diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 00000000..73090700 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,61 @@ +name: docs +on: [push, pull_request] + +permