the markdown files don't actually appear, but are virtually part of the site build. +The files must still be referenced in the `nav:` section of `mkdocs.yml`, for example: + +!!! example "mkdocs.yml" + ```yaml + - nav: + - Code Reference: + - vast_pipeline: + - image: + - main.py: reference/image/main.md + - utils.py: reference/image/utils.md + ``` + +The files are virtually created relative to the doc path that is stated in `gen_doc_stubs.py`. +For example, using the `vast_pipeline` as the base for the python files and `reference` as the doc path, the markdown file for the docstrings in `vast_pipeline/image/main.py` is created at `reference/image/main.md`. + +Please refer to the [`mkdocstrings` documentation ](https://mkdocstrings.github.io){:target="_blank"} for full details of the options available to declare in `mkdocs.yml`. ## Deployment to GitHub pages diff --git a/docs/developing/github.md b/docs/developing/github.md index 2dd47b191..0d41f65d0 100644 --- a/docs/developing/github.md +++ b/docs/developing/github.md @@ -1,54 +1,86 @@ -# GitHub platform guidelines +# GitHub Platform Guidelines -This section explains how to interact with GitHub platform for opening Issues and Pull Requests, and some notes how to make a release of the pipeline if you are a mantainer of the code base. +This section explains how to interact with GitHub platform for opening issues, starting discussions, creating pull requests (PR), and some notes how to make a release of the pipeline if you are a maintainer of the code base. -## Issues Guidelines +The VAST team uses the "git flow" branching model which we briefly summarise here. More detail can be found [here](https://nvie.com/posts/a-successful-git-branching-model/). -* Please search for a similar issue before opening a new one by run a search on the [issue page](https://github.com/askap-vast/vast-pipeline/issues){:target="_blank"} with specific key-words. -* When opening a new issue, please specify the issue type (e.g. bug, feature, etc.) and provide a detailed description with use cases if applied. +There are two main branches, both with infinite lifetimes (they are never deleted): +- `master` for stable, production-ready code that has been released, and +- `dev` for the latest reviewed updates for the next release. -## Pull Request Guideline +Other branches for bug fixes and new features are created as needed, branching off and merging back into `dev`. An exception to this is for critical patches for a released version called a "hotfix". These are branched off `master` and merged back into both `master` and `dev`. -### Opening a PR +Branches are also created for each new release candidate, which are branched off `dev` and merged into `master` and `dev` when completed. See the [Releases](#releases) section below for more information. + +## Issues + +An issue can be created by anyone with access to the repository. Users are encouraged to create issues for problems they encounter while using the pipeline or to request a new feature be added to the software. Issues are created by clicking the "New issue" button near the top-right of the [issues page](https://github.com/askap-vast/vast-pipeline/issues){:target="_blank"}. + +When creating a new issue, please consider the following: -!!! tip "First consider . . ." +* Search for a similar issue before opening a new one by using the search box near the top of the issues page. +* When opening a new issue, please specify the issue type (e.g. bug, feature, etc.) and provide a detailed description with use cases when appropriate. - 1. search among the issues for similar problems/bugs/etc - 2. opening an issue before creating/issuing the PR. +## Discussions - So we can separate problems from solutions. +GitHub repositories also have a discussions page which serves as a collaborative forum to discuss ideas and ask questions. Users are encouraged to ask general questions, or start a conversation about potential new features to the software by creating a new discussion thread on the [discussions page](https://github.com/askap-vast/vast-pipeline/discussions){:target="_blank"}. Note that new software features may also be requested by creating an issue, but a discussion thread is more appropriate if the details of the new feature are still yet to be determined or require wider discussion – issues can be created from discussions once a consensus is reached. + +## Pull Requests + +Pull requests are created when a developer wishes to merge changes they have made in a branch into another branch. They enable others to review the changes and make comments. While issues typically describe in detail a specific problem or proposed feature, pull requests contain a detailed description and the required code changes for a solution to a problem or implementation of a new feature. + +### Opening a PR + +!!! tip "First consider ..." + + 1. Search existing issues for similar problems or feature proposals. + 2. Opening an issue to describe the problem or feature before creating a PR. This will help separate problems from solutions. Steps to issue a pull request: -1. Open an issue (e.g. `My issue blah`, GitHub will assign a id e.g. `#123`). -2. Branch off `master` by naming your branch `fix-#123-my-issue-blah` (keep it short please). -3. Do your changes. -4. Run test locally with `./manage.py test vast_pipeline` (see the [complete guide on the test](./tests.md) for more details). -5. Run the webserver and check the functionality. -6. Commit and issue the PR. -7. Assign the review to one or more reviewers if none are assigned by default. +1. Create a new issue on GitHub, giving it a succinct title and describe the problem. GitHub will assign an ID e.g. `#123`. +2. Create a new branch off the `dev` branch and name the branch based on the issue title, e.g. `fix-123-some-problem` (keep it short please). +3. Make your changes. +4. Run the test suite locally with `python manage.py test vast_pipeline`. See the [complete guide on the test](./tests.md) for more details. +5. Run the webserver and check the functionality. This is important as the test suite does not currently check the web UI. +6. Commit the changes to your branch, push it to GitHub, and open a PR for the branch. +7. Update the `CHANGELOG.md` file by adding the link to your PR and briefly describing the changes. An example of the change log format can be found [here](https://github.com/apache/incubator-superset/blob/dev/CHANGELOG.md){:target="_blank"} +8. Assign the review to one or more reviewers if none are assigned by default. !!! warning "Warning" - PRs not branched off master will be __rejected__!. + PRs not branched off dev will be __rejected__!. + +### Reviewing a PR -### Pull Request Review Guidelines The guidelines to dealing with reviews and conversations on GitHub are essentially: * Be nice :smile: with the review and do not offend the author of the PR: __Nobody is a perfect developer or born so!__ * The reviewers will in general mark the conversation as "resolved" (e.g. he/she is satisfied with the answer from the PR author). * The PR author will re-request the review by clicking on the :octicons-sync-16: on the top right corner and might ping the reviewer on a comment if necessary with `@github_name`. -* When the PR is approved by at least one reviewer you might want to merge it to master (you should have that privileges), unless you want to make sure that such PR is reviewed by another reviewer (e.g. you are doing big changes or important changes or you want to make sure that other person is aware/updated about the changes in that PR). - -## Releasing Guidelines - -In to order to make a release, please follow these steps (example: making the `0.1.0` release): - -1. Make sure that every new feature and PR will be merged to master, before continuing with the releasing process. -2. Update the [`CHANGELOG.md`](https://github.com/askap-vast/vast-pipeline/blob/master/CHANGELOG.md){:target="_blank"} on `master` directly (only admin can and need to force-push the changes) with the list of changes. An example of format can be found [here](https://github.com/apache/incubator-superset/blob/master/CHANGELOG.md){:target="_blank"}. -3. The `0.2.X` branch will be updated by merging `master` into `0.2.X`. -4. Branch off `0.2.X` and call it `0.2.1`, then change the `package.json` with the version of the release, commit and tag the commit. Push commit and tag to origin. -5. Make a release in GitHub using that tag. - -__NOTE__: keep the version on `master` branch to something like 99.99.99dev and in `0.2.X` branch to something like 0.2.99dev. In the release branch, change only the version in [`package.json`](https://github.com/askap-vast/vast-pipeline/blob/master/package.json){:target="_blank"}. +* When the PR is approved by at least one reviewer you might want to merge it to dev (you should have that privileges), unless you want to make sure that such PR is reviewed by another reviewer (e.g. you are doing big changes or important changes or you want to make sure that other person is aware/updated about the changes in that PR). + +## Releases + +In to order to make a release, please follow these steps: + +1. Make sure that all new feature and bug fix PRs that should be part of the new release have been merged to `dev`. +2. Checkout the `dev` branch and update it with `git pull`. Ensure that there are no uncommitted changes. +3. Create a new branch off `dev`, naming it `release-vX.Y.Z` where `X.Y.Z` is the new version. Typically, patch version increments for bug fixes, minor version increments for new features that do not break backward compatibility with previous versions (i.e. no database schema changes), and major version increments for large changes or for changes that would break backward compatibility. +4. Bump the version number of the Python package using Poetry, i.e. `poetry version X.Y.Z`. This will update the version number in `pyproject.toml`. +5. Update the version in `package.json` and `vast_pipeline/_version.py` to match the new version number, then run `npm install` to update the `package-lock.json` file. +6. Update the "announcement bar" in the documentation to refer to the new release. This can be found in `docs/theme/main.html` at line 37. +7. Update the [`CHANGELOG.md`](https://github.com/askap-vast/vast-pipeline/blob/master/CHANGELOG.md){:target="_blank"} by making a copy of the "Unreleased" heading at the top, and renaming the second one to the new version. Include a link to the release - it won't exist yet, so just follow the format of the others. After this there should be an "Unreleased" heading at the top, immediately followed by another heading with the new version number, which is followed by all the existing changes. +8. Commit all the changes made above to the new branch and push it to GitHub. +9. Open a PR to merge the new branch into `master`. Note that the default target branch is `dev` so you will need to change this to `master` when creating the PR. +10. Once the PR has been reviewed and approved, merge the branch into `master`. This can only be done by administrators of the repository. +11. Tag the merge commit on `master` with the version, i.e. `git tag vX.Y.Z`, then push the tag to GitHub. + + !!! warning + If you merged the release branch into `master` with the GitHub web UI, you will need to sync that merge to your local copy and checkout `master` before creating the tag. You cannot create tags with the GitHub web UI. + +12. Push the tag to GitHub, i.e. `git push origin vX.Y.Z`. +13. Merge the release branch into `dev`, resolving any conflicts. +14. Append "dev" to the version numbers in `pyproject.toml`, `package.json` and `vast_pipeline/_version.py`, then run `npm install` to update `package-lock.json`, and commit the changes to `dev`. This can either be done as a new commit, or while resolving merge conflicts in the previous step, if appropriate. +15. Create a [new release](https://github.com/askap-vast/vast-pipeline/releases/new) on GitHub that points to the tagged commit on master. diff --git a/docs/developing/intro.md b/docs/developing/intro.md index 18be98621..169ca1fcd 100644 --- a/docs/developing/intro.md +++ b/docs/developing/intro.md @@ -1,12 +1,7 @@ # Contributing and Developing Guidelines -This section explains how to contribute to the project code base and collaborate on GitHub platform. A very exahustive set of general guidelines can be follow [here](https://github.com/apache/incubator-superset/blob/master/CONTRIBUTING.md){:target="_blank"}, but I think the following will suffice for our purpose. The next sections describes: - -* [GitHub Platform](github.md) -* [Local Development Enviroment](localdevenv.md) -* [Tests](tests.md) -* [Docs](docsdev.md) -* [Bechmarks](profiling.md) +This section explains how to contribute to the project code base and collaborate on GitHub platform. +Please use the section navigator to left to visit pages for specific details on areas of development. ## Terminology @@ -16,3 +11,6 @@ These below is the terminology used to identify pipeline objects. * Measurement -> the extracted measurement from the source finder of a single astrophysical source from an image, referred in the code as `measurement(s), meas, ...` * Source -> A collection of single measurements for the same astrophysical source, referred as `src, source, ...` in the code +## Docstrings + +All docstrings must be done using the [Google format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html){target="_blank"} to ensure compatibility with the documentation. \ No newline at end of file diff --git a/docs/developing/localdevenv.md b/docs/developing/localdevenv.md index 65db7c8a5..5b7c6aeb8 100644 --- a/docs/developing/localdevenv.md +++ b/docs/developing/localdevenv.md @@ -6,7 +6,7 @@ This section describes how to set up a local development environment more in det ### Installation -The installation instructions are the same as the ones describes in the [quickstart section](../quickstart/installation.md) with one key difference. Rather than installing the Python dependencies with pip, you will need to install and use [Poetry](https://python-poetry.org){:target="_blank"}. After installing Poetry, running the command below will install the pipeline dependencies defined in `poetry.lock` into a virtual environment. The main difference between using Poetry and pip is that pip will only install the dependencies necessary for using the pipeline, whereas Poetry will also install development dependencies required for contributing (e.g. tools to build the documentation). +The installation instructions are the same as the ones describes in the [Getting Started section](../gettingstarted/installation.md) with one key difference. Rather than installing the Python dependencies with pip, you will need to install and use [Poetry](https://python-poetry.org){:target="_blank"}. After installing Poetry, running the command below will install the pipeline dependencies defined in `poetry.lock` into a virtual environment. The main difference between using Poetry and pip is that pip will only install the dependencies necessary for using the pipeline, whereas Poetry will also install development dependencies required for contributing (e.g. tools to build the documentation). ```console poetry install @@ -15,99 +15,11 @@ poetry install !!! note Poetry will automatically create a virtual environment if it detects that your shell isn't currently using one. This should be fine for most users. If you prefer to use an alternative virtual environment manager (e.g. Miniconda), you can [prevent Poetry from creating virtual environments](https://python-poetry.org/docs/faq/#i-dont-want-poetry-to-manage-my-virtual-environments-can-i-disable-it){:target="_blank"}. However, even if you are using something like Miniconda, allowing Poetry to manage the virtualenv (the default behaviour) is fine. The development team only uses this option during our automated testing since our test runner machines only contain a single Python environment so using virtualenvs is redundant. -### Solving your `models.py`/migrations issues +### Changes to the data models -First of all the `makemigrations` command must be run only if you modified the `models.py` or you pull down changes (i.e. `git pull`) that modify `models.py`. So please refer to the cases below: +When changes are made to the data models defined in `vast_pipeline/models.py`, the database schema needs to be updated to reflect those changes. Django can handle this for you by generating migration files that contain the necessary code to update the schema. Migration files are generated with the Django management command `python manage.py makemigrations` and applied to the database with `python manage.py migrate`. Depending on the nature of the changes, this may break backward compatibility, i.e. runs created with previous versions of the pipeline may not be compatible with your changes. -#### 1. You modify `models.py` - -In this case there are 2 situations that arise: - -1. You currently don't have a production environment and/or you are comfortable in dropping all the data in the database. In this case, you don't need to update the production environment with multiple migration files even though Django docs promote making as many migrations as you need to ([see Django migration guidelines](https://docs.djangoproject.com/en/3.0/topics/migrations/#squashing-migrations){:target="_blank"}). For such reasons please consider doing the following steps: - - 1.1. Make your changes to `models.py`. - - 1.2. Remove all the migration files including `0002_q3c.py`. - - 1.3. Run `./manage.py makemigrations`. This will generate a __NEW__ `0001_initial.py` file. - - 1.4. Commit the new migraton file `0001_initial.py` as well as `models.py` within a single commit, and add an appropriate message (e.g. add field X to model Y). __DO NOT__ commit the removal of `0002_q3c.py`. - - 1.5. Get back the Q3C migration file `git checkout pipeline/migrations/0002_q3c.py`. - -2. You currently have a production environment and/or you do not want to lose all the data in the database. In this situation, you need to be careful not to mess up with the producation database, so please consider doing the following steps: - - 2.1. Make a copy ("dump") of the production database as it is, e.g. (by logging remotely to the server) `pg_dump -h DBHOST_PROD -p DBPORT_PROD -U DBUSER_PROD -Fc -o DBNAME_PROD > prod-backup-$(date +"%F_%H%M").sql`. - - 2.2. Upload the copy to your local development database, e.g. `pg_restore -h DBHOST_DEV -p DBPORT_DEV --verbose --clean --no-acl --no-owner -U DBUSER_DEV -d DBNAME_DEV prod-backup.sql`. - - 2.3. Make your changes to `models.py`. - - 2.4. Run `./manage.py makemigrations` with optional but strongly recommended `-n 'my_migration_name'`. This will generate a new migration file `000X_my_migration_name.py` where X is incremented by 1 with respect the last migration file. - - 2.5. Commit the new migraton file `000X_my_migration_name.py` as well as `models.py` within a single commit, and add an appropriate message (e.g. add field X to model Y) - - !!! warning - Do not modify the `0002_q3c.py` file as it relates to migration operations for using Q3C plugin and related functions! - -#### 2. Someone else modified `models.py` and you pull the changes - -Situation: - -```console -~/vast-pipeline [master]$ git fetch && git pull -Updating abc123..321cba -Fast-forward - pipeline/models.py | 4 +++- - pipeline/migrations/0001_initial.py | 5 ++++- - 2 file changed, 9 insertions(+), 2 deletions(-) -``` - -You realise that you are in this situation when: - -- In the command above you see changes (i.e. `+` or `-`) in `models.py` and/or in migrations (i.e. `XXXX_some_migration.py`) - -- Running the webserver, a message reports - - ```console - You have unapplied migrations; - your app may not work properly until they are applied. - Run 'python manage.py migrate' to apply them. - ``` - -- Running the pipeline you have errors related to the database models - -Solutions to such scenario: - -If you don't mind losing all the data in your database just follow the [Reset the database](#reset-the-database) instructions to drop all the data. But if you want to keep your data, you have to fix these changes by trying to run `makemigrations` and `migrate`. But ideally you should follow the following steps: - -1. Identify the previous commit before pulling the changes (when your migration and model files were working): - - ```console - ~/vast-pipeline [master]$ git show -1 pipeline/models.py #OR - ~/vast-pipeline [master]$ git show -2 pipeline/models.py #OR - ~/vast-pipeline [master]$ git show -1 pipeline/migrations/XXXX_my_migration.py - ``` - - Or even better - - ```console - ~/vast-pipeline [master]$ git log -p pipeline/models.py - ``` - -2. Take note of the commit hash of the old changes (i.e. before pulling down the new changes). Checkout __ONLY__ your old migration files, for example like this: - - ```console - ~/vast-pipeline [master]$ git checkout 37cabac84785742437927c785b63a767aa8ac5ff pipeline/migrations/0001_initial.py - ``` - -3. Make the migrations `./manage.py makemigrations && ./manage.py migrate` - -4. Run the pipeline and the webserver to see that everything is working fine - -5. Squash the migrations using [Django migration guidelines](https://docs.djangoproject.com/en/3.0/topics/migrations/#squashing-migrations){:target="_blank"} - -6. Continue with the normal development cycle (i.e. branch off master, do changes, commit everything, _including your changes in the models/migrations even done with the squashing!_) +Database migrations must be committed to source control so that others can pull in your model changes. They can sometimes be complex and require additional attention. If you have any difficulty with migrations, please contact the VAST development team for help. More information can be found in the [Django documentation on migrations](https://docs.djangoproject.com/en/3.2/topics/migrations/). ### Removing/Clearing Data @@ -175,7 +87,7 @@ npm ci ... ``` -For installing future additional dependecies you can run `npm install --save my-package` or `npm install --save-dev my-dev-package` (to save a development module), and after that commit __both__ `package.json` and `package-lock.json` files. For details about the installed packages and npm scripts see [`package.json`](https://github.com/apache/incubator-superset/blob/master/package.json){:target="_blank"}. +For installing future additional dependencies you can run `npm install --save my-package` or `npm install --save-dev my-dev-package` (to save a development module), and after that commit __both__ `package.json` and `package-lock.json` files. For details about the installed packages and npm scripts see [`package.json`](https://github.com/apache/incubator-superset/blob/master/package.json){:target="_blank"}. ### FrontEnd Tasks with `gulp` @@ -183,7 +95,7 @@ Using `gulp` and `npm` scripts you can: 1. Install dependencies under the `./static/vendor` folder. 2. Building (e.g. minify/uglify) CSS and/or Javascript files. -3. Run a developement server that "hot-reload" your web page when any HTML, CSS or Javascript file is modified. +3. Run a development server that "hot-reload" your web page when any HTML, CSS or Javascript file is modified. The command to list all the `gulp` "tasks" and sub-tasks is (you might need `gulp-cli` installed globally, i.e. `npm i --global gulp-cli`, more info [here](https://gulpjs.com/docs/en/getting-started/quick-start){:target="_blank"}): @@ -297,7 +209,7 @@ gulp css to run just the minification of the CSS files. -#### 3. Run Developement Server +#### 3. Run Development Server Start your normal Django server with (__NOTE__: do not change the default port!): @@ -317,7 +229,7 @@ The latter will open your dev server, that will auto reload and apply your lates #### 4. Debug Task -This task is for debugging the paths used in the others task, but also serve as a palce hodler to debug commands. +This task is for debugging the paths used in the others task, but also serve as a place holder to debug commands. ```bash npm run debug @@ -347,4 +259,4 @@ This command will collect all static assets (Javascript and CSS files) and copy The `js9staticprod` gulp task is necessary if you specify a `STATIC_URL` and a `BASE_URL` different than the default, for example if you need to prefix the site `/` with a base url because you are running another webserver (e.g. another web server is running on `https://my-astro-platform.com/` so you want to run the pipeline on the same server/domain `https://my-astro-platform.com/pipeline`, so you need to set `BASE_URL='/pipeline/'` and `STATIC_URL=/pipeline-static/` in `settings.py`). __We recommend to run this in any case!__ -Then you can move that folder to where it can be served by the production static files server ([Ningx](https://www.nginx.com/){:target="_blank"} or [Apache](https://httpd.apache.org/){:target="_blank"} are usually good choices, in case refere to the [Django documentation](https://docs.djangoproject.com/en/3.1/howto/deployment/){:target="_blank"}). +Then you can move that folder to where it can be served by the production static files server ([Ningx](https://www.nginx.com/){:target="_blank"} or [Apache](https://httpd.apache.org/){:target="_blank"} are usually good choices, in case refer to the [Django documentation](https://docs.djangoproject.com/en/3.1/howto/deployment/){:target="_blank"}). diff --git a/docs/developing/tests.md b/docs/developing/tests.md index 15ffa01e0..0a9236978 100644 --- a/docs/developing/tests.md +++ b/docs/developing/tests.md @@ -20,10 +20,10 @@ To run one test file or class, use: (pipeline_env)$ ./manage.py test ``` -for example, to run the test class `CheckRunConfigValidationTest` located in [`test_runpipeline.py`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/test_runpipeline.py){:target="_blank"}, use: +for example, to run the test class `CheckRunConfigValidationTest` located in [`test_pipelineconfig.py`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/test_pipelineconfig.py){:target="_blank"}, use: ```bash -(pipeline_env)$ ./manage.py test vast_pipeline.tests.test_runpipeline.CheckRunConfigValidationTest +(pipeline_env)$ ./manage.py test vast_pipeline.tests.test_pipelineconfig.CheckRunConfigValidationTest ``` to run the tests located in [`test_webserver.py`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/test_webserver.py){:target="_blank"}, use: @@ -34,17 +34,17 @@ to run the tests located in [`test_webserver.py`](https://github.com/askap-vast/ ## Regression Tests -Regression tests located in [`test_regression.py`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/test_regression.py){:target="_blank"} require the use of the _VAST_2118-06A_ field test dataset which is not a part of the repository. This data is downloadable from [cloudstor](https://cloudstor.aarnet.edu.au/plus/s/xjh0aRr1EGY6Bt3){:target="_blank"}. You can use the script located in [tests/regression-data/](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"}: +Regression tests located in [`test_regression`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/test_regression/){:target="\_blank"} require the use of the _VAST\_2118-06A_ field test dataset which is not a part of the repository. This data is downloadable from [cloudstor](https://cloudstor.aarnet.edu.au/plus/s/xjh0aRr1EGY6Bt3){:target="_blank"}. You can use the script located in [tests/regression-data/](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"}: ```bash -$ cd vast_pipeline/tests/regression-data/ && ./download.sh +cd vast_pipeline/tests/regression-data/ && ./download.sh ``` -to download the _VAST_2118-06A_ field test dataset into the [`regression-data`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"} folder. Or manually by clicking the button below: +to download the _VAST\_2118-06A_ field test dataset into the [`regression-data`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"} folder. Or manually by clicking the button below: [Download data for test :material-cloud-download-outline:](https://cloudstor.aarnet.edu.au/plus/s/xjh0aRr1EGY6Bt3/download){: .md-button target="_blank"} -and place the _VAST_2118-06A_ field test dataset into the [`regression-data`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"} folder. These regression tests are skipped if the dataset is not present. +and place the _VAST\_2118-06A_ field test dataset into the [`regression-data`](https://github.com/askap-vast/vast-pipeline/blob/master/vast_pipeline/tests/regression-data/){:target="_blank"} folder. These regression tests are skipped if the dataset is not present. All tests should be run before pushing to master. Running all the tests takes a few minutes, so it is not recommended to run them for every change. diff --git a/docs/exploringwebsite/admintools.md b/docs/exploringwebsite/admintools.md index da3489140..a126ca945 100644 --- a/docs/exploringwebsite/admintools.md +++ b/docs/exploringwebsite/admintools.md @@ -5,11 +5,11 @@ Users designated as administrators of the pipeline instance being explored (controlled by GitHub team membership) will be able to see the admin button at the top of the navbar as shown below. -[![Admin Navbar](../img/admin-navbar.png){: loading=lazy }](../img/admin-navbar.png) +![!Admin navbar option.](../img/admin-navbar.png){: loading=lazy } Clicking this button and then selecting the `Django` open will take the user to the Django admin backend interface shown below. -[![Admin Homepage](../img/admin-homepage.png){: loading=lazy }](../img/admin-homepage.png) +![!Admin tools homepage.](../img/admin-homepage.png){: loading=lazy } ## Authentification and Authorization diff --git a/docs/exploringwebsite/datatables.md b/docs/exploringwebsite/datatables.md new file mode 100644 index 000000000..27088fce2 --- /dev/null +++ b/docs/exploringwebsite/datatables.md @@ -0,0 +1,18 @@ +# DataTables + +Much of the data is presented using tables that share consistent functionality across the website. +An example of a table is shown below, note the interactive features across the top of the table, these are explained after the screenshot. + +![!Datatable example.](../img/datatables.png){: loading=lazy } + +* **Show 10 entries**: A selectable limiter of how many rows to display at once (maximum 100). +* **Column visibility**: Enables the user to hide and show columns columns. In the screenshot below the `compactness` column is hidden by deselecting it in the presented list. + ![!Datatable column visibility menu.](../img/datatables-colvis.png){: loading=lazy } +* **CSV**: Will download a CSV file of the data currently shown on screen. +* **Excel**: Will download an Excel file of the data currently shown on screen. + + !!! warning + Note the statement **currently shown on screen** - only this data will be downloaded to the CSV and Excel files. All the records are not able to be downloaded + in this manner - for this it is recommened to interact with the output [parquet files](../outputs/outputs.md). + +* **Search**: A search bar for the user to filter the table to the row they require. The search will take into account all appropriate columns when searching. \ No newline at end of file diff --git a/docs/exploringwebsite/imagepages.md b/docs/exploringwebsite/imagepages.md index 6cedfd7f8..922532997 100644 --- a/docs/exploringwebsite/imagepages.md +++ b/docs/exploringwebsite/imagepages.md @@ -6,15 +6,15 @@ This page details the website pages for information on the images. Shown on this page is a list of images that have been ingested into the pipeline database from **all** pipeline runs, along with their statistics. From this page the full detail page of a specific image can be accessed by clicking on the image name. -Explanation of the table options can be found on the overview page [here](websiteoverview.md#data-tables). +Explanation of the table options can be found in the [DataTables section](datatables.md). -[![VAST Pipeline Images List](../img/image-list.png){: loading=lazy }](../img/image-list.png) +![!Pipeline images table.](../img/image-list.png){: loading=lazy } ## Image Detail Page This page presents all the information about the selected image. -[![VAST Pipeline Image Detail](../img/image-detail1.png){: loading=lazy }](../img/image-detail1.png) +![!Image detail page.](../img/image-detail1.png){: loading=lazy } ### Previous & Next Buttons @@ -44,10 +44,10 @@ Users are able to read and post comments on an image using this form. This table displays all the `Selavy` measurements that were ingested with the image (no forced measurements appear here as they are run specific). The measurement detail page can be reached by clicking the measurement name. -[![VAST Pipeline Image Detail](../img/image-detail2.png){: loading=lazy }](../img/image-detail2.png) +![!Image detail page: measurements table.](../img/image-detail2.png){: loading=lazy } ### Pipeline Runs Table This table displays all the pipeline runs that use the current image. The pipeline detail page can be reached by clicking the run name. -[![VAST Pipeline Image Detail](../img/image-detail3.png){: loading=lazy }](../img/image-detail3.png) +![!Image detail page: runs table.](../img/image-detail3.png){: loading=lazy } diff --git a/docs/exploringwebsite/measurementpages.md b/docs/exploringwebsite/measurementpages.md index 6a87613dc..80a146a78 100644 --- a/docs/exploringwebsite/measurementpages.md +++ b/docs/exploringwebsite/measurementpages.md @@ -6,15 +6,15 @@ This page details the website pages for information on the measurements. A list of measurements that have been ingested into the pipeline database from **all** pipeline runs, along with their statistics, is shown on this page. From this page the full detail page of a specific measurement can be accessed by clicking on the name of the measurement. -Explanation of the table options can be found on the overview page [here](websiteoverview.md#data-tables). +Explanation of the table options can be found in the [DataTables section](datatables.md). -[![VAST Pipeline Measurements List](../img/measurements-list.png){: loading=lazy }](../img/measurements-list.png) +![!Pipeline measurements table.](../img/measurements-list.png){: loading=lazy } ## Measurement Detail Page This page presents all the information about the selected measurement, including a postage stamp cutout of the component. -[![VAST Pipeline Measurements Detail](../img/measurement-detail1.png){: loading=lazy }](../img/measurement-detail1.png) +![!Measurement detail page.](../img/measurement-detail1.png){: loading=lazy } ### SIMBAD, NED, Previous & Next Buttons @@ -29,13 +29,6 @@ These buttons do the following: A text representation of details of the measurement. -### Aladin Lite Viewer - -[Aladin Lite Documentation](https://aladin.u-strasbg.fr/AladinLite/doc/){ target=_blank }. - -The central panel contains an Aladin Lite viewer, which by default displays the HIPS image from the [Rapid ASKAP Continuum Survey](https://research.csiro.au/racs/){ target=_blank }, centred on the location of the measurement. -Other surveys are available such as all epochs of the VAST Pilot Survey (including Stokes V) and other wavelength surveys such as 2MASS. - ### JS9 Viewer [JS9 website](https://js9.si.edu){ target=_blank }. @@ -45,18 +38,25 @@ The right panel contains a JS9 viewer showing the postage stamp FITS image of th !!! note If the image data is removed from its location when the pipeline run was processed the JS9 viewer will no longer work. +### Aladin Lite Viewer + +[Aladin Lite Documentation](https://aladin.u-strasbg.fr/AladinLite/doc/){ target=_blank }. + +The central panel contains an Aladin Lite viewer, which by default displays the HIPS image from the [Rapid ASKAP Continuum Survey](https://research.csiro.au/racs/){ target=_blank }, centred on the location of the measurement. +Other surveys are available such as all epochs of the VAST Pilot Survey (including Stokes V) and other wavelength surveys such as 2MASS. + ### User Comments Users are able to read and post comments on a measurement using this form. -[![VAST Pipeline Measurements Detail](../img/measurement-detail2.png){: loading=lazy }](../img/measurement-detail2.png) +![!Measurement detail page: user comments.](../img/measurement-detail2.png){: loading=lazy } ### Sources Table The sources table shows all the sources, from all pipeline runs, that the measurement is associated to. Explanation of the table options can be found on the overview page [here](websiteoverview.md#data-tables). -[![VAST Pipeline Measurements Detail](../img/measurement-detail3.png){: loading=lazy }](../img/measurement-detail3.png) +![!Measurement detail page: source and siblings tables.](../img/measurement-detail3.png){: loading=lazy } ### Siblings Table diff --git a/docs/exploringwebsite/runpages.md b/docs/exploringwebsite/runpages.md index 831ea36d6..3d01efc55 100644 --- a/docs/exploringwebsite/runpages.md +++ b/docs/exploringwebsite/runpages.md @@ -6,9 +6,9 @@ This page details the website pages for information on the pipeline runs. A list of the pipeline runs that have been processed or initialised are presented on this page along with basic statistics, including the run status. From this page the full detail page of a specific pipeline run can be accessed by clicking on the name of the pipeline run. -Explanation of the table options can be found on the overview page [here](websiteoverview.md#data-tables). +Explanation of the table options can be found in the [DataTables section](datatables.md). -[![VAST Pipeline Runs Table](../img/pipeline-runs.png){: loading=lazy }](../img/pipeline-runs.png) +![!Pipeline Runs table.](../img/pipeline-runs.png){: loading=lazy } ## Pipeline Run Detail Page @@ -17,7 +17,7 @@ This page presents all the information about the pipeline run, including options !!! note For full details on how to process a run please refer to [this page](../using/processrun.md). -[![VAST Pipeline Run Detail](../img/run-detail1.png){: loading=lazy }](../img/run-detail1.png) +![!Pipeline Run detail page.](../img/run-detail1.png){: loading=lazy } ### Summary Cards The cards at the top of the page give a summary of the total numbers of: @@ -43,13 +43,13 @@ A sky map showing the area of sky covered by the images associated with the pipe ### Configuration File -[![VAST Pipeline Run Detail](../img/run-detail2.png){: loading=lazy }](../img/run-detail2.png) +![!Pipeline Run detail page.](../img/run-detail2.png){: loading=lazy } Here the pipeline run configuration file can be viewed, edited and validated. #### Editing the Configuration File -[![VAST Pipeline Run Detail](../img/run-detail3.png){: loading=lazy align=right width=350px}](../img/run-detail3.png) +![!Pipeline Run detail page.](../img/run-detail3.png){: loading=lazy align=right width=350px} To edit the configuration file first select the `Toggle on/off Config Edit` option, that is shown in the screenshot to the right. This will enter edit mode on the configuration file as denoted by the `--Edit Mode--` message shown in the screenshot below. @@ -57,7 +57,7 @@ This will enter edit mode on the configuration file as denoted by the `--Edit Mo !!! warning Do not toggle off edit mode without first selecting `Wrtie Current Config` otherwise changes will be lost. -[![VAST Pipeline Run Detail](../img/run-detail6.png){: loading=lazy }](../img/run-detail6.png) +![!VAST Pipeline Run Detail](../img/run-detail6.png){: loading=lazy } When all changes are applied, select the `Write Current Config` to save the changes. @@ -65,9 +65,9 @@ When all changes are applied, select the `Write Current Config` to save the chan From the configuration file menu select the `Validate Config` option. A feedback modal will then appear with feedback stating whether the configuration validation was successful or failed. -The feeback may take a moment to appear as the check is performed. +The feedback may take a moment to appear as the check is performed. -[![VAST Pipeline Run Detail](../img/run-detail7.png){: loading=lazy }](../img/run-detail7.png) +![!Configuration is valid confirmation.](../img/run-detail7.png){: loading=lazy } ### User Comments @@ -75,7 +75,7 @@ Users are able to read and post comments on a pipeline run using this form. ### Log File -[![VAST Pipeline Run Detail](../img/run-detail4.png){: loading=lazy }](../img/run-detail4.png) +![!Run log file.](../img/run-detail4.png){: loading=lazy } The full log file of the pipeline run is able to viewed. diff --git a/docs/exploringwebsite/sourcepages.md b/docs/exploringwebsite/sourcepages.md index 4a64ee334..281426fe4 100644 --- a/docs/exploringwebsite/sourcepages.md +++ b/docs/exploringwebsite/sourcepages.md @@ -11,7 +11,7 @@ Once the form is submitted the results are dynamically updated in the results ta The following sections provide further details on the form. -[![VAST Pipeline Source Query](../img/source-query-form.png){: loading=lazy }](../img/source-query-form.png) +![!The source query form.](../img/source-query-form.png){: loading=lazy } ### Data Source @@ -35,8 +35,8 @@ The format of the coordinates should be in a standard format that is recognised Galactic coordinates can also be entered by selecting `Galactic` from the dropdown menu that is set to `ICRS` by default. Feedback will be given immediately whether the coordinates are valid, as shown in the screenshots below: -[![VAST Pipeline Source Query Cone Search](../img/cone-search-ok.png){: loading=lazy }](../img/cone-search-ok.png) -[![VAST Pipeline Source Query Cone Search](../img/cone-search-bad.png){: loading=lazy }](../img/cone-search-bad.png) +![!Cone search: accepted coordinate input.](../img/cone-search-ok.png){: loading=lazy } +![!Cone search: rejected coordinate input.](../img/cone-search-bad.png){: loading=lazy } Once the coordinates have been entered the radius value must also be specified as shown in the screenshot above. Use the dropdown menu to change the radius unit to be `arcsec`, `arcmin` or `deg`. @@ -45,11 +45,11 @@ Once the coordinates have been entered the radius value must also be specified a To use the name resolver, the name of the source should be entered into the `Object Name` field (e.g. `PSR J2129-04`), select the name resolver service and then click the `Resolve` button. The coordinates will then be automatically filled on a successful match. -[![VAST Pipeline Source Query Cone Search](../img/cone-search-resolve.png){: loading=lazy }](../img/cone-search-resolve.png) +![!Cone search: successful name resolver.](../img/cone-search-resolve.png){: loading=lazy } if no match is found then this will be communicated by the form as below: -[![VAST Pipeline Source Query Cone Search](../img/cone-search-resolver-bad.png){: loading=lazy }](../img/cone-search-resolver-bad.png) +![!Cone search: unsuccessful name resolver.](../img/cone-search-resolver-bad.png){: loading=lazy } ### Table Filters @@ -60,13 +60,13 @@ The following options are not standard source metrics: #### Include and Exclude Tags -Users can attach tags to sources (see [Tags and Favourites](#tags-and-favourites)) and here tags can be selected to include or exclude in the source search. +Users can attach tags to sources (see [Source Tags and Favourites](sourcetagsfavs.md)) and here tags can be selected to include or exclude in the source search. #### Source Selection Here specific sources can be searched for by entering the source names, or source database `id` values, in a comma-separated list. For example: -* `ASKAP_011816.05-730747.77,ASKAP_011816.05-730747.77,ASKAP_213221.21-040900.42` +* `J011816.05-730747.77,J011816.05-730747.77,J213221.21-040900.42` * `1031,1280,52` are valid entries to this search field. Use the dropdown menu to declare whether `name` (default) or `id` values are being searched. @@ -75,21 +75,21 @@ are valid entries to this search field. Use the dropdown menu to declare whether Located directly below the form is the results table which is dynamically updated once the form is submitted. The full detail page of a specific source can be accessed by clicking on the source name in the table. -Explanation of the table options can be found on the overview page [here](websiteoverview.md#data-tables). +Explanation of the table options can be found in the [DataTables section](datatables.md). -[![VAST Pipeline Source Query](../img/source-query-results.png){: loading=lazy }](../img/source-query-results.png) +![!Source query results table.](../img/source-query-results.png){: loading=lazy } ## Source Detail Page This page presents all the information about the selected source, including a light curve and cutouts of all the measurements that are associated to the source. -[![VAST Pipeline Source Detail](../img/source-detail1.png){: loading=lazy }](../img/source-detail1.png) +![!Source detail page.](../img/source-detail1.png){: loading=lazy } ### Star, SIMBAD, NED, Previous & Next Buttons These buttons do the following: -* **Star**: Adds the source to the user's favourites, see [Tags and Favourites](#tags-and-favourites). +* **Star**: Adds the source to the user's favourites, see [Source Tags and Favourites](sourcetagsfavs.md). * **SIMBAD**: Performs a cone search on SIMBAD with a radius of 10 arcmin centered on the source location. * **NED**: Performs a cone search on NED with a radius of 10 arcmin centered on the source location. * **Previous**: Navigates to the previous source that was returned in the source query. @@ -97,11 +97,11 @@ These buttons do the following: ### Details -A text representation of details of the measurement. +A text representation of details of the source, including position, number of measurements and whether the source is defined as `new`. -### User Comments & Tags +### First Detection Postage Stamp -Users are able to read and post comments on a measurement using this form, in addition to adding and removing tags, see [Tags and Favourites](#tags-and-favourites). +Shown in this panel is a postage stamp of the first detection of the source in the pipeline run. Postage stamps of all measurements can be seen in the [main postage stamp section](#js9-viewer-postage-stamps) lower on the page. ### Aladin Lite Viewer @@ -110,12 +110,16 @@ Users are able to read and post comments on a measurement using this form, in ad The central panel contains an Aladin Lite viewer, which by default displays the HIPS image from the [Rapid ASKAP Continuum Survey](https://research.csiro.au/racs/){ target=_blank }, centred on the location of the source. Other surveys are available such as all epochs of the VAST Pilot Survey (including Stokes V) and other wavelength surveys such as 2MASS. +### Flux & Variability Details + +The flux details, both integrated and peak, of the source. Also shown are the variability parameters calculated by the pipeline. + +![!Source detail page: Flux and variability details, light curve and the node graph.](../img/source-detail2.png){: loading=lazy } + ### Light Curve The light curve of the source is shown. The peak or integrated flux can be selected by using the radio selection buttons. -[![VAST Pipeline Source Detail](../img/source-detail2.png){: loading=lazy }](../img/source-detail2.png) - ### Two-epoch Node Graph The node graph is a visual representation of what two-epoch pairings have significant variability metric values. @@ -126,6 +130,12 @@ If an epoch pairing is significant then they are joined by a line on the graph. This table shows the result of a query to the SIMBAD and NED services for astronomical sources within 1 arcmin of the source location. Along with the name and coordinate of the matches, the on-sky separation between the source is shown along with the source type. +![!Source detail page: External results table and the user comments field.](../img/source-detail3.png){: loading=lazy } + +### User Comments & Tags + +Users are able to read and post comments on a measurement using this form, in addition to adding and removing tags, see [Source Tags and Favourites](sourcetagsfavs.md). + ### JS9 Viewer Postage Stamps [JS9 website](https://js9.si.edu){ target=_blank }. @@ -135,63 +145,14 @@ The JS9 viewer is used to show the postage stamp FITS images of the measurements !!! note If the image data is removed from its location when the pipeline run was processed the JS9 viewer will no longer work. -[![VAST Pipeline Source Detail](../img/source-detail3.png){: loading=lazy }](../img/source-detail3.png) +![!Source detail page: postage stamps.](../img/source-detail4.png){: loading=lazy } ### Source Measurements Table This table displays the measurements that are associated with the source. The detail page for the measurement can be reached by clicking the name of the respective measurement. -[![VAST Pipeline Source Detail](../img/source-detail4.png){: loading=lazy }](../img/source-detail4.png) +![!Source detail page: measurement and related tables.](../img/source-detail5.png){: loading=lazy } ### Related Sources Table This table displays the sources that are a relation of the source in question. For further information refer to the [Relations](../design/association.md#relations) section in the association documentation. - -## Tags and Favourites - -Users are able to save a source as a favourite for later reference, in addition to adding `tags` to sources that can be used in source queries. - -### Adding a Source to Favourites - -A source can be added to a user's favourites by: - -1. Selecting the 'star' button at the top of the source detail page as shown below. - - [![VAST Pipeline Source Favourite](../img/source-add-fav.png){: loading=lazy width=600px }](../img/source-add-fav.png) - -2. A modal window will open to confirm the saving of the source as a favourite. An optional comment can be entered. - - [![VAST Pipeline Source Favourite](../img/source-add-fav-modal.png){: loading=lazy }](../img/source-add-fav-modal.png) - -3. Select `Add to Favourites` and a confirmation alert will be shown to signify the source has been added successfully. - - [![VAST Pipeline Source Favourite](../img/source-add-fav-confirm.png){: loading=lazy width=600px }](../img/source-add-fav-confirm.png) - - -### Viewing Favourite Sources - -A user can access their favourite sources by selecting the `Favourite Sources` option from the menu when clicking on their username at the top right-hand corner of the page. - -[![VAST Pipeline User Favourites](../img/source-user-fav.png){: loading=lazy width=400px }](../img/source-user-fav.png) - -The user will then be navigated to their favourite sources table as shown below. - -[![VAST Pipeline User Favourites](../img/user-fav-sources.png){: loading=lazy }](../img/user-fav-sources.png) - -### Adding a Tag - -Follow these steps to add a tag to a source: - -1. Type the tag to be added into the field tag field. -2. If the tag has already been used it will appear in the dropdown text options and can be selected by clicking the text. To add a new tag, enter the complete text of the new tag and again click the text in the dropdown text. -3. After clicking the text the tag will then show as a bordered tag in the input field. -4. Finally, click the submit button (a comment is optional) and the tag will be saved as shown below. A comment will appear stating the addition of the tag. - -[![VAST Pipeline Source Add Tag](../img/source-add-tag1.png){: loading=lazy align=left width=350px }](../img/source-add-tag1.png) -[![VAST Pipeline Source Add Tag](../img/source-add-tag3.png){: loading=lazy align=right width=350px }](../img/source-add-tag3.png) - -### Removing a Tag - -Click the `x` on the tag to remove it and then click the `Submit` button to save the removal. - -[![VAST Pipeline Source Add Tag](../img/source-tag-remove.png){: loading=lazy width=350px }](../img/source-tag-remove.png) diff --git a/docs/exploringwebsite/sourcetagsfavs.md b/docs/exploringwebsite/sourcetagsfavs.md new file mode 100644 index 000000000..8aabde012 --- /dev/null +++ b/docs/exploringwebsite/sourcetagsfavs.md @@ -0,0 +1,48 @@ +# Source Tags and Favourites + +Users are able to save a source as a favourite for later reference, in addition to adding `tags` to sources that can be used in source queries. + +## Adding a Source to Favourites + +A source can be added to a user's favourites by: + +1. Selecting the 'star' button at the top of the source detail page as shown below. + + ![!Add to favourites button on the source detail page.](../img/source-add-fav.png){: loading=lazy width=600px } + +2. A modal window will open to confirm the saving of the source as a favourite. An optional comment can be entered. + + ![!Add source to favourites confirmation.](../img/source-add-fav-modal.png){: loading=lazy } + +3. Select `Add to Favourites` and a confirmation alert will be shown to signify the source has been added successfully. + + ![!Source added to favourites confirmation.](../img/source-add-fav-confirm.png){: loading=lazy width=600px } + + +## Viewing Favourite Sources + +A user can access their favourite sources by selecting the `Favourite Sources` option from the menu when clicking on their username at the top right-hand corner of the page. + +![!View favourite sources menu.](../img/source-user-fav.png){: loading=lazy width=400px } + +The user will then be navigated to their favourite sources table as shown below. + +![!User favourite sources page.](../img/user-fav-sources.png){: loading=lazy } + +## Adding a Tag + +Follow these steps to add a tag to a source: + +1. Type the tag to be added into the field tag field. +2. If the tag has already been used it will appear in the dropdown text options and can be selected by clicking the text. To add a new tag, enter the complete text of the new tag and again click the text in the dropdown text. +3. After clicking the text the tag will then show as a bordered tag in the input field. +4. Finally, click the submit button (a comment is optional) and the tag will be saved as shown below. A comment will appear stating the addition of the tag. + +![!Adding a source tag entry.](../img/source-add-tag1.png){: loading=lazy align=left width=350px } +![!Adding a source tag success.](../img/source-add-tag3.png){: loading=lazy align=right width=350px } + +## Removing a Tag + +Click the `x` on the tag to remove it and then click the `Submit` button to save the removal. + +![!Source tag removed confirmation.](../img/source-tag-remove.png){: loading=lazy width=350px } diff --git a/docs/exploringwebsite/websiteoverview.md b/docs/exploringwebsite/websiteoverview.md index 3161ea797..31242d6a4 100644 --- a/docs/exploringwebsite/websiteoverview.md +++ b/docs/exploringwebsite/websiteoverview.md @@ -4,11 +4,11 @@ This page gives an overview of the pipeline website, with links to main pages on Refer to [Accessing the Pipeline](../using/access.md) for details on how to access the pipeline instance that is hosted by the VAST collaboration. -For admins, refer to the following pages for details of the configuration and set up of the web server: [Configuration](../quickstart/configuration.md), [Deployment](../quickstart/deployment.md) and [Web App Admin Usage](../adminusage/app.md). +For admins, refer to the following pages for details of the configuration and set up of the web server: [Configuration](../gettingstarted/configuration.md), [Deployment](../gettingstarted/deployment.md) and [Web App Admin Usage](../adminusage/app.md). ## Homepage -[![VAST Pipeline Homepage](../img/homepage.png){: loading=lazy }](../img/homepage.png) +![!VAST Pipeline homepage.](../img/homepage.png){: loading=lazy } The homepage provides a summary of the data currently held in the pipeline instance that has been processed. The four cards at the top of the homepage provide total values for the amount of pipeline runs, images, measurements and sources that are stored in the database. Clicking any of them will take you to the respective overview page for the data type. @@ -21,7 +21,7 @@ Also displayed is a sky region map that shows all the areas of the sky that have ## Navbar -[![VAST Pipeline Navbar](../img/navbar.png){: loading=lazy align=right width=80px }](../img/navbar.png) +![!VAST Pipeline navbar.](../img/navbar.png){: loading=lazy align=right width=80px } The navbar, shown to the right, acts as the main method in which to navigate around the website. The following sections link to the respective documentation pages explainging the features of each link. @@ -76,22 +76,3 @@ From here users can also access the detail page for individual images. - **JupyterHub**: Links to the VAST hosted JupyterHub instance which includes access to the pipeline results and `vast-tools`. - **Website**: Links to the VAST collaboration website. - **Wiki**: Links to the VAST Wiki which is hosted on GitHub. - -## Data Tables - -Much of the data is presented using tables that share consistent functionality across the website. -An example of a table is shown below, note the interactive features across the top of the table, these are explained after the screenshot. - -[![VAST Pipeline Datatable](../img/datatables.png){: loading=lazy }](../img/datatables.png) - -* **Show 10 entries**: A selectable limiter of how many rows to display at once (maximum 100). -* **Column visibility**: Enables the user to hide and show columns columns. In the screenshot below the `compactness` column is hidden by deselecting it in the presented list. - [![VAST Pipeline Datatable Column Visibility](../img/datatables-colvis.png){: loading=lazy }](../img/datatables-colvis.png) -* **CSV**: Will download a CSV file of the data currently shown on screen. -* **Excel**: Will download an Excel file of the data currently shown on screen. - - !!! warning - Note the statement **currently shown on screen** - only this data will be downloaded to the CSV and Excel files. All