From f64a3d34c92617a2db4eea2e31bcc80e05ebdf9f Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 2 Feb 2024 14:07:49 -0500 Subject: [PATCH 01/19] Simplify and document dependency management --- .pre-commit-config.yaml | 1 + .vscode/settings.json | 7 +- CONTRIBUTING.md | 195 +- README.md | 36 +- algorithm_config.yaml | 6 +- bin/build-dps.sh | 7 + bin/build.sh | 128 + bin/conda-prefix.sh | 47 + bin/generate-lock-file.sh | 11 + subset.sh => bin/subset.sh | 14 +- build.sh | 45 - conda-lock.yml | 20900 ++++++++++++++++++++++ {src/gedi_subset => docs}/MAAP_USAGE.md | 0 environment-dev.yml | 24 + environment.yml | 29 + environment/conda-linux-64.lock | 203 - environment/conda-lock.yml | 6089 ------- environment/conda-osx-64.lock | 186 - environment/environment-dev.yml | 22 - environment/environment-maappy.yml | 8 - environment/environment.yml | 14 - 21 files changed, 21348 insertions(+), 6624 deletions(-) create mode 100755 bin/build-dps.sh create mode 100755 bin/build.sh create mode 100755 bin/conda-prefix.sh create mode 100755 bin/generate-lock-file.sh rename subset.sh => bin/subset.sh (72%) delete mode 100755 build.sh create mode 100644 conda-lock.yml rename {src/gedi_subset => docs}/MAAP_USAGE.md (100%) create mode 100644 environment-dev.yml create mode 100644 environment.yml delete mode 100644 environment/conda-linux-64.lock delete mode 100644 environment/conda-lock.yml delete mode 100644 environment/conda-osx-64.lock delete mode 100644 environment/environment-dev.yml delete mode 100644 environment/environment-maappy.yml delete mode 100644 environment/environment.yml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 02cf478..433446d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,6 +7,7 @@ repos: rev: v4.4.0 hooks: - id: check-added-large-files + exclude: conda-lock.yml - id: check-case-conflict - id: check-executables-have-shebangs - id: check-json diff --git a/.vscode/settings.json b/.vscode/settings.json index 95a7c42..e311585 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,11 +1,6 @@ { - "deepscan.enable": true, - "python.linting.mypyEnabled": true, "python.analysis.stubPath": "./gedi-subset/typings", - "python.formatting.provider": "black", "python.analysis.extraPaths": [ "./gedi-subset/src" - ], - "mypy.runUsingActiveInterpreter": true, - "mypy.configFile": "gedi-subset/pyproject.toml" + ] } diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4889f61..6af62cf 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,45 +1,155 @@ # Contributing +- [Development Setup](#development-setup) +- [Managing Dependencies](#managing-dependencies) +- [Creating an Algorithm Release](#creating-an-algorithm-release) +- [Registering an Algorithm Release](#registering-an-algorithm-release) + ## Development Setup To contribute to this work, you must obtain access to the following: -1. [MAAP GEDI Subsetter hosted on GitHub]: For creating new versions - (releases) of the algorithms implemented in the repository. -1. [NASA MAAP]: Where the ADE resides, and thus where algorithms can be - registered. - -To prepare for contributing, do the following in an ADE workspace: +1. [MAAP GEDI Subsetter repository]: For creating new versions (releases) of the + algorithms implemented in the repository. +1. [NASA MAAP]: Where the Algorithm Development Environment (ADE) resides, and + thus where algorithms can be registered. + +On your development system (not necessarily the ADE), you must have the +following installed: + +- `git`: [pre-installed in the ADE] On macOS, using Homebrew is highly + recommended: `brew install git`. Otherwise, see + . +- `conda`: [pre-installed in the ADE] On macOS, using Homebrew to install + Miniforge (containing `conda`) is highly recommended: + `brew install --cask miniforge`. Otherwise, see + . +- `conda-lock`: On macOS, using Homebrew is highly recommended: + `brew install conda-lock`. Otherwise, see + . +- `pre-commit`: On macOS, using Homebrew is highly recommended: + `brew install pre-commit`. Otherwise, see . + +To prepare for contributing, do the following on your development system (again, +not necessarily the ADE): 1. Clone this GitHub repository. 1. Change directory to the cloned repository. -1. Create the `gedi_subset` virtual environment (**NOTE:** _you will need to - repeat this step whenever your restart your ADE workspace_): +1. Create the `gedi_subset` virtual environment. + + **NOTE:** _If you're working in the ADE, use the `--prefix` option shown + (excluding the square brackets), otherwise you will need to repeat this step + whenever your restart your ADE workspace_. Outside of the ADE, there's no + such need to use the `--prefix` option, unless you prefer to use a + non-default location: ```bash - ./build.sh --dev + bin/build.sh [--prefix "${HOME}/envs/gedi_subset"] ``` -1. Activate the `gedi_subset` virtual environment: + Note that you may also supply additional options, all of which are passed + through to the `conda-lock install` command. For a list of options, see + . + + **TROUBLESHOOTING:** If the command above fails with the error message + `conda: command not found`, you must first run `conda activate base`, then + rerun the command above. + +1. Activate the `gedi_subset` virtual environment. + + If you did _not_ specify the `--prefix` option in the previous step, you can + use the following command: ```bash conda activate gedi_subset ``` + Otherwise, you must instead use the following command (alter the value if you + specified a different prefix in the previous step): + + ```bash + conda activate "${HOME}/envs/gedi_subset" + ``` + 1. Install Git pre-commit hooks: ```bash pre-commit install --install-hooks ``` -If you plan to do any development work outside of the ADE (such as on your local -workstation), perform the steps above in that location as well. **NOTE:** _This -means that you must have `conda` installed (see [conda installation]) in your -desired development location outside of the ADE workspace._ - During development, you will create PRs against the GitHub repository, as explained below. +## Managing Dependencies + +To minimize the time it takes to install dependencies on the Docker image +created during algorithm registration, we leverage `conda-lock` to pre-resolve +dependencies and generate a lock file, so that dependency resolution does not +take place during registration. This means that we manage dependencies and +update the lock file as follows: + +1. Dependencies required by the algorithm are specified in `environment.yml`. + (These are the only dependencies that will be installed in DPS.) +1. Development dependencies (for testing, static code analysis, etc.) are + specified in `environment-dev.yml`. +1. We use `conda-lock` to generate the lock file `conda-lock.yml` from the files + above whenever we either make a change to one (or both) of the files, or wish + to simply update dependencies (specified in those files) to their latest + versions that satisfy the specified version constraints (see below). + +Within `environment.yml` and `environment-dev.yml` we intentionally _avoid_ +specifying _exact_ (`==`) versions to avoid resolution conflicts that would +prevent successful dependency resolution by giving the resolver enough +flexibility to satisfy all requirements. When versions are specified, they are +only to ensure we use versions with necessary features or without known bugs we +want to avoid, and typically use the [compatible release operator] (`~=`) to +constrain only the _major_ version of a dependency. + +The lock file, `conda-lock.yml`, was generated with the following command: + +```plain +bin/generate-lock-file.sh +``` + +Whenever a dependency is added, removed, or has its version constraint changed +within either source file (`environment.yml` or `environment-dev.yml`), the same +command above should be performed, and all of the updated files should be +committed to Git. + +If you simply want to update some (or all) packages to their latest versions +compatible with their version constraints, run the following command instead: + +```plain +conda lock --update TEXT +``` + +where `TEXT` is one or more (comma-separated) packages specified in +`environment.yml` or `environment-dev.yml`. To update _all_ of the packages to +their latest versions matching their constraints, specify empty quotes in place +of `TEXT` (either `''` or `""`), otherwise `conda-lock` will complain. + +The lock file (`conda-lock.yml`) is a unified, multi-platform lock file, so it +can be used on various platforms (Linux, macOS, and Windows) to create (or +update) the `gedi_subset` conda environment, which is precisely what the +`build.sh` script does. + +**IMPORTANT:** Whenever you regenerate or update the lock file, you must also +update your `gedi_subset` conda environment on your development workstation so +that all dependency changes are applied to it, because updating the lock file +does not apply the changes to your conda environment. Therefore, you must +again run `bin/build.sh` command (with appropriate options). + +Note, as indicated in a later section, the `bin/build-dps.sh` script is used to +install the dependencies from the lock file during algorithm registration. +Specifically, it calls `bin/build.sh` with options appropriate for the DPS +environment. + +Using the conda lock file in both development and DPS environments is an +intentional consistency for dependency installation designed to eliminate +possible differences in dependencies that might otherwise allow development and +testing to succeed, but later result in a failure in DPS, either during +algorithm registration, or worse, during algorithm execution. + ## Creating an Algorithm Release 1. Create a new branch based on an appropriate existing branch (typically based @@ -63,8 +173,7 @@ explained below. 1. Submit a PR to the GitHub repository. 1. _Only when_ the PR is on a branch to be merged into the `main` branch _and_ it has been approved and merged, create a new release in GitHub as follows: - 1. Go to - + 1. Go to 1. Click the **Choose a tag** dropdown. 1. In the input box that appears, enter the _same_ value as the new value of `version` in `algorithm_config.yml`, and click the **Create a new tag** @@ -80,48 +189,58 @@ explained below. Once a release is published in the GitHub repository (see above), the algorithm must be registered in the ADE. To do so, follow these steps: + 1. Within an ADE workspace, open a **New Launcher** tab and underneath the **MAAP Extensions** section, select **Register Algorithm**. - **Terminal** launcher. 1. On the main registration page: 1. Under Repository Information: - Enter the **Repository URL** as `https://github.com/MAAP-Project/gedi-subsetter.git`. - - Enter the **Repository Branch** as the name of the release tag (e.g., `1.0.0`). - - Enter the **Run Command** as `gedi-subsetter/subset.sh`. - - Enter the **Build Command** as `gedi-subsetter/build.sh`. + - Enter the **Repository Branch** as the name of the release tag (e.g., + `1.0.0`). + - Enter the **Run Command** as `gedi-subsetter/bin/subset.sh`. + - Enter the **Build Command** as `gedi-subsetter/bin/build-dps.sh`. 1. Under General Information: - Enter the **Algorithm Name** as `gedi-subset`. - - Enter the **Algorithm Description** as `Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI)`. + - Enter the **Algorithm Description** as + `Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI)`. - Enter the **Disk Space** as `20`. - Enter the **Resource Allocation** as `maap-dps-worker-32gb`. - - Enter the **Container URL** as `mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.0.1`. + - Enter the **Container URL** as + `mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.4`. 1. Under Input Types, add the following Name, Description pairs: 1. For File Inputs: - `aoi`: Area of Interest GeoJSON file 1. For Positional Inputs: - - `doi`: Digital Object Identifier (DOI) of the GEDI collection to subset, or a logical name representing such a DOI - - `temporal`: (Default: full temporal range): Temporal range to subset. + - `doi`: Digital Object Identifier (DOI) of the GEDI collection to + subset, or a logical name representing such a DOI + - `temporal`: (Default: `-`, which means the full temporal range): + Temporal range to subset. - `lat`: Name of the dataset used for latitude. - `lon`: Name of the dataset used for longitude. - - `beams`: (Default: `all`): `all`, `coverage`, or `power`, or a comma-separated list of specific beam names, with or without the `BEAM` prefix (e.g., `BEAM0000,BEAM0001` or `0000,0001`). - - `columns`: One or more column names, separated by commas, to include in the output file. - - `query`: (Default: no query): Query expression for subsetting the rows in the output file. - - `limit`: (Default: 1_000): Maximum number of GEDI granule data files to download from the CMR + - `beams`: (Default: `all`): `all`, `coverage`, or `power`, or a + comma-separated list of specific beam names, with or without the + `BEAM` prefix (e.g., `BEAM0000,BEAM0001` or `0000,0001`). + - `columns`: One or more column names, separated by commas, to include + in the output file. + - `query`: (Default: no query): Query expression for subsetting the + rows in the output file. + - `limit`: (Default: 1_000): Maximum number of GEDI granule data files + to download from the CMR - `output`: Name to use for the output file. 1. Once finished, click **Register Algorithm** 1. Check the build job status at - . If the job - fails, you will need to correct the issue (and likely create a patch release, - following the release steps again). Otherwise, you should now be able to - open the **Jobs** menu, choose **View & Submit Jobs**, and find - the new version of the algorithm in the dropdown list of the **Submit** tab. - -[conda installation]: - https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html + . If the + job fails, you will need to correct the issue (and likely create a patch + release, following the release steps again). Otherwise, you should now be + able to open the **Jobs** menu, choose **View & Submit Jobs**, and find the + new version of the algorithm in the dropdown list of the **Submit** tab. + +[compatible release operator]: + https://peps.python.org/pep-0440/#compatible-release [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/ -[MAAP GEDI Subsetter hosted on GitHub]: +[MAAP GEDI Subsetter repository]: https://github.com/MAAP-Project/gedi-subsetter.git [NASA MAAP]: https://maap-project.org/ diff --git a/README.md b/README.md index ba65888..037a927 100644 --- a/README.md +++ b/README.md @@ -4,20 +4,46 @@ ## History -The GEDI Subsetter tool was developed in response to the release of [Global Ecosystem Dynamics Investigation](https://www.earthdata.nasa.gov/sensors/gedi) (GEDI) data and the subsequent interest from the [University of Maryland biomass group](https://geog.umd.edu/). The group expressed interest in studying various regions, which requires obtaining all granules that intersect any given region. Due to GEDI products being an orbit of the International Space Station (ISS), the challenge was to efficiently subset all granules passing through the area of interest. So while the existing methods would work for a small number of granules, the users were seeking a highly scalable, automated approach that would allow them to efficiently gather their data points without the need to process each file separately. +The GEDI Subsetter tool was developed in response to the release of +[Global Ecosystem Dynamics Investigation](https://www.earthdata.nasa.gov/sensors/gedi) +(GEDI) data and the subsequent interest from the +[University of Maryland biomass group](https://geog.umd.edu/). The group +expressed interest in studying various regions, which requires obtaining all +granules that intersect any given region. Due to GEDI products being an orbit +of the International Space Station (ISS), the challenge was to efficiently +subset all granules passing through the area of interest. So while the existing +methods would work for a small number of granules, the users were seeking a +highly scalable, automated approach that would allow them to efficiently gather +their data points without the need to process each file separately. ## About GEDI -GEDI is a [LIDAR](https://www.earthdata.nasa.gov/technology/lidar) instrument on the International Space Station that generates high-resolution laser ranging observations of the 3D features of the Earth. GEDI’s precise measurements of forest canopy height, canopy vertical structure, and surface elevation greatly advance our ability to characterize important carbon and water cycling processes, biodiversity, and habitat. +GEDI is a [LIDAR](https://www.earthdata.nasa.gov/technology/lidar) instrument on +the International Space Station that generates high-resolution laser ranging +observations of the 3D features of the Earth. GEDI’s precise measurements of +forest canopy height, canopy vertical structure, and surface elevation greatly +advance our ability to characterize important carbon and water cycling +processes, biodiversity, and habitat. ## The Subsetter -The Subsetter utilizes the Multi-Mission Algorithm and Analysis Platform’s (MAAP) async job queuing system that runs on AWS. The tool automatically handles authentication (AWS S3 direct access) and auto-refreshes tokens. Users are able to pass a number of inputs to the Subsetter’s job to refine the results. By querying NASA's Common Metadata Repository (CMR) to gather all the granules that pass through a specified region, the Subsetter is able to parallelize the process to download the granules and then append the subsetted results to a single [GeoPackage](https://www.geopackage.org/) (GPKG) file. +The Subsetter utilizes the Multi-Mission Algorithm and Analysis Platform’s +(MAAP) async job queuing system that runs on AWS. The tool automatically +handles authentication (AWS S3 direct access) and auto-refreshes tokens. Users +are able to pass a number of inputs to the Subsetter’s job to refine the +results. By querying NASA's Common Metadata Repository (CMR) to gather all the +granules that pass through a specified region, the Subsetter is able to +parallelize the process to download the granules and then append the subsetted +results to a single [GeoPackage](https://www.geopackage.org/) (GPKG) file. -To read more about its specifications and usage in MAAP, please see the [MAAP Usage Guide](src/gedi_subset/MAAP_USAGE.md). +To read more about its specifications and usage in MAAP, please see the +[MAAP Usage Guide](docs/MAAP_USAGE.md). For contributing to the Subsetter, please see the [Contributing Guide](./CONTRIBUTING.md). ## Beyond -The Subsetter could be generalized to work with other datasets, pass back different data formats, directly read from S3, and more. The Subsetter is a great example of how MAAP can help users with their data processing needs. Future examples could demonstrate its usage outside of MAAP. +The Subsetter could be generalized to work with other datasets, pass back +different data formats, directly read from S3, and more. The Subsetter is a +great example of how MAAP can help users with their data processing needs. +Future examples could demonstrate its usage outside of MAAP. diff --git a/algorithm_config.yaml b/algorithm_config.yaml index 3344965..1f724fd 100644 --- a/algorithm_config.yaml +++ b/algorithm_config.yaml @@ -1,12 +1,12 @@ description: Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI) algo_name: gedi-subset -version: 0.6.0 +version: 0.6.2 environment: ubuntu repository_url: https://repo.ops.maap-project.org/data-team/gedi-subsetter.git docker_url: mas.dit.maap-project.org/root/maap-workspaces/base_images/r:dit queue: maap-dps-worker-32gb -build_command: gedi-subsetter/build.sh -run_command: gedi-subsetter/subset.sh +build_command: gedi-subsetter/bin/build-dps.sh +run_command: gedi-subsetter/bin/subset.sh disk_space: 20GB inputs: - name: aoi diff --git a/bin/build-dps.sh b/bin/build-dps.sh new file mode 100755 index 0000000..9ecd30d --- /dev/null +++ b/bin/build-dps.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +set -euo pipefail + +basedir=$(dirname "$(readlink -f "$0")") + +"${basedir}/build.sh" --yes --no-dev diff --git a/bin/build.sh b/bin/build.sh new file mode 100755 index 0000000..d3e0a3b --- /dev/null +++ b/bin/build.sh @@ -0,0 +1,128 @@ +#!/usr/bin/env bash + +set -euo pipefail + +function usage() { + echo 1>&2 "Usage: $0 [OPTIONS]" + echo 1>&2 "" + echo 1>&2 "Build the gedi_subset conda environment from a conda lock file." + echo 1>&2 "" + echo 1>&2 "Options:" + echo 1>&2 " -h, --help Show this help message and exit" + echo 1>&2 " -y, --yes Sets any confirmation values to 'yes' automatically." + echo 1>&2 " Users will not be asked to confirm installation of" + echo 1>&2 " conda-lock within the conda base environment." + echo 1>&2 "" + echo 1>&2 "All options not listed above will be passed to 'conda lock install'." + echo 1>&2 "See https://conda.github.io/conda-lock/cli/gen/#conda-lock-install." +} + +# Apply dirname twice to get the parent directory of the directory containing +# this script. +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") + +conda_env=() +conda_base_deps=("conda~=23.0") +conda_lock_dep="conda-lock~=2.0" +conda_lock_args=() +yes= + +while ((${#})); do + case "${1}" in + -h | --help) + usage + exit 0 + ;; + -y | --yes) + yes=1 + shift + ;; + -n | --name) + conda_env=("--name" "${2}") + shift 2 + ;; + --name=?*) + conda_env=("${1}") + shift + ;; + -p | --prefix) + conda_env=("--prefix" "${2}") + shift 2 + ;; + --prefix=?*) + conda_env=("${1}") + shift + ;; + *) + conda_lock_args+=("${1}") + shift + ;; + esac +done + +# If no environment name or prefix was provided, use the default name. +if [[ "${#conda_env[@]}" == "0" ]]; then + conda_env=("--name" "gedi_subset") +fi + +conda_lock_args+=("${conda_env[@]}") + +if [[ ! $(type conda-lock 2>/dev/null) ]]; then + if [[ -n "${yes}" ]]; then + conda_base_deps+=("${conda_lock_dep}") + else + read -r -p "NOTE: conda-lock is not installed + +If you wish to install conda-lock yourself, answer 'no' to the following +question, and see installation options at https://github.com/conda/conda-lock. + +Would you like to install conda-lock into your conda base environment? [y/N] " yn + case "${yn}" in + [Yy]*) + conda_base_deps+=("${conda_lock_dep}") + ;; + *) + exit 0 + ;; + esac + fi +fi + +set -x + +# Install conda 'base' environment dependencies. +# conda install --yes --solver libmamba --name base --channel conda-forge "${conda_base_deps[@]}" + +# Install dependencies from the conda lock file for speed and reproducibility. +# Since there is at least one package (maap-py) that is not available on conda, +# we need to use pip to install it (conda does this for us), so we must set +# PIP_REQUIRE_VENV=0 to avoid complaints about installing packages outside of a +# virtual environment. +PIP_REQUIRE_VENV=0 conda lock install "${conda_lock_args[@]}" "${basedir}/conda-lock.yml" + +# pip install gedi-subsetter in editable mode. +PIP_REQUIRE_VENV=0 conda run --no-capture-output "${conda_env[@]}" \ + python -m pip install -e "${basedir}" --no-deps + +# Fail build if finicky mix of fiona and gdal isn't correct, so that we don't +# have to wait to execute a DPS job to find out. +conda run --no-capture-output "${conda_env[@]}" python -c ' +import geopandas as gpd +import tempfile +import warnings +from shapely.geometry import Point + +# Make sure pip install worked +from maap.maap import MAAP +# Make sure MAAP can be instantiated +maap = MAAP() + +warnings.filterwarnings("ignore", message=".*initial implementation of Parquet.*") + +d = {"col1": ["name1", "name2"], "geometry": [Point(1, 2), Point(2, 1)]} +gdf = gpd.GeoDataFrame(d, crs="EPSG:4326") + +with tempfile.TemporaryFile() as fp: + gdf.to_parquet(fp) + assert gdf.equals(gpd.read_parquet(fp)) +' diff --git a/bin/conda-prefix.sh b/bin/conda-prefix.sh new file mode 100755 index 0000000..6ae5bd7 --- /dev/null +++ b/bin/conda-prefix.sh @@ -0,0 +1,47 @@ +#!/usr/bin/env bash + +python -c " +import json +import os +import sys + +prefix = os.getenv('GEDI_SUBSET_CONDA_PREFIX') + +if prefix: + print(prefix) + sys.exit(0) + +envs = json.loads('''$(conda env list --json)''')['envs'] +prefixes = tuple(env for env in envs if env.endswith('/gedi_subset')) + +if len(prefixes) == 0: + print( + ' '.join( + [ + 'ERROR: Could not find the gedi_subset conda environment. If', + 'you have not created the environment, run bin/build.sh. If', + 'you have already created it, but used a different name, set', + 'the GEDI_SUBSET_CONDA_PREFIX environment variable to the', + 'absolute path of the environment.' + ] + ), + file=sys.stderr, + ) + sys.exit(1) + +if len(prefixes) > 1: + print( + ' '.join( + [ + 'ERROR: Found multiple conda environments named gedi_subset:', + f'{prefixes}. Please remove all but one, or set the', + 'GEDI_SUBSET_CONDA_PREFIX environment variable to the full', + 'path of the desired environment.', + ] + ), + file=sys.stderr, + ) + sys.exit(1) + +print(prefixes[0]) +" diff --git a/bin/generate-lock-file.sh b/bin/generate-lock-file.sh new file mode 100755 index 0000000..822fbf1 --- /dev/null +++ b/bin/generate-lock-file.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +set -euo pipefail + +# Apply dirname twice to get the parent directory of the directory containing +# this script. +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") + +set -x + +conda lock --mamba -f "${basedir}/environment.yml" -f "${basedir}/environment-dev.yml" diff --git a/subset.sh b/bin/subset.sh similarity index 72% rename from subset.sh rename to bin/subset.sh index 8a11700..dca77e8 100755 --- a/subset.sh +++ b/bin/subset.sh @@ -1,14 +1,18 @@ #!/usr/bin/env bash -set -xuo pipefail +set -xeuo pipefail -basedir=$(dirname "$(readlink -f "$0")") -subset_py="conda run --no-capture-output -n gedi_subset ${basedir}/src/gedi_subset/subset.py" +# Apply dirname twice to get to the top of the repo, since this script is in the +# `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") +conda_env_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_env_prefix}") +subset_py="${basedir}/src/gedi_subset/subset.py" -if ! test -d "input"; then +if ! test -d "${basedir}/input"; then # There is no `input` sub-directory of the current working directory, so # simply pass all arguments through to the Python script. - ${subset_py} --verbose "$@" + "${conda_run[@]}" "${subset_py}" --verbose "$@" else # There is an `input` sub-directory of the current working directory, so # assume the AOI file is the sole file within the `input` sub-directory. diff --git a/build.sh b/build.sh deleted file mode 100755 index b287567..0000000 --- a/build.sh +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env bash - -set -xeuo pipefail - -basedir=$(dirname "$(readlink -f "$0")") - -# Make sure conda is updated to a version that supports the --no-capture-output option -conda install -y -n base -c conda-forge "conda>=4.13.0" - -# Create conda env containing only conda-lock -conda create -y -n gedi_subset conda-lock - -# Install dependencies from lock file for speed and reproducibility -conda run --no-capture-output -n gedi_subset conda lock install -n gedi_subset "${basedir}/environment/conda-lock.yml" - -# Install maap-py, since it cannot be specified in the lock file -PIP_REQUIRE_VENV=0 conda env update -n gedi_subset --file "${basedir}/environment/environment-maappy.yml" - -# Install development environment dependencies if the --dev flag is supplied -if [[ "${1:-}" == "--dev" ]]; then - PIP_REQUIRE_VENV=0 conda env update -n gedi_subset --file "${basedir}/environment/environment-dev.yml" -fi - -conda run --no-capture-output -n gedi_subset PIP_REQUIRE_VENV=0 python -m pip install -e "${basedir}" - -# Fail build if finicky mix of fiona and gdal isn't correct, so that we don't -# have to wait to execute a DPS job to find out. -conda run --no-capture-output -n gedi_subset python -c ' -import geopandas as gpd -import tempfile -import warnings -from shapely.geometry import Point - -# Make sure pip install worked -from maap.maap import MAAP - -warnings.filterwarnings("ignore", message=".*initial implementation of Parquet.*") - -d = {"col1": ["name1", "name2"], "geometry": [Point(1, 2), Point(2, 1)]} -gdf = gpd.GeoDataFrame(d, crs="EPSG:4326") - -with tempfile.TemporaryFile() as fp: - gdf.to_parquet(fp) - assert gdf.equals(gpd.read_parquet(fp)) -' diff --git a/conda-lock.yml b/conda-lock.yml new file mode 100644 index 0000000..3df1024 --- /dev/null +++ b/conda-lock.yml @@ -0,0 +1,20900 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV --file conda-lock.yml +# This lock contains optional development dependencies. Include them in the installed environment with: +# conda-lock install --dev-dependencies -n YOURENV --file conda-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f environment.yml -f environment-dev.yml --lockfile conda-lock.yml +version: 1 +metadata: + content_hash: + linux-64: 9460fe242d653e9c0e1f7a775d476616b1e9957c41c51f1f84d928c02d06efc2 + osx-arm64: 9861d7bd045838dc96cf6071032d02671378fd5f3a31f52a34955f596a56a84a + osx-64: 6d0eb564e6e6efe84c7d9435b84bed4f353b9e364e086658b4e0130952b4778c + win-64: c3c2d4491f2d77631bf1ec9d1f7ef230eb00f6d8b8038e30bc56f13e5b304c4f + channels: + - url: conda-forge + used_env_vars: [] + - url: defaults + used_env_vars: [] + platforms: + - linux-64 + - osx-64 + - osx-arm64 + - win-64 + sources: + - environment.yml 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boto3-stubs~=1.33 + - boto3-stubs-essential~=1.33 + - botocore-stubs~=1.33 + - contextily~=1.3 + - ipykernel~=6.23 + - isort~=5.12 + - moto~=4.1 + - mypy~=1.2 + # pandas-stubs constraint should align with pandas constraint in environment.yml + - pandas-stubs~=2.0 + - pre-commit~=3.3 + - pytest~=7.3 + - types-cachetools~=5.3 + - types-requests~=2.30 diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..402f776 --- /dev/null +++ b/environment.yml @@ -0,0 +1,29 @@ +name: gedi_subset +channels: + - conda-forge + - defaults + +# For details on dependecies includef for pandas performance see +# https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#performance-dependencies-recommended + +dependencies: + - python~=3.11 + + - boto3~=1.33 + - bottleneck~=1.3 # pandas performance + - cachetools~=5.3 + - geopandas~=0.14 + - h5py~=3.9 + - numba~=0.56 # pandas performance + - numexpr~=2.8 # pandas performance + - pandas~=2.0 + - pip~=23.1 + - 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-https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.6.0-pyhd8ed1ab_0.tar.bz2#900e74d8547fbea3af028937df28ed77 -https://conda.anaconda.org/conda-forge/noarch/boto3-1.24.1-pyhd8ed1ab_0.tar.bz2#fac37c00c482669b383f39de1e40d2f8 -https://conda.anaconda.org/conda-forge/noarch/geopandas-0.10.2-pyhd8ed1ab_1.tar.bz2#0682614964c1319304cfa554cbce90f0 diff --git a/environment/environment-dev.yml b/environment/environment-dev.yml deleted file mode 100644 index d3e1c1f..0000000 --- a/environment/environment-dev.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: gedi_subset -channels: - - conda-forge - - defaults -dependencies: - - backoff>=2.2 - - black>=23.3 - - boto3-stubs>=1.26 - - boto3-stubs-essential>=1.26 - - botocore-stubs>=1.29 - - contextily>=1.3 - - ipykernel>=6.23 - - isort>=5.12 - - memray>=1.7 - - moto>=4.1 - - mypy>=1.2 - - pandas-stubs - - pip>=23.1 - - pre-commit>=3.3 - - pytest>=7.3 - - types-cachetools>=5.3 - - types-requests>=2.30 diff --git a/environment/environment-maappy.yml b/environment/environment-maappy.yml deleted file mode 100644 index b7f1eea..0000000 --- a/environment/environment-maappy.yml +++ /dev/null @@ -1,8 +0,0 @@ -name: gedi_subset -channels: - - conda-forge - - defaults -dependencies: - - pip=23.0.1 - - pip: - - git+https://github.com/MAAP-Project/maap-py.git@v3.1.3#egg=maappy diff --git a/environment/environment.yml b/environment/environment.yml deleted file mode 100644 index 6f4c613..0000000 --- a/environment/environment.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: gedi_subset -channels: - - conda-forge - - defaults -dependencies: - - python==3.11.3 - - boto3 - - cachetools - - returns>=0.20.0 - - typer - - geopandas - - h5py - - pyarrow - - shapely From 3429fdacefda51390c4b384c475a3ed8ca174dc4 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Wed, 7 Feb 2024 19:19:11 -0500 Subject: [PATCH 02/19] Support scalene profiling --- CHANGELOG.md | 38 ++++++----- CONTRIBUTING.md | 150 +++++++++++++++++++++++++++--------------- algorithm_config.yaml | 2 + bin/build.sh | 12 +++- bin/subset.sh | 64 +++++++++++++----- docs/MAAP_USAGE.md | 21 ++++++ 6 files changed, 201 insertions(+), 86 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ae12e89..ee7ccb2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,21 +5,30 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog], and this project adheres to [Semantic Versioning]. -## [0.6.2] - 2023-12-05 +## Unreleased + +### Added + +- [#57](https://github.com/MAAP-Project/gedi-subsetter/issues/57) Users may + choose to profile their jobs by specifying command-line options for the + `scalene` profiling tool. See `docs/MAAP_USAGE.md` for more information. + +## 0.6.2 ### Fixed - Updated to use v3.1.3 of maap-py in environment-maappy.yml. Previous versions of maap-py were using the deprecated MAAP Query Service API endpoint. -## [0.6.1] - 2023-09-26 +## 0.6.1 ### Fixed -- [#49](https://github.com/MAAP-Project/gedi-subsetter/issues/49) Remove all - API urls that contain ops as they have now been retired (eg. api.ops.maap-project.org). +- [#49](https://github.com/MAAP-Project/gedi-subsetter/issues/49) Remove all API + URLs that contain ops as they have now been retired (e.g., + api.ops.maap-project.org). -## [0.6.0] - 2023-06-02 +## 0.6.0 ### Fixed @@ -42,8 +51,7 @@ The format is based on [Keep a Changelog], and this project adheres to ### Changed - Upgraded Python to version 3.11 to take advantage of the addition of - [fine-grained error locations in tracebacks](https://docs.python.org/3/whatsnew/3.11.html#whatsnew311-pep657) - to help with debugging errors. + [fine-grained error locations in tracebacks] to help with debugging errors. - The `beam` column is no longer automatically included in the output file. If you wish to include the `beam` column, you must specify it explicitly in the `columns` input. @@ -57,12 +65,12 @@ The format is based on [Keep a Changelog], and this project adheres to - [#38](https://github.com/MAAP-Project/gedi-subsetter/issues/38): Temporal filtering is now supported, such that specifying a temporal range will limit the granules downloaded from the CMR, pulling only granules obtained - within the specified range. See [README.md] for more information. + within the specified range. See `docs/MAAP_USAGE.md` for more information. - Added an input parameter named `output` to allow user to specify the name of the output file, rather than hard-code the name to `gedi-subset.gpkg`. See - [README.md] for more information. + `docs/MAAP_USAGE.md` for more information. -## [0.5.0] - 2023-04-11 +## 0.5.0 ### Changed @@ -71,14 +79,14 @@ The format is based on [Keep a Changelog], and this project adheres to wish to query the MAAP CMR until it is taken down, you may still use an earlier version of this algorithm (ideally, 0.4.0). -## [0.4.0] - 2022-11-14 +## 0.4.0 ### Added - [#6](https://github.com/MAAP-Project/gedi-subsetter/issues/6): Allow user to specify which BEAMs to subset -## [0.3.0] - 2022-10-31 +## 0.3.0 ### Fixed @@ -102,7 +110,7 @@ The format is based on [Keep a Changelog], and this project adheres to - [#8](https://github.com/MAAP-Project/gedi-subsetter/issues/8): Specifying a query is now optional, to allow selecting all rows for specified columns. -## [0.2.7] - 2022-10-18 +## 0.2.7 ### Added @@ -110,11 +118,11 @@ The format is based on [Keep a Changelog], and this project adheres to [MAAP-Project/maap-documentation-examples] repository. This `0.2.7` version replicates the `gedi-subset-0.2.7` version released from that repository. +[fine-grained error locations in tracebacks]: + https://docs.python.org/3/whatsnew/3.11.html#whatsnew311-pep657 [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/ [Semantic Versioning]: https://semver.org/spec/v2.0.0.html [MAAP-Project/maap-documentation-examples]: https://github.com/MAAP-Project/maap-documentation-examples -[README.md]: - README.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6af62cf..a307750 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,9 @@ # Contributing - [Development Setup](#development-setup) + - [Create the conda environment](#create-the-conda-environment) + - [Activate the conda environment](#activate-the-conda-environment) + - [Install Git pre-commit hooks](#install-git-pre-commit-hooks) - [Managing Dependencies](#managing-dependencies) - [Creating an Algorithm Release](#creating-an-algorithm-release) - [Registering an Algorithm Release](#registering-an-algorithm-release) @@ -35,50 +38,101 @@ not necessarily the ADE): 1. Clone this GitHub repository. 1. Change directory to the cloned repository. -1. Create the `gedi_subset` virtual environment. +1. Create the `gedi_subset` conda environment (see below). +1. Activate the `gedi_subset` conda environment (see below). +1. Install Git pre-commit hooks (see below). + +### Create the conda environment + +Once you have cloned this repository and changed directory to the clone, you +must create the `gedi_subset` conda environment. To do so, you'll use the +script `bin/build.sh`, as instructed below, which is a script that serves +double-duty as the script that also builds the DPS environment for executing the +algorithm, by ensuring that all necessary Python packages are installed. + +**IMPORTANT:** If you're working in the ADE, the default location for conda +environments is ephemeral, meaning that whenever your ADE workspace is +restarted, all of the conda environments in the default location are lost. This +requires you to recreate any such conda environments that you wish to use after +a workspace restart. To prevent this from occurring, you must provide a +location that persists across restarts via the `--prefix` option with the +`bin/build.sh` script, as described below. _However_, taking this approach +means that creation of the conda environment may take significantly more time +(possibly 10s of minutes) because the persistent location is an AWS S3 bucket. + +If you're not working in the ADE, or you are, but aren't bothered by having to +rerun the following command every time you want to use the `gedi_subset` after +a workspace restart, you may create the conda environment simply as follows: + +```bash +bin/build.sh +``` - **NOTE:** _If you're working in the ADE, use the `--prefix` option shown - (excluding the square brackets), otherwise you will need to repeat this step - whenever your restart your ADE workspace_. Outside of the ADE, there's no - such need to use the `--prefix` option, unless you prefer to use a - non-default location: +_Alternatively_, if you _are_ using the ADE, and you _do_ want the `gedi_subset` +conda environment to persist across workspace restarts, use the following +command instead: - ```bash - bin/build.sh [--prefix "${HOME}/envs/gedi_subset"] - ``` +```bash +bin/build.sh --prefix "${HOME}/envs/gedi_subset" +``` - Note that you may also supply additional options, all of which are passed - through to the `conda-lock install` command. For a list of options, see - . +Note that you may supply additional options, all of which are passed through to +the `conda-lock install` command (see +[Managing Dependencies](#managing-dependencies)). For a list of options, see +[conda-lock install](https://conda.github.io/conda-lock/cli/gen/#conda-lock-install). +By default, all _development_ dependencies will be installed along with all of +the main dependencies (i.e., the `--dev` option is implicit). - **TROUBLESHOOTING:** If the command above fails with the error message - `conda: command not found`, you must first run `conda activate base`, then - rerun the command above. +**TROUBLESHOOTING:** If the command above fails with an error that includes the +message `conda: command not found`, it is likely due to `conda` initialization +being skipped when your terminal window is initialized. Here are 2 options for +resolving this issue (do one, not both): -1. Activate the `gedi_subset` virtual environment. +**Option 1:** Edit your `${HOME}/.bash_profile` file by adding the following +line at the top of the file: - If you did _not_ specify the `--prefix` option in the previous step, you can - use the following command: +```bash +source "${HOME}/.bashrc" +``` - ```bash - conda activate gedi_subset - ``` +**Option 2:** Move the conda initialization block from `${HOME}/.bashrc` to +`${HOME}/.bash_profile`. The conda initialization block is the block of lines +that looks like the following: - Otherwise, you must instead use the following command (alter the value if you - specified a different prefix in the previous step): +```plain +# >>> conda initialize >>> +# !! Contents within this block are managed by 'conda init' !! +... (contents elided) ... +# <<< conda initialize <<< +``` + +Move that block in it's entirety (_including_ the leading and trailing comment +lines) from `${HOME}/.bashrc` to `${HOME}/.bash_profile`. - ```bash - conda activate "${HOME}/envs/gedi_subset" - ``` +### Activate the conda environment -1. Install Git pre-commit hooks: +If you did _not_ specify the `--prefix` option to `bin/build.sh`, you can use +the following command: - ```bash - pre-commit install --install-hooks - ``` +```bash +conda activate gedi_subset +``` -During development, you will create PRs against the GitHub repository, as -explained below. +Otherwise, you must instead use the following command (alter the value if you +specified a different prefix with the `bin/build.sh` command earlier): + +```bash +conda activate "${HOME}/envs/gedi_subset" +``` + +### Install Git pre-commit hooks + +We leverage `pre-commit` to help with some housekeeping tasks. To enable the +configured hooks, run the following from the root of the repository: + +```bash +pre-commit install --install-hooks +``` ## Managing Dependencies @@ -145,31 +199,21 @@ Specifically, it calls `bin/build.sh` with options appropriate for the DPS environment. Using the conda lock file in both development and DPS environments is an -intentional consistency for dependency installation designed to eliminate -possible differences in dependencies that might otherwise allow development and -testing to succeed, but later result in a failure in DPS, either during -algorithm registration, or worse, during algorithm execution. +intentional consistency for dependency installation designed to greatly reduce, +if not eliminate, possible differences in dependencies that might otherwise +allow development and testing to succeed, but later result in a failure in DPS, +either during algorithm registration, or worse, during algorithm execution. ## Creating an Algorithm Release 1. Create a new branch based on an appropriate existing branch (typically based on `main`). 1. Add your desired code and/or configuration changes. -1. Add appropriate entries to the [Changelog](./CHANGELOG.md), according to - the [Keep a Changelog] convention. In particular: - - Add a new, second-level section of the following form: - - ```plain - ## [VERSION] - YYYY-MM-DD - ``` - - where: - - `VERSION` is the value of `version` specified in `algorithm_config.yaml` - - `YYYY-MM-DD` is the date that you expect to create the release (see the - following steps), which may or may not be the current date, depending - upon when you expect your PR (next step) to be approved and merged. - - Add appropriate third-level sections under the new version section (for - additions, changes, and fixes). Again, see [Keep a Changelog]. +1. Add appropriate entries to the [Changelog](./CHANGELOG.md), according to the + [Keep a Changelog] convention. See existing sections in the Changelog for + guidance on structure and format. In general, you should add entries under + the `Unreleased` section at the top. A release manager will relable the + `Unreleased` section to the appropriate release number upon the next release. 1. Submit a PR to the GitHub repository. 1. _Only when_ the PR is on a branch to be merged into the `main` branch _and_ it has been approved and merged, create a new release in GitHub as follows: @@ -181,8 +225,8 @@ algorithm registration, or worse, during algorithm execution. 1. In the **Release title** input, also enter the _same_ value as the new value of `version` in `algorithm_config.yml`. 1. In the description text box, copy and paste from the Changelog file only - the _new version section_ you added earlier to the Changelog, including - the new version heading. + the _new version section_ you added earlier to the Changelog, + **excluding** the new version heading. 1. Click the **Publish release** button. ## Registering an Algorithm Release diff --git a/algorithm_config.yaml b/algorithm_config.yaml index 1f724fd..b3829dc 100644 --- a/algorithm_config.yaml +++ b/algorithm_config.yaml @@ -29,3 +29,5 @@ inputs: download: False - name: output download: False + - name: scalene_args + download: False diff --git a/bin/build.sh b/bin/build.sh index d3e0a3b..e178100 100755 --- a/bin/build.sh +++ b/bin/build.sh @@ -80,6 +80,9 @@ Would you like to install conda-lock into your conda base environment? [y/N] " y case "${yn}" in [Yy]*) conda_base_deps+=("${conda_lock_dep}") + echo + echo "Installing conda-lock into conda base environment." + echo ;; *) exit 0 @@ -88,10 +91,17 @@ Would you like to install conda-lock into your conda base environment? [y/N] " y fi fi +if [[ ! $(type conda 2>/dev/null) ]]; then + echo "ERROR: conda was not found. Make sure conda is installed. If conda is" >&2 + echo "installed, this may be due to conda's base environment being shadowed by" >&2 + echo "some other active environment. Run 'conda activate base' and try again." >&2 + exit 1 +fi + set -x # Install conda 'base' environment dependencies. -# conda install --yes --solver libmamba --name base --channel conda-forge "${conda_base_deps[@]}" +conda install --yes --solver libmamba --name base --channel conda-forge "${conda_base_deps[@]}" # Install dependencies from the conda lock file for speed and reproducibility. # Since there is at least one package (maap-py) that is not available on conda, diff --git a/bin/subset.sh b/bin/subset.sh index dca77e8..bf6b3a7 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -1,17 +1,20 @@ #!/usr/bin/env bash -set -xeuo pipefail +set -euo pipefail # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") -conda_env_prefix=$("${basedir}/bin/conda-prefix.sh") -conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_env_prefix}") +conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") subset_py="${basedir}/src/gedi_subset/subset.py" if ! test -d "${basedir}/input"; then # There is no `input` sub-directory of the current working directory, so - # simply pass all arguments through to the Python script. + # simply pass all arguments through to the Python script. This is useful + # for testing in a non-DPS environment, where there is no `input` directory + # since the DPS system creates the `input` directory and places the AOI file + # within it. "${conda_run[@]}" "${subset_py}" --verbose "$@" else # There is an `input` sub-directory of the current working directory, so @@ -21,21 +24,48 @@ else n_actual=${#} n_expected=9 - if test ${n_actual} -gt 0 -a ${n_actual} -ne ${n_expected}; then + if test ${n_actual} -lt ${n_expected} -o ${n_actual} -gt $((n_expected + 1)); then echo "Expected ${n_expected} inputs, but got ${n_actual}:$(printf " '%b'" "$@")" >&2 exit 1 fi - options=() - [[ "${1:--}" != "-" ]] && options=("${options[@]}" --doi "${1:--}") - [[ "${2:--}" != "-" ]] && options=("${options[@]}" --temporal "${2:--}") - [[ "${3:--}" != "-" ]] && options=("${options[@]}" --lat "${3:--}") - [[ "${4:--}" != "-" ]] && options=("${options[@]}" --lon "${4:--}") - [[ "${5:--}" != "-" ]] && options=("${options[@]}" --beams "${5:--}") - [[ "${6:--}" != "-" ]] && options=("${options[@]}" --columns "${6:--}") - [[ "${7:--}" != "-" ]] && options=("${options[@]}" --query "${7:--}") - [[ "${8:--}" != "-" ]] && options=("${options[@]}" --limit "${8:--}") - [[ "${9:--}" != "-" ]] && options=("${options[@]}" --output "${9:--}") - - ${subset_py} --verbose --aoi "${aoi}" "${options[@]}" + inputs=() + + # Workaround for DPS bug where default input values must be quoted in order + # for algorithm registration to work. We strip surrounding quotes from all + # arguments, either double or single quotes, if found. + while ((${#})); do + input=${1} + + if [[ "${input}" =~ \".*\" ]]; then + input=${1%\"} # Strip leading quote + input=${input#\"} # Strip trailing quote + elif [[ "${input}" =~ \'.*\' ]]; then + input=${input%\'} # Strip leading quote + input=${input#\'} # Strip trailing quote + fi + + inputs+=("${input}") + shift + done + + args=(--verbose --aoi "${aoi}") + args+=(--doi "${inputs[0]}") # doi is required + [[ "${inputs[1]}" != "-" ]] && args+=(--temporal "${inputs[1]}") + args+=(--lat "${inputs[2]}") # lat is required + args+=(--lon "${inputs[3]}") # lon is required + [[ "${inputs[4]}" != "-" ]] && args+=(--beams "${inputs[4]}") + args+=(--columns "${inputs[5]}") # columns is required + [[ "${inputs[6]}" != "-" ]] && args+=(--query "${inputs[6]}") + [[ "${inputs[7]}" != "-" ]] && args+=(--limit "${inputs[7]}") + [[ "${inputs[8]}" != "-" ]] && args+=(--output "${inputs[8]}") + + if [[ "${inputs[9]:--}" != "-" ]]; then + # The last argument is not a hyphen, so we expect it to be arguments to + # pass to scalene for profiling our algorithm. + IFS=' ' read -ra scalene_args <<<"${inputs[9]}" + "${conda_run[@]}" scalene "${scalene_args[@]}" --no-browser "${subset_py}" --- "${args[@]}" + else + "${conda_run[@]}" "${subset_py}" "${args[@]}" + fi fi diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 71435bb..351c897 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -153,6 +153,25 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. _New in version 0.6.0_ +- `scalene_args` (_optional_): Arguments to pass to [Scalene] for performance + profiling. If you do not want to profile performance of the algorithm, do + not specify a value for this input. + + Otherwise, when this input is supplied, the algorithm will be run via the + `scalene` command, and the value of this input will be passed as arguments to + the command. For a list of the available command-line options, see + . + + For first-time users of `scalene`, the recommended value for this input is + `--reduced-profile`. Note that since no browser is available in DPS, when any + value is supplied for this input, the `--no-browser` option will be included + automatically, which will produce HTML output to a file named `profile.html`, + if you do not specify a different name via the `--outfile` option. The + profiling output file will appear in the same directory as the algorithm + output file. + + _New in version 0.6.3_ + ### Specifying an AOI If your AOI is a publicly available geoBoundary, see @@ -448,3 +467,5 @@ administrative boundaries. PLoS ONE 15(4): e0231866. https://www.geoboundaries.org [geoBoundaries API]: https://www.geoboundaries.org/api.html +[Scalene]: + https://github.com/plasma-umass/scalene From cff739de0d52c1545fdc76425c58ab3d3dad0116 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Thu, 8 Feb 2024 11:50:09 -0500 Subject: [PATCH 03/19] Update algorithm_config.yaml to use latest structure and names --- algorithm_config.yaml | 94 ++++++++++++++++++++++++++++++------------- 1 file changed, 65 insertions(+), 29 deletions(-) diff --git a/algorithm_config.yaml b/algorithm_config.yaml index b3829dc..1f5fc25 100644 --- a/algorithm_config.yaml +++ b/algorithm_config.yaml @@ -1,33 +1,69 @@ -description: Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI) -algo_name: gedi-subset -version: 0.6.2 -environment: ubuntu -repository_url: https://repo.ops.maap-project.org/data-team/gedi-subsetter.git -docker_url: mas.dit.maap-project.org/root/maap-workspaces/base_images/r:dit +algorithm_description: Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI) +algorithm_name: gedi-subset +algorithm_version: 0.6.2 +repository_url: https://github.com/MAAP-Project/gedi-subsetter.git +docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.4 +disk_space: 20GB queue: maap-dps-worker-32gb build_command: gedi-subsetter/bin/build-dps.sh run_command: gedi-subsetter/bin/subset.sh -disk_space: 20GB inputs: - - name: aoi - download: True - - name: doi - download: False - - name: temporal - download: False - - name: lat - download: False - - name: lon - download: False - - name: beams - download: False - - name: columns - download: False - - name: query - download: False - - name: limit - download: False - - name: output - download: False - - name: scalene_args - download: False + config: [] + file: + - name: aoi + description: URL of a file representing the Area of Interest (e.g., GeoJSON file) + required: true + default: "" + positional: + - name: doi + description: "Digital Object Identifier (DOI) of the GEDI collection to subset, + or one of these logical names: L1B, L2A, L2B, L4A" + required: true + default: "" + - name: temporal + description: Temporal range to subset, formatted as an ISO 8601 Time Interval. + For example, 2021-01-01T00:00:00Z/2021-12-31T23:59:59Z. See + https://en.wikipedia.org/wiki/ISO_8601#Time_intervals. If not provided, + the entire temporal range of the GEDI collection is used. + required: false + default: "-" + - name: lat + description: Name of the dataset containing latitude values + required: true + default: "" + - name: lon + description: Name of the dataset containing longitude values + required: true + default: "" + - name: beams + description: "Which beams to include: all, coverage, power, or a comma-separated + list of specific beam names, with or without the BEAM prefix (e.g., + BEAM0000,BEAM0001 or 0000,0001)" + required: false + default: all + - name: columns + description: One or more column names, separated by commas, to include in the + output file + required: true + default: "" + - name: query + description: Boolean query expression for subsetting the rows in the output file. + If not provided, all rows are included. See + https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.query.html. + required: false + default: "-" + - name: limit + description: Maximum number of GEDI granule data files to download from the CMR, + regardless of the number of granules within the AOI. + required: false + default: "1000" + - name: output + description: Name of the output file produced by the algorithm. Defaults to + using the AOI file name (without the extension) with the suffix "_subset.gpkg". + required: false + default: "-" + - name: scalene_args + description: Arguments to pass to Scalene for memory and CPU profiling. If not + provided, Scalene will not be used. + required: false + default: "-" From 0a980c991f8550fdc64570ac16f1b529124b0310 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Thu, 8 Feb 2024 19:46:44 -0500 Subject: [PATCH 04/19] Add script to register algorithm --- CONTRIBUTING.md | 178 +++++++++++++++++++++++--------------- bin/register-algorithm.sh | 61 +++++++++++++ 2 files changed, 169 insertions(+), 70 deletions(-) create mode 100755 bin/register-algorithm.sh diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a307750..1523d62 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -5,8 +5,9 @@ - [Activate the conda environment](#activate-the-conda-environment) - [Install Git pre-commit hooks](#install-git-pre-commit-hooks) - [Managing Dependencies](#managing-dependencies) -- [Creating an Algorithm Release](#creating-an-algorithm-release) -- [Registering an Algorithm Release](#registering-an-algorithm-release) +- [Development Process](#development-process) +- [Registering a Version of the Algorithm](#registering-a-version-of-the-algorithm) +- [Creating a Release](#creating-a-release) ## Development Setup @@ -204,81 +205,116 @@ if not eliminate, possible differences in dependencies that might otherwise allow development and testing to succeed, but later result in a failure in DPS, either during algorithm registration, or worse, during algorithm execution. -## Creating an Algorithm Release +## Development Process -1. Create a new branch based on an appropriate existing branch (typically based - on `main`). +To work on a feature or bug fix, you'll generally want to follow these steps: + +1. Create a branch from the `main` branch. 1. Add your desired code and/or configuration changes. 1. Add appropriate entries to the [Changelog](./CHANGELOG.md), according to the [Keep a Changelog] convention. See existing sections in the Changelog for guidance on structure and format. In general, you should add entries under the `Unreleased` section at the top. A release manager will relable the `Unreleased` section to the appropriate release number upon the next release. -1. Submit a PR to the GitHub repository. -1. _Only when_ the PR is on a branch to be merged into the `main` branch _and_ - it has been approved and merged, create a new release in GitHub as follows: - 1. Go to - 1. Click the **Choose a tag** dropdown. - 1. In the input box that appears, enter the _same_ value as the new value of - `version` in `algorithm_config.yml`, and click the **Create a new tag** - label that appears immediately below the input box. - 1. In the **Release title** input, also enter the _same_ value as the new - value of `version` in `algorithm_config.yml`. - 1. In the description text box, copy and paste from the Changelog file only - the _new version section_ you added earlier to the Changelog, - **excluding** the new version heading. - 1. Click the **Publish release** button. - -## Registering an Algorithm Release - -Once a release is published in the GitHub repository (see above), the algorithm -must be registered in the ADE. To do so, follow these steps: - -1. Within an ADE workspace, open a **New Launcher** tab and underneath the - **MAAP Extensions** section, select **Register Algorithm**. -1. On the main registration page: - 1. Under Repository Information: - - Enter the **Repository URL** as - `https://github.com/MAAP-Project/gedi-subsetter.git`. - - Enter the **Repository Branch** as the name of the release tag (e.g., - `1.0.0`). - - Enter the **Run Command** as `gedi-subsetter/bin/subset.sh`. - - Enter the **Build Command** as `gedi-subsetter/bin/build-dps.sh`. - 1. Under General Information: - - Enter the **Algorithm Name** as `gedi-subset`. - - Enter the **Algorithm Description** as - `Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI)`. - - Enter the **Disk Space** as `20`. - - Enter the **Resource Allocation** as `maap-dps-worker-32gb`. - - Enter the **Container URL** as - `mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.4`. - 1. Under Input Types, add the following Name, Description pairs: - 1. For File Inputs: - - `aoi`: Area of Interest GeoJSON file - 1. For Positional Inputs: - - `doi`: Digital Object Identifier (DOI) of the GEDI collection to - subset, or a logical name representing such a DOI - - `temporal`: (Default: `-`, which means the full temporal range): - Temporal range to subset. - - `lat`: Name of the dataset used for latitude. - - `lon`: Name of the dataset used for longitude. - - `beams`: (Default: `all`): `all`, `coverage`, or `power`, or a - comma-separated list of specific beam names, with or without the - `BEAM` prefix (e.g., `BEAM0000,BEAM0001` or `0000,0001`). - - `columns`: One or more column names, separated by commas, to include - in the output file. - - `query`: (Default: no query): Query expression for subsetting the - rows in the output file. - - `limit`: (Default: 1_000): Maximum number of GEDI granule data files - to download from the CMR - - `output`: Name to use for the output file. -1. Once finished, click **Register Algorithm** -1. Check the build job status at - . If the - job fails, you will need to correct the issue (and likely create a patch - release, following the release steps again). Otherwise, you should now be - able to open the **Jobs** menu, choose **View & Submit Jobs**, and find the - new version of the algorithm in the dropdown list of the **Submit** tab. +1. Register a version of the algorithm (see next section). +1. Test your registered version, and repeat as necessary. +1. Once you're satsified with your changes, delete your registered version. +1. Submit a PR to the GitHub repository, targeting the `main` branch. + +## Registering a Version of the Algorithm + +To register a new version of the algorithm, simply run the following, +where `YAML_FILE` is optional, and defaults to `algorithm_config.yaml`: + +```plain +bin/register-algorithm.sh [YAML_FILE] +``` + +When on the `main` branch (typically only after creating a release of the +algorithm, as described in the next section), and the current commit (`HEAD`) is +tagged, the script will check whether or not the value of `algorithm_version` in +the specified YAML file matches the value of the git tag. If so, the YAML file +will be registered as-is. If not, the script will report the version-tag +mismatch. A match is expected when registering from the `main` branch, as +that's where tagging/releasing should take place. + +However, you will likely want to register a version of the algorithm from +another branch when to test your changes on the branch, before opening a Pull +Request. In this case, when registering from another branch, the script ignores +the value of `algorithm_version` in the YAML file, and the script will instead +use the name of the current branch as the algorithm version during registration +(the YAML file is _not_ modified). + +Once such an unreleased version is registered, you may submit jobs against it to +test it. Once you're satisified that your unreleased version of the algorithm +works properly, you should delete (unregister) it, and create a Pull Request +against the `main` branch. If you need to make adjustments to your branch, you +can rerun registration to replace your unreleased version of the algorithm as +often as necessary until you're satisfied. + +Upon successful registration, you should see output similar to the following +(abridged): + +```plain +{ + "code": 200, + "message": { + "id": "...", + ..., + "title": "Registering algorithm: gedi-subset", + "message": "Registering algorithm: gedi-subset", + ..., + "status": "created", + ..., + "job_web_url": "https://repo.maap-project.org/root/register-job-hysds-v4/-/jobs/XXXXX", + "job_log_url": "https://repo.maap-project.org/root/register-job-hysds-v4/-/jobs/XXXXX/raw" + } +} +``` + +This indicates that the registration succeeded (code 200), and that the image +for the algorithm is being built. To see the progress of the build, open a +browser to the `"job_web_url"` value shown in your output. Note that although +registration succeeded, the image build process may fail, so it is important to +make sure the build succeeds. If it does, then the new version of the algorithm +should be visible in the **Algorithm** list on the form shown in the ADE after +choosing **Jobs > Submit Jobs** menu item. + +If registration fails, or it succeeds, but the image build fails, analyze the +error message from the failed registration or failed build. If it does not +provide the information you need to correct the problem, reach out to the +platform team for assistance. + +## Creating a Release + +After one or more Pull Requests have landed on the `main` branch to constitute +a new release: + +1. Checkout the latest changes to the `main` branch. +1. Create a new branch named `release/VERSION`, where `VERSION` is an + appropriate version number, according to [Semantic Versioning]. +1. In `algorithm_config.yaml` change the value of `algorithm_version` to the + same value as `VERSION` from the previous step. +1. In the [Changelog](./CHANGELOG.md), change the `Unreleased` heading to the + same value as `VERSION` from the previous step, and then, above the new + version heading, add a new `Unreleased` section, for future changes. +1. Commit the changes, and open a Pull Request to `main`. +1. Once the PR is approved and merged, go to + +1. Click the **Choose a tag** dropdown. +1. In the input box that appears, enter the _same_ value as the value of + `VERSION` from previous steps, and click the **Create a new tag** label that + appears immediately below the input box. +1. In the **Release title** input, also enter the _same_ value as the value of + `VERSION` in the previous step. +1. In the description text box, copy and paste the content of only the _new + version section_ you added earlier to the Changelog, **excluding** the new + version heading. +1. Click the **Publish release** button. +1. Checkout and pull the `main` branch in order to pull down the new tag created + by the release process. +1. Register the new release of the algorithm as described in the previous + section. [compatible release operator]: https://peps.python.org/pep-0440/#compatible-release @@ -288,3 +324,5 @@ must be registered in the ADE. To do so, follow these steps: https://github.com/MAAP-Project/gedi-subsetter.git [NASA MAAP]: https://maap-project.org/ +[Semantic Versioning]: + https://semver.org/spec/v2.0.0.html diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh new file mode 100755 index 0000000..b070ce2 --- /dev/null +++ b/bin/register-algorithm.sh @@ -0,0 +1,61 @@ +#!/usr/bin/env bash + +yaml_file=${1:-algorithm_config.yaml} +tag=$(git tag --points-at HEAD) +branch=$(git rev-parse --abbrev-ref HEAD) +version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') + +function stderr() { + echo 1>&2 "${1}" +} + +if [[ "${branch}" =~ "/" ]]; then + # Slashes in branch names are not acceptable because the DPS system uses the + # branch name as part of the Docker image tag (which cannot contain slashes). + stderr "ERROR: Branch names cannot contain slashes. Please rename the branch and try again." + exit 1 +elif [[ "${branch}" != "main" ]]; then + version=${branch//\//-} +elif [[ -z "${tag}" ]]; then + stderr "ERROR: You're on the main branch, but there's no tag for the current commit." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +elif [[ "${tag}" != "${version}" ]]; then + stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +fi + +stderr "Registering algorithm version ${version} of ${yaml_file}..." + +# Apply dirname twice to get to the top of the repo, since this script is in the +# `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") +conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") + +"${conda_run[@]}" python -c " +import json +import sys +import tempfile + +import yaml +from maap.maap import MAAP + +maap = MAAP('api.maap-project.org') + +with open('${yaml_file}') as f: + config = yaml.safe_load(f) + +with tempfile.NamedTemporaryFile('w+') as f: + config['algorithm_version'] = '${version}' + json.dump(config, f, indent=2) + f.seek(0) + + try: + r = maap.register_algorithm_from_yaml_file(f.name) + print(json.dumps(r.json(), indent=2)) + except Exception as e: + print(e, file=sys.stderr) + sys.exit(1) +" From f1bee349d7c1b916bb71d6df5e0b12556a0d83e0 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 04:51:14 -0500 Subject: [PATCH 05/19] Adjust input path to be relative to run script --- bin/subset.sh | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/bin/subset.sh b/bin/subset.sh index bf6b3a7..5425657 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -9,12 +9,14 @@ conda_prefix=$("${basedir}/bin/conda-prefix.sh") conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") subset_py="${basedir}/src/gedi_subset/subset.py" -if ! test -d "${basedir}/input"; then +if ! test -d "${basedir}/bin/input"; then + echo "No input directory found, assuming local development environment: ${basedir}/input" >&2 # There is no `input` sub-directory of the current working directory, so # simply pass all arguments through to the Python script. This is useful # for testing in a non-DPS environment, where there is no `input` directory # since the DPS system creates the `input` directory and places the AOI file # within it. + set -x "${conda_run[@]}" "${subset_py}" --verbose "$@" else # There is an `input` sub-directory of the current working directory, so @@ -37,13 +39,13 @@ else while ((${#})); do input=${1} - if [[ "${input}" =~ \".*\" ]]; then - input=${1%\"} # Strip leading quote - input=${input#\"} # Strip trailing quote - elif [[ "${input}" =~ \'.*\' ]]; then - input=${input%\'} # Strip leading quote - input=${input#\'} # Strip trailing quote - fi + # if [[ "${input}" =~ \".*\" ]]; then + # input=${1%\"} # Strip leading quote + # input=${input#\"} # Strip trailing quote + # elif [[ "${input}" =~ \'.*\' ]]; then + # input=${input%\'} # Strip leading quote + # input=${input#\'} # Strip trailing quote + # fi inputs+=("${input}") shift @@ -64,8 +66,10 @@ else # The last argument is not a hyphen, so we expect it to be arguments to # pass to scalene for profiling our algorithm. IFS=' ' read -ra scalene_args <<<"${inputs[9]}" + set -x "${conda_run[@]}" scalene "${scalene_args[@]}" --no-browser "${subset_py}" --- "${args[@]}" else + set -x "${conda_run[@]}" "${subset_py}" "${args[@]}" fi fi From 926d5e53147d7d6f3d3fdcd47be224cd83ee970e Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 08:52:17 -0500 Subject: [PATCH 06/19] Add script to delete an algorithm version --- bin/delete-algorithm.sh | 52 +++++++++++++++++++++++++++++++++++++++++ bin/subset.sh | 15 ++++++++---- 2 files changed, 62 insertions(+), 5 deletions(-) create mode 100755 bin/delete-algorithm.sh diff --git a/bin/delete-algorithm.sh b/bin/delete-algorithm.sh new file mode 100755 index 0000000..5407ede --- /dev/null +++ b/bin/delete-algorithm.sh @@ -0,0 +1,52 @@ +#!/usr/bin/env bash + +yaml_file=${1:-algorithm_config.yaml} +tag=$(git tag --points-at HEAD) +branch=$(git rev-parse --abbrev-ref HEAD) +name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') +version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') + +function stderr() { + echo >&2 "${1}" +} + +if [[ "${branch}" != "main" ]]; then + version=${branch//\//-} +elif [[ -z "${tag}" ]]; then + stderr "ERROR: You're on the main branch, but there's no tag for the current commit." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +elif [[ "${tag}" != "${version}" ]]; then + stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +fi + +# TODO: add confirmation prompt! + +algorithm_id="${name}:${version}" +stderr "Deleting algorithm version '${algorithm_id}'..." + +# Apply dirname twice to get to the top of the repo, since this script is in the +# `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") +conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") + +"${conda_run[@]}" python -c " +import json +import sys +import tempfile + +import yaml +from maap.maap import MAAP + +maap = MAAP('api.maap-project.org') + +try: + r = maap.deleteAlgorithm('${algorithm_id}') + print(json.dumps(r.json(), indent=2)) +except Exception as e: + print(e, file=sys.stderr) + sys.exit(1) +" diff --git a/bin/subset.sh b/bin/subset.sh index 5425657..35678d6 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -4,13 +4,18 @@ set -euo pipefail # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). -basedir=$(dirname "$(dirname "$(readlink -f "$0")")") -conda_prefix=$("${basedir}/bin/conda-prefix.sh") +base_dir=$(dirname "$(dirname "$(readlink -f "$0")")") +input_dir="${base_dir}/input" +conda_prefix=$("${base_dir}/bin/conda-prefix.sh") conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") -subset_py="${basedir}/src/gedi_subset/subset.py" +subset_py="${base_dir}/src/gedi_subset/subset.py" -if ! test -d "${basedir}/bin/input"; then - echo "No input directory found, assuming local development environment: ${basedir}/input" >&2 +echo "--- listing files in ${base_dir} ---" +ls "${base_dir}/*" +echo "---" + +if ! test -d "${input_dir}"; then + echo "No input directory found, assuming local development environment: ${input_dir}" >&2 # There is no `input` sub-directory of the current working directory, so # simply pass all arguments through to the Python script. This is useful # for testing in a non-DPS environment, where there is no `input` directory From ed3664d9aa8f3803f6227d9d57292fb442e0edaa Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 09:44:18 -0500 Subject: [PATCH 07/19] Debug missing 'input' dir --- bin/subset.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/bin/subset.sh b/bin/subset.sh index 35678d6..83d2f7d 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -10,8 +10,14 @@ conda_prefix=$("${base_dir}/bin/conda-prefix.sh") conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") subset_py="${base_dir}/src/gedi_subset/subset.py" +echo "--- listing files in $(dirname "${base_dir}") ---" +ls -l "$(dirname "${base_dir}")" || true echo "--- listing files in ${base_dir} ---" -ls "${base_dir}/*" +ls -l "${base_dir}" || true +echo "--- listing files in ${base_dir}/bin ---" +ls -l "${base_dir}/bin" || true +echo "--- listing files in ${input_dir} ---" +ls -l "${input_dir}" || true echo "---" if ! test -d "${input_dir}"; then From 95dcdf2ce0c4f8215c8fcff4f35b9ebc42036eee Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 14:02:05 -0500 Subject: [PATCH 08/19] Add algorithm management scripts --- bin/build.sh | 32 +++++++++++++++++++++----- bin/delete-algorithm.sh | 2 +- bin/describe-algorithm.sh | 48 +++++++++++++++++++++++++++++++++++++++ bin/register-algorithm.sh | 28 +++++++++++++++++------ 4 files changed, 96 insertions(+), 14 deletions(-) create mode 100755 bin/describe-algorithm.sh diff --git a/bin/build.sh b/bin/build.sh index e178100..3e53a8f 100755 --- a/bin/build.sh +++ b/bin/build.sh @@ -25,6 +25,8 @@ conda_env=() conda_base_deps=("conda~=23.0") conda_lock_dep="conda-lock~=2.0" conda_lock_args=() +# conda-lock defaults to --dev when neither --dev nor --no-dev is provided. +dev=1 yes= while ((${#})); do @@ -37,6 +39,11 @@ while ((${#})); do yes=1 shift ;; + --no-dev) + dev= + conda_lock_args+=("${1}") + shift + ;; -n | --name) conda_env=("--name" "${2}") shift 2 @@ -65,8 +72,6 @@ if [[ "${#conda_env[@]}" == "0" ]]; then conda_env=("--name" "gedi_subset") fi -conda_lock_args+=("${conda_env[@]}") - if [[ ! $(type conda-lock 2>/dev/null) ]]; then if [[ -n "${yes}" ]]; then conda_base_deps+=("${conda_lock_dep}") @@ -101,18 +106,33 @@ fi set -x # Install conda 'base' environment dependencies. -conda install --yes --solver libmamba --name base --channel conda-forge "${conda_base_deps[@]}" +conda install \ + --yes \ + --solver libmamba \ + --name base \ + --channel conda-forge "${conda_base_deps[@]}" # Install dependencies from the conda lock file for speed and reproducibility. # Since there is at least one package (maap-py) that is not available on conda, # we need to use pip to install it (conda does this for us), so we must set # PIP_REQUIRE_VENV=0 to avoid complaints about installing packages outside of a # virtual environment. -PIP_REQUIRE_VENV=0 conda lock install "${conda_lock_args[@]}" "${basedir}/conda-lock.yml" +PIP_REQUIRE_VENV=0 conda lock install \ + "${conda_env[@]}" "${conda_lock_args[@]}" "${basedir}/conda-lock.yml" # pip install gedi-subsetter in editable mode. -PIP_REQUIRE_VENV=0 conda run --no-capture-output "${conda_env[@]}" \ - python -m pip install -e "${basedir}" --no-deps +PIP_REQUIRE_VENV=0 conda run --no-capture-output \ + "${conda_env[@]}" python -m pip install -e "${basedir}" --no-deps + +# If development dependencies were installed, let's also install the conda +# environment as a Jupyter kernel. +if [[ -n "${dev}" ]]; then + conda run --no-capture-output \ + "${conda_env[@]}" python -m ipykernel install \ + --user \ + --name gedi_subset \ + --display-name "GEDI Subsetter (Python)" +fi # Fail build if finicky mix of fiona and gdal isn't correct, so that we don't # have to wait to execute a DPS job to find out. diff --git a/bin/delete-algorithm.sh b/bin/delete-algorithm.sh index 5407ede..dd769f3 100755 --- a/bin/delete-algorithm.sh +++ b/bin/delete-algorithm.sh @@ -25,7 +25,7 @@ fi # TODO: add confirmation prompt! algorithm_id="${name}:${version}" -stderr "Deleting algorithm version '${algorithm_id}'..." +stderr "Deleting algorithm '${algorithm_id}'..." # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). diff --git a/bin/describe-algorithm.sh b/bin/describe-algorithm.sh new file mode 100755 index 0000000..4d6f4d9 --- /dev/null +++ b/bin/describe-algorithm.sh @@ -0,0 +1,48 @@ +#!/usr/bin/env bash + +yaml_file=${1:-algorithm_config.yaml} +tag=$(git tag --points-at HEAD) +branch=$(git rev-parse --abbrev-ref HEAD) +name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') +version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') + +function stderr() { + echo >&2 "${1}" +} + +if [[ "${branch}" != "main" ]]; then + version=${branch//\//-} +elif [[ -z "${tag}" ]]; then + stderr "ERROR: You're on the main branch, but there's no tag for the current commit." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +elif [[ "${tag}" != "${version}" ]]; then + stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 +fi + +algorithm_id="${name}:${version}" + +# Apply dirname twice to get to the top of the repo, since this script is in the +# `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). +basedir=$(dirname "$(dirname "$(readlink -f "$0")")") +conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") + +"${conda_run[@]}" python -c " +import json +import sys +import tempfile + +import yaml +from maap.maap import MAAP + +maap = MAAP('api.maap-project.org') + +if r := maap.describeAlgorithm('${algorithm_id}'): + print(r.text) +else: + print(r.text, file=sys.stderr) + sys.exit(1) +" diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index b070ce2..0b8f1b8 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -3,7 +3,8 @@ yaml_file=${1:-algorithm_config.yaml} tag=$(git tag --points-at HEAD) branch=$(git rev-parse --abbrev-ref HEAD) -version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') +algorithm_name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') +algorithm_version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') function stderr() { echo 1>&2 "${1}" @@ -15,22 +16,35 @@ if [[ "${branch}" =~ "/" ]]; then stderr "ERROR: Branch names cannot contain slashes. Please rename the branch and try again." exit 1 elif [[ "${branch}" != "main" ]]; then - version=${branch//\//-} + algorithm_version=${branch} elif [[ -z "${tag}" ]]; then stderr "ERROR: You're on the main branch, but there's no tag for the current commit." stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." exit 1 -elif [[ "${tag}" != "${version}" ]]; then - stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." +elif [[ "${tag}" != "${algorithm_version}" ]]; then + stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${algorithm_version}'." stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." exit 1 fi -stderr "Registering algorithm version ${version} of ${yaml_file}..." - # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") + +algorithm_id="${algorithm_name}:${algorithm_version}" +stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." + +if [[ $("${basedir}/bin/describe-algorithm.sh") ]]; then + stderr "" + stderr "ERROR: Algorithm '${algorithm_id}' already exists." + stderr "" + stderr "If you want to re-register the algorithm, you must first delete it:" + stderr "" + stderr " bin/delete-algorithm.sh" + stderr "" + exit 1 +fi + conda_prefix=$("${basedir}/bin/conda-prefix.sh") conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") @@ -48,7 +62,7 @@ with open('${yaml_file}') as f: config = yaml.safe_load(f) with tempfile.NamedTemporaryFile('w+') as f: - config['algorithm_version'] = '${version}' + config['algorithm_version'] = '${algorithm_version}' json.dump(config, f, indent=2) f.seek(0) From 914a3efee14195452d40e130ee848681877fd3b8 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 14:38:42 -0500 Subject: [PATCH 09/19] Still debugging location of input dir --- CONTRIBUTING.md | 42 +++++++++++++++++++++++++-------------- bin/register-algorithm.sh | 2 +- bin/subset.sh | 2 ++ 3 files changed, 30 insertions(+), 16 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 1523d62..70ef46c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -223,35 +223,33 @@ To work on a feature or bug fix, you'll generally want to follow these steps: ## Registering a Version of the Algorithm -To register a new version of the algorithm, simply run the following, -where `YAML_FILE` is optional, and defaults to `algorithm_config.yaml`: +To register a new version of the algorithm, you must do so within the ADE in +order to obtain automatic authorization. If you have not been using the ADE for +development, be sure to clone and/or pull the latest code from the branch from +which you want to register the algorithm. + +Then, simply run the following to register the algorithm described in +`algorithm_config.yaml`: ```plain -bin/register-algorithm.sh [YAML_FILE] +bin/register-algorithm.sh ``` When on the `main` branch (typically only after creating a release of the algorithm, as described in the next section), and the current commit (`HEAD`) is tagged, the script will check whether or not the value of `algorithm_version` in -the specified YAML file matches the value of the git tag. If so, the YAML file -will be registered as-is. If not, the script will report the version-tag -mismatch. A match is expected when registering from the `main` branch, as -that's where tagging/releasing should take place. +the YAML file matches the value of the git tag. If so, the YAML file will be +registered as-is. If not, the script will report the version-tag mismatch. A +match is expected when registering from the `main` branch, as that's where +tagging/releasing should take place. However, you will likely want to register a version of the algorithm from -another branch when to test your changes on the branch, before opening a Pull +another branch when test your changes on the branch, before opening a Pull Request. In this case, when registering from another branch, the script ignores the value of `algorithm_version` in the YAML file, and the script will instead use the name of the current branch as the algorithm version during registration (the YAML file is _not_ modified). -Once such an unreleased version is registered, you may submit jobs against it to -test it. Once you're satisified that your unreleased version of the algorithm -works properly, you should delete (unregister) it, and create a Pull Request -against the `main` branch. If you need to make adjustments to your branch, you -can rerun registration to replace your unreleased version of the algorithm as -often as necessary until you're satisfied. - Upon successful registration, you should see output similar to the following (abridged): @@ -285,6 +283,20 @@ error message from the failed registration or failed build. If it does not provide the information you need to correct the problem, reach out to the platform team for assistance. +Once the registration build succeeds, you may submit jobs against the algorithm. + +For unreleased versions, once you're satisified that your unreleased version of +the algorithm works properly, you should delete it as follows: + +```bash +bin/delete-algorithm.sh +``` + +Then create a Pull Request against the `main` branch. If you need to make +adjustments to your branch, you can rerun registration to replace your +unreleased version of the algorithm as often as necessary until you're +satisfied. + ## Creating a Release After one or more Pull Requests have landed on the `main` branch to constitute diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index 0b8f1b8..1a96a08 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -34,7 +34,7 @@ basedir=$(dirname "$(dirname "$(readlink -f "$0")")") algorithm_id="${algorithm_name}:${algorithm_version}" stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." -if [[ $("${basedir}/bin/describe-algorithm.sh") ]]; then +if [[ $("${basedir}/bin/describe-algorithm.sh" 2>&1 >/dev/null) ]]; then stderr "" stderr "ERROR: Algorithm '${algorithm_id}' already exists." stderr "" diff --git a/bin/subset.sh b/bin/subset.sh index 83d2f7d..0c7ef88 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -2,6 +2,8 @@ set -euo pipefail +set -x + # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). base_dir=$(dirname "$(dirname "$(readlink -f "$0")")") From 06f1f8428466433bdccd8357ce35cc5a548590b0 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 14:42:53 -0500 Subject: [PATCH 10/19] Time build.sh when in DPS --- bin/build-dps.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/build-dps.sh b/bin/build-dps.sh index 9ecd30d..44e2958 100755 --- a/bin/build-dps.sh +++ b/bin/build-dps.sh @@ -4,4 +4,4 @@ set -euo pipefail basedir=$(dirname "$(readlink -f "$0")") -"${basedir}/build.sh" --yes --no-dev +time "${basedir}/build.sh" --yes --no-dev From 82497cda1d80c2b89556b919b13d01ead5b9fdb6 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 14:48:31 -0500 Subject: [PATCH 11/19] Fix stderr redirection --- bin/register-algorithm.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index 1a96a08..50de86f 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -34,7 +34,7 @@ basedir=$(dirname "$(dirname "$(readlink -f "$0")")") algorithm_id="${algorithm_name}:${algorithm_version}" stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." -if [[ $("${basedir}/bin/describe-algorithm.sh" 2>&1 >/dev/null) ]]; then +if [[ $("${basedir}/bin/describe-algorithm.sh" >/dev/null 2>&1) ]]; then stderr "" stderr "ERROR: Algorithm '${algorithm_id}' already exists." stderr "" From cf27c7b4d78d998baf6d8d579d1ce0c8f3dd6f79 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 18:09:29 -0500 Subject: [PATCH 12/19] Fix scripts --- bin/delete-algorithm.sh | 55 +++++++++++++++---------- bin/describe-algorithm.sh | 32 ++++++--------- bin/register-algorithm.sh | 84 ++++++++++++++++++++++++--------------- bin/subset.sh | 82 ++++++++++++-------------------------- 4 files changed, 123 insertions(+), 130 deletions(-) diff --git a/bin/delete-algorithm.sh b/bin/delete-algorithm.sh index dd769f3..99258a6 100755 --- a/bin/delete-algorithm.sh +++ b/bin/delete-algorithm.sh @@ -1,39 +1,52 @@ #!/usr/bin/env bash -yaml_file=${1:-algorithm_config.yaml} -tag=$(git tag --points-at HEAD) -branch=$(git rev-parse --abbrev-ref HEAD) -name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') -version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') - function stderr() { echo >&2 "${1}" } -if [[ "${branch}" != "main" ]]; then - version=${branch//\//-} -elif [[ -z "${tag}" ]]; then - stderr "ERROR: You're on the main branch, but there's no tag for the current commit." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 -elif [[ "${tag}" != "${version}" ]]; then - stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 -fi +yes= + +while ((${#})); do + case "${1}" in + -y | --yes) + yes=1 + ;; + *) + stderr "ERROR: unrecognized argument: ${1}" + exit 1 + ;; + esac + shift +done + +# Obtain the algorithm name and version from the algorithm_config.yaml file, but +# use the current branch name as the version if the current branch is not `main`. -# TODO: add confirmation prompt! +yaml_file=${1:-algorithm_config.yaml} +branch=$(git rev-parse --abbrev-ref HEAD) +algorithm_name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') +algorithm_version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') +[[ "${branch}" != "main" ]] && algorithm_version=${branch} +algorithm_id="${algorithm_name}:${algorithm_version}" + +if [[ -z "${yes}" ]]; then + read -rp "Are you sure you want to delete algorithm '${algorithm_id}'? [yes/NO] " + + if [[ ! "${REPLY}" =~ ^[Yy][Ee][Ss]$ ]]; then + stderr "Aborted." + exit 1 + fi +fi -algorithm_id="${name}:${version}" stderr "Deleting algorithm '${algorithm_id}'..." # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") + conda_prefix=$("${basedir}/bin/conda-prefix.sh") -conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") -"${conda_run[@]}" python -c " +conda run --no-capture-output --prefix "${conda_prefix}" python -c " import json import sys import tempfile diff --git a/bin/describe-algorithm.sh b/bin/describe-algorithm.sh index 4d6f4d9..490de51 100755 --- a/bin/describe-algorithm.sh +++ b/bin/describe-algorithm.sh @@ -1,36 +1,26 @@ #!/usr/bin/env bash -yaml_file=${1:-algorithm_config.yaml} -tag=$(git tag --points-at HEAD) -branch=$(git rev-parse --abbrev-ref HEAD) -name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') -version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') - function stderr() { echo >&2 "${1}" } -if [[ "${branch}" != "main" ]]; then - version=${branch//\//-} -elif [[ -z "${tag}" ]]; then - stderr "ERROR: You're on the main branch, but there's no tag for the current commit." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 -elif [[ "${tag}" != "${version}" ]]; then - stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${version}'." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 -fi +# Obtain the algorithm name and version from the algorithm_config.yaml file, but +# use the current branch name as the version if the current branch is not `main`. -algorithm_id="${name}:${version}" +yaml_file=${1:-algorithm_config.yaml} +branch=$(git rev-parse --abbrev-ref HEAD) +algorithm_name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') +algorithm_version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') +[[ "${branch}" != "main" ]] && algorithm_version=${branch} +algorithm_id="${algorithm_name}:${algorithm_version}" # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") + conda_prefix=$("${basedir}/bin/conda-prefix.sh") -conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") -"${conda_run[@]}" python -c " +conda run --no-capture-output --prefix "${conda_prefix}" python -c " import json import sys import tempfile @@ -41,6 +31,8 @@ from maap.maap import MAAP maap = MAAP('api.maap-project.org') if r := maap.describeAlgorithm('${algorithm_id}'): + # This response is XML, not JSON, unfortunately, so the output is not + # convenient to read. print(r.text) else: print(r.text, file=sys.stderr) diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index 50de86f..af10add 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -1,54 +1,71 @@ #!/usr/bin/env bash +function stderr() { + echo 1>&2 "${1}" +} + +yes= + +while ((${#})); do + case "${1}" in + -y | --yes) + yes=${1} + ;; + *) + stderr "ERROR: unrecognized argument: ${1}" + exit 1 + ;; + esac + shift +done + +# Obtain the algorithm name and version from the algorithm_config.yaml file, but +# use the current branch name as the version if the current branch is not `main`. + yaml_file=${1:-algorithm_config.yaml} tag=$(git tag --points-at HEAD) branch=$(git rev-parse --abbrev-ref HEAD) algorithm_name=$(grep "^algorithm_name:" "${yaml_file}" | sed -E 's/algorithm_name: ([^[:space:]]+).*/\1/') algorithm_version=$(grep "^algorithm_version:" "${yaml_file}" | sed -E 's/algorithm_version: ([^[:space:]]+).*/\1/') +[[ "${branch}" != "main" ]] && algorithm_version=${branch} +algorithm_id="${algorithm_name}:${algorithm_version}" -function stderr() { - echo 1>&2 "${1}" -} - -if [[ "${branch}" =~ "/" ]]; then +if [[ "${algorithm_version}" =~ "/" ]]; then # Slashes in branch names are not acceptable because the DPS system uses the # branch name as part of the Docker image tag (which cannot contain slashes). stderr "ERROR: Branch names cannot contain slashes. Please rename the branch and try again." exit 1 -elif [[ "${branch}" != "main" ]]; then - algorithm_version=${branch} -elif [[ -z "${tag}" ]]; then - stderr "ERROR: You're on the main branch, but there's no tag for the current commit." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 -elif [[ "${tag}" != "${algorithm_version}" ]]; then - stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${algorithm_version}'." - stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." - exit 1 +fi + +if [[ "${branch}" == "main" ]]; then + if [[ -z "${tag}" ]]; then + stderr "ERROR: You're on the main branch, but there's no tag for the current commit." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 + elif [[ "${tag}" != "${algorithm_version}" ]]; then + stderr "ERROR: The tag for the current commit is '${tag}', but the version in algorithm_config.yaml is '${algorithm_version}'." + stderr "Please follow the instructions for creating a new release in CONTRIBUTING.md." + exit 1 + fi fi # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") -algorithm_id="${algorithm_name}:${algorithm_version}" -stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." - -if [[ $("${basedir}/bin/describe-algorithm.sh" >/dev/null 2>&1) ]]; then - stderr "" - stderr "ERROR: Algorithm '${algorithm_id}' already exists." - stderr "" - stderr "If you want to re-register the algorithm, you must first delete it:" - stderr "" - stderr " bin/delete-algorithm.sh" - stderr "" - exit 1 +# If the algorithm already exists, delete it first. +if [[ $("${basedir}/bin/describe-algorithm.sh") ]]; then + stderr "Algorithm '${algorithm_id}' already exists, so it must be deleted first." + # ${yes} is intentionally unquoted to allow it to be empty. + # shellcheck disable=SC2086 + "${basedir}/bin/delete-algorithm.sh" ${yes} + [[ $? ]] && exit 1 fi +stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." conda_prefix=$("${basedir}/bin/conda-prefix.sh") -conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") -"${conda_run[@]}" python -c " +conda run --no-capture-output --prefix "${conda_prefix}" python -c " import json import sys import tempfile @@ -59,11 +76,14 @@ from maap.maap import MAAP maap = MAAP('api.maap-project.org') with open('${yaml_file}') as f: - config = yaml.safe_load(f) + algorithm_config = yaml.safe_load(f) with tempfile.NamedTemporaryFile('w+') as f: - config['algorithm_version'] = '${algorithm_version}' - json.dump(config, f, indent=2) + # Replace the algorithm version, write the modified config to a temporary + # file, then rewind the file pointer to the beginning so it can be read for + # registration. + algorithm_config['algorithm_version'] = '${algorithm_version}' + json.dump(algorithm_config, f, indent=2) f.seek(0) try: diff --git a/bin/subset.sh b/bin/subset.sh index 0c7ef88..1430d17 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -2,39 +2,24 @@ set -euo pipefail -set -x - # Apply dirname twice to get to the top of the repo, since this script is in the # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). base_dir=$(dirname "$(dirname "$(readlink -f "$0")")") -input_dir="${base_dir}/input" -conda_prefix=$("${base_dir}/bin/conda-prefix.sh") -conda_run=("conda" "run" "--no-capture-output" "--prefix" "${conda_prefix}") -subset_py="${base_dir}/src/gedi_subset/subset.py" -echo "--- listing files in $(dirname "${base_dir}") ---" -ls -l "$(dirname "${base_dir}")" || true -echo "--- listing files in ${base_dir} ---" -ls -l "${base_dir}" || true -echo "--- listing files in ${base_dir}/bin ---" -ls -l "${base_dir}/bin" || true -echo "--- listing files in ${input_dir} ---" -ls -l "${input_dir}" || true -echo "---" +input_dir="${PWD}/input" +subset_py="${base_dir}/src/gedi_subset/subset.py" if ! test -d "${input_dir}"; then - echo "No input directory found, assuming local development environment: ${input_dir}" >&2 # There is no `input` sub-directory of the current working directory, so # simply pass all arguments through to the Python script. This is useful # for testing in a non-DPS environment, where there is no `input` directory # since the DPS system creates the `input` directory and places the AOI file # within it. - set -x - "${conda_run[@]}" "${subset_py}" --verbose "$@" + command=("${subset_py}" --verbose "$@") else # There is an `input` sub-directory of the current working directory, so # assume the AOI file is the sole file within the `input` sub-directory. - aoi="$(ls input/*)" + aoi="$(ls "${input_dir}"/*)" n_actual=${#} n_expected=9 @@ -44,45 +29,28 @@ else exit 1 fi - inputs=() - - # Workaround for DPS bug where default input values must be quoted in order - # for algorithm registration to work. We strip surrounding quotes from all - # arguments, either double or single quotes, if found. - while ((${#})); do - input=${1} - - # if [[ "${input}" =~ \".*\" ]]; then - # input=${1%\"} # Strip leading quote - # input=${input#\"} # Strip trailing quote - # elif [[ "${input}" =~ \'.*\' ]]; then - # input=${input%\'} # Strip leading quote - # input=${input#\'} # Strip trailing quote - # fi - - inputs+=("${input}") - shift - done - args=(--verbose --aoi "${aoi}") - args+=(--doi "${inputs[0]}") # doi is required - [[ "${inputs[1]}" != "-" ]] && args+=(--temporal "${inputs[1]}") - args+=(--lat "${inputs[2]}") # lat is required - args+=(--lon "${inputs[3]}") # lon is required - [[ "${inputs[4]}" != "-" ]] && args+=(--beams "${inputs[4]}") - args+=(--columns "${inputs[5]}") # columns is required - [[ "${inputs[6]}" != "-" ]] && args+=(--query "${inputs[6]}") - [[ "${inputs[7]}" != "-" ]] && args+=(--limit "${inputs[7]}") - [[ "${inputs[8]}" != "-" ]] && args+=(--output "${inputs[8]}") - - if [[ "${inputs[9]:--}" != "-" ]]; then - # The last argument is not a hyphen, so we expect it to be arguments to - # pass to scalene for profiling our algorithm. - IFS=' ' read -ra scalene_args <<<"${inputs[9]}" - set -x - "${conda_run[@]}" scalene "${scalene_args[@]}" --no-browser "${subset_py}" --- "${args[@]}" + args+=(--doi "${1}") # doi is required + [[ "${2}" != "-" ]] && args+=(--temporal "${2}") + args+=(--lat "${3}") # lat is required + args+=(--lon "${4}") # lon is required + [[ "${5}" != "-" ]] && args+=(--beams "${5}") + args+=(--columns "${6}") # columns is required + [[ "${7}" != "-" ]] && args+=(--query "${7}") + [[ "${8}" != "-" ]] && args+=(--limit "${8}") + [[ "${9}" != "-" ]] && args+=(--output "${9}") + + # If the last argument is not a hyphen, we expect it to be arguments to pass + # to scalene for profiling our algorithm. + if [[ "${10:--}" != "-" ]]; then + # Split the 10th argument into an array of arguments to pass to scalene. + IFS=' ' read -ra scalene_args <<<"${10}" + command=(scalene "${scalene_args[@]}" --no-browser "${subset_py}" --- "${args[@]}") else - set -x - "${conda_run[@]}" "${subset_py}" "${args[@]}" + command=("${subset_py}" "${args[@]}") fi fi + +set -x +conda_prefix=$("${base_dir}/bin/conda-prefix.sh") +conda run --no-capture-output --prefix "${conda_prefix}" "${command[@]}" From 1f3047dd2651da0a178e1ad1c637def7ef062294 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 9 Feb 2024 19:05:38 -0500 Subject: [PATCH 13/19] Make scalene write to DPS output dir --- bin/subset.sh | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/bin/subset.sh b/bin/subset.sh index 1430d17..ea7e239 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -7,6 +7,7 @@ set -euo pipefail base_dir=$(dirname "$(dirname "$(readlink -f "$0")")") input_dir="${PWD}/input" +output_dir="${PWD}/output" subset_py="${base_dir}/src/gedi_subset/subset.py" if ! test -d "${input_dir}"; then @@ -42,15 +43,25 @@ else # If the last argument is not a hyphen, we expect it to be arguments to pass # to scalene for profiling our algorithm. - if [[ "${10:--}" != "-" ]]; then + if [[ "${10:--}" == "-" ]]; then + command=("${subset_py}" "${args[@]}") + else # Split the 10th argument into an array of arguments to pass to scalene. IFS=' ' read -ra scalene_args <<<"${10}" - command=(scalene "${scalene_args[@]}" --no-browser "${subset_py}" --- "${args[@]}") - else - command=("${subset_py}" "${args[@]}") + # Force output to be written to the output directory by adding the + # `--outfile` argument after any user-provided arguments. If the user + # provides their own `--outfile` argument, it will be ignored. + command=( + scalene \ + "${scalene_args[@]}" \ + --no-browser \ + --outfile "${output_dir}"/profile.html \ + "${subset_py}" --- "${args[@]}" + ) fi fi set -x +mkdir -p "${output_dir}" conda_prefix=$("${base_dir}/bin/conda-prefix.sh") conda run --no-capture-output --prefix "${conda_prefix}" "${command[@]}" From 3b7766b3a1c71ed1fe43ef9e293556f808ef4945 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Sat, 10 Feb 2024 14:05:29 -0500 Subject: [PATCH 14/19] Force HTML profile output --- bin/delete-algorithm.sh | 20 +++++++------------- bin/register-algorithm.sh | 27 ++++++++++++++++++--------- bin/subset.sh | 1 + docs/MAAP_USAGE.md | 10 +++++----- 4 files changed, 31 insertions(+), 27 deletions(-) diff --git a/bin/delete-algorithm.sh b/bin/delete-algorithm.sh index 99258a6..fcefc82 100755 --- a/bin/delete-algorithm.sh +++ b/bin/delete-algorithm.sh @@ -46,20 +46,14 @@ basedir=$(dirname "$(dirname "$(readlink -f "$0")")") conda_prefix=$("${basedir}/bin/conda-prefix.sh") -conda run --no-capture-output --prefix "${conda_prefix}" python -c " -import json -import sys -import tempfile - -import yaml +message=$(conda run --no-capture-output --prefix "${conda_prefix}" python -c " from maap.maap import MAAP maap = MAAP('api.maap-project.org') -try: - r = maap.deleteAlgorithm('${algorithm_id}') - print(json.dumps(r.json(), indent=2)) -except Exception as e: - print(e, file=sys.stderr) - sys.exit(1) -" +if not (r := maap.deleteAlgorithm('${algorithm_id}')): + print(r.json()['message']) +") + +echo "${message}" +[[ -z "${message}" ]] || exit 1 diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index af10add..a1111a9 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -54,18 +54,21 @@ fi basedir=$(dirname "$(dirname "$(readlink -f "$0")")") # If the algorithm already exists, delete it first. -if [[ $("${basedir}/bin/describe-algorithm.sh") ]]; then +if "${basedir}/bin/describe-algorithm.sh" >/dev/null 2>&1; then stderr "Algorithm '${algorithm_id}' already exists, so it must be deleted first." - # ${yes} is intentionally unquoted to allow it to be empty. + # ${yes} is intentionally unquoted to allow it to be empty. Otherwise, the + # script would receive an empty string as an argument, rather than no argument. # shellcheck disable=SC2086 - "${basedir}/bin/delete-algorithm.sh" ${yes} - [[ $? ]] && exit 1 + if ! message=$("${basedir}/bin/delete-algorithm.sh" ${yes}); then + stderr "Failed to delete algorithm '${algorithm_id}': ${message}" + exit 1 + fi fi stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." conda_prefix=$("${basedir}/bin/conda-prefix.sh") -conda run --no-capture-output --prefix "${conda_prefix}" python -c " +script=" import json import sys import tempfile @@ -86,10 +89,16 @@ with tempfile.NamedTemporaryFile('w+') as f: json.dump(algorithm_config, f, indent=2) f.seek(0) - try: - r = maap.register_algorithm_from_yaml_file(f.name) + if r := maap.register_algorithm_from_yaml_file(f.name): print(json.dumps(r.json(), indent=2)) - except Exception as e: - print(e, file=sys.stderr) + else: + print(r.json()['message']) sys.exit(1) " + +if message=$(conda run --no-capture-output --prefix "${conda_prefix}" python -c "${script}" 2>/dev/null); then + echo "${message}" +else + stderr "Failed to register algorithm '${algorithm_id}': ${message}" + exit 1 +fi diff --git a/bin/subset.sh b/bin/subset.sh index ea7e239..089cb43 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -54,6 +54,7 @@ else command=( scalene \ "${scalene_args[@]}" \ + --html \ --no-browser \ --outfile "${output_dir}"/profile.html \ "${subset_py}" --- "${args[@]}" diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 351c897..3ca28e5 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -165,12 +165,12 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. For first-time users of `scalene`, the recommended value for this input is `--reduced-profile`. Note that since no browser is available in DPS, when any value is supplied for this input, the `--no-browser` option will be included - automatically, which will produce HTML output to a file named `profile.html`, - if you do not specify a different name via the `--outfile` option. The - profiling output file will appear in the same directory as the algorithm - output file. + to prevent Scalene from attempting to open a browser. However, the `--html` + option will also be included, which will produce HTML output to a file named + `profile.html`. The profiling output file will appear in the same directory + as the algorithm output file. - _New in version 0.6.3_ + _New in version 0.7.0_ ### Specifying an AOI From 09bf504990a028c52062b56645c1576ff36abbf5 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Sat, 10 Feb 2024 16:28:17 -0500 Subject: [PATCH 15/19] Use --web, not --html w/scalene --- bin/subset.sh | 2 +- docs/MAAP_USAGE.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/subset.sh b/bin/subset.sh index 089cb43..0f1fccf 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -54,7 +54,7 @@ else command=( scalene \ "${scalene_args[@]}" \ - --html \ + --web \ --no-browser \ --outfile "${output_dir}"/profile.html \ "${subset_py}" --- "${args[@]}" diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 3ca28e5..163554e 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -165,7 +165,7 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. For first-time users of `scalene`, the recommended value for this input is `--reduced-profile`. Note that since no browser is available in DPS, when any value is supplied for this input, the `--no-browser` option will be included - to prevent Scalene from attempting to open a browser. However, the `--html` + to prevent Scalene from attempting to open a browser. However, the `--web` option will also be included, which will produce HTML output to a file named `profile.html`. The profiling output file will appear in the same directory as the algorithm output file. From 9feb0cde15b1e9fc1a8ff8a45bc259867409ce48 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Sat, 10 Feb 2024 16:53:22 -0500 Subject: [PATCH 16/19] Eliminate dash (-) as default for optional fields --- algorithm_config.yaml | 32 ++++++++++++++++---------------- bin/subset.sh | 18 +++++++++--------- docs/MAAP_USAGE.md | 41 +++++++++++++++-------------------------- 3 files changed, 40 insertions(+), 51 deletions(-) diff --git a/algorithm_config.yaml b/algorithm_config.yaml index 1f5fc25..189d219 100644 --- a/algorithm_config.yaml +++ b/algorithm_config.yaml @@ -20,13 +20,6 @@ inputs: or one of these logical names: L1B, L2A, L2B, L4A" required: true default: "" - - name: temporal - description: Temporal range to subset, formatted as an ISO 8601 Time Interval. - For example, 2021-01-01T00:00:00Z/2021-12-31T23:59:59Z. See - https://en.wikipedia.org/wiki/ISO_8601#Time_intervals. If not provided, - the entire temporal range of the GEDI collection is used. - required: false - default: "-" - name: lat description: Name of the dataset containing latitude values required: true @@ -35,12 +28,6 @@ inputs: description: Name of the dataset containing longitude values required: true default: "" - - name: beams - description: "Which beams to include: all, coverage, power, or a comma-separated - list of specific beam names, with or without the BEAM prefix (e.g., - BEAM0000,BEAM0001 or 0000,0001)" - required: false - default: all - name: columns description: One or more column names, separated by commas, to include in the output file @@ -51,7 +38,20 @@ inputs: If not provided, all rows are included. See https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.query.html. required: false - default: "-" + default: "" + - name: temporal + description: Temporal range to subset, formatted as an ISO 8601 Time Interval. + For example, 2021-01-01T00:00:00Z/2021-12-31T23:59:59Z. See + https://en.wikipedia.org/wiki/ISO_8601#Time_intervals. If not provided, + the entire temporal range of the GEDI collection is used. + required: false + default: "" + - name: beams + description: "Which beams to include: all, coverage, power, or a comma-separated + list of specific beam names, with or without the BEAM prefix (e.g., + BEAM0000,BEAM0001 or 0000,0001)" + required: false + default: all - name: limit description: Maximum number of GEDI granule data files to download from the CMR, regardless of the number of granules within the AOI. @@ -61,9 +61,9 @@ inputs: description: Name of the output file produced by the algorithm. Defaults to using the AOI file name (without the extension) with the suffix "_subset.gpkg". required: false - default: "-" + default: "" - name: scalene_args description: Arguments to pass to Scalene for memory and CPU profiling. If not provided, Scalene will not be used. required: false - default: "-" + default: "" diff --git a/bin/subset.sh b/bin/subset.sh index 0f1fccf..a9b6651 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -32,18 +32,18 @@ else args=(--verbose --aoi "${aoi}") args+=(--doi "${1}") # doi is required - [[ "${2}" != "-" ]] && args+=(--temporal "${2}") - args+=(--lat "${3}") # lat is required - args+=(--lon "${4}") # lon is required - [[ "${5}" != "-" ]] && args+=(--beams "${5}") - args+=(--columns "${6}") # columns is required - [[ "${7}" != "-" ]] && args+=(--query "${7}") - [[ "${8}" != "-" ]] && args+=(--limit "${8}") - [[ "${9}" != "-" ]] && args+=(--output "${9}") + args+=(--lat "${2}") # lat is required + args+=(--lon "${3}") # lon is required + args+=(--columns "${4}") # columns is required + [[ -n "${5}" ]] && args+=(--query "${5}") + [[ -n "${6}" ]] && args+=(--temporal "${6}") + [[ -n "${7}" ]] && args+=(--beams "${7}") + [[ -n "${8}" ]] && args+=(--limit "${8}") + [[ -n "${9}" ]] && args+=(--output "${9}") # If the last argument is not a hyphen, we expect it to be arguments to pass # to scalene for profiling our algorithm. - if [[ "${10:--}" == "-" ]]; then + if [[ -z "${10}" ]]; then command=("${subset_py}" "${args[@]}") else # Split the 10th argument into an array of arguments to pass to scalene. diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 163554e..9d8ed0c 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -31,11 +31,7 @@ At a high level, the GEDI subsetting algorithm does the following: ## Algorithm Inputs -To run a GEDI subsetting DPS job, you must supply the following inputs. - -|**IMPORTANT:**| -|:---| -| _When **submitting a job via the ADE's user interface**, to indicate that you do not want to specify a particular value for an **optional** input, you must enter a single dash/hyphen (`-`) in the input text box. This will indicate that you wish to use the default value indicated for that optional input._ When **submitting a job via code, such as in a notebook**, if you wish to use the default value for an optional input, simply exclude the input name and value from the dictionary of inputs. +To run a GEDI subsetting DPS job, you must supply the following inputs: - `aoi` (_required_): URL to a GeoJSON file representing your area of interest (see [Specifying an AOI](#specifying-an-aoi)). This may contain multiple @@ -86,15 +82,6 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. quality_flag == 1 and `geolocation/sensitivity_a2` > 0.95 ``` - Alternatively, "dot" (`.`) notation may be used in place of using slashes. - This eliminates the need to use backticks to surround a path. Note, however, - that the **corresponding columns in the output will still contain slashes in - their names**: - - ```plain - quality_flag == 1 and geolocation.sensitivity_a2 > 0.95 - ``` - - `limit` (_optional_; default: 1_000): Maximum number of GEDI granule data files to download from the CMR, among those that intersect the specified AOI's bounding box, and fall within the specified temporal range (if supplied). @@ -104,8 +91,8 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. under 1000 granules for downloading, so a larger default value might only lead to longer CMR query times. -- `doi` (_required_): [Digital Object Identifier] (DOI) of the GEDI collection to - subset, or a logical name representing such a DOI (see +- `doi` (_required_): [Digital Object Identifier] (DOI) of the GEDI collection + to subset, or a logical name representing such a DOI (see [Specifying a DOI](#specifying-a-doi)) _New in version 0.3.0_ @@ -118,17 +105,17 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. _New in version 0.3.0_ -- `beams` (_optional_; default: `"all"`): Which beams to include in the subset. +- `beams` (_optional_; default: `all`): Which beams to include in the subset. If supplied, must be one of logical names `all`, `coverage`, or `power`, _OR_ a comma-separated list of specific beam names, with or without the `BEAM` prefix (e.g., `BEAM0000,BEAM0001` or `0000,0001`) _New in version 0.4.0_ -- `temporal` (_optional_; default: full temporal range available): Temporal range - to subset. You may specify either a closed range, with start and end dates, - or a half-open range, with either a start date or an end date. For full - details on the valid formats, see the NASA CMR's documentation on +- `temporal` (_optional_; default: full temporal range available): Temporal + range to subset. You may specify either a closed range, with start and end + dates, or a half-open range, with either a start date or an end date. For + full details on the valid formats, see the NASA CMR's documentation on [temporal range searches](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html#temporal-range-searches). _New in version 0.6.0_ @@ -145,7 +132,8 @@ To run a GEDI subsetting DPS job, you must supply the following inputs. Examples showing how the value specified for `output` is mapped to a final output file: - - Unspecified -> `myaoi.gpkg`, where `myaoi.geojson` is the name of the AOI file + - Unspecified -> `myaoi.gpkg`, where `myaoi.geojson` is the name of the AOI + file - `myoutput` -> `myoutput.gpkg` - `myoutput.gpkg` -> `myoutput.gpkg` - `myoutput.h5` -> `myoutput.gpkg` @@ -188,8 +176,8 @@ form within the ADE (where `path/to/aio.geojson` can be any path and filename for your AOI): ```plain -~/my-public-bucket/path/to/aoi.geojson -^^^^^^^^^^^^^^^^^^ +/projects/my-public-bucket/path/to/aoi.geojson +-------------------------- ``` You would then supply the following URL as the `aoi` input value when running @@ -197,8 +185,9 @@ this algorithm as a DPS job, where `` is your ADE username: ```plain https://maap-ops-workspace.s3.amazonaws.com/shared//path/to/aoi.geojson -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Replace "~/my-public-bucket" with this URL prefix +------------------------------------------------------------- + | + +-- Replace "/projects/my-public-bucket" with this URL prefix ``` ### Specifying a DOI From 06bdbd465355dde3896c4b0eff6f9510dd9209ca Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Sat, 10 Feb 2024 17:50:26 -0500 Subject: [PATCH 17/19] Widen scalene report --- bin/subset.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/subset.sh b/bin/subset.sh index a9b6651..8d25259 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -54,7 +54,8 @@ else command=( scalene \ "${scalene_args[@]}" \ - --web \ + --column-width 165 \ + --html \ --no-browser \ --outfile "${output_dir}"/profile.html \ "${subset_py}" --- "${args[@]}" From 4432641a762af1b4d94ac1662cd88dec33b8fb43 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Mon, 12 Feb 2024 09:11:05 -0500 Subject: [PATCH 18/19] Clarify use of `--scalene_args` option --- docs/MAAP_USAGE.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 9d8ed0c..5471445 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -158,6 +158,13 @@ To run a GEDI subsetting DPS job, you must supply the following inputs: `profile.html`. The profiling output file will appear in the same directory as the algorithm output file. + Starting with `--reduced-profile` produces a relatively brief report that may + aid in more quickly identifying hotspots than a fully profile would. However, + to produce a full profile where you want to use all of Scalene's default + values, you must supply _some_ value for this input, so the simplest valid + Scalene option is `--on`. Otherwise, as mentioned above, when no value is + supplied for this input, Scalene will not be used at all. + _New in version 0.7.0_ ### Specifying an AOI From a5d7c84fedc50e6085362c112b2977bdcada6ed3 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Tue, 13 Feb 2024 09:55:05 -0500 Subject: [PATCH 19/19] Add/clarify script comments --- CHANGELOG.md | 14 ++++----- CONTRIBUTING.md | 42 ++++++++++++-------------- bin/build-dps.sh | 6 ++++ bin/conda-prefix.py | 62 +++++++++++++++++++++++++++++++++++++++ bin/conda-prefix.sh | 47 ----------------------------- bin/delete-algorithm.sh | 14 ++++++++- bin/describe-algorithm.sh | 16 +++++++++- bin/register-algorithm.sh | 17 +++++++++-- bin/subset.sh | 18 ++++++------ docs/MAAP_USAGE.md | 30 ++++++++++--------- 10 files changed, 161 insertions(+), 105 deletions(-) create mode 100755 bin/conda-prefix.py delete mode 100755 bin/conda-prefix.