the records are not able to be downloaded - in this manner - for this it is recommened to interact with the output [parquet files](../outputs/outputs.md). - -* **Search**: A search bar for the user to filter the table to the row they require. The search will take into account all appropriate columns when searching. \ No newline at end of file diff --git a/docs/faqs.md b/docs/faq.md similarity index 68% rename from docs/faqs.md rename to docs/faq.md index 07c7061da..d15a40daa 100644 --- a/docs/faqs.md +++ b/docs/faq.md @@ -20,3 +20,19 @@ Please open a discussion or issue on GitHub if you intend to give this a go! This is unintentional as there is nothing special about the FITS headers being read. Worth to check if anyone goes down this path. - Adam, March 2021. +### Does the pipeline support any other Stokes products such as Stokes V? + +Currently the pipeline only supports Stokes I data. + +Users can view Stokes V HIPS maps of the RACS and VAST surveys in the Aladin Lite tool on the [source detail page](exploringwebsite/sourcepages.md#source-detail-page). + +The support of Stokes V is [planned in a future update](https://github.com/askap-vast/vast-pipeline/issues/223){:target="_blank"}. + +### Can the pipeline handle multi-frequency datasets? + +Currently the pipeline does not support multi-frequency datasets. Any images that are put through in a run are assumed by the pipeline to be directly comparable to one another. +For example, all variability metrics are calculated directly on the fluxes provided from the source catalogues. + +Multi-frequency support is [planned in a future update](https://github.com/askap-vast/vast-pipeline/issues/467). + + diff --git a/docs/gen_doc_stubs.py b/docs/gen_doc_stubs.py index 28e5de6a2..29249b125 100755 --- a/docs/gen_doc_stubs.py +++ b/docs/gen_doc_stubs.py @@ -11,7 +11,7 @@ # See https://github.com/mkdocstrings/mkdocstrings/issues/141 # __init__ is there just to avoid building these. # TODO: Fix Django pages for mkdocs. -problem_files = ['serializers.py', 'views.py', '__init__.py'] +problem_files = ['serializers.py', 'views.py', '__init__.py', '_version.py'] for path in Path("vast_pipeline").glob("**/*.py"): diff --git a/docs/quickstart/configuration.md b/docs/gettingstarted/configuration.md similarity index 52% rename from docs/quickstart/configuration.md rename to docs/gettingstarted/configuration.md index de0640f5f..ab85d18f3 100644 --- a/docs/quickstart/configuration.md +++ b/docs/gettingstarted/configuration.md @@ -52,7 +52,7 @@ The following instructions, will get you started in setting up the database and Done! ``` -2. Copy the setting configuration file template and modify it with your desired settings (see [defaults](https://github.com/askap-vast/vast-pipeline/blob/master/webinterface/.env.template){:target="_blank"}). +2. Copy the setting configuration file template and modify it with your desired settings. Please refer to the [.env File](#.env-file) section on this page for further details about the settings that are set in this file along with their defaults. ```console cp webinterface/.env.template webinterface/.env @@ -77,7 +77,6 @@ The following instructions, will get you started in setting up the database and 5. Create the pipeline data directories. The pipeline has several directories that can be configured in `webinterface/.env`: * `PIPELINE_WORKING_DIR`: location to store various pipeline output files. - * `SURVEYS_WORKING_DIR`: location of reference survey catalogues, e.g. NVSS, SUMSS. * `RAW_IMAGE_DIR`: default location that the pipeline will search for input images and catalogues to ingest during a pipeline run. Data inputs can also be defined as absolute paths in a pipeline run configuration file, so this setting only affects relative paths in the pipeline run configuration. * `HOME_DATA_DIR`: additional location to search for input images and catalogues that is relative to the user's home directory. Intended for multi-user server deployments and unlikely to be useful for local installations. @@ -86,7 +85,6 @@ The following instructions, will get you started in setting up the database and ```console mkdir -p /data/vast-pipeline mkdir /data/vast-pipeline/pipeline-runs - mkdir /data/vast-pipeline/reference-surveys mkdir /data/vast-pipeline/raw-images mkdir /data/vast-pipeline/vast-pipeline-extra-data ``` @@ -95,14 +93,100 @@ The following instructions, will get you started in setting up the database and ```bash PIPELINE_WORKING_DIR=/data/vast-pipeline/pipeline-runs - SURVEYS_WORKING_DIR=/data/vast-pipeline/reference-surveys RAW_IMAGE_DIR=/data/vast-pipeline/raw-images HOME_DATA_DIR=/data/vast-pipeline/vast-pipeline-extra-data ``` +## .env File + +The `.env` file contains various top-level settings that apply to Django, authentication and the running of the pipeline itself. +Shown below is the [`.env.template`](https://github.com/askap-vast/vast-pipeline/blob/master/webinterface/.env.template){:target="_blank"} file which is provided to be able to copy in step 3 above. + +!!! example ".env.template" + ```console + # Django + DEBUG=True + SECRET_KEY=FillMeUPWithSomeComplicatedString + # see https://django-environ.readthedocs.io/en/latest/#tips + DATABASE_URL=psql://FILLMYUSER:FILLMYPASSWORD@FILLMYHOST:FILLMYPORT/FILLMYDBNAME + # BASE_URL=this for append a base url in a production deployment + STATIC_ROOT=./staticfiles/ + STATIC_URL=/static/ + # STATICFILES_DIRS= uncomment and fill to use + # EXTRA_APPS= uncomment and fill to use + # EXTRA_MIDDLEWARE= uncomment and fill to use + ALLOWED_HOSTS=localhost + + # Github Authentication + GITHUB_AUTH_TYPE='org' + SOCIAL_AUTH_GITHUB_KEY=fillMeUp + SOCIAL_AUTH_GITHUB_SECRET=fillMeUp + SOCIAL_AUTH_GITHUB_ORG_NAME=fillMeUp + SOCIAL_AUTH_GITHUB_ADMIN_TEAM=fillMeUp + + # Pipeline + PIPELINE_WORKING_DIR=pipeline-runs + FLUX_DEFAULT_MIN_ERROR=0.001 + POS_DEFAULT_MIN_ERROR=0.01 + RAW_IMAGE_DIR=raw-images + HOME_DATA_DIR=vast-pipeline-extra-data + # PIPELINE_MAINTAINANCE_MESSAGE=Uncomment and fill to show + MAX_PIPELINE_RUNS=3 + MAX_PIPERUN_IMAGES=200 + ``` + +The available settings are grouped into three distinct categories: + +### Django + +These settings are standard Django settings that are commonly set in the `settings.py` file of Django projects. +Please see [this page](https://docs.djangoproject.com/en/3.2/ref/settings/){:target="_blank"} in the Django documentation for explanations on their meaning. +Multiple entries for settings such as `EXTRA_APPS` or `EXTRA_MIDDLEWARE` can be entered as comma-separated strings like the following example: + +```console +EXTRA_APPS=django_extensions,debug_toolbar +``` + +### GitHub Authentication + +The settings in this section control the GitHub organization authentication method. +Please refer to the [Python Social Auth documentation](https://python-social-auth.readthedocs.io/en/latest/backends/github.html){:target="_blank"} for descriptions of the required settings. + +!!! note + By default the pipeline is set up for authentication using GitHub organizations. Note that switching to teams will require changes to `settings.py`. + Please refer to the instructions in the [Python Social Auth documentation](https://python-social-auth.readthedocs.io/en/latest/backends/github.html){:target="_blank"}. + +### Pipeline + +These settings apply to various aspects of the VAST pipeline itself. The table below provides descriptions of each setting. + +| Setting | Default Value | Description | +| ------------------------ | ------- | ----------- | +| `PIPELINE_WORKING_DIR` | pipeline-runs | The name of the working directory where pipeline run directories are created. The pipeline location acts as the root directory. | +| `FLUX_DEFAULT_MIN_ERROR` | 0.001 | In the event a measurement is ingested with a flux error of 0 from Selavy, the error is replaced with this default value (mJy). | +| `POS_DEFAULT_MIN_ERROR` | 0.01 | In the event a measurement is ingested with an positional error of 0 from Selavy, the error is replaced with this default value (arcsec). | +| `RAW_IMAGE_DIR` | raw-images | Directory where the majority of raw ASKAP FITS images are expected to be stored. This directory is scanned to provide user with an image list when configuration a job using the website interface. | +| `HOME_DATA_DIR` | vast-pipeline-extra-data | Not currently used. Safe to ignore. | +| `PIPELINE_MAINTAINANCE_MESSAGE` | Disabled | The message to display at the top of the webserver. See image below this table for an example. Comment out the setting to disable. | +| `MAX_PIPELINE_RUNS` | 3 | The allowed maximum number of concurrent pipeline runs. | +| `MAX_PIPERUN_IMAGES` | 200 | The allowed maximum number of images in a single pipeline run (non-admins). | + +#### Maintenance Message Example + +```console +PIPELINE_MAINTAINANCE_MESSAGE=This website is subject to rapid changes which may result in data loss and may go offline with minimal warning. Please be mindful of usage. +``` + +![!Maintenance message example.](../img/maintenance-message.png){: loading=lazy } + ## Authentication -The pipeline supports two authentication methods: GitHub Teams, intended to multi-user server deployments; and local Django administrator. For a single-user local installation, we recommend creating a Django superuser account. +The pipeline supports two authentication methods: GitHub Organizations, intended to multi-user server deployments; and local Django administrator. For a single-user local installation, we recommend creating a Django superuser account. + +### GitHub Organizations + +Please refer to the [Python Social Auth documentation](https://python-social-auth.readthedocs.io/en/latest/backends/github.html){:target="_blank"} for a complete description on this authentication method and how to set up the GitHub app used for authentication. +All settings are entered into the `.env` file as detailed in the [above section](#.env-file). ### Django superuser diff --git a/docs/quickstart/deployment.md b/docs/gettingstarted/deployment.md similarity index 86% rename from docs/quickstart/deployment.md rename to docs/gettingstarted/deployment.md index 5ea1655c7..b1e76ef92 100644 --- a/docs/quickstart/deployment.md +++ b/docs/gettingstarted/deployment.md @@ -52,7 +52,9 @@ The following steps describes how to set up the Django side of the production de ### Extra Service(s) Deployment -In order to run a pipeline run from the Web App, the `Django-Q` process need to be started and managed as a service by the OS. In order to do so we recommend building a unit/systemd file to manage the `Django-Q` process, in a similar way of the `gunicorn` process (following the [Jupyter Hub docs](https://jupyterhub.readthedocs.io/en/stable/installation-guide-hard.html#setup-systemd-service){:target="_blank"}): +#### Django Q + +In order to run a pipeline run from the Web App, the `Django Q` process needs to be started and managed as a service by the OS. In order to do so we recommend building a unit/systemd file to manage the `Django Q` process, in a similar way of the `gunicorn` process (following the [Jupyter Hub docs](https://jupyterhub.readthedocs.io/en/stable/installation-guide-hard.html#setup-systemd-service){:target="_blank"}): ```bash ... @@ -62,7 +64,7 @@ ExecStart=/opt/vast-pipeline/venv/bin/python manage.py qcluster ``` !!! tip "Tip" - In the examples above I decided to install the Python virtual enviroment of the pipeline, in `venv` folder under the cloned repository + In the examples above, the Python virtual enviroment used by the pipeline is installed in the `venv` folder under the cloned repository. ## Security diff --git a/docs/quickstart/installation.md b/docs/gettingstarted/installation.md similarity index 100% rename from docs/quickstart/installation.md rename to docs/gettingstarted/installation.md diff --git a/docs/help_and_acknowledgements.md b/docs/help_and_acknowledgements.md new file mode 100644 index 000000000..bc349c509 --- /dev/null +++ b/docs/help_and_acknowledgements.md @@ -0,0 +1,32 @@ +# Help and Acknowledgements + +## Getting Help + +The best way to get help with the VAST Pipeline software is to contact the development team on GitHub. If you have encountered a specific problem while using the pipeline or attempting to install any of the components, please open a [new issue](https://github.com/askap-vast/vast-pipeline/issues/new). If you have a more general question or an idea for a new feature, please create a [new discussion thread](https://github.com/askap-vast/vast-pipeline/discussions/new). + +General enquiries may also be sent via email to the VAST project Principal Investigators: + +* [Tara Murphy](mailto:tara.murphy@sydney.edu.au) +* [David Kaplan](mailto:kaplan@uwm.edu) + +## Contributors + +* Sergio Pintaldi – [Sydney Informatics Hub](https://informatics.sydney.edu.au) +* Adam Stewart – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) +* Andrew O'Brien – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/) +* Tara Murphy – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) +* David Kaplan – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/) +* Shibli Saleheen – [ADACS](https://adacs.org.au/who-we-are/our-team/) +* David Liptai – [ADACS](https://adacs.org.au/who-we-are/our-team/) +* Ella Xi Wang – [ADACS](https://adacs.org.au/who-we-are/our-team/) + +## Acknowledgements + +The VAST Pipeline development was supported by: + +* The Australian Research Council through grants FT150100099 and DP190100561. +* The Sydney Informatics Hub (SIH), a core research facility at the University of Sydney. +* Software support resources awarded under the Astronomy Data and Computing Services (ADACS) Merit Allocation Program. ADACS is funded from the Astronomy National Collaborative Research Infrastructure Strategy (NCRIS) allocation provided by the Australian Government and managed by Astronomy Australia Limited (AAL). +* NSF grant AST-1816492. + +The developers thank the creators of [SB Admin 2](https://github.com/StartBootstrap/startbootstrap-sb-admin-2) to make the dashboard template freely available. diff --git a/docs/img/add-images-config.png b/docs/img/add-images-config.png index 18248b80c..7205337e5 100644 Binary files a/docs/img/add-images-config.png and b/docs/img/add-images-config.png differ diff --git a/docs/img/association_false_variability_lc.png b/docs/img/association_false_variability_lc.png new file mode 100644 index 000000000..52fb52d32 Binary files /dev/null and b/docs/img/association_false_variability_lc.png differ diff --git a/docs/img/association_false_variability_lc_relation.png b/docs/img/association_false_variability_lc_relation.png new file mode 100644 index 000000000..033b30f86 Binary files /dev/null and b/docs/img/association_false_variability_lc_relation.png differ diff --git a/docs/img/association_false_variability_stamps.png b/docs/img/association_false_variability_stamps.png new file mode 100644 index 000000000..daf715635 Binary files /dev/null and b/docs/img/association_false_variability_stamps.png differ diff --git a/docs/img/docs-home.png b/docs/img/docs-home.png new file mode 100644 index 000000000..758916168 Binary files /dev/null and b/docs/img/docs-home.png differ diff --git a/docs/img/maintenance-message.png b/docs/img/maintenance-message.png new file mode 100644 index 000000000..6df7a4ac9 Binary files /dev/null and b/docs/img/maintenance-message.png differ diff --git a/docs/img/measurement-detail1.png b/docs/img/measurement-detail1.png index bd8a6b835..63d0f37f9 100644 Binary files a/docs/img/measurement-detail1.png and b/docs/img/measurement-detail1.png differ diff --git a/docs/img/measurement-detail2.png b/docs/img/measurement-detail2.png index f78d5014b..62dbbb122 100644 Binary files a/docs/img/measurement-detail2.png and b/docs/img/measurement-detail2.png differ diff --git a/docs/img/process-run-modal.png b/docs/img/process-run-modal.png index 3399cec92..54c1c547f 100644 Binary files a/docs/img/process-run-modal.png and b/docs/img/process-run-modal.png differ diff --git a/docs/img/rundetail-validate-config-feedback.png b/docs/img/rundetail-validate-config-feedback.png index e4fa46889..2f1ed661c 100644 Binary files a/docs/img/rundetail-validate-config-feedback.png and b/docs/img/rundetail-validate-config-feedback.png differ diff --git a/docs/img/rundetail-validate-config.png b/docs/img/rundetail-validate-config.png index f8f26ac6e..acd958bba 100644 Binary files a/docs/img/rundetail-validate-config.png and b/docs/img/rundetail-validate-config.png differ diff --git a/docs/img/schema.png b/docs/img/schema.png index 5593a4848..9db429fb2 100644 Binary files a/docs/img/schema.png and b/docs/img/schema.png differ diff --git a/docs/img/schema_pipeline.png b/docs/img/schema_pipeline.png index 59e52feeb..a6dc31e17 100644 Binary files a/docs/img/schema_pipeline.png and b/docs/img/schema_pipeline.png differ diff --git a/docs/img/source-detail-full copy 2.png b/docs/img/source-detail-full copy 2.png deleted file mode 100644 index 8c96cb776..000000000 Binary files a/docs/img/source-detail-full copy 2.png and /dev/null differ diff --git a/docs/img/source-detail1.png b/docs/img/source-detail1.png index 581c3bc55..502e4788f 100644 Binary files a/docs/img/source-detail1.png and b/docs/img/source-detail1.png differ diff --git a/docs/img/source-detail2.png b/docs/img/source-detail2.png index a87eb8348..8a0a698f1 100644 Binary files a/docs/img/source-detail2.png and b/docs/img/source-detail2.png differ diff --git a/docs/img/source-detail3.png b/docs/img/source-detail3.png index c6d57f433..d7f770685 100644 Binary files a/docs/img/source-detail3.png and b/docs/img/source-detail3.png differ diff --git a/docs/img/source-detail4.png b/docs/img/source-detail4.png index 535a8de44..e09597fe5 100644 Binary files a/docs/img/source-detail4.png and b/docs/img/source-detail4.png differ diff --git a/docs/img/source-detail5.png b/docs/img/source-detail5.png new file mode 100644 index 000000000..1eeb44f69 Binary files /dev/null and b/docs/img/source-detail5.png differ diff --git a/docs/img/vast-logo.png b/docs/img/vast-logo.png new file mode 100644 index 000000000..cec4b3170 Binary files /dev/null and b/docs/img/vast-logo.png differ diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 000000000..d1c3314a8 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,4 @@ +--- +title: VAST Pipeline +template: home.html +--- diff --git a/docs/outputs/outputs.md b/docs/outputs/outputs.md index cc139fbaf..754eee30e 100644 --- a/docs/outputs/outputs.md +++ b/docs/outputs/outputs.md @@ -1,26 +1,27 @@ + # Outputs Overview This page gives details on the output files that the pipeline writes to disk. ## Pipeline Run Output Overview -The output for a pipeline run will be located in the pipeline working directory, which is defined at the pipeline configuration stage (see [Pipeline Configuration](../quickstart/configuration.md#pipeline-configuration)). -A sub-directory will exist for each pipeline run that contains the output products for the run. +The output for a pipeline run will be located in the pipeline working directory, which is defined at the pipeline configuration stage (see [Pipeline Configuration](../gettingstarted/configuration.md#pipeline-configuration)). +A sub-directory will exist for each pipeline run that contains the output products for the run. !!! note If you do not administrate your system or do not have access to a `vast-tools` notebook interface, please contact your system admin to confirm the working directory and how to best access the files. The pipeline uses the [Apache Parquet](https://parquet.apache.org){:target="_blank"} file format to write results to disk. Details on how to read these files can be found below in [Reading the Outputs](#reading-the-outputs). -Below is the output structure for a pipeline run named `new-test-data` when the pipeline run option `CREATE_MEASUREMENTS_ARROW_FILES` has been set to `True` and the working directory is named `pipeline-runs` (see [File Details](#file-details) for descriptions): +Below is the output structure for a pipeline run named `new-test-data` when the pipeline run option `measurements.write_arrow_files` has been set to `True` and the working directory is named `pipeline-runs` (see [File Details](#file-details) for descriptions): ```bash pipeline-runs ├── new-test-data │   ├── associations.parquet │   ├── bands.parquet -│   ├── config.py -│   ├── config_prev.py +│   ├── config.yaml +│   ├── config_prev.yaml │   ├── forced_measurements_VAST_0127-73A_EPOCH01_I_cutout_fits.parquet │   ├── forced_measurements_VAST_0127-73A_EPOCH05x_I_cutout_fits.parquet │   ├── forced_measurements_VAST_0127-73A_EPOCH06x_I_cutout_fits.parquet @@ -46,8 +47,9 @@ pipeline-runs ``` ### Arrow Files -Large pipeline runs (hundreds of images) mean that to read the measurements, hundreds of parquet files need to be read in, and can contain millions of rows. -This can be slow using libraries such as pandas, and also consumes a lot of system memory. + +Large pipeline runs (hundreds of images) mean that to read the measurements, hundreds of parquet files need to be read in, and can contain millions of rows. +This can be slow using libraries such as pandas, and also consumes a lot of system memory. A solution to this is to save all the measurements associated with the pipeline run into one single file in the [Apache Arrow](https://arrow.apache.org/overview/){:target="_blank"} format. The library `vaex` is able to open `.arrow` files in an out-of-core context so the memory footprint is hugely reduced along with the reading of the file being very fast. @@ -56,10 +58,10 @@ The two-epoch measurement pairs are also saved to arrow format due to the same r !!! note At the time of development `vaex` could not open parquets in an out-of-core context. This will be reviewed in the future if such functionality is added to `vaex`. -!!! bug - Currently the arrow files cannot be generated by runs that are processed through the website. In this case please contact the pipeline administrator who can generate the arrow files after a run has successfully completed (refer to the admin command [`createmaeasarrow`](../adminusage/cli.md#createmeasarrow)). +!!! tip + The arrow files can be generated after a run has successfully completed (must be done by an administrator, refer to the admin command [`createmaeasarrow`](../adminusage/cli.md#createmeasarrow)). -To enable the arrow files to be produced, the option `CREATE_MEASUREMENTS_ARROW_FILES` is required to be set to `True` in the pipeline run config. +To enable the arrow files to be produced, the option `measurements.write_arrow_files` is required to be set to `True` in the pipeline run config. ### Image Data @@ -106,8 +108,8 @@ Here, for each image, the selavy measurements that have been ingested are stored | ---- | ----------- | | `associations.parquet` | Contains the association information between sources and measurements. | | `bands.parquet` | Contains the information of the bands associated with the pipeline run. | -| `config.py` | The pipeline run configuration file. | -| `config_prev.py` | The previous pipeline run configuration file used by the [add image](../using/addtorun.md) mode. | +| `config.yaml` | The pipeline run configuration file. | +| `config_prev.yaml` | The previous pipeline run configuration file used by the [add image](../using/addtorun.md) mode. | | `forced_measurements*.parquet` | Multiple files that contain the forced measurements extracted from the respective image denoted in the filename. | | `images.parquet` | Contains the information of the images processed in the pipeline run. | | `log.txt` | The log file of the pipeline run. | diff --git a/docs/theme/assets/stylesheets/overrides.css b/docs/theme/assets/stylesheets/overrides.css new file mode 100644 index 000000000..eb96c7f95 --- /dev/null +++ b/docs/theme/assets/stylesheets/overrides.css @@ -0,0 +1,287 @@ +.md-header { + position: initial +} + +.md-main__inner { + margin: 0 +} + +.md-footer-copyright { + display: none +} + +.md-footer-nav__inner { + display: none +} + +.md-content { + display: none +} + +.md-footer-meta__inner { + align-content: center; + display: flex; + align-items: center; + justify-content: center +} + +.tx-container { + height: fit-content; + padding-top: 0rem; + background: url("data:image/svg+xml;utf8,") no-repeat bottom, linear-gradient(to bottom, var(--md-primary-fg-color), #2a978d 99%, #fff 99%) +} + +[data-md-color-scheme="slate"] .tx-container { + background: url("data:image/svg+xml;utf8,") no-repeat bottom, linear-gradient(to bottom, var(--md-primary-fg-color), #e86100 99%, #fff 99%) +} + +.tx-hero { + color: var(--md-primary-bg-color); + justify-content: right; +} + +.tx-hero h1 { + margin-bottom: 0rem; + color: currentColor; + font-weight: 700 +} + +.tx-hero__content { + padding-bottom: 9rem; + justify-content: left; + padding-right: 3rem; +} + +.tx-hero__content_small {x; + justify-content: left; + padding-right: 3rem; +} + +.tx-hero__image { + max-width: 100%; + max-height: 100%; + order: 1; + padding-right: 2.5rem; +} + +.tx-hero .md-button { + margin-top: .5rem; + margin-right: .5rem; + color: var(--md-primary-bg-color) +} + +.tx-hero .md-button--primary { + background-color: var(--md-primary-bg-color); + color: var(--md-primary-fg-color); + border-color: var(--md-primary-bg-color) +} + +.tx-hero .md-button:focus, +.tx-hero .md-button:hover { + background-color: var(--md-accent-fg-color); + color: var(--md-default-bg-color); + border-color: var(--md-accent-fg-color) +} + +.tx-container-2 { + padding: 0rem; + background-color: white; + margin-bottom: 0px; +} + +.tx-hero__image-2 { + max-width: 100%; + max-height: 100%; + order: 1; + padding-right: 0.5rem; + padding-left: 0rem; + padding-bottom: 0px; + float: left; +} + +.tx-hero__content-2 { + margin-left: 50px; + justify-content: left; + color: #2a978d; + font-weight: 300; + padding: 0 0px; + padding-bottom: 40px; + word-break: break-word; + 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align-items: center; + justify-content: center; +} + +.tx-hero__content-footer { + justify-content: left; + color: #2a978d; + font-weight: 300; + padding: 0 0px; + word-break: break-word; + float: left; +} + +.tx-footer p { + font-size: 12px; + line-height: 1.8em; + text-rendering: optimizeLegibility; + color: black; + display: block; + font-family: inherit; +} + +/**/ +/*Adjusting Mobile UI */ +/**/ +@media screen and (max-width: 30em) { + .tx-hero h1 { + font-size: 1.4rem + } + + .tx-hero__content { + margin-left: 20px; + margin-right: 20px; + } + + .tx-hero__content_small { + margin-left: 20px; + margin-right: 20px; + } + + .tx-hero__content-2 { + margin-left: 20px; + margin-right: 20px; + } + + .tx-hero__content-3 { + margin-left: 20px; + margin-right: 20px; + } +} + +@media screen and (min-width: 60em) { + .md-sidebar--secondary { + display: none + } + + .tx-hero { + display: flex; + align-items: center; + justify-content: center; + } + + .tx-hero__content { + max-width: 22rem; + margin-top: 3.5rem; + margin-bottom: 3.5rem; + margin-left: 1.0rem; + margin-right: 4.0rem; + align-items: center; + } +} + +@media screen and (min-width: 76.25em) { + .md-sidebar--primary { + display: none + } + + .top-hr { + width: 100%; + display: flex; + max-width: 61rem; + margin-right: auto; + margin-left: auto; + padding: 0 .2rem; + } + + .bottom-hr { + margin-top: 10px; + width: 100%; + display: flex; + max-width: 61rem; + margin-right: auto; + margin-left: auto; + padding: 0 .2rem; + } +} + +.text-center { + text-align: center; + padding-right: 15px; + padding-left: 15px; + margin-right: auto; + margin-left: auto; + margin-top: 15px; + font-size: 23px; + font-weight: 300; + padding-bottom: 10px; +} + +.logos { + display: flex; + align-items: center; + justify-content: center; + flex-flow: row wrap; + margin: 0 auto; +} + +.logos img { + flex: 1 1 auto; + padding: 25px; + max-height: 130px; + vertical-align: middle; +} \ No newline at end of file diff --git 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--git a/docs/theme/fonts/lg.ttf b/docs/theme/fonts/lg.ttf new file mode 100644 index 000000000..213afec14 Binary files /dev/null and b/docs/theme/fonts/lg.ttf differ diff --git a/docs/theme/fonts/lg.woff b/docs/theme/fonts/lg.woff new file mode 100644 index 000000000..27a2b8ea4 Binary files /dev/null and b/docs/theme/fonts/lg.woff differ diff --git a/docs/theme/home.html b/docs/theme/home.html new file mode 100644 index 000000000..851dc126d --- /dev/null +++ b/docs/theme/home.html @@ -0,0 +1,67 @@ +{#- +This file was automatically generated - do not edit +NOTE: At line 9 -> 'background:' has the current color for the botom part of the cover +- current | #2a978d (OK w/ mkdocs.yaml -> palette -> /docs/assets/stylesheets) +- before | #2a978d (OK w/ mkdocs.yaml -> palette -> primary: "teal" +-#} + +{% extends "main.html" %} + + +{% block tabs %} +{{ super() }} + + + + + + +
+
+
+ + +
+ +
+ + +
+