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index ee7ccb2..dd8165a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,14 +13,14 @@ The format is based on [Keep a Changelog], and this project adheres to choose to profile their jobs by specifying command-line options for the `scalene` profiling tool. See `docs/MAAP_USAGE.md` for more information. -## 0.6.2 +## 0.6.2 (2023-12-05) ### Fixed - Updated to use v3.1.3 of maap-py in environment-maappy.yml. Previous versions of maap-py were using the deprecated MAAP Query Service API endpoint. -## 0.6.1 +## 0.6.1 (2023-09-28) ### Fixed @@ -28,7 +28,7 @@ The format is based on [Keep a Changelog], and this project adheres to URLs that contain ops as they have now been retired (e.g., api.ops.maap-project.org). -## 0.6.0 +## 0.6.0 (2023-06-02) ### Fixed @@ -70,7 +70,7 @@ The format is based on [Keep a Changelog], and this project adheres to the output file, rather than hard-code the name to `gedi-subset.gpkg`. See `docs/MAAP_USAGE.md` for more information. -## 0.5.0 +## 0.5.0 (2023-04-11) ### Changed @@ -79,14 +79,14 @@ The format is based on [Keep a Changelog], and this project adheres to wish to query the MAAP CMR until it is taken down, you may still use an earlier version of this algorithm (ideally, 0.4.0). -## 0.4.0 +## 0.4.0 (2022-11-14) ### Added - [#6](https://github.com/MAAP-Project/gedi-subsetter/issues/6): Allow user to specify which BEAMs to subset -## 0.3.0 +## 0.3.0 (2022-11-10) ### Fixed @@ -110,7 +110,7 @@ The format is based on [Keep a Changelog], and this project adheres to - [#8](https://github.com/MAAP-Project/gedi-subsetter/issues/8): Specifying a query is now optional, to allow selecting all rows for specified columns. -## 0.2.7 +## 0.2.7 (2022-10-18) ### Added diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 70ef46c..e62b252 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,27 +51,17 @@ script `bin/build.sh`, as instructed below, which is a script that serves double-duty as the script that also builds the DPS environment for executing the algorithm, by ensuring that all necessary Python packages are installed. -**IMPORTANT:** If you're working in the ADE, the default location for conda -environments is ephemeral, meaning that whenever your ADE workspace is -restarted, all of the conda environments in the default location are lost. This -requires you to recreate any such conda environments that you wish to use after -a workspace restart. To prevent this from occurring, you must provide a -location that persists across restarts via the `--prefix` option with the -`bin/build.sh` script, as described below. _However_, taking this approach -means that creation of the conda environment may take significantly more time -(possibly 10s of minutes) because the persistent location is an AWS S3 bucket. - -If you're not working in the ADE, or you are, but aren't bothered by having to -rerun the following command every time you want to use the `gedi_subset` after -a workspace restart, you may create the conda environment simply as follows: +You may create the conda environment simply as follows: ```bash bin/build.sh ``` -_Alternatively_, if you _are_ using the ADE, and you _do_ want the `gedi_subset` -conda environment to persist across workspace restarts, use the following -command instead: +**IMPORTANT:** If you're working in the ADE, to persist your conda environment +across restarts use the `--prefix` option with the `bin/build.sh` script. See +also the [MAAP documentation on custom environments]. _However_, taking this +approach takes significantly more time (possibly ~20 minutes), but is required +only once: ```bash bin/build.sh --prefix "${HOME}/envs/gedi_subset" @@ -303,13 +293,15 @@ After one or more Pull Requests have landed on the `main` branch to constitute a new release: 1. Checkout the latest changes to the `main` branch. -1. Create a new branch named `release/VERSION`, where `VERSION` is an - appropriate version number, according to [Semantic Versioning]. +1. Create a new branch named `release-VERSION`, where `VERSION` is an + appropriate version number for the changes being made, according to + [Semantic Versioning]. 1. In `algorithm_config.yaml` change the value of `algorithm_version` to the same value as `VERSION` from the previous step. -1. In the [Changelog](./CHANGELOG.md), change the `Unreleased` heading to the - same value as `VERSION` from the previous step, and then, above the new - version heading, add a new `Unreleased` section, for future changes. +1. In the [Changelog](./CHANGELOG.md), immediately below the `Unreleased` + heading add a new heading (at the same level) using the format + `VERSION (YYYY-MM-DD)`, where `VERSION` is as above, and `YYYY-MM-DD` is the + expected release date. 1. Commit the changes, and open a Pull Request to `main`. 1. Once the PR is approved and merged, go to @@ -321,7 +313,7 @@ a new release: `VERSION` in the previous step. 1. In the description text box, copy and paste the content of only the _new version section_ you added earlier to the Changelog, **excluding** the new - version heading. + version heading (since it would be redundant with the release title). 1. Click the **Publish release** button. 1. Checkout and pull the `main` branch in order to pull down the new tag created by the release process. @@ -329,12 +321,14 @@ a new release: section. [compatible release operator]: - https://peps.python.org/pep-0440/#compatible-release + https://peps.python.org/pep-0440/#compatible-release [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/ +[MAAP documentation on custom environments]: + https://docs.maap-project.org/en/develop/system_reference_guide/custom-environments.html#Basic-custom-environment [MAAP GEDI Subsetter repository]: https://github.com/MAAP-Project/gedi-subsetter.git [NASA MAAP]: https://maap-project.org/ [Semantic Versioning]: - https://semver.org/spec/v2.0.0.html + https://semver.org/spec/v2.0.0.html diff --git a/bin/build-dps.sh b/bin/build-dps.sh index 44e2958..01f79b3 100755 --- a/bin/build-dps.sh +++ b/bin/build-dps.sh @@ -1,5 +1,11 @@ #!/usr/bin/env bash +# Builds the gedi_subset conda environment from a conda lock file, specifically +# for the DPS system. This script is intended to be specified as the algorithm +# configuration's `build_command` because that configuration value does not +# accept any arguments. This script is a wrapper around the `build.sh` script +# using specific options that are appropriate for the DPS system. + set -euo pipefail basedir=$(dirname "$(readlink -f "$0")") diff --git a/bin/conda-prefix.py b/bin/conda-prefix.py new file mode 100755 index 0000000..7deb0f5 --- /dev/null +++ b/bin/conda-prefix.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python + +# NOTE: Not intended for direct use. This is used by other scripts. + +# Finds the conda environment prefix for the gedi_subset environment, whether it +# was created in the default conda env location, or via an explicit prefix, and +# prints it to stdout. If the environment is not found, or multiple are found, +# an error message is printed to stderr and the script exits with a non-zero +# status code. +# +# If the environment variable GEDI_SUBSET_CONDA_PREFIX is set, it is used as the +# prefix, rather than searching the list of conda envs, but it is not checked +# for existence. + +import json +import os +import subprocess +import sys + +if prefix := os.getenv("GEDI_SUBSET_CONDA_PREFIX"): + print(prefix) + sys.exit(0) + +proc = subprocess.run(["conda", "env", "list", "--json"], capture_output=True) + +if proc.returncode: + print(proc.stderr.decode("utf-8"), file=sys.stderr) + sys.exit(1) + +envs = json.loads(proc.stdout)["envs"] +prefixes = tuple(env for env in envs if env.endswith("/gedi_subset")) + +if not prefixes: + print( + " ".join( + [ + "ERROR: Could not find the gedi_subset conda environment. If", + "you have not created the environment, run bin/build.sh. If", + "you have already created it, but used a different name, set", + "the GEDI_SUBSET_CONDA_PREFIX environment variable to the", + "absolute path of the environment.", + ] + ), + file=sys.stderr, + ) + sys.exit(1) + +if len(prefixes) > 1: + print( + " ".join( + [ + "ERROR: Found multiple conda environments named gedi_subset:", + f"{prefixes}. Please remove all but one, or set the", + "GEDI_SUBSET_CONDA_PREFIX environment variable to the full", + "path of the desired environment.", + ] + ), + file=sys.stderr, + ) + sys.exit(1) + +print(prefixes[0]) diff --git a/bin/conda-prefix.sh b/bin/conda-prefix.sh deleted file mode 100755 index 6ae5bd7..0000000 --- a/bin/conda-prefix.sh +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env bash - -python -c " -import json -import os -import sys - -prefix = os.getenv('GEDI_SUBSET_CONDA_PREFIX') - -if prefix: - print(prefix) - sys.exit(0) - -envs = json.loads('''$(conda env list --json)''')['envs'] -prefixes = tuple(env for env in envs if env.endswith('/gedi_subset')) - -if len(prefixes) == 0: - print( - ' '.join( - [ - 'ERROR: Could not find the gedi_subset conda environment. If', - 'you have not created the environment, run bin/build.sh. If', - 'you have already created it, but used a different name, set', - 'the GEDI_SUBSET_CONDA_PREFIX environment variable to the', - 'absolute path of the environment.' - ] - ), - file=sys.stderr, - ) - sys.exit(1) - -if len(prefixes) > 1: - print( - ' '.join( - [ - 'ERROR: Found multiple conda environments named gedi_subset:', - f'{prefixes}. Please remove all but one, or set the', - 'GEDI_SUBSET_CONDA_PREFIX environment variable to the full', - 'path of the desired environment.', - ] - ), - file=sys.stderr, - ) - sys.exit(1) - -print(prefixes[0]) -" diff --git a/bin/delete-algorithm.sh b/bin/delete-algorithm.sh index fcefc82..fc8ecd2 100755 --- a/bin/delete-algorithm.sh +++ b/bin/delete-algorithm.sh @@ -1,5 +1,17 @@ #!/usr/bin/env bash +# Deletes the version of the algorithm that is currently checked out. If the +# current branch is not `main`, uses the current branch name as the version. +# Otherwise, uses the version from the `algorithm_config.yaml` file, if and only +# if the current commit is tagged with that version. +# +# Prompts for confirmation before deleting the algorithm, unless the `-y` or +# `--yes` option is given: +# +# delete-algorithm.sh [-y|--yes] + +set -euo pipefail + function stderr() { echo >&2 "${1}" } @@ -44,7 +56,7 @@ stderr "Deleting algorithm '${algorithm_id}'..." # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") -conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_prefix=$("${basedir}/bin/conda-prefix.py") message=$(conda run --no-capture-output --prefix "${conda_prefix}" python -c " from maap.maap import MAAP diff --git a/bin/describe-algorithm.sh b/bin/describe-algorithm.sh index 490de51..6082762 100755 --- a/bin/describe-algorithm.sh +++ b/bin/describe-algorithm.sh @@ -1,5 +1,19 @@ #!/usr/bin/env bash +# Describes the version of the algorithm that is currently checked out. If the +# current branch is not `main`, uses the current branch name as the version. +# Otherwise, uses the version from the `algorithm_config.yaml` file, if and only +# if the current commit is tagged with that version: +# +# describe-algorithm.sh +# +# Currently, this script only prints the XML response from the MAAP API, which +# is not very useful. It would be better to parse the XML and print a more +# human-readable description of the algorithm. For now, this script is used +# mainly for other scripts to check whether or not the algorithm exists. + +set -euo pipefail + function stderr() { echo >&2 "${1}" } @@ -18,7 +32,7 @@ algorithm_id="${algorithm_name}:${algorithm_version}" # `bin` directory (i.e., first dirname gets to `bin`, second gets to the top). basedir=$(dirname "$(dirname "$(readlink -f "$0")")") -conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_prefix=$("${basedir}/bin/conda-prefix.py") conda run --no-capture-output --prefix "${conda_prefix}" python -c " import json diff --git a/bin/register-algorithm.sh b/bin/register-algorithm.sh index a1111a9..4b2ae7d 100755 --- a/bin/register-algorithm.sh +++ b/bin/register-algorithm.sh @@ -1,5 +1,18 @@ #!/usr/bin/env bash +# Registers the version of the algorithm that is currently checked out. If the +# current branch is not `main`, uses the current branch name as the version. +# Otherwise, uses the version from the `algorithm_config.yaml` file, if and only +# if the current commit is tagged with that version. +# +# If the algorithm already exists, it is first deleted (`delete-algorithm.sh`). +# Prompts for confirmation before deleting the algorithm, unless the `-y` or +# `--yes` option is given: +# +# register-algorithm.sh [-y|--yes] + +set -euo pipefail + function stderr() { echo 1>&2 "${1}" } @@ -60,13 +73,13 @@ if "${basedir}/bin/describe-algorithm.sh" >/dev/null 2>&1; then # script would receive an empty string as an argument, rather than no argument. # shellcheck disable=SC2086 if ! message=$("${basedir}/bin/delete-algorithm.sh" ${yes}); then - stderr "Failed to delete algorithm '${algorithm_id}': ${message}" + [[ -z "${message}" ]] || stderr "Failed to delete algorithm '${algorithm_id}': ${message}" exit 1 fi fi stderr "Registering algorithm '${algorithm_id}' (${yaml_file})..." -conda_prefix=$("${basedir}/bin/conda-prefix.sh") +conda_prefix=$("${basedir}/bin/conda-prefix.py") script=" import json diff --git a/bin/subset.sh b/bin/subset.sh index 8d25259..26b0efc 100755 --- a/bin/subset.sh +++ b/bin/subset.sh @@ -23,9 +23,9 @@ else aoi="$(ls "${input_dir}"/*)" n_actual=${#} - n_expected=9 + n_expected=10 - if test ${n_actual} -lt ${n_expected} -o ${n_actual} -gt $((n_expected + 1)); then + if test ${n_actual} -ne ${n_expected}; then echo "Expected ${n_expected} inputs, but got ${n_actual}:$(printf " '%b'" "$@")" >&2 exit 1 fi @@ -40,14 +40,13 @@ else [[ -n "${7}" ]] && args+=(--beams "${7}") [[ -n "${8}" ]] && args+=(--limit "${8}") [[ -n "${9}" ]] && args+=(--output "${9}") + # Split the 10th argument into an array of arguments to pass to scalene. + IFS=' ' read -ra scalene_args <<<"${10}" - # If the last argument is not a hyphen, we expect it to be arguments to pass - # to scalene for profiling our algorithm. - if [[ -z "${10}" ]]; then + if [[ ${#scalene_args[@]} -eq 0 ]]; then + # There are no scalene arguments, so don't use scalene command=("${subset_py}" "${args[@]}") else - # Split the 10th argument into an array of arguments to pass to scalene. - IFS=' ' read -ra scalene_args <<<"${10}" # Force output to be written to the output directory by adding the # `--outfile` argument after any user-provided arguments. If the user # provides their own `--outfile` argument, it will be ignored. @@ -58,12 +57,13 @@ else --html \ --no-browser \ --outfile "${output_dir}"/profile.html \ - "${subset_py}" --- "${args[@]}" + --- \ + "${subset_py}" "${args[@]}" ) fi fi set -x mkdir -p "${output_dir}" -conda_prefix=$("${base_dir}/bin/conda-prefix.sh") +conda_prefix=$("${base_dir}/bin/conda-prefix.py") conda run --no-capture-output --prefix "${conda_prefix}" "${command[@]}" diff --git a/docs/MAAP_USAGE.md b/docs/MAAP_USAGE.md index 5471445..493a1c3 100644 --- a/docs/MAAP_USAGE.md +++ b/docs/MAAP_USAGE.md @@ -142,29 +142,31 @@ To run a GEDI subsetting DPS job, you must supply the following inputs: _New in version 0.6.0_ - `scalene_args` (_optional_): Arguments to pass to [Scalene] for performance - profiling. If you do not want to profile performance of the algorithm, do - not specify a value for this input. + profiling. Normal usage should leave this argument blank. - Otherwise, when this input is supplied, the algorithm will be run via the - `scalene` command, and the value of this input will be passed as arguments to - the command. For a list of the available command-line options, see - . + Fill this in if you want to collect performance metrics (i.e. CPU and RAM + usage). The recommended value for this input is `--reduced-profile` (see + below for more advanced usage). When used, you will find `profile.html` in + your algorithm output folder. - For first-time users of `scalene`, the recommended value for this input is - `--reduced-profile`. Note that since no browser is available in DPS, when any - value is supplied for this input, the `--no-browser` option will be included - to prevent Scalene from attempting to open a browser. However, the `--web` - option will also be included, which will produce HTML output to a file named - `profile.html`. The profiling output file will appear in the same directory - as the algorithm output file. + When this input is supplied, the algorithm will be run via the `scalene` + command, and the value of this input will be passed as arguments to the + command. For a list of the available command-line options, see + . Starting with `--reduced-profile` produces a relatively brief report that may - aid in more quickly identifying hotspots than a fully profile would. However, + aid in more quickly identifying hotspots than a full profile would. However, to produce a full profile where you want to use all of Scalene's default values, you must supply _some_ value for this input, so the simplest valid Scalene option is `--on`. Otherwise, as mentioned above, when no value is supplied for this input, Scalene will not be used at all. + > **Note:** that since no browser is available in DPS, when any value is + > supplied for this input, the `--no-browser` option will be included to + > prevent Scalene from attempting to open a browser. However, the `--web` + > option will also be included, which will produce HTML output to a file named + > `profile.html`. + _New in version 0.7.0_ ### Specifying an AOI