The VAST Pipeline

+ +

+ A fast and modern image-plane radio transient detection + pipeline for the Variables and Slow Transients (VAST) survey + science project using data from the Australian Square + Kilometre Array Pathfinder. + +

+ + + Get started + + + + Go to GitHub + + +
+
+
+
+ +{% block content %}{% endblock %} +{% block footer %}{% endblock %} +{% endblock %} diff --git a/docs/theme/img/loading.gif b/docs/theme/img/loading.gif new file mode 100644 index 000000000..d3bbc8062 Binary files /dev/null and b/docs/theme/img/loading.gif differ diff --git a/docs/theme/js/extra.js b/docs/theme/js/extra.js index adc3163b5..309949081 100644 --- a/docs/theme/js/extra.js +++ b/docs/theme/js/extra.js @@ -1,10 +1,11 @@ function addGoToTop() { - document.querySelectorAll('[aria-label="Table of contents"]')[1].innerHTML += 'Back to top'; + let toc = document.querySelectorAll('[aria-label="Table of contents"]'); + // only add the link if the TOC is on the page (it's the second one) + if (toc.length > 1) { + toc[1].innerHTML += 'Back to top'; + } } -// window.open = addGoToTop(); -document.addEventListener('scroll', addGoToTop()) - window.MathJax = { tex: { inlineMath: [["\\(", "\\)"]], @@ -17,3 +18,28 @@ window.MathJax = { processHtmlClass: "arithmatex" } }; + +/* +mkdocs-material loads local pages via XHR (they call it "instant loading") which speeds +up navigation by preventing a full page reload. This means that any custom JS is only +run on the first page load and skipped on subsequent loads. Below, we add functions +that should be called on each page load by subsribing them to the document$ observable, +i.e. any time the document changes, execute the following. +*/ +// render MathJax +document$.subscribe(() => { + MathJax.typesetPromise() +}) + +// configure images to use lightgallery +document$.subscribe(function() { + var elements = document.getElementsByClassName("lightgallery"); + for(var i=0; i { + addGoToTop(); +}) diff --git a/docs/theme/js/lg-zoom.js b/docs/theme/js/lg-zoom.js new file mode 100644 index 000000000..e8bc629b8 --- /dev/null +++ b/docs/theme/js/lg-zoom.js @@ -0,0 +1,715 @@ +/**! + * lg-zoom.js | 1.3.0-beta.0 | October 5th 2020 + * http://sachinchoolur.github.io/lg-zoom.js + * Copyright (c) 2016 Sachin N; + * @license GPLv3 + */(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.LgZoom = f()}})(function(){var define,module,exports;return (function(){function r(e,n,t){function o(i,f){if(!n[i]){if(!e[i]){var c="function"==typeof require&&require;if(!f&&c)return c(i,!0);if(u)return u(i,!0);var a=new Error("Cannot find module '"+i+"'");throw a.code="MODULE_NOT_FOUND",a}var p=n[i]={exports:{}};e[i][0].call(p.exports,function(r){var n=e[i][1][r];return o(n||r)},p,p.exports,r,e,n,t)}return n[i].exports}for(var u="function"==typeof require&&require,i=0;i 1) { + utils.addClass(_this.core.outer, 'lg-zoomed'); + } else { + _this.resetZoom(); + } + + if (scale < 1) { + scale = 1; + } + + zoom(scale); + }; + + var actualSize = function actualSize(event, image, index, fromIcon) { + var w = image.clientWidth; + var nw; + if (_this.core.s.dynamic) { + nw = _this.core.s.dynamicEl[index].width || image.naturalWidth || w; + } else { + nw = _this.core.items[index].getAttribute('data-width') || image.naturalWidth || w; + } + + var _scale; + + if (utils.hasClass(_this.core.outer, 'lg-zoomed')) { + scale = 1; + } else { + if (nw > w) { + _scale = nw / w; + scale = _scale || 2; + } + } + + if (fromIcon) { + _this.pageX = window.innerWidth / 2; + _this.pageY = window.innerHeight / 2 + (document.documentElement.scrollTop || document.body.scrollTop); + } else { + _this.pageX = event.pageX || event.targetTouches[0].pageX; + _this.pageY = event.pageY || event.targetTouches[0].pageY; + } + + callScale(); + setTimeout(function () { + utils.removeClass(_this.core.outer, 'lg-grabbing'); + utils.addClass(_this.core.outer, 'lg-grab'); + }, 10); + }; + + var tapped = false; + + // event triggered after appending slide content + utils.on(_this.core.el, 'onAferAppendSlide.lgtmzoom', function (event) { + + var index = event.detail.index; + + // Get the current element + var image = _this.core.___slide[index].querySelector('.lg-image'); + + if (!_this.core.isTouch) { + utils.on(image, 'dblclick', function (event) { + actualSize(event, image, index); + }); + } + + if (_this.core.isTouch) { + utils.on(image, 'touchstart', function (event) { + if (!tapped) { + tapped = setTimeout(function () { + tapped = null; + }, 300); + } else { + clearTimeout(tapped); + tapped = null; + actualSize(event, image, index); + } + + event.preventDefault(); + }); + } + }); + + // Update zoom on resize and orientationchange + utils.on(window, 'resize.lgzoom scroll.lgzoom orientationchange.lgzoom', function () { + _this.pageX = window.innerWidth / 2; + _this.pageY = window.innerHeight / 2 + (document.documentElement.scrollTop || document.body.scrollTop); + zoom(scale); + }); + + utils.on(document.getElementById('lg-zoom-out'), 'click.lg', function () { + if (_this.core.outer.querySelector('.lg-current .lg-image')) { + scale -= _this.core.s.scale; + callScale(); + } + }); + + utils.on(document.getElementById('lg-zoom-in'), 'click.lg', function () { + if (_this.core.outer.querySelector('.lg-current .lg-image')) { + scale += _this.core.s.scale; + callScale(); + } + }); + + utils.on(document.getElementById('lg-actual-size'), 'click.lg', function (event) { + actualSize(event, _this.core.___slide[_this.core.index].querySelector('.lg-image'), _this.core.index, true); + }); + + // Reset zoom on slide change + utils.on(_this.core.el, 'onBeforeSlide.lgtm', function () { + scale = 1; + _this.resetZoom(); + }); + + // Drag option after zoom + if (!_this.core.isTouch) { + _this.zoomDrag(); + } + + if (_this.core.isTouch) { + _this.zoomSwipe(); + } + }; + + Zoom.prototype.getModifier = function (rotateValue, axis, el) { + var originalRotate = rotateValue; + rotateValue = Math.abs(rotateValue); + var transformValues = this.getCurrentTransform(el); + if (!transformValues) { + return 1; + } + var modifier = 1; + if (axis === 'X') { + var flipHorizontalValue = Math.sign(parseFloat(transformValues[0])); + if (rotateValue === 0 || rotateValue === 180) { + modifier = 1; + } else if (rotateValue === 90) { + if (originalRotate === -90 && flipHorizontalValue === 1 || originalRotate === 90 && flipHorizontalValue === -1) { + modifier = -1; + } else { + modifier = 1; + } + } + modifier = modifier * flipHorizontalValue; + } else { + var flipVerticalValue = Math.sign(parseFloat(transformValues[3])); + if (rotateValue === 0 || rotateValue === 180) { + modifier = 1; + } else if (rotateValue === 90) { + var sinX = parseFloat(transformValues[1]); + var sinMinusX = parseFloat(transformValues[2]); + modifier = Math.sign(sinX * sinMinusX * originalRotate * flipVerticalValue); + } + modifier = modifier * flipVerticalValue; + } + return modifier; + }; + + Zoom.prototype.getImageSize = function ($image, rotateValue, axis) { + var imageSizes = { + y: 'offsetHeight', + x: 'offsetWidth' + }; + if (rotateValue === 90) { + // Swap axis + if (axis === 'x') { + axis = 'y'; + } else { + axis = 'x'; + } + } + return $image[imageSizes[axis]]; + }; + + Zoom.prototype.getDragCords = function (e, rotateValue) { + if (rotateValue === 90) { + return { + x: e.pageY, + y: e.pageX + }; + } else { + return { + x: e.pageX, + y: e.pageY + }; + } + }; + Zoom.prototype.getSwipeCords = function (e, rotateValue) { + var x = e.targetTouches[0].pageX; + var y = e.targetTouches[0].pageY; + if (rotateValue === 90) { + return { + x: y, + y: x + }; + } else { + return { + x: x, + y: y + }; + } + }; + + Zoom.prototype.getPossibleDragCords = function ($image, rotateValue) { + + var minY = (this.core.outer.querySelector('.lg').clientHeight - this.getImageSize($image, rotateValue, 'y')) / 2; + var maxY = Math.abs(this.getImageSize($image, rotateValue, 'y') * Math.abs($image.getAttribute('data-scale')) - this.core.outer.querySelector('.lg').clientHeight + minY); + var minX = (this.core.outer.querySelector('.lg').clientWidth - this.getImageSize($image, rotateValue, 'x')) / 2; + var maxX = Math.abs(this.getImageSize($image, rotateValue, 'x') * Math.abs($image.getAttribute('data-scale')) - this.core.outer.querySelector('.lg').clientWidth + minX); + if (rotateValue === 90) { + return { + minY: minX, + maxY: maxX, + minX: minY, + maxX: maxY + }; + } else { + return { + minY: minY, + maxY: maxY, + minX: minX, + maxX: maxX + }; + } + }; + + Zoom.prototype.getDragAllowedAxises = function ($image, rotateValue) { + var allowY = this.getImageSize($image, rotateValue, 'y') * $image.getAttribute('data-scale') > this.core.outer.querySelector('.lg').clientHeight; + var allowX = this.getImageSize($image, rotateValue, 'x') * $image.getAttribute('data-scale') > this.core.outer.querySelector('.lg').clientWidth; + if (rotateValue === 90) { + return { + allowX: allowY, + allowY: allowX + }; + } else { + return { + allowX: allowX, + allowY: allowY + }; + } + }; + + /** + * + * @param {Element} el + * @return matrix(cos(X), sin(X), -sin(X), cos(X), 0, 0); + * Get the current transform value + */ + Zoom.prototype.getCurrentTransform = function (el) { + if (!el) { + return 0; + } + var st = window.getComputedStyle(el, null); + var tm = st.getPropertyValue('-webkit-transform') || st.getPropertyValue('-moz-transform') || st.getPropertyValue('-ms-transform') || st.getPropertyValue('-o-transform') || st.getPropertyValue('transform') || 'none'; + if (tm !== 'none') { + return tm.split('(')[1].split(')')[0].split(','); + } + return 0; + }; + + Zoom.prototype.getCurrentRotation = function (el) { + if (!el) { + return 0; + } + var values = this.getCurrentTransform(el); + if (values) { + return Math.round(Math.atan2(values[1], values[0]) * (180 / Math.PI)); + // If you want rotate in 360 + //return (angle < 0 ? angle + 360 : angle); + } + return 0; + }; + + // Reset zoom effect + Zoom.prototype.resetZoom = function () { + utils.removeClass(this.core.outer, 'lg-zoomed'); + for (var i = 0; i < this.core.___slide.length; i++) { + if (this.core.___slide[i].querySelector('.lg-img-wrap')) { + this.core.___slide[i].querySelector('.lg-img-wrap').removeAttribute('style'); + this.core.___slide[i].querySelector('.lg-img-wrap').removeAttribute('data-x'); + this.core.___slide[i].querySelector('.lg-img-wrap').removeAttribute('data-y'); + } + } + + for (var j = 0; j < this.core.___slide.length; j++) { + if (this.core.___slide[j].querySelector('.lg-image')) { + this.core.___slide[j].querySelector('.lg-image').removeAttribute('style'); + this.core.___slide[j].querySelector('.lg-image').removeAttribute('data-scale'); + } + } + + // Reset pagx pagy values to center + this.pageX = window.innerWidth / 2; + this.pageY = window.innerHeight / 2 + (document.documentElement.scrollTop || document.body.scrollTop); + }; + + Zoom.prototype.zoomSwipe = function () { + var _this = this; + var startCoords = {}; + var endCoords = {}; + var isMoved = false; + + // Allow x direction drag + var allowX = false; + + // Allow Y direction drag + var allowY = false; + + var rotateValue = 0; + var rotateEl; + + for (var i = 0; i < _this.core.___slide.length; i++) { + + /*jshint loopfunc: true */ + utils.on(_this.core.___slide[i], 'touchstart.lg', function (e) { + + if (utils.hasClass(_this.core.outer, 'lg-zoomed')) { + var $image = _this.core.___slide[_this.core.index].querySelector('.lg-object'); + + rotateEl = _this.core.___slide[_this.core.index].querySelector('.lg-img-rotate'); + rotateValue = _this.getCurrentRotation(rotateEl); + + var dragAllowedAxises = _this.getDragAllowedAxises($image, Math.abs(rotateValue)); + allowY = dragAllowedAxises.allowY; + allowX = dragAllowedAxises.allowX; + + if (allowX || allowY) { + e.preventDefault(); + startCoords = _this.getSwipeCords(e, Math.abs(rotateValue)); + } + } + }); + } + + for (var j = 0; j < _this.core.___slide.length; j++) { + + /*jshint loopfunc: true */ + utils.on(_this.core.___slide[j], 'touchmove.lg', function (e) { + + if (utils.hasClass(_this.core.outer, 'lg-zoomed')) { + + var _el = _this.core.___slide[_this.core.index].querySelector('.lg-img-wrap'); + var distanceX; + var distanceY; + + e.preventDefault(); + isMoved = true; + + endCoords = _this.getSwipeCords(e, Math.abs(rotateValue)); + + // reset opacity and transition duration + utils.addClass(_this.core.outer, 'lg-zoom-dragging'); + + if (allowY) { + distanceY = -Math.abs(_el.getAttribute('data-y')) + (endCoords.y - startCoords.y) * _this.getModifier(rotateValue, 'Y', rotateEl); + } else { + distanceY = -Math.abs(_el.getAttribute('data-y')); + } + + if (allowX) { + distanceX = -Math.abs(_el.getAttribute('data-x')) + (endCoords.x - startCoords.x) * _this.getModifier(rotateValue, 'X', rotateEl); + } else { + distanceX = -Math.abs(_el.getAttribute('data-x')); + } + + if (Math.abs(endCoords.x - startCoords.x) > 15 || Math.abs(endCoords.y - startCoords.y) > 15) { + + if (_this.core.s.useLeftForZoom) { + _el.style.left = distanceX + 'px'; + _el.style.top = distanceY + 'px'; + } else { + utils.setVendor(_el, 'Transform', 'translate3d(' + distanceX + 'px, ' + distanceY + 'px, 0)'); + } + } + } + }); + } + + for (var k = 0; k < _this.core.___slide.length; k++) { + + /*jshint loopfunc: true */ + utils.on(_this.core.___slide[k], 'touchend.lg', function () { + if (utils.hasClass(_this.core.outer, 'lg-zoomed')) { + if (isMoved) { + isMoved = false; + utils.removeClass(_this.core.outer, 'lg-zoom-dragging'); + _this.touchendZoom(startCoords, endCoords, allowX, allowY, rotateValue); + } + } + }); + } + }; + + Zoom.prototype.zoomDrag = function () { + + var _this = this; + var startCoords = {}; + var endCoords = {}; + var isDraging = false; + var isMoved = false; + + // Allow x direction drag + var allowX = false; + + // Allow Y direction drag + var allowY = false; + + var rotateValue = 0; + var rotateEl; + + for (var i = 0; i < _this.core.___slide.length; i++) { + + /*jshint loopfunc: true */ + utils.on(_this.core.___slide[i], 'mousedown.lgzoom', function (e) { + + // execute only on .lg-object + var $image = _this.core.___slide[_this.core.index].querySelector('.lg-object'); + + rotateEl = _this.core.___slide[_this.core.index].querySelector('.lg-img-rotate'); + rotateValue = _this.getCurrentRotation(rotateEl); + + var dragAllowedAxises = _this.getDragAllowedAxises($image, Math.abs(rotateValue)); + allowY = dragAllowedAxises.allowY; + allowX = dragAllowedAxises.allowX; + + if (utils.hasClass(_this.core.outer, 'lg-zoomed')) { + if (utils.hasClass(e.target, 'lg-object') && (allowX || allowY)) { + e.preventDefault(); + startCoords = _this.getDragCords(e, Math.abs(rotateValue)); + + isDraging = true; + + // ** Fix for webkit cursor issue https://code.google.com/p/chromium/issues/detail?id=26723 + _this.core.outer.scrollLeft += 1; + _this.core.outer.scrollLeft -= 1; + + utils.removeClass(_this.core.outer, 'lg-grab'); + utils.addClass(_this.core.outer, 'lg-grabbing'); + } + } + }); + } + + utils.on(window, 'mousemove.lgzoom', function (e) { + if (isDraging) { + var _el = _this.core.___slide[_this.core.index].querySelector('.lg-img-wrap'); + var distanceX; + var distanceY; + + isMoved = true; + endCoords = _this.getDragCords(e, Math.abs(rotateValue)); + + // reset opacity and transition duration + utils.addClass(_this.core.outer, 'lg-zoom-dragging'); + + if (allowY) { + distanceY = -Math.abs(_el.getAttribute('data-y')) + (endCoords.y - startCoords.y) * _this.getModifier(rotateValue, 'Y', rotateEl); + } else { + distanceY = -Math.abs(_el.getAttribute('data-y')); + } + + if (allowX) { + distanceX = -Math.abs(_el.getAttribute('data-x')) + (endCoords.x - startCoords.x) * _this.getModifier(rotateValue, 'X', rotateEl); + } else { + distanceX = -Math.abs(_el.getAttribute('data-x')); + } + + if (_this.core.s.useLeftForZoom) { + _el.style.left = distanceX + 'px'; + _el.style.top = distanceY + 'px'; + } else { + utils.setVendor(_el, 'Transform', 'translate3d(' + distanceX + 'px, ' + distanceY + 'px, 0)'); + } + } + }); + + utils.on(window, 'mouseup.lgzoom', function (e) { + + if (isDraging) { + isDraging = false; + utils.removeClass(_this.core.outer, 'lg-zoom-dragging'); + + // Fix for chrome mouse move on click + if (isMoved && (startCoords.x !== endCoords.x || startCoords.y !== endCoords.y)) { + endCoords = _this.getDragCords(e, Math.abs(rotateValue)); + _this.touchendZoom(startCoords, endCoords, allowX, allowY, rotateValue); + } + + isMoved = false; + } + + utils.removeClass(_this.core.outer, 'lg-grabbing'); + utils.addClass(_this.core.outer, 'lg-grab'); + }); + }; + + Zoom.prototype.touchendZoom = function (startCoords, endCoords, allowX, allowY, rotateValue) { + + var _this = this; + var _el = _this.core.___slide[_this.core.index].querySelector('.lg-img-wrap'); + var image = _this.core.___slide[_this.core.index].querySelector('.lg-object'); + var rotateEl = _this.core.___slide[_this.core.index].querySelector('.lg-img-rotate'); + var distanceX = -Math.abs(_el.getAttribute('data-x')) + (endCoords.x - startCoords.x) * _this.getModifier(rotateValue, 'X', rotateEl); + var distanceY = -Math.abs(_el.getAttribute('data-y')) + (endCoords.y - startCoords.y) * _this.getModifier(rotateValue, 'Y', rotateEl); + var possibleDragCords = _this.getPossibleDragCords(image, Math.abs(rotateValue)); + + if (Math.abs(endCoords.x - startCoords.x) > 15 || Math.abs(endCoords.y - startCoords.y) > 15) { + if (allowY) { + if (distanceY <= -possibleDragCords.maxY) { + distanceY = -possibleDragCords.maxY; + } else if (distanceY >= -possibleDragCords.minY) { + distanceY = -possibleDragCords.minY; + } + } + + if (allowX) { + if (distanceX <= -possibleDragCords.maxX) { + distanceX = -possibleDragCords.maxX; + } else if (distanceX >= -possibleDragCords.minX) { + distanceX = -possibleDragCords.minX; + } + } + + if (allowY) { + _el.setAttribute('data-y', Math.abs(distanceY)); + } else { + distanceY = -Math.abs(_el.getAttribute('data-y')); + } + + if (allowX) { + _el.setAttribute('data-x', Math.abs(distanceX)); + } else { + distanceX = -Math.abs(_el.getAttribute('data-x')); + } + + if (_this.core.s.useLeftForZoom) { + _el.style.left = distanceX + 'px'; + _el.style.top = distanceY + 'px'; + } else { + utils.setVendor(_el, 'Transform', 'translate3d(' + distanceX + 'px, ' + distanceY + 'px, 0)'); + } + } + }; + + Zoom.prototype.destroy = function () { + + var _this = this; + + // Unbind all events added by lightGallery zoom plugin + utils.off(_this.core.el, '.lgzoom'); + utils.off(window, '.lgzoom'); + for (var i = 0; i < _this.core.___slide.length; i++) { + utils.off(_this.core.___slide[i], '.lgzoom'); + } + + utils.off(_this.core.el, '.lgtmzoom'); + _this.resetZoom(); + clearTimeout(_this.zoomabletimeout); + _this.zoomabletimeout = false; + }; + + window.lgModules.zoom = Zoom; +}); + +},{}]},{},[1])(1) +}); diff --git a/docs/theme/js/lightgallery.min.js b/docs/theme/js/lightgallery.min.js new file mode 100644 index 000000000..9548d8e63 --- /dev/null +++ b/docs/theme/js/lightgallery.min.js @@ -0,0 +1,7 @@ +/**! + * lightgallery.js | 1.4.1-beta.0 | October 29th 2020 + * http://sachinchoolur.github.io/lightgallery.js/ + * Copyright (c) 2016 Sachin N; + * @license GPLv3 + */ +!function(e){if("object"==typeof exports&&"undefined"!=typeof module)module.exports=e();else if("function"==typeof define&&define.amd)define([],e);else{var t;t="undefined"!=typeof window?window:"undefined"!=typeof global?global:"undefined"!=typeof self?self:this,t.Lightgallery=e()}}(function(){var e,t,s;return function(){function e(t,s,l){function i(r,a){if(!s[r]){if(!t[r]){var d="function"==typeof require&&require;if(!a&&d)return d(r,!0);if(o)return o(r,!0);var n=new Error("Cannot find module '"+r+"'");throw n.code="MODULE_NOT_FOUND",n}var u=s[r]={exports:{}};t[r][0].call(u.exports,function(e){return i(t[r][1][e]||e)},u,u.exports,e,t,s,l)}return s[r].exports}for(var o="function"==typeof require&&require,r=0;r2&&void 0!==arguments[2]?arguments[2]:null;if(t){var i=new CustomEvent(s,{detail:l});t.dispatchEvent(i)}},Listener:{uid:0},on:function e(s,l,i){var o=this;s&&l.split(" ").forEach(function(e){var l=o.getAttribute(s,"lg-event-uid")||"";t.Listener.uid++,l+="&"+t.Listener.uid,o.setAttribute(s,"lg-event-uid",l),t.Listener[e+t.Listener.uid]=i,s.addEventListener(e.split(".")[0],i,!1)})},off:function e(s,l){if(s){var i=this.getAttribute(s,"lg-event-uid");if(i){i=i.split("&");for(var o=0;o-1&&(s.removeEventListener(a.split(".")[0],t.Listener[a]),this.setAttribute(s,"lg-event-uid",this.getAttribute(s,"lg-event-uid").replace("&"+i[o],"")),delete t.Listener[a]);else s.removeEventListener(r.split(".")[0],t.Listener[r]),this.setAttribute(s,"lg-event-uid",this.getAttribute(s,"lg-event-uid").replace("&"+i[o],"")),delete t.Listener[r]}}}},param:function e(t){return Object.keys(t).map(function(e){return encodeURIComponent(e)+"="+encodeURIComponent(t[e])}).join("&")}};e.default=t})},{}],2:[function(t,s,l){!function(s,i){if("function"==typeof e&&e.amd)e(["./lg-utils"],i);else if(void 0!==l)i(t("./lg-utils"));else{var o={exports:{}};i(s.lgUtils),s.lightgallery=o.exports}}(this,function(e){"use strict";function t(e){return e&&e.__esModule?e:{default:e}}function s(e,t){if(this.el=e,this.s=i({},o,t),this.s.dynamic&&"undefined"!==this.s.dynamicEl&&this.s.dynamicEl.constructor===Array&&!this.s.dynamicEl.length)throw"When using dynamic mode, you must also define dynamicEl as an Array.";return this.modules={},this.lGalleryOn=!1,this.lgBusy=!1,this.hideBartimeout=!1,this.isTouch="ontouchstart"in document.documentElement,this.s.slideEndAnimatoin&&(this.s.hideControlOnEnd=!1),this.items=[],this.s.dynamic?this.items=this.s.dynamicEl:"this"===this.s.selector?this.items.push(this.el):""!==this.s.selector?this.s.selectWithin?this.items=document.querySelector(this.s.selectWithin).querySelectorAll(this.s.selector):this.items=this.el.querySelectorAll(this.s.selector):this.items=this.el.children,this.___slide="",this.outer="",this.init(),this}var l=t(e),i=Object.assign||function(e){for(var t=1;te.items.length&&(e.s.preload=e.items.length);var t=window.location.hash;if(t.indexOf("lg="+this.s.galleryId)>0&&(e.index=parseInt(t.split("&slide=")[1],10),l.default.addClass(document.body,"lg-from-hash"),l.default.hasClass(document.body,"lg-on")||(l.default.addClass(document.body,"lg-on"),setTimeout(function(){e.build(e.index)}))),e.s.dynamic)l.default.trigger(this.el,"onBeforeOpen"),e.index=e.s.index||0,l.default.hasClass(document.body,"lg-on")||(l.default.addClass(document.body,"lg-on"),setTimeout(function(){e.build(e.index)}));else for(var s=0;s1&&(t.arrow(),setTimeout(function(){t.enableDrag(),t.enableSwipe()},50),t.s.mousewheel&&t.mousewheel()),t.counter(),t.closeGallery(),l.default.trigger(t.el,"onAfterOpen"),t.s.hideBarsDelay>0){var i=setTimeout(function(){l.default.addClass(t.outer,"lg-hide-items")},t.s.hideBarsDelay);l.default.on(t.outer,"mousemove.lg click.lg touchstart.lg",function(){clearTimeout(i),l.default.removeClass(t.outer,"lg-hide-items"),clearTimeout(t.hideBartimeout),t.hideBartimeout=setTimeout(function(){l.default.addClass(t.outer,"lg-hide-items")},t.s.hideBarsDelay)})}},s.prototype.structure=function(){var e="",t="",s=0,i="",o,r=this;for(document.body.insertAdjacentHTML("beforeend",'
'),l.default.setVendor(document.querySelector(".lg-backdrop"),"TransitionDuration",this.s.backdropDuration+"ms"),s=0;s';if(this.s.controls&&this.items.length>1&&(t='
"),".lg-sub-html"===this.s.appendSubHtmlTo&&(i='
'),o='",document.body.insertAdjacentHTML("beforeend",o),this.outer=document.querySelector(".lg-outer"),this.outer.focus(),this.___slide=this.outer.querySelectorAll(".lg-item"),this.s.useLeft?(l.default.addClass(this.outer,"lg-use-left"),this.s.mode="lg-slide"):l.default.addClass(this.outer,"lg-use-css3"),r.setTop(),l.default.on(window,"resize.lg orientationchange.lg",function(){setTimeout(function(){r.setTop()},100)}),l.default.addClass(this.___slide[this.index],"lg-current"),this.doCss()?l.default.addClass(this.outer,"lg-css3"):(l.default.addClass(this.outer,"lg-css"),this.s.speed=0),l.default.addClass(this.outer,this.s.mode),this.s.enableDrag&&this.items.length>1&&l.default.addClass(this.outer,"lg-grab"),this.s.showAfterLoad&&l.default.addClass(this.outer,"lg-show-after-load"),this.doCss()){var a=this.outer.querySelector(".lg-inner");l.default.setVendor(a,"TransitionTimingFunction",this.s.cssEasing),l.default.setVendor(a,"TransitionDuration",this.s.speed+"ms")}setTimeout(function(){l.default.addClass(document.querySelector(".lg-backdrop"),"in")}),setTimeout(function(){l.default.addClass(r.outer,"lg-visible")},this.s.backdropDuration),this.s.download&&this.outer.querySelector(".lg-toolbar").insertAdjacentHTML("beforeend",''),this.prevScrollTop=document.documentElement.scrollTop||document.body.scrollTop},s.prototype.setTop=function(){if("100%"!==this.s.height){var e=window.innerHeight,t=(e-parseInt(this.s.height,10))/2,s=this.outer.querySelector(".lg");e>=parseInt(this.s.height,10)?s.style.top=t+"px":s.style.top="0px"}},s.prototype.doCss=function(){return!!function e(){var t=["transition","MozTransition","WebkitTransition","OTransition","msTransition","KhtmlTransition"],s=document.documentElement,l=0;for(l=0;l'+(parseInt(this.index,10)+1)+' / '+this.items.length+"")},s.prototype.addHtml=function(e){var t=null,s;if(this.s.dynamic?t=this.s.dynamicEl[e].subHtml:(s=this.items[e],t=s.getAttribute("data-sub-html"),this.s.getCaptionFromTitleOrAlt&&!t&&(t=s.getAttribute("title"))&&s.querySelector("img")&&(t=s.querySelector("img").getAttribute("alt"))),void 0!==t&&null!==t){var i=t.substring(0,1);"."!==i&&"#"!==i||(t=this.s.subHtmlSelectorRelative&&!this.s.dynamic?s.querySelector(t).innerHTML:document.querySelector(t).innerHTML)}else t="";".lg-sub-html"===this.s.appendSubHtmlTo?this.outer.querySelector(this.s.appendSubHtmlTo).innerHTML=t:this.___slide[e].insertAdjacentHTML("beforeend",t),void 0!==t&&null!==t&&(""===t?l.default.addClass(this.outer.querySelector(this.s.appendSubHtmlTo),"lg-empty-html"):l.default.removeClass(this.outer.querySelector(this.s.appendSubHtmlTo),"lg-empty-html")),l.default.trigger(this.el,"onAfterAppendSubHtml",{index:e})},s.prototype.preload=function(e){var t=1,s=1;for(t=1;t<=this.s.preload&&!(t>=this.items.length-e);t++)this.loadContent(e+t,!1,0);for(s=1;s<=this.s.preload&&!(e-s<0);s++)this.loadContent(e-s,!1,0)},s.prototype.loadContent=function(e,t,s){var i=this,o=!1,r,a,d,n,u,c,g,f=function e(t){for(var s=[],l=[],i=0;ir){a=l[d];break}};if(i.s.dynamic){if(i.s.dynamicEl[e].poster&&(o=!0,d=i.s.dynamicEl[e].poster),c=i.s.dynamicEl[e].html,a=i.s.dynamicEl[e].src,g=i.s.dynamicEl[e].alt,i.s.dynamicEl[e].responsive){f(i.s.dynamicEl[e].responsive.split(","))}n=i.s.dynamicEl[e].srcset,u=i.s.dynamicEl[e].sizes}else{if(i.items[e].getAttribute("data-poster")&&(o=!0,d=i.items[e].getAttribute("data-poster")),c=i.items[e].getAttribute("data-html"),a=i.items[e].getAttribute("href")||i.items[e].getAttribute("data-src"),g=i.items[e].getAttribute("title"),i.items[e].querySelector("img")&&(g=g||i.items[e].querySelector("img").getAttribute("alt")),i.items[e].getAttribute("data-responsive")){f(i.items[e].getAttribute("data-responsive").split(","))}n=i.items[e].getAttribute("data-srcset"),u=i.items[e].getAttribute("data-sizes")}var h=!1;i.s.dynamic?i.s.dynamicEl[e].iframe&&(h=!0):"true"===i.items[e].getAttribute("data-iframe")&&(h=!0);var m=i.isVideo(a,e);if(!l.default.hasClass(i.___slide[e],"lg-loaded")){if(h)i.___slide[e].insertAdjacentHTML("afterbegin",'
');else if(o){var p="";p=m&&m.youtube?"lg-has-youtube":m&&m.vimeo?"lg-has-vimeo":"lg-has-html5",i.___slide[e].insertAdjacentHTML("beforeend",'
')}else m?(i.___slide[e].insertAdjacentHTML("beforeend",'
'),l.default.trigger(i.el,"hasVideo",{index:e,src:a,html:c})):(g=g?'alt="'+g+'"':"",i.___slide[e].insertAdjacentHTML("beforeend",'
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e=this,t=!1;l.default.on(this.outer.querySelector(".lg-close"),"click.lg",function(){e.destroy()}),e.s.closable&&(l.default.on(e.outer,"mousedown.lg",function(e){t=!!(l.default.hasClass(e.target,"lg-outer")||l.default.hasClass(e.target,"lg-item")||l.default.hasClass(e.target,"lg-img-wrap"))}),l.default.on(e.outer,"mouseup.lg",function(s){(l.default.hasClass(s.target,"lg-outer")||l.default.hasClass(s.target,"lg-item")||l.default.hasClass(s.target,"lg-img-wrap")&&t)&&(l.default.hasClass(e.outer,"lg-dragging")||e.destroy())}))},s.prototype.destroy=function(e){var t=this;if(e||l.default.trigger(t.el,"onBeforeClose"),document.body.scrollTop=t.prevScrollTop,document.documentElement.scrollTop=t.prevScrollTop,e){if(!t.s.dynamic)for(var s=0;s +{% block extrahead %} + + + {% set title = config.site_name %} + {% if page and page.title and not page.is_homepage %} + {% set title = config.site_name ~ " - " ~ page.title | striptags %} + {% endif %} + + + + + + + + + + + +{% endblock %} + + +{% block announce %} + + + + New in version 1.0.0: Documentation, add epoch mode and more 🙌. Check the release notes! + +{% endblock %} + +{% block styles %} + {{ super() }} + +{% endblock styles %} + +{% block libs %} + {{ super() }} + + +{% endblock libs %} diff --git a/docs/using/access.md b/docs/using/access.md index 0e34da666..40dd1cceb 100644 --- a/docs/using/access.md +++ b/docs/using/access.md @@ -5,17 +5,17 @@ Access to the pipeline website is done using GitHub as the authentification meth !!! note If you are attempting to access an instance of the VAST pipeline not hosted by the VAST group, confirm with the administrator what GitHub organisation membership is required. - Adminstrators can refer to [Pipeline Login](../quickstart/configuration.md#pipeline-login) for information on how to configure the login system. + Adminstrators can refer to [Pipeline Login](../gettingstarted/configuration.md#pipeline-login) for information on how to configure the login system. ## Logging In 1. Navigate to the [VAST Pipeline](https://data.vast-survey.org/pipeline/) (or other hosted instance) and the following page will appear. -[![VAST Pipeline Login](../img/login.png){: loading=lazy }](../img/login.png) +![!VAST Pipeline login page.](../img/login.png){: loading=lazy #fixed-size } 2. Click the `Login with GitHub` button and you will be presented with the following page to enter you GitHub details. Note that if you are already logged into GitHub in your browser then you will likely not see this page. -[![VAST Pipeline Signin GitHub](../img/signin-github.png){: loading=lazy }](../img/signin-github.png) +![!VAST Pipeline GitHub sign-in page.](../img/signin-github.png){: loading=lazy } 3. After a successful login you will then be redirected to the Pipeline homepage. -[![VAST Pipeline Homepage](../img/homepage.png){: loading=lazy }](../img/homepage.png) +![!VAST Pipeline homepage.](../img/homepage.png){: loading=lazy } ## Troubleshooting diff --git a/docs/using/addtorun.md b/docs/using/addtorun.md index b9bc30800..4949e9b8f 100644 --- a/docs/using/addtorun.md +++ b/docs/using/addtorun.md @@ -4,37 +4,41 @@ This page describes how to add images to a completed run, including how to resto !!! note Adding images to an existing run will update the sources already present from the respective run, such that the existing source IDs, comments, and tags are retained. If a full re-run was used instead then new IDs would be created and the comments and tags lost. - + There is no limit on how many times images may be added to a run. ## Step-by-step Guide !!! warning A run must have a `Completed` status before images can be added to it. - + No other settings other than the input data can be changed in the config. ### 1. Navigate to the Run Detail Page + Navigate to the detail page of the run you wish to process, and confirm that the job is marked as `Completed`. -[![VAST Pipeline Runs Add Images Detail](../img/add-images-detail.png){: loading=lazy }](../img/add-images-detail.png) +![!Pipeline run detail page.](../img/add-images-detail.png){: loading=lazy } ### 2. Add the New Images to the Configuration + Scroll to the configuration editor, enter edit mode and add the new images to the existing data inputs. If using epoch mode notation, add a new epoch(s) to the file. Once all the images, selavy files, rms images and background images have been added, select the `Write Current Config` option to save the file. !!! warning Do not remove the previous images from the configuration inputs or change any other options! - + Remember to make sure the order of the new input data is consistent between types! -[![VAST Pipeline Runs Add Images Config](../img/add-images-config.png){: loading=lazy }](../img/add-images-config.png) +![!New images added to the run configuration.](../img/add-images-config.png){: loading=lazy } ### 3. Perform a Config Validation + Check that the configuration file is still valid by selecting `Validate Config` from the same menu as shown in the previous step 2 screenshot. ### 4. Process the Run + Select the `Add Images or Re-Process Run` button at the top right of the run detail page to open the processing modal window. Select whether to turn debugging log output `On` or `Off` and when ready select the `Schedule Run`. !!! warning @@ -42,17 +46,20 @@ Select the `Add Images or Re-Process Run` button at the top right of the run det You can refresh the page to check the status of the run. You can confirm that the images have been added correctly by consulting the log output found below the configuration file. New images should have been ingested and output similar to the following should be present: -```console -2021-01-31 12:20:37,885 association INFO Association mode selected: basic. -2021-01-31 12:20:37,975 association INFO Found 2 images to add to the run. -2021-01-31 12:20:37,979 association INFO Association iteration: #1 -``` +!!! example "log.txt" + + ```console + 2021-04-02 21:17:00,628 association INFO Starting association. + 2021-04-02 21:17:00,628 association INFO Association mode selected: basic. + 2021-04-02 21:17:00,708 association INFO Found 7 images to add to the run. + ``` Once the processing has `Completed` the run detail page will now show the updated statistics and information of the run. -[![VAST Pipeline Runs Add Images Finished](../img/add-images-finished.png){: loading=lazy }](../img/add-images-finished.png) +![!Pipeline run successfully completed after adding images.](../img/add-images-finished.png){: loading=lazy } ## Restore Run to Pre-Add Version + When images are added to a run, a backup is made of the run before proceeding which can be used to restore the run to the pre-addition version. For example, perhaps the wrong images were added or an error occured mid-addition that could not be resolved. This command is currently unavailable to perform through the website interface but can be performed by an administrator of the pipeline via the command line interface. Please contact the adminstrator for the pipeline instance to request a run restoration. diff --git a/docs/using/initrun.md b/docs/using/initrun.md index 4ef5dd014..165b58e69 100644 --- a/docs/using/initrun.md +++ b/docs/using/initrun.md @@ -13,13 +13,13 @@ This page outlines the steps required to create a pipeline run through the web i ### 1. Navigate to the Pipeline Runs Overview Page Navigate to the Pipeline Runs overview page by clicking on the `Pipeline Runs` option in the left hand side navigation bar, as highlighted below. -[![VAST Pipeline Runs selection](../img/piperuns-navbar.png){: loading=lazy }](../img/piperuns-navbar.png) +![!Navbar 'Pipeline Runs' selection.](../img/piperuns-navbar.png){: loading=lazy } ### 2. Select the New Pipeline Run Option From the Pipeline Runs overview page, select the `New Pipeline Run` button as highlighted in the screenshot below. This will open up a modal window to begin the run initialisation process. -[![VAST Pipeline Runs New Run Button](../img/piperuns-newrun.png){: loading=lazy }](../img/piperuns-newrun.png) -[![VAST Pipeline Runs Modal 1](../img/initrun-modal1.png){: loading=lazy }](../img/initrun-modal1.png) +![!'New Pipeline Run' button.](../img/piperuns-newrun.png){: loading=lazy } +![!Pipeline run creation modal.](../img/initrun-modal1.png){: loading=lazy } ### 3. Fill in the Run Details Fill in the name and description of the run and then press next to navigate to the next form to enter and select the configuration options. @@ -33,9 +33,9 @@ For full details on how to configure a pipeline run see the [Run Configuration]( Once you have finished filling in the configuration options, press the `create` button. -[![VAST Pipeline Runs Modal 2](../img/initrun-modal2.png){: loading=lazy }](../img/initrun-modal2.png) -[![VAST Pipeline Runs Modal 3](../img/initrun-modal3.png){: loading=lazy }](../img/initrun-modal3.png) -[![VAST Pipeline Runs Modal 4](../img/initrun-modal4.png){: loading=lazy }](../img/initrun-modal4.png) +![!Pipeline run creation modal.](../img/initrun-modal2.png){: loading=lazy } +![!Pipeline run creation modal form (part 1).](../img/initrun-modal3.png){: loading=lazy } +![!Pipeline run creation modal form (part 2).](../img/initrun-modal4.png){: loading=lazy } ### 4. The Run Detail Page @@ -53,4 +53,4 @@ For full details on: * how to submit the job to be processed see [Processing a Run](processrun.md), * and how to add images to a run that has already been processed [Adding Images to a Run](addtorun.md). -[![VAST Pipeline Run Detail](../img/rundetail-create.png){: loading=lazy }](../img/rundetail-create.png) +![!Run creation confirmation.](../img/rundetail-create.png){: loading=lazy } diff --git a/docs/using/processrun.md b/docs/using/processrun.md index c4cad8ea0..17860290d 100644 --- a/docs/using/processrun.md +++ b/docs/using/processrun.md @@ -2,29 +2,35 @@ This page describes how to submit a pipeline run for processing. -!!! note +!!! tip "Admin Tip" Administrators please refer to [this section](../../adminusage/cli/#runpipeline) in the admin documentation for instructions on how to process a pipeline run via the command line interface. - + +!!! warning "Admin Warning" + The `Django Q` service must be running in order for pipeline runs to be processed. See the [Deployment](../gettingstarted/deployment.md#django-q) page for further details. + !!! tip Use the editor window on the run detail page to make adjustments to the run configuration file before processing. ## Step-by-step Guide ### 1. Navigate to the Run Detail Page + Navigate to the detail page of the run you wish to process. -[![VAST Pipeline Runs Detail](../img/run-detail.png){: loading=lazy }](../img/run-detail.png) +![!Run detail page.](../img/run-detail.png){: loading=lazy } ### 2. Run a config validation + Before processing it is recommended to check that the configuration file is valid. This is done by scrolling down to the config file card on the page and selecting the `Validate Config` option accessed by clicking the three dots menu button. Doing this will check if the configuration contains any errors prior to processing. Feedback will be provided on whether the configuration file is valid. In the event of an error, this can be corrected by using the edit option found in the same menu. -[![VAST Pipeline Runs Validate Config](../img/rundetail-validate-config.png){: loading=lazy }](../img/rundetail-validate-config.png) +![!Pipeline run validate configuration file option.](../img/rundetail-validate-config.png){: loading=lazy } -[![VAST Pipeline Runs Validate Config Feedback](../img/rundetail-validate-config-feedback.png){: loading=lazy }](../img/rundetail-validate-config-feedback.png) +![!Pipeline run validate configuration success.](../img/rundetail-validate-config-feedback.png){: loading=lazy } ### 3. Confirm Processing + With a successful configuration validation, scroll back up to the top of the page and click the `Process Run` button. This will open a modal window for you to confirm processing. For a newly initialised run, the only option that requires attention is whether to toggle the `Debug Log Output` on. This can be helpful if processing a new set of images which the pipeline hasn't seen before. @@ -36,19 +42,20 @@ Once ready, press the `Schedule Run` button which will send the run to the queue !!! warning For non-admin users, by default there is a run image limit of 200. -[![VAST Pipeline Runs Process Button](../img/process-run-button.png){: loading=lazy }](../img/process-run-button.png) - -[![VAST Pipeline Runs Process Modal](../img/process-run-modal.png){: loading=lazy }](../img/process-run-modal.png) +![!Process run button.](../img/process-run-button.png){: loading=lazy } -[![VAST Pipeline Runs Process Success](../img/process-run-success.png){: loading=lazy }](../img/process-run-success.png) +![!Process run modal.](../img/process-run-modal.png){: loading=lazy } +![!Process runs success.](../img/process-run-success.png){: loading=lazy } ## Monitoring the Run + You can check the status of the run by refreshing the run detail page and seeing if the `Run Status` field has been updated. You can also check the log output by scrolling down to the log file card found below the configuration file. There is currently no automated notification on completion or errors. ## Full Re-Run + A full re-run will be required if the run configuration needs to be changed, or in the event that an initial run has errored. !!! warning @@ -58,4 +65,5 @@ A full re-run will be required if the run configuration needs to be changed, or If images have been added to a run and the processing errors, there is a one time undo option that may avoid having to use the `Full Re-Run` command. ## Adding Images to a Run + See the dedicated documentation page [here](addtorun.md). diff --git a/docs/using/runconfig.md b/docs/using/runconfig.md index 59b631195..859c93f53 100644 --- a/docs/using/runconfig.md +++ b/docs/using/runconfig.md @@ -3,312 +3,400 @@ This page gives an overview of the configuration options available for a pipeline run. ## Default Configuration File -Below is an example of a default `config.py` file. Note that no images or other input files have been provided. The file can be either edited directly or through the editor available on the run detail page. - -```python -# This file specifies the pipeline configuration for the current pipeline run. -# You should review these settings before processing any images - some of the default -# values will probably not be appropriate. - -import os - -# path of the pipeline run -PIPE_RUN_PATH = os.path.dirname(os.path.realpath(__file__)) - - -# Images settings -# NOTE: all the paths !!!MUST!!! match with each other, e.g. -# IMAGE_FILES[0] image matches SELAVY_FILES[0] file -IMAGE_FILES = [ - # insert images file path(s) here - ] - -# Selavy catalogue files -SELAVY_FILES = [ - # insert Selavy file path(s) here - ] - -# Noise or RMS files -NOISE_FILES = [ - # insert RMS file path(s) here - ] - -# background map files -BACKGROUND_FILES = [ - # insert background map file path(s) here - ] - - -### -# SOURCE FINDER OPTIONS -### -# source finder used for this pipeline run -SOURCE_FINDER = 'selavy' - -### -# SOURCE MONITORING OPTIONS -### -# Source monitoring can be done both forward and backward in 'time'. -# Monitoring backward means re-opening files that were previously processed and can be slow. -MONITOR = False -# MONITOR_MIN_SIGMA defines the minimum SNR ratio a source has to be if it was placed in the -# area of minimum rms in the image from which it is to be extracted from. If lower than this -# value it is skipped -MONITOR_MIN_SIGMA = 3.0 -# MONITOR_EDGE_BUFFER_SCALE is a multiplicative scaling factor to the buffer size of the -# forced photometry from the image edge. -MONITOR_EDGE_BUFFER_SCALE = 1.2 -# MONITOR_CLUSTER_THRESHOLD represents the cluster_threshold parameter used in the forced -# extraction. If unsure leave as default. -MONITOR_CLUSTER_THRESHOLD = 3.0 -# MONITOR_ALLOW_NAN governs whether a source is attempted to be fit even if there are NaN's -# present in the rms or background maps. -MONITOR_ALLOW_NAN = False - -# The position uncertainty is in reality a combination of the fitting errors and the -# astrometric uncertainty of the image/survey/instrument. -# These two uncertainties are combined in quadrature. -# These two parameters are the astrometric uncertainty in ra/dec and they may be different -ASTROMETRIC_UNCERTAINTY_RA = 1.0 # arcsec -ASTROMETRIC_UNCERTAINTY_DEC = 1.0 # arcsec - -### -# OPTIONS THAT CONTROL THE SOURCE ASSOCIATION -### -ASSOCIATION_METHOD = 'basic' # 'basic', 'advanced' or 'deruiter' - -# options that apply to basic and advanced association -ASSOCIATION_RADIUS = 10.0 # arcsec, basic and advanced only - -# options that apply to deruiter association -ASSOCIATION_DE_RUITER_RADIUS = 5.68 # unitless, deruiter only -ASSOCIATION_BEAMWIDTH_LIMIT = 1.5 # multiplicative factor, deruiter only - -# If ASSOCIATION_PARALLEL is set to 'True' then the input images will be split into -# 'sky region groups' and association run on these groups in parallel and combined at the end. -# Setting to 'True' is best used when you have a large dataset with multiple patches of the sky, -# for smaller searches of only 3 or below sky regions it is recommened to keep as 'False'. -ASSOCIATION_PARALLEL = False - -# If images have been submitted in epoch dictionaries then an attempt will be made by the pipeline to -# remove duplicate sources. To do this a crossmatch is made between catalgoues to match 'the same' -# measurements from different catalogues. This parameter governs the distance for which a match is made. -# Default is 2.5 arcsec (which is typically 1 pixel in ASKAP images). -ASSOCIATION_EPOCH_DUPLICATE_RADIUS = 2.5 # arcsec - -### -# OPTIONS THAT CONTROL THE NEW SOURCE ANALYSIS -### - -# controls whether a source is labelled as a new source. The source in question -# must meet the requirement of: -# MIN_NEW_SOURCE_SIGMA > (source_peak_flux / lowest_previous_image_min_rms) -NEW_SOURCE_MIN_SIGMA = 5.0 - -# Default survey. -# Used by the website for analysis plots. -DEFAULT_SURVEY = None # 'NVSS' - -# Minimum error to apply to all flux measurements. The actual value used will be the measured/ -# reported value or this value, whichever is greater. -# This is a fraction, 0 = No minimum error -FLUX_PERC_ERROR = 0.0 #percent 0.05 is 5% - -# Replace the selavy errors with -USE_CONDON_ERRORS = True - -# Sometimes the local rms for a source is reported as 0 by selavy. -# Choose a value to use for the local rms in these cases -SELAVY_LOCAL_RMS_ZERO_FILL_VALUE = 0.2 # mJy - -# Create 'measurements.arrow' and 'measurement_pairs.arrow' files at the end of -# a successful run -CREATE_MEASUREMENTS_ARROW_FILES = False - -# Hide astropy warnings -SUPPRESS_ASTROPY_WARNINGS = True - -# Only measurement pairs where the Vs metric exceeds this value are selected for the -# aggregate pair metrics that are stored in Source objects. -SOURCE_AGGREGATE_PAIR_METRICS_MIN_ABS_VS = 4.3 -``` -## Configuration Options - -### Images and Selavy Files -**`IMAGE_FILES`** -List or Dictionary. The full paths to the image FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. - -=== "Normal mode" - - ```python - IMAGE_FILES = [ - "/full/path/to/image1.fits", "/full/path/to/image2.fits", "/full/path/to/image3.fits" - ] - ``` - -=== "Epoch mode" +Below is an example of a default `config.yaml` file. Note that no images or other input files have been provided. The file can be either edited directly or through the editor available on the run detail page. - ```python - IMAGE_FILES = { - "epoch01": ["/full/path/to/image1.fits", "/full/path/to/image2.fits"], - "epoch02": ["/full/path/to/image3.fits"], - } - ``` +!!! warning + Similarly to Python files, the indentation in the run configuration YAML file is important as it defines nested parameters. + +!!! example "config.yaml" + ```yaml + # This file specifies the pipeline configuration for the current pipeline run. + # You should review these settings before processing any images - some of the default + # values will probably not be appropriate. + + run: + # Path of the pipeline run + path: ... # auto-filled by pipeline initpiperun command + + # Hide astropy warnings during the run execution. + suppress_astropy_warnings: True + + inputs: + # NOTE: all the inputs must match with each other, i.e. the catalogue for the first + # input image (inputs.image[0]) must be the first input catalogue (inputs.selavy[0]) + # and so on. + image: + # list input images here, e.g. (note the leading hyphens) + # - /path/to/image1.fits + # - /path/to/image2.fits + + selavy: + # list input selavy catalogues here, as above with the images + + noise: + # list input noise (rms) images here, as above with the images + + # Required only if source_monitoring.monitor is true, otherwise optional. If not providing + # background images, remove the entire background section below. + background: + # list input background images here, as above with the images + + + source_monitoring: + # Source monitoring can be done both forward and backward in 'time'. + # Monitoring backward means re-opening files that were previously processed and can be slow. + monitor: True + + # Minimum SNR ratio a source has to be if it was placed in the area of minimum rms in + # the image from which it is to be extracted from. If lower than this value it is skipped + min_sigma: 3.0 + + # Multiplicative scaling factor to the buffer size of the forced photometry from the + # image edge + edge_buffer_scale: 1.2 + + # Passed to forced-phot as `cluster_threshold`. See docs for details. If unsure, leave + # as default. + cluster_threshold: 3.0 + + # Attempt forced-phot fit even if there are NaN's present in the rms or background maps. + allow_nan: False + + source_association: + # basic, advanced, or deruiter + method: basic + + # Maximum source separation allowed during basic and advanced association in arcsec + radius: 10.0 + + # Options that apply only to deruiter association + deruiter_radius: 5.68 # unitless + deruiter_beamwidth_limit: 1.5 # multiplicative factor + + # Split input images into sky region groups and run the association on these groups in + # parallel. Best used when there are a large number of input images with multiple + # non-overlapping patches of the sky. + # Not recommended for smaller searches of <= 3 sky regions. + parallel: False + + # If images have been submitted in epoch dictionaries then an attempt will be made by + # the pipeline to remove duplicate sources. To do this a crossmatch is made between + # catalgoues to match 'the same' measurements from different catalogues. This + # parameter governs the distance for which a match is made in arcsec. Default is 2.5 + # arcsec which is typically 1 pixel in ASKAP images. + epoch_duplicate_radius: 2.5 # arcsec + + new_sources: + # Controls when a source is labelled as a new source. The source in question must meet + # the requirement of: min sigma > (source_peak_flux / lowest_previous_image_min_rms) + min_sigma: 5.0 + + measurements: + # Source finder used to produce input catalogues. Only selavy is currently supported. + source_finder: selavy + + # Minimum error to apply to all flux measurements. The actual value used will either + # be the catalogued value or this value, whichever is greater. This is a fraction, e.g. + # 0.05 = 5% error, 0 = no minimum error. + flux_fractional_error: 0.0 + + # Replace the selavy errors with Condon (1997) errors. + condon_errors: True + + # Sometimes the local rms for a source is reported as 0 by selavy. + # Choose a value to use for the local rms in these cases in mJy/beam. + selavy_local_rms_fill_value: 0.2 + + # Create 'measurements.arrow' and 'measurement_pairs.arrow' files at the end of + # a successful run. + write_arrow_files: False + + # The positional uncertainty of a measurement is in reality the fitting errors and the + # astrometric uncertainty of the image/survey/instrument combined in quadrature. + # These two parameters are the astrometric uncertainty in RA/Dec and they may be different. + ra_uncertainty: 1.0 # arcsec + dec_uncertainty: 1.0 # arcsec + + variability: + # Only measurement pairs where the Vs metric exceeds this value are selected for the + # aggregate pair metrics that are stored in Source objects. + source_aggregate_pair_metrics_min_abs_vs: 4.3 -!!! tip - Use `glob` to easily list a large amount of files. E.g. - ```python - from glob import glob - ... - IMAGE_FILES = glob("/full/path/to/image*.fits") ``` - This can also be applied to any of the input options below. - -**`SELAVY_FILES`** -List or Dictionary. The full paths to the selavy text files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. -=== "Normal mode" - - ```python - SELAVY_FILES = [ - "/full/path/to/image1_selavy.txt", "/full/path/to/image2_selavy.txt", "/full/path/to/image3_selavy.txt" - ] - ``` +!!! note + Throughout the documentation we use dot-notation to refer to nested parameters, for example `inputs.image` refers to the list of input images. + This page on [YAML syntax](https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html) from the Ansible documentation is a good brief primer on the basics. -=== "Epoch mode" +## Configuration Options - ```python - SELAVY_FILES = { - "epoch01": ["/full/path/to/image1_selavy.txt", "/full/path/to/image2_selavy.txt"], - "epoch02": ["/full/path/to/image3_selavy.txt"], - } - ``` +### General Run Options -**`NOISE_FILES`** -List or Dictionary. The full paths to the image noise (RMS) FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. +**`run.path`** +Path to the directory for the pipeline run. This parameter will be automatically filled if the configuration file is generate with the [`initpiperun` management command](../adminusage/cli.md#initpiperun) or if the run was created with the web interface. -=== "Normal mode" +**`run.suppress_astropy_warnings`** +Boolean. Astropy warnings are suppressed in the logging output if set to `True`. Defaults to `True`. - ```python - NOISE_FILES = [ - "/full/path/to/image1_rms.fits", "/full/path/to/image2_rms.fits", "/full/path/to/image3_rms.fits" - ] +### Input Images and Selavy Files + +**`inputs.image`** +Line entries or epoch headed entries. The full paths to the image FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. + + +!!! example "config.yaml" + === "Normal mode" + + ```yaml + inputs: + image: + - /full/path/to/image1.fits + - /full/path/to/image2.fits + - /full/path/to/image3.fits + ``` + + === "Epoch mode" + + ```yaml + inputs: + image: + epoch01: + - /full/path/to/image1.fits + - /full/path/to/image2.fits + epoch02: + - /full/path/to/image3.fits + ``` + + +**`inputs.selavy`** +Line entries or epoch headed entries. The full paths to the selavy text files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. + +!!! example "config.yaml" + + === "Normal mode" + + ```yaml + inputs: + selavy: + - /full/path/to/image1_selavy.txt + - /full/path/to/image2_selavy.txt + - /full/path/to/image3_selavy.txt + ``` + + === "Epoch mode" + + ```yaml + inputs: + selavy: + epoch01: + - /full/path/to/image1_selavy.txt + - /full/path/to/image2_selavy.txt + epoch02: + - /full/path/to/image3_selavy.txt + ``` + + +**`inputs.noise`** +Line entries or epoch headed entries. The full paths to the image noise (RMS) FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. + +!!! example "config.yaml" + + === "Normal mode" + + ```yaml + inputs: + noise: + - /full/path/to/image1_rms.fits + - /full/path/to/image2_rms.fits + - /full/path/to/image3_rms.fits + ``` + + === "Epoch mode" + + ```yaml + inputs: + noise: + epoch01: + - /full/path/to/image1_rms.fits + - /full/path/to/image2_rms.fits + epoch02: + - /full/path/to/image3_rms.fits + ``` + + +**`inputs.background`** +Line entries or epoch headed entries. The full paths to the image background (mean) FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. Only required to be defined if `source_monitoring.monitor` is set to `True`. + +!!! example "config.yaml" + + === "Normal mode" + + ```yaml + inputs: + background: + - /full/path/to/image1_bkg.fits + - /full/path/to/image2_bkg.fits + - /full/path/to/image3_bkg.fits + ``` + + === "Epoch mode" + + ```yaml + inputs: + background: + epoch01: + - /full/path/to/image1_bkg.fits + - /full/path/to/image2_bkg.fits + epoch02: + - /full/path/to/image3_bkg.fits + ``` + + +#### Using glob expressions + +Instead of providing each input file explicitly, the inputs can be given as glob expressions which are resolved and sorted. Glob expressions must be provided as a mapping with the key `glob`. Both normal and epoch mode are supported. + +For example, the image input examples given above can be equivalently specified with the following glob expressions. + +!!! example "config.yaml" + + === "Normal mode" + + ```yaml + inputs: + image: + glob: /full/path/to/image*.fits + ``` + + === "Epoch mode" + + ```yaml + inputs: + image: + epoch01: + glob: /full/path/to/image[12].fits + epoch02: + - /full/path/to/image3.fits + ``` + + +Multiple glob expressions can also be provided as a list, in which case they are resolved and sorted in the order they are given. For example: + + +!!! example "config.yaml" + ```yaml + inputs: + image: + glob: + - /full/path/to/A/image*.fits + - /full/path/to/B/image*.fits ``` - -=== "Epoch mode" - - ```python - NOISE_FILES = { - "epoch01": ["/full/path/to/image1_rms.fits", "/full/path/to/image2_rms.fits"], - "epoch02": ["/full/path/to/image3_rms.fits"], - } + + +Note that it is not valid YAML to mix a sequence/list and a mapping/dictionary, meaning that for each input type (or epoch if using epoch mode), the files may be given _either_ as glob expressions or explicit file paths. For example, the following is **invalid**: + + +!!! failure "Invalid config.yaml" + ```yaml + inputs: + image: + # Invalid! Thou shalt not mix sequences and mappings in YAML + - /full/path/to/A/image1.fits + glob: /full/path/to/B/image*.fits ``` - -**`BACKGROUND_FILES`** -List or Dictionary. The full paths to the image background (mean) FITS files to be processed. Also accepts a dictionary format that will activate _epoch mode_ (see [Epoch Based Association](../design/association.md#epoch-based-association)) in which case all inputs must also be in dictionary format. The order of the entries must be consistent with the other input types. Only required to be defined if `MONITOR` is set to `True`. - -=== "Normal mode" - - ```python - BACKGROUND_FILES = [ - "/full/path/to/image1_bkg.fits", "/full/path/to/image2_bkg.fits", "/full/path/to/image3_bkg.fits" - ] + + +However, an explicit file path is a valid glob expression, so adding explicit paths alongside glob expressions is still possible by simply including the path in a list of glob expressions. For example, the following is valid: + + +!!! success "config.yaml" + ```yaml + inputs: + image: + glob: + - /full/path/to/A/image1.fits + - /full/path/to/B/image*.fits ``` + -=== "Epoch mode" - - ```python - BACKGROUND_FILES = { - "epoch01": ["/full/path/to/image1_bkg.fits", "/full/path/to/image2_bkg.fits"], - "epoch02": ["/full/path/to/image3_bkg.fits"], - } - ``` - -### Source Finder Format -**`SOURCE_FINDER`** -String. Signifies the format of the source finder text file read by the pipeline. Currently only supports `"selavy"`. - -!!! warning - Source finding is not performed by the pipeline and must be completed prior to processing. +In the above example, the final resolved image input list would contain the image `/full/path/to/A/image1.fits`, followed by all files matching `image*.fits` in `/full/path/to/B`. ### Source Monitoring -**`MONITOR`** -Boolean. Turns on or off forced extractions for non detections. If set to `True` then `BACKGROUND_IMAGES` must also be defined. Defaults to `False`. -**`MONITOR_MIN_SIGMA`** +**`source_monitoring.monitor`** +Boolean. Turns on or off forced extractions for non detections. If set to `True` then `inputs.background` must also be defined. Defaults to `False`. + +**`source_monitoring.min_sigma`** Float. For forced extractions to be performed they must meet a minimum signal-to-noise threshold with respect to the minimum rms value of the respective image. If the proposed forced measurement does not meet the threshold then it is not performed. I.e. $$ -\frac{f_{peak}}{\text{rms}_{image, min}} \geq \small{\text{MONITOR_MIN_SIGMA}}\text{,} +\frac{f_{peak}}{\text{rms}_{image, min}} \geq \small{\text{source_monitoring.min_sigma}}\text{,} $$ where $f_{peak}$ is the initial detection peak flux measurement of the source in question and $\text{rms}_{image, min}$ is the minimum RMS value of the image where the forced extraction is to take place. Defaults to `3.0`. -**`MONITOR_EDGE_BUFFER_SCALE`** +**`source_monitoring.edge_buffer_scale`** Float. Monitor forced extractions are not performed when the location is within 3 beamwidths of the image edge. This parameter scales this distance by the value set, which can help avoid errors when the 3 beamwidth limit is insufficient to avoid extraction failures. Defaults to 1.2. -**`MONITOR_CLUSTER_THRESHOLD`** +**`source_monitoring.cluster_threshold`** Float. A argument directly passed to the [forced photometry package](https://github.com/askap-vast/forced_phot/) used by the pipeline. It defines the multiple of `major_axes` to use for identifying clusters. Defaults to 3.0. -**`MONITOR_ALLOW_NAN`** +**`source_monitoring.allow_nan`** Boolean. A argument directly passed to the [forced photometry package](https://github.com/askap-vast/forced_phot/) used by the pipeline. It defines whether `NaN` values are allowed to be present in the extraction area in the rms or background maps. `True` would mean that `NaN` values are allowed. Defaults to False. ### Association !!! tip - Refer to the association documentation for full details on the association methods. - -**`ASTROMETRIC_UNCERTAINTY_RA`** -Float. Defines an uncertainty error to the RA that will be added in quadrature to the existing source extraction error. Used to represent a systematic positional error. Unit is arcseconds. Defaults to 1.0. - -**`ASTROMETRIC_UNCERTAINTY_DEC`** -Float. Defines an uncertainty error to the Dec that will be added in quadrature to the existing source extraction error. Used to represent systematic positional error. Unit is arcseconds. Defaults to 1.0. + Refer to the [association documentation](../design/association.md) for full details on the association methods. -**`ASSOCIATION_METHOD`** +**`source_association.method`** String. Select whether to use the `basic`, `advanced` or `deruiter` association method, entered as a string of the method name. Defaults to `"basic"`. -**`ASSOCIATION_RADIUS`** +**`source_association.radius`** Float. The distance limit to use during `basic` and `advanced` association. Unit is arcseconds. Defaults to `10.0`. -**`ASSOCIATION_DE_RUITER_RADIUS`** +**`source_association.deruiter_radius`** Float. The de Ruiter radius limit to use during `deruiter` association only. The parameter is unitless. Defaults to `5.68`. -**`ASSOCIATION_BEAMWIDTH_LIMIT`** +**`source_association.deruiter_beamwidth_limit`** Float. The beamwidth limit to use during `deruiter` association only. Multiplicative factor. Defaults to `1.5`. -**`ASSOCIATION_PARALLEL`** +**`source_association.parallel`** Boolean. When `True`, association is performed in parallel on non-overlapping groups of sky regions. Defaults to `False`. -**`ASSOCIATION_EPOCH_DUPLICATE_RADIUS`** +**`source_association.epoch_duplicate_radius`** Float. Applies to epoch based association only. Defines the limit at which a duplicate source is identified. Unit is arcseconds. Defaults to `2.5` (commonly one pixel for ASKAP images). ### New Sources -**`NEW_SOURCE_MIN_SIGMA`** -Float. Defines the limit at which a source is classed as a new source based upon the would-be significance of detections in previous images where no detection was made. I.e. +**`new_sources.min_sigma`** +Float. Defines the limit at which a source is classed as a new source based upon the would-be significance of detections in previous images where no detection was made. i.e. $$ -\frac{f_{peak}}{\text{rms}_{image, min}} \geq \small{\text{NEW_SOURCE_MIN_SIGMA}}\text{,} +\frac{f_{peak}}{\text{rms}_{image, min}} \geq \small{\text{new_sources.min_sigma}}\text{,} $$ where $f_{peak}$ is the initial detection peak flux measurement of the source in question and $\text{rms}_{image, min}$ is the minimum RMS value of the previous image(s) where no detection was made. If the requirement is met in any previous image then the source is flagged as new. Defaults to `5.0`. -### General +### Measurements + +**`measurements.source_finder`** +String. Signifies the format of the source finder text file read by the pipeline. Currently only supports `"selavy"`. -**`DEFAULT_SURVEY`** -Currently not used hence this option can be safely ignored. +!!! warning + Source finding is not performed by the pipeline and must be completed prior to processing. -**`FLUX_PERC_ERROR`** -Define a percentage flux error that will be added in quadrature to the extracted sources. Note that this will be reflected in the final source statistics and will not be applied directly to the measurements. Entered as a float between 0 - 1.0 which represents 0 - 100%. Defaults to `0.0`. +**`measurements.flux_fractional_error`** +Define a fractional flux error that will be added in quadrature to the extracted sources. Note that this will be reflected in the final source statistics and will not be applied directly to the measurements. Entered as a float between 0 - 1.0 which represents 0 - 100%. Defaults to `0.0`. -**`USE_CONDON_ERRORS`** +**`measurements.condon_errors`** Boolean. Calculate the Condon errors of the extractions when read in from the source extraction file. If `False` then the errors directly from the source finder output are used. Recommended to set to `True` for selavy extractions. Defaults to `True`. -**`SELAVY_LOCAL_RMS_ZERO_FILL_VALUE`** +**`measurements.selavy_local_rms_fill_value`** Float. Value to substitute for the `local_rms` parameter in selavy extractions if a `0.0` value is found. Unit is mJy. Defaults to `0.2`. -**`CREATE_MEASUREMENTS_ARROW_FILES`** +**`measurements.write_arrow_files`** Boolean. When `True` then two `arrow` format files are produced: * `measurements.arrow` - an arrow file containing all the measurements associated with the run. @@ -317,10 +405,15 @@ Boolean. When `True` then two `arrow` format files are produced: Producing these files for large runs (200+ images) is recommended for post-processing. Defaults to `False`. !!! note - The arrow files can be produced after the run has completed by an administrator. + The arrow files can optionally be produced after the run has completed by an administrator. -**`SUPPRESS_ASTROPY_WARNINGS`** -Boolean. Astropy warnings are suppressed in the logging output if set to `True`. Defaults to `True`. +**`measurements.ra_uncertainty`** +Float. Defines an uncertainty error to the RA that will be added in quadrature to the existing source extraction error. Used to represent a systematic positional error. Unit is arcseconds. Defaults to 1.0. + +**`measurements.dec_uncertainty`** +Float. Defines an uncertainty error to the Dec that will be added in quadrature to the existing source extraction error. Used to represent systematic positional error. Unit is arcseconds. Defaults to 1.0. + +### Variability -**`SOURCE_AGGREGATE_PAIR_METRICS_MIN_ABS_VS`** -Float. Defines the minimum `Vs` two-epoch metric value threshold used to attach the most significant pair value to the source. Defaults to `4.3`. +**`variability.source_aggregate_pair_metrics_min_abs_vs`** +Float. Defines the minimum $V_s$ two-epoch metric value threshold used to attach the most significant pair value to the source. Defaults to `4.3`. diff --git a/gulpfile.js b/gulpfile.js index d17eb032a..2f337052d 100644 --- a/gulpfile.js +++ b/gulpfile.js @@ -168,8 +168,8 @@ function clean() { // Bring third party dependencies from node_modules into vendor directory function modules() { - // Bootstrap JS - var bootstrapJS = gulp.src('./node_modules/bootstrap/dist/js/*') + // Bootstrap JS + var bootstrapJS = gulp.src('./node_modules/startbootstrap-sb-admin-2/vendor/bootstrap/js/*') .pipe(gulp.dest(paths.vendor + '/bootstrap/js')); // Bootstrap Select @@ -249,7 +249,7 @@ function modules() { // PrismJs var prismJs = gulp.src('./node_modules/prismjs/prism.js') .pipe(gulp.dest(paths.vendor + '/prismjs')); - var prismJsPy = gulp.src('./node_modules/prismjs/components/prism-python.min.js') + var prismJsYaml = gulp.src('./node_modules/prismjs/components/prism-yaml.min.js') .pipe(gulp.dest(paths.vendor + '/prismjs')); var prismJsLineNum = gulp.src('./node_modules/prismjs/plugins/line-numbers/prism-line-numbers.min.js') .pipe(gulp.dest(paths.vendor + '/prismjs/line-numbers')); @@ -258,7 +258,7 @@ function modules() { var prismJsLineNumCss = gulp.src('./node_modules/prismjs/plugins/line-numbers/prism-line-numbers.css') .pipe(gulp.dest(paths.vendor + '/prismjs/line-numbers')); - return merge(bootstrapJS, bootstrapSbAdmin2, bootstrap4toggle, bokehJS, dataTables, dataTablesButtons, fontAwesome, jquery, jqueryEasing, jszip, d3Celestial, d3CelestialData, d3CelestialImage, particlesJs, prismJs, prismJsPy, prismJsLineNum, prismJsCss, prismJsLineNumCss); + return merge(bootstrapJS, bootstrapSbAdmin2, bootstrap4toggle, bokehJS, dataTables, dataTablesButtons, fontAwesome, jquery, jqueryEasing, jszip, d3Celestial, d3CelestialData, d3CelestialImage, particlesJs, prismJs, prismJsYaml, prismJsLineNum, prismJsCss, prismJsLineNumCss); } // SCSS task diff --git a/mkdocs.yml b/mkdocs.yml index 3622a52ef..84ba0b0e4 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -7,7 +7,7 @@ copyright: Copyright © 2020 - 2025 Vast Development Team, University of Syd repo_url: https://github.com/askap-vast/vast-pipeline repo_name: askap-vast/vast-pipeline -edit_uri: "" +edit_uri: "tree/dev/docs/" dev_addr: localhost:8008 docs_dir: docs @@ -16,9 +16,28 @@ site_dir: docs_build theme: name: material favicon: img/favicon.png - logo: img/vast.png + logo: img/vast-logo.png features: - navigation.instant + - navigation.tabs + - navigation.sections + custom_dir: docs/theme + palette: + # Light mode + - media: "(prefers-color-scheme: light)" + scheme: default + accent: indigo + toggle: + icon: material/toggle-switch-off-outline + name: Switch to dark mode + + # Dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + accent: blue + toggle: + icon: material/toggle-switch + name: Switch to light mode # Extensions extra_css: @@ -45,23 +64,14 @@ markdown_extensions: - toc: toc_depth: 4 permalink: true + - lightgallery nav: - - Home: README.md - - Quickstart: - - Installation: quickstart/installation.md - - Configuration: quickstart/configuration.md - - Deployment: quickstart/deployment.md - - Admin Usage: - - CLI: adminusage/cli.md - - Web App: adminusage/app.md - - Pipeline Features and Design: - - Pipeline Steps Overview: design/overview.md - - Image & Selavy Catalogue Ingest: design/imageingest.md - - Source Association: design/association.md - - New Sources: design/newsources.md - - Forced Measurements: design/monitor.md - - Source Statistics: design/sourcestats.md + - Home: index.md + - Getting Started: + - Installation: gettingstarted/installation.md + - Configuration: gettingstarted/configuration.md + - Deployment: gettingstarted/deployment.md - Using the Pipeline: - Accessing the Pipeline: using/access.md - Initialising a Run: using/initrun.md @@ -69,79 +79,95 @@ nav: - Processing a Run: using/processrun.md - Adding Images to a Run: using/addtorun.md - Deleting a Run: using/deleterun.md - - Exploring the Pipeline Website: - - Overview: exploringwebsite/websiteoverview.md - - Admin Tools: exploringwebsite/admintools.md - - Pipeline Run Pages: exploringwebsite/runpages.md - - Source Pages: exploringwebsite/sourcepages.md - - Measurement Pages: exploringwebsite/measurementpages.md - - Image Pages: exploringwebsite/imagepages.md - - Pipeline Outputs: - - Outputs Overview: outputs/outputs.md - - Using the Outputs: outputs/usingoutputs.md - - Column Descriptions: outputs/coldesc.md + - Exploring the Pipeline Website: + - Overview: exploringwebsite/websiteoverview.md + - DataTables: exploringwebsite/datatables.md + - Pipeline Run Pages: exploringwebsite/runpages.md + - Source Pages: exploringwebsite/sourcepages.md + - Source Tags & Favourites: exploringwebsite/sourcetagsfavs.md + - Measurement Pages: exploringwebsite/measurementpages.md + - Image Pages: exploringwebsite/imagepages.md + - Pipeline Outputs: + - Outputs Overview: outputs/outputs.md + - Using the Outputs: outputs/usingoutputs.md + - Column Descriptions: outputs/coldesc.md + - Admin Usage: + - CLI: adminusage/cli.md + - Web App: adminusage/app.md + - Web App Admin Tools: exploringwebsite/admintools.md + - Features & Design: + - Pipeline Steps Overview: design/overview.md + - Image & Selavy Catalogue Ingest: design/imageingest.md + - Source Association: design/association.md + - New Sources: design/newsources.md + - Forced Measurements: design/monitor.md + - Source Statistics: design/sourcestats.md + - Architecture: + - Architecture Overview: architecture/intro.md + - Database Schema: architecture/database.md + # - Production: architecture/nimbus.md - Contributing and Developing: - - Intro: developing/intro.md + - Development Guidlines: developing/intro.md - GitHub Platform: developing/github.md - Local Development Environment: developing/localdevenv.md - Tests: developing/tests.md - - Docs: developing/docsdev.md - - Bechmarks: developing/profiling.md + - Documentation: developing/docsdev.md + - Benchmarks: developing/profiling.md # - Tips: developing/tips.md like this https://stackoverflow.com/questions/60160823/how-to-properly-parallelize-generic-code-with-numba-dask - - Code Reference: - - vast_pipeline: - - image: - - main.py: reference/image/main.md - - utils.py: reference/image/utils.md - - management: - - commands: - - clearpiperun.py: reference/management/commands/clearpiperun.md - - createmeasarrow.py: reference/management/commands/createmeasarrow.md - - debugrun.py: reference/management/commands/debugrun.md - - importsurvey.py: reference/management/commands/importsurvey.md - - initpiperun.py: reference/management/commands/initpiperun.md - - restorepiperun.py: reference/management/commands/restorepiperun.md - - runpipeline.py: reference/management/commands/runpipeline.md - - helpers.py: reference/management/helpers.md - - pipeline: - - association.py: reference/pipeline/association.md - - errors.py: reference/pipeline/errors.md - - finalise.py: reference/pipeline/finalise.md - - forced_extraction.py: reference/pipeline/forced_extraction.md - - loading.py: reference/pipeline/loading.md - - main.py: reference/pipeline/main.md - - model_generator.py: reference/pipeline/model_generator.md - - new_sources.py: reference/pipeline/new_sources.md - - utils.py: reference/pipeline/utils.md - - survey: - - catalogue.py: reference/survey/catalogue.md - - translators.py: reference/survey/translators.md - - utils: - - auth.py: reference/utils/auth.md - - unit_tags.py: reference/utils/unit_tags.md - - utils.py: reference/utils/utils.md - - view.py: reference/utils/view.md - - admin.py: reference/admin.md - - apps.py: reference/apps.md - - context_processors.py: reference/context_processors.md - - converters.py: reference/converters.md - - forms.py: reference/forms.md - - models.py: reference/models.md - - plots.py: reference/plots.md - # - serializers.py: reference/serializers.md - - urls.py: reference/urls.md - # - views.py: reference/views.md - - Architecture: - - Architecture Intro: architecture/intro.md - - Database Schema: architecture/database.md - # - Production: architecture/nimbus.md - - FAQs: faqs.md - - Changelog: changelog.md - - Code of Conduct: code_of_conduct.md - - License: license.md + - FAQ: faq.md + - Help and Acknowledgements: help_and_acknowledgements.md + - Reference: + - Changelog: changelog.md + - Code of Conduct: code_of_conduct.md + - License: license.md + - Code Reference: + - vast_pipeline: + - image: + - main.py: reference/image/main.md + - utils.py: reference/image/utils.md + - management: + - commands: + - clearpiperun.py: reference/management/commands/clearpiperun.md + - createmeasarrow.py: reference/management/commands/createmeasarrow.md + - debugrun.py: reference/management/commands/debugrun.md + - initpiperun.py: reference/management/commands/initpiperun.md + - restorepiperun.py: reference/management/commands/restorepiperun.md + - runpipeline.py: reference/management/commands/runpipeline.md + - helpers.py: reference/management/helpers.md + - pipeline: + - association.py: reference/pipeline/association.md + - config.py: reference/pipeline/config.md + - errors.py: reference/pipeline/errors.md + - finalise.py: reference/pipeline/finalise.md + - forced_extraction.py: reference/pipeline/forced_extraction.md + - loading.py: reference/pipeline/loading.md + - main.py: reference/pipeline/main.md + - model_generator.py: reference/pipeline/model_generator.md + - new_sources.py: reference/pipeline/new_sources.md + - utils.py: reference/pipeline/utils.md + - survey: + - translators.py: reference/survey/translators.md + - utils: + - auth.py: reference/utils/auth.md + - unit_tags.py: reference/utils/unit_tags.md + - utils.py: reference/utils/utils.md + - view.py: reference/utils/view.md + - admin.py: reference/admin.md + - apps.py: reference/apps.md + - context_processors.py: reference/context_processors.md + - converters.py: reference/converters.md + - forms.py: reference/forms.md + - models.py: reference/models.md + - plots.py: reference/plots.md + # - serializers.py: reference/serializers.md + - urls.py: reference/urls.md + # - views.py: reference/views.md plugins: - search + - git-revision-date-localized: + fallback_to_build_date: true + enable_creation_date: true - gen-files: scripts: # - docs/gen_credits.py @@ -173,10 +199,5 @@ extra: - icon: fontawesome/brands/github link: https://github.com/askap-vast/vast-pipeline name: vast-pipeline source on GitHub - - icon: fontawesome/brands/slack - link: https://askap-vast.slack.com/ - - icon: fontawesome/solid/paper-plane - link: mailto:transients@mailman.sydney.edu.au - name: Email ASKAP VAST - icon: fontawesome/solid/globe link: https://vast-survey.org diff --git a/package-lock.json b/package-lock.json index b194ee9aa..b82686c7f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,284 +1,9496 @@ { "name": "vast-pipeline", - "version": "99.99.99dev", - "lockfileVersion": 1, + "version": "1.0.0", + "lockfileVersion": 2, "requires": true, + "packages": { + "": { + "version": 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a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "vast-pipeline", - "version": "99.99.99dev", + "version": "1.0.0", "description": "Vast Pipeline code base for processing and analysing telescope images from the Square Kilometre Pathfinder", "main": "gulpfile.js", "scripts": { @@ -36,26 +36,26 @@ }, "homepage": "https://github.com/askap-vast/vast-pipeline#readme", "dependencies": { - "@bokeh/bokehjs": "2.2.0", + "@bokeh/bokehjs": "2.3.0", "@fortawesome/fontawesome-free": "5.12.0", - "bootstrap": "4.4.1", "bootstrap-select": "^1.13.18", "bootstrap4-toggle": "3.6.1", - "d3-celestial": "^0.7.34", + "d3-celestial": "^0.7.35", "datatables.net-bs4": "1.10.22", "datatables.net-buttons-bs4": "1.6.5", - "dotenv": "^8.2.0", - "jquery": "^3.5.1", + "dotenv": "^8.6.0", + "jquery": "^3.6.0", "jquery.easing": "^1.4.1", - "js9": "git+https://github.com/ericmandel/js9.git#v3.0", + "js9": "^3.4.0", "jszip": "3.5.0", "particles.js": "^2.0.0", "prismjs": "^1.23.0", - "startbootstrap-sb-admin-2": "^4.1.2" + "startbootstrap-sb-admin-2": "^4.1.4" }, "devDependencies": { - "@babel/core": "^7.12.3", - "@babel/preset-env": "^7.12.1", + "@babel/core": "^7.14.3", + "@babel/preset-env": "^7.14.2", + "@mr-hope/gulp-sass": "^2.0.0", "browser-sync": "^2.26.14", "del": "5.1.0", "gulp": "4.0.2", @@ -64,7 +64,6 @@ "gulp-clean-css": "4.2.0", "gulp-rename": "2.0.0", "gulp-run-command": "0.0.10", - "@mr-hope/gulp-sass": "^2.0.0", "gulp-sourcemaps": "^2.6.5", "gulp-uglify": "3.0.2", "merge-stream": "2.0.0" diff --git a/poetry.lock b/poetry.lock index db067b964..c37ff45fe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6,14 +6,6 @@ category = "main" optional = false python-versions = "*" -[[package]] -name = "aplus" -version = "0.11.0" -description = "UNKNOWN" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "appdirs" version = "1.4.4" @@ -32,7 +24,7 @@ python-versions = "*" [[package]] name = "arrow" -version = "1.0.3" +version = "1.1.0" description = "Better dates & times for Python" category = "main" optional = false @@ -44,18 +36,21 @@ typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "asgiref" -version = "3.3.1" +version = "3.3.4" description = "ASGI specs, helper code, and adapters" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" + +[package.dependencies] +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] -tests = ["pytest", "pytest-asyncio"] +tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"] [[package]] name = "astropy" -version = "4.2" +version = "4.2.1" description = "Astronomy and astrophysics core library" category = "main" optional = false @@ -101,6 +96,17 @@ python-versions = "*" [package.dependencies] six = ">=1.6.1,<2.0" +[[package]] +name = "babel" +version = "2.9.1" +description = "Internationalization utilities" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.dependencies] +pytz = ">=2015.7" + [[package]] name = "backcall" version = "0.2.0" @@ -255,41 +261,30 @@ sdist = ["setuptools-rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] test = ["pytest (>=6.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] -[[package]] -name = "cycler" -version = "0.10.0" -description = "Composable style cycles" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -six = "*" - [[package]] name = "dask" -version = "2021.3.0" +version = "2021.4.1" description = "Parallel PyData with Task Scheduling" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -fsspec = {version = ">=0.6.0", optional = true, markers = "extra == \"dataframe\""} -numpy = {version = ">=1.15.1", optional = true, markers = "extra == \"dataframe\""} +cloudpickle = ">=1.1.1" +fsspec = ">=0.6.0" +numpy = {version = ">=1.16", optional = true, markers = "extra == \"dataframe\""} pandas = {version = ">=0.25.0", optional = true, markers = "extra == \"dataframe\""} -partd = {version = ">=0.3.10", optional = true, markers = "extra == \"dataframe\""} +partd = ">=0.3.10" pyyaml = "*" -toolz = {version = ">=0.8.2", optional = true, markers = "extra == \"dataframe\""} +toolz = ">=0.8.2" [package.extras] -array = ["numpy (>=1.15.1)", "toolz (>=0.8.2)"] -bag = ["cloudpickle (>=0.2.2)", "fsspec (>=0.6.0)", "toolz (>=0.8.2)", "partd (>=0.3.10)"] -complete = ["bokeh (>=1.0.0,!=2.0.0)", "cloudpickle (>=0.2.2)", "distributed (>=2021.03.0)", "fsspec (>=0.6.0)", "numpy (>=1.15.1)", "pandas (>=0.25.0)", "partd (>=0.3.10)", "toolz (>=0.8.2)"] -dataframe = ["numpy (>=1.15.1)", "pandas (>=0.25.0)", "toolz (>=0.8.2)", "partd (>=0.3.10)", "fsspec (>=0.6.0)"] -delayed = ["cloudpickle (>=0.2.2)", "toolz (>=0.8.2)"] +array = ["numpy (>=1.16)"] +complete = ["bokeh (>=1.0.0,!=2.0.0)", "distributed (>=2021.04.1)", "numpy (>=1.16)", "pandas (>=0.25.0)"] +dataframe = ["numpy (>=1.16)", "pandas (>=0.25.0)"] diagnostics = ["bokeh (>=1.0.0,!=2.0.0)"] -distributed = ["distributed (>=2021.03.0)"] +distributed = ["distributed (>=2021.04.1)"] +test = ["pytest", "pytest-rerunfailures", "pytest-xdist"] [[package]] name = "decorator" @@ -320,19 +315,19 @@ graph = ["objgraph (>=1.7.2)"] [[package]] name = "django" -version = "3.1.7" +version = "3.2.2" description = "A high-level Python Web framework that encourages rapid development and clean, pragmatic design." category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -asgiref = ">=3.2.10,<4" +asgiref = ">=3.3.2,<4" pytz = "*" sqlparse = ">=0.2.2" [package.extras] -argon2 = ["argon2-cffi (>=16.1.0)"] +argon2 = ["argon2-cffi (>=19.1.0)"] bcrypt = ["bcrypt"] [[package]] @@ -345,7 +340,7 @@ python-versions = ">=3.5" [[package]] name = "django-debug-toolbar" -version = "3.2" +version = "3.2.1" description = "A configurable set of panels that display various debug information about the current request/response." category = "dev" optional = false @@ -365,12 +360,15 @@ python-versions = "*" [[package]] name = "django-extensions" -version = "3.1.1" +version = "3.1.3" description = "Extensions for Django" category = "dev" optional = false python-versions = ">=3.6" +[package.dependencies] +Django = ">=2.2" + [[package]] name = "django-picklefield" version = "3.0.1" @@ -403,6 +401,31 @@ django-picklefield = "*" rollbar = ["django-q-rollbar (>=0.1)"] sentry = ["django-q-sentry (>=0.1)"] +[[package]] +name = "django-stubs" +version = "1.8.0" +description = "Mypy stubs for Django" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +django = "*" +django-stubs-ext = "*" +mypy = ">=0.790" +typing-extensions = "*" + +[[package]] +name = "django-stubs-ext" +version = "0.2.0" +description = "Monkey-patching and extensions for django-stubs" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +django = "*" + [[package]] name = "django-tagulous" version = "1.1.0" @@ -432,7 +455,7 @@ django = ">=2.2" [[package]] name = "djangorestframework-datatables" -version = "0.5.2" +version = "0.5.1" description = "Seamless integration between Django REST framework and Datatables (https://datatables.net)" category = "main" optional = false @@ -443,7 +466,7 @@ djangorestframework = ">=3.5.0" [[package]] name = "flake8" -version = "3.9.0" +version = "3.9.2" description = "the modular source code checker: pep8 pyflakes and co" category = "dev" optional = false @@ -474,29 +497,27 @@ scipy = "*" type = "git" url = "https://github.com/askap-vast/forced_phot.git" reference = "master" -resolved_reference = "507a682ce5372da7eaaa380ff84aee329ac4bef2" +resolved_reference = "8f4307825781743755d189418a9cb9111aaf0b63" [[package]] name = "fsspec" -version = "0.8.7" +version = "2021.4.0" description = "File-system specification" category = "main" optional = false -python-versions = ">3.6" - -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} +python-versions = ">=3.6" [package.extras] abfs = ["adlfs"] adl = ["adlfs"] dask = ["dask", "distributed"] dropbox = ["dropboxdrivefs", "requests", "dropbox"] +entrypoints = ["importlib-metadata"] gcs = ["gcsfs"] git = ["pygit2"] github = ["requests"] gs = ["gcsfs"] -hdfs = ["pyarrow"] +hdfs = ["pyarrow (>=1)"] http = ["requests", "aiohttp"] s3 = ["s3fs"] sftp = ["paramiko"] @@ -507,7 +528,7 @@ ssh = ["paramiko"] name = "future" version = "0.18.2" description = "Clean single-source support for Python 3 and 2" -category = "main" +category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" @@ -532,9 +553,32 @@ monitor = ["psutil (>=5.7.0)"] recommended = ["dnspython (>=1.16.0,<2.0)", "idna", "cffi (>=1.12.2)", "selectors2", "backports.socketpair", "psutil (>=5.7.0)"] test = ["dnspython (>=1.16.0,<2.0)", "idna", "requests", "objgraph", "cffi (>=1.12.2)", "selectors2", "futures", "mock", "backports.socketpair", "contextvars (==2.4)", "coverage (>=5.0)", "coveralls (>=1.7.0)", "psutil (>=5.7.0)"] +[[package]] +name = "gitdb" +version = "4.0.7" +description = "Git Object Database" +category = "dev" +optional = false +python-versions = ">=3.4" + +[package.dependencies] +smmap = ">=3.0.1,<5" + +[[package]] +name = "gitpython" +version = "3.1.15" +description = "Python Git Library" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +gitdb = ">=4.0.1,<5" +typing-extensions = ">=3.7.4.0" + [[package]] name = "greenlet" -version = "1.0.0" +version = "1.1.0" description = "Lightweight in-process concurrent programming" category = "main" optional = false @@ -545,15 +589,15 @@ docs = ["sphinx"] [[package]] name = "gunicorn" -version = "20.0.4" +version = "20.1.0" description = "WSGI HTTP Server for UNIX" category = "main" optional = true -python-versions = ">=3.4" +python-versions = ">=3.5" [package.extras] -eventlet = ["eventlet (>=0.9.7)"] -gevent = ["gevent (>=0.13)"] +eventlet = ["eventlet (>=0.24.1)"] +gevent = ["gevent (>=1.4.0)"] setproctitle = ["setproctitle"] tornado = ["tornado (>=0.2)"] @@ -593,7 +637,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "3.7.3" +version = "4.0.1" description = "Read metadata from Python packages" category = "main" optional = false @@ -605,7 +649,7 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "ipdb" @@ -621,7 +665,7 @@ toml = {version = ">=0.10.2", markers = "python_version > \"3.6\""} [[package]] name = "ipython" -version = "7.21.0" +version = "7.23.1" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -633,6 +677,7 @@ backcall = "*" colorama = {version = "*", markers = "sys_platform == \"win32\""} decorator = "*" jedi = ">=0.16" +matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} pickleshare = "*" prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0" @@ -640,7 +685,7 @@ pygments = "*" traitlets = ">=4.2" [package.extras] -all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.14)", "pygments", "qtconsole", "requests", "testpath"] +all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.16)", "pygments", "qtconsole", "requests", "testpath"] doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] @@ -648,7 +693,7 @@ nbformat = ["nbformat"] notebook = ["notebook", "ipywidgets"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.14)"] +test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.16)"] [[package]] name = "ipython-genutils" @@ -700,7 +745,7 @@ i18n = ["Babel (>=0.8)"] [[package]] name = "jinxed" -version = "1.0.1" +version = "1.1.0" description = "Jinxed Terminal Library" category = "main" optional = false @@ -744,12 +789,15 @@ docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"] [[package]] -name = "kiwisolver" -version = "1.3.1" -description = "A fast implementation of the Cassowary constraint solver" -category = "main" +name = "lightgallery" +version = "0.5" +description = "Markdown extension to wrap images in lightbox/lightgallery" +category = "dev" optional = false -python-versions = ">=3.6" +python-versions = "*" + +[package.dependencies] +markdown = ">=3.0" [[package]] name = "livereload" @@ -810,20 +858,15 @@ optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" [[package]] -name = "matplotlib" -version = "3.4.0" -description = "Python plotting package" -category = "main" +name = "matplotlib-inline" +version = "0.1.2" +description = "Inline Matplotlib backend for Jupyter" +category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.5" [package.dependencies] -cycler = ">=0.10" -kiwisolver = ">=1.0.1" -numpy = ">=1.16" -pillow = ">=6.2.0" -pyparsing = ">=2.2.1" -python-dateutil = ">=2.7" +traitlets = "*" [[package]] name = "mccabe" @@ -864,7 +907,7 @@ mkdocs = ">=1.1,<2.0" [[package]] name = "mkdocs-gen-files" -version = "0.3.1" +version = "0.3.2" description = "MkDocs plugin to programmatically generate documentation pages during the build" category = "dev" optional = false @@ -873,9 +916,22 @@ python-versions = ">=3.7,<4.0" [package.dependencies] mkdocs = ">=1.0,<2.0" +[[package]] +name = "mkdocs-git-revision-date-localized-plugin" +version = "0.9.2" +description = "Mkdocs plugin that enables displaying the localized date of the last git modification of a markdown file." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +babel = ">=2.7.0" +GitPython = "*" +mkdocs = ">=1.0" + [[package]] name = "mkdocs-material" -version = "7.0.6" +version = "7.1.4" description = "A Material Design theme for MkDocs" category = "dev" optional = false @@ -953,24 +1009,16 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "nest-asyncio" -version = "1.5.1" -description = "Patch asyncio to allow nested event loops" -category = "main" -optional = false -python-versions = ">=3.5" - [[package]] name = "networkx" -version = "2.5" +version = "2.5.1" description = "Python package for creating and manipulating graphs and networks" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -decorator = ">=4.3.0" +decorator = ">=4.3,<5" [package.extras] all = ["numpy", "scipy", "pandas", "matplotlib", "pygraphviz", "pydot", "pyyaml", "lxml", "pytest"] @@ -987,11 +1035,11 @@ scipy = ["scipy"] [[package]] name = "nltk" -version = "3.5" +version = "3.6.2" description = "Natural Language Toolkit" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.5.*" [package.dependencies] click = "*" @@ -1000,16 +1048,16 @@ regex = "*" tqdm = "*" [package.extras] -all = ["requests", "numpy", "python-crfsuite", "scikit-learn", "twython", "pyparsing", "scipy", "matplotlib", "gensim"] +all = ["matplotlib", "twython", "scipy", "numpy", "gensim (<4.0.0)", "python-crfsuite", "pyparsing", "scikit-learn", "requests"] corenlp = ["requests"] -machine_learning = ["gensim", "numpy", "python-crfsuite", "scikit-learn", "scipy"] +machine_learning = ["gensim (<4.0.0)", "numpy", "python-crfsuite", "scikit-learn", "scipy"] plot = ["matplotlib"] tgrep = ["pyparsing"] twitter = ["twython"] [[package]] name = "numpy" -version = "1.20.1" +version = "1.20.2" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -1041,7 +1089,7 @@ pyparsing = ">=2.0.2" [[package]] name = "pandas" -version = "1.2.3" +version = "1.2.4" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -1057,7 +1105,7 @@ test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"] [[package]] name = "parso" -version = "0.8.1" +version = "0.8.2" description = "A Python Parser" category = "dev" optional = false @@ -1069,7 +1117,7 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "partd" -version = "1.1.0" +version = "1.2.0" description = "Appendable key-value storage" category = "main" optional = false @@ -1111,7 +1159,7 @@ python-versions = "*" [[package]] name = "pillow" -version = "8.1.2" +version = "8.2.0" description = "Python Imaging Library (Fork)" category = "main" optional = false @@ -1132,22 +1180,6 @@ click = ">=7" coverage = ["pytest-cov"] testing = ["mock", "pytest", "pytest-rerunfailures"] -[[package]] -name = "progressbar2" -version = "3.53.1" -description = "A Python Progressbar library to provide visual (yet text based) progress to long running operations." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -python-utils = ">=2.3.0" -six = "*" - -[package.extras] -docs = ["sphinx (>=1.7.4)"] -tests = ["flake8 (>=3.7.7)", "pytest (>=4.6.9)", "pytest-cov (>=2.6.1)", "pytest-flakes (>=4.0.0)", "pytest-pep8 (>=1.0.6)", "freezegun (>=0.3.11)", "sphinx (>=1.8.5)"] - [[package]] name = "prompt-toolkit" version = "3.0.18" @@ -1215,7 +1247,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pyerfa" -version = "1.7.2" +version = "1.7.3" description = "Python bindings for ERFA" category = "main" optional = false @@ -1238,7 +1270,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.8.1" +version = "2.9.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false @@ -1254,7 +1286,7 @@ python-versions = ">=3.7" [[package]] name = "pyjwt" -version = "2.0.1" +version = "2.1.0" description = "JSON Web Token implementation in Python" category = "main" optional = false @@ -1268,7 +1300,7 @@ tests = ["pytest (>=6.0.0,<7.0.0)", "coverage[toml] (==5.0.4)"] [[package]] name = "pymdown-extensions" -version = "8.1.1" +version = "8.2" description = "Extension pack for Python Markdown." category = "dev" optional = false @@ -1296,17 +1328,6 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" [package.dependencies] six = ">=1.5" -[[package]] -name = "python-utils" -version = "2.5.6" -description = "Python Utils is a module with some convenient utilities not included with the standard Python install" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -six = "*" - [[package]] name = "python3-openid" version = "3.2.0" @@ -1324,11 +1345,11 @@ postgresql = ["psycopg2"] [[package]] name = "pytkdocs" -version = "0.11.0" +version = "0.11.1" description = "Load Python objects documentation." category = "dev" optional = false -python-versions = ">=3.6,<4.0" +python-versions = ">=3.6.1,<4.0.0" [package.dependencies] astunparse = {version = ">=1.6.3,<2.0.0", markers = "python_version < \"3.9\""} @@ -1364,7 +1385,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [[package]] name = "regex" -version = "2021.3.17" +version = "2021.4.4" description = "Alternative regular expression module, to replace re." category = "dev" optional = false @@ -1403,6 +1424,40 @@ requests = ">=2.0.0" [package.extras] rsa = ["oauthlib[signedtoken] (>=3.0.0)"] +[[package]] +name = "rope" +version = "0.18.0" +description = "a python refactoring library..." +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +dev = ["pytest"] + +[[package]] +name = "ruamel.yaml" +version = "0.17.4" +description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" +category = "main" +optional = false +python-versions = ">=3" + +[package.dependencies] +"ruamel.yaml.clib" = {version = ">=0.1.2", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.10\""} + +[package.extras] +docs = ["ryd"] +jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] + +[[package]] +name = "ruamel.yaml.clib" +version = "0.2.2" +description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "scipy" version = "1.6.1" @@ -1428,12 +1483,20 @@ jeepney = ">=0.6" [[package]] name = "six" -version = "1.15.0" +version = "1.16.0" description = "Python 2 and 3 compatibility utilities" category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "smmap" +version = "4.0.0" +description = "A pure Python implementation of a sliding window memory map manager" +category = "dev" +optional = false +python-versions = ">=3.5" + [[package]] name = "social-auth-app-django" version = "3.4.0" @@ -1482,7 +1545,7 @@ python-versions = ">=3.6" [[package]] name = "sqlalchemy" -version = "1.4.3" +version = "1.4.14" description = "Database Abstraction Library" category = "main" optional = false @@ -1520,11 +1583,23 @@ category = "main" optional = false python-versions = ">=3.5" +[[package]] +name = "strictyaml" +version = "1.4.0" +description = "Strict, typed YAML parser" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +python-dateutil = ">=2.6.0" +"ruamel.yaml" = ">=0.14.2" + [[package]] name = "tabulate" version = "0.8.9" description = "Pretty-print tabular data" -category = "main" +category = "dev" optional = false python-versions = "*" @@ -1557,7 +1632,7 @@ python-versions = ">= 3.5" [[package]] name = "tqdm" -version = "4.59.0" +version = "4.60.0" description = "Fast, Extensible Progress Meter" category = "dev" optional = false @@ -1584,7 +1659,7 @@ test = ["pytest"] [[package]] name = "typed-ast" -version = "1.4.2" +version = "1.4.3" description = "a fork of Python 2 and 3 ast modules with type comment support" category = "dev" optional = false @@ -1592,7 +1667,7 @@ python-versions = "*" [[package]] name = "typing-extensions" -version = "3.7.4.3" +version = "3.10.0.0" description = "Backported and Experimental Type Hints for Python 3.5+" category = "main" optional = false @@ -1611,44 +1686,6 @@ secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "cer socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] brotli = ["brotlipy (>=0.6.0)"] -[[package]] -name = "vaex-arrow" -version = "0.5.1" -description = "Arrow support for vaex" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -matplotlib = ">=1.3.1" -pillow = "*" -pyarrow = ">=0.15" -vaex-core = ">=2.0.0,<3" - -[[package]] -name = "vaex-core" -version = "2.0.3" -description = "Core of vaex" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -aplus = "*" -astropy = ">=2" -cloudpickle = "*" -dask = {version = "*", extras = ["array"]} -future = ">=0.15.2" -nest-asyncio = ">=1.3.3" -numpy = ">=1.16" -pandas = "*" -progressbar2 = "*" -psutil = ">=1.2.1" -pyyaml = "*" -requests = "*" -six = 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Team"] license = "MIT" @@ -9,7 +9,7 @@ license = "MIT" python = "^3.7.1" astropy = "^4.0" astroquery = "^0.4.0" -bokeh = "^2.2.0" +bokeh = "2.3.0" # must align with @bokeh/bokehjs version in package.json cloudpickle = "^1.5.0" dask = {extras = ["dataframe"], version = "^2021.3.0"} dill = "^0.3.3" @@ -17,7 +17,7 @@ Django = "^3.1.7" django-crispy-forms = "^1.9.2" django-environ = "^0.4.5" djangorestframework = "^3.11.0" -djangorestframework-datatables = "^0.5.1" +djangorestframework-datatables = "0.5.1" django-q = "^1.3.3" django-tagulous = "^1.1.0" jinja2 = "^2.11.2" @@ -35,10 +35,10 @@ whitenoise = "^5.2.0" gevent = { version = "^21.1.2", optional = true } gunicorn = { version = "^20.0.4", optional = true } forced-phot = { git = "https://github.com/askap-vast/forced_phot.git" } -vaex-arrow = "^0.5.1" +strictyaml = "^1.3.2" [tool.poetry.dev-dependencies] -mkdocs-material = "^7.0.5" +mkdocs-material = "^7.1.4" mkdocstrings = "^0.15.0" mkdocs-minify-plugin = "^0.4.0" mkdocs-material-extensions = "^1.0.1" @@ -53,6 +53,10 @@ flake8 = "^3.9.0" mypy = "^0.812" black = "^20.8b1" django-extensions = "^3.1.1" +rope = "^0.18.0" +django-stubs = "^1.7.0" +lightgallery = "^0.5" +mkdocs-git-revision-date-localized-plugin = "^0.9" [tool.poetry.extras] prod = ["gevent", "gunicorn"] diff --git a/scss/pipeline.scss b/scss/pipeline.scss index 8bfe3f4d7..5f1d8e108 100644 --- a/scss/pipeline.scss +++ b/scss/pipeline.scss @@ -69,17 +69,17 @@ justify-content: flex-end; } -.breadcrumb { - display: block !important; +// make the breadcrumb truncate instead of wrap on narrow viewports +#content > nav > ol.breadcrumb { + margin-bottom: 0rem; + flex-wrap: nowrap !important; + + .breadcrumb-item { + display: list-item; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; - margin-bottom: unset; - margin-block-end: 0px; -} - -.breadcrumb .breadcrumb-item { - display: inline; + } } .sidebar { diff --git a/static/js/aladin-script.js b/static/js/aladin-script.js index a36596516..6d4f08f58 100644 --- a/static/js/aladin-script.js +++ b/static/js/aladin-script.js @@ -86,12 +86,13 @@ function configureAladin(aladin, aladinConf) { aladin.getBaseImageLayer().getColorMap().reverse(); if (aladinConf.hasOwnProperty('aladin_box_ra')) { var overlay = A.graphicOverlay({color: '#ee2345', lineWidth: 2}); + var COS_DEC = Math.cos(aladinConf.aladin_dec * (Math.PI / 180.0)) aladin.addOverlay(overlay); overlay.addFootprints([A.polygon([ - [aladinConf.aladin_ra + (aladinConf.aladin_box_ra / 2) , aladinConf.aladin_dec - (aladinConf.aladin_box_dec / 2)], - [aladinConf.aladin_ra + (aladinConf.aladin_box_ra / 2) , aladinConf.aladin_dec + (aladinConf.aladin_box_dec / 2)], - [aladinConf.aladin_ra - (aladinConf.aladin_box_ra / 2) , aladinConf.aladin_dec + (aladinConf.aladin_box_dec / 2)], - [aladinConf.aladin_ra - (aladinConf.aladin_box_ra / 2) , aladinConf.aladin_dec - (aladinConf.aladin_box_dec / 2)], + [aladinConf.aladin_ra + (aladinConf.aladin_box_ra / COS_DEC / 2) , aladinConf.aladin_dec - (aladinConf.aladin_box_dec / 2)], + [aladinConf.aladin_ra + (aladinConf.aladin_box_ra / COS_DEC / 2) , aladinConf.aladin_dec + (aladinConf.aladin_box_dec / 2)], + [aladinConf.aladin_ra - (aladinConf.aladin_box_ra / COS_DEC / 2) , aladinConf.aladin_dec + (aladinConf.aladin_box_dec / 2)], + [aladinConf.aladin_ra - (aladinConf.aladin_box_ra / COS_DEC / 2) , aladinConf.aladin_dec - (aladinConf.aladin_box_dec / 2)], ])]); } } diff --git a/static/js/datatables-pipeline.js b/static/js/datatables-pipeline.js index 7edf83d5e..9d7e43224 100644 --- a/static/js/datatables-pipeline.js +++ b/static/js/datatables-pipeline.js @@ -254,7 +254,7 @@ $(document).ready(function() { */ .DataTable({ "searching": false, - "pageLength": 5, + "pageLength": 15, "lengthChange": false, // need a different dom for external results table "dom": ( diff --git a/templates/base.html b/templates/base.html index d6d3c9068..502057b9c 100644 --- a/templates/base.html +++ b/templates/base.html @@ -279,7 +279,7 @@ @@ -308,7 +308,7 @@ - + diff --git a/templates/generic_table.html b/templates/generic_table.html index d85d448ca..b7e29dcc4 100644 --- a/templates/generic_table.html +++ b/templates/generic_table.html @@ -264,17 +264,6 @@
-
- - - -
- -
diff --git a/templates/image_detail.html b/templates/image_detail.html index 12da266d5..c1e41de4a 100644 --- a/templates/image_detail.html +++ b/templates/image_detail.html @@ -62,10 +62,8 @@
Details

Position: {{ image.ra_hms }} {{ image.dec_dms }}
- Position (Decimal): {{ image.ra|floatformat:6 }} - {{ image.dec|floatformat:6 }}
- Position (Galactic): {{ image.l|floatformat:6 }} - {{ image.b|floatformat:6 }}
+ Position (Decimal): {{ image.ra|floatformat:6 }} {{ image.dec|floatformat:6 }}
+ Position (Galactic): {{ image.l|floatformat:6 }} {{ image.b|floatformat:6 }}

diff --git a/templates/index.html b/templates/index.html index 0e87da5d6..563bd53f7 100644 --- a/templates/index.html +++ b/templates/index.html @@ -21,6 +21,9 @@

Welcome back {{ user.first_name }}!

{% else %}

Welcome back!

{% endif %} +
+ VAST Pipeline version {% if pipeline_version_url %}{% endif %}{{ pipeline_version }}{% if pipeline_version_url %}{% endif %}. +
@@ -116,11 +119,11 @@
Welcome to the VAST Pipeline!

Use the navigation sidebar to explore the website. Where to go for common tasks:

 -

If you find an issue please use the raise an issue on Github. This link is always available via the sidebar.

+

If you find an issue please raise an issue on Github. This link is always available via the sidebar. For ideas or features that require more discussion, or to ask a general question about the pipeline, there is also a link to start a discussion on Github.

Links to other VAST servies such as the JupyterHub or Wiki can be found under 'VAST Links' in the sidebar.

-

Currently users are unable to launch processing of their own run from the website. This feature is coming soon. In the meantime please contact the admin team if you wish to process your own run.

+

Full pipeline documentation is available on the documentation website.

diff --git a/templates/measurement_detail.html b/templates/measurement_detail.html index 51f8fbddf..0f3c209f8 100644 --- a/templates/measurement_detail.html +++ b/templates/measurement_detail.html @@ -75,7 +75,7 @@
Details

Name: {{ measurement.name }}
Island ID: {{ measurement.island_id }}
- Image: Image: {{ measurement.image_name }}

@@ -83,12 +83,9 @@

Details
Table)

- Position: {{ measurement.ra_hms }} - {{ measurement.dec_dms }}
- Position (Decimal): {{ measurement.ra }} - {{ measurement.dec }}
- Position (Galactic): {{ measurement.l|floatformat:6 }} - {{ measurement.b|floatformat:6 }} + Position: {{ measurement.ra_hms }} {{ measurement.dec_dms }}
+ Position (Decimal): {{ measurement.ra }} {{ measurement.dec }}
+ Position (Galactic): {{ measurement.l|floatformat:6 }} {{ measurement.b|floatformat:6 }}

@@ -139,13 +136,6 @@
Details
- -
-
-
-
-
-
@@ -157,6 +147,15 @@
Postage Stamp
+ + +
+
+
+
+
+ +
@@ -267,7 +266,7 @@
- + diff --git a/templates/run_detail.html b/templates/run_detail.html index f234f6eeb..1816c1414 100644 --- a/templates/run_detail.html +++ b/templates/run_detail.html @@ -197,7 +197,7 @@
- 
{{ p_run.config_txt }}
+ 
{{ p_run.config_txt }}
@@ -339,10 +339,6 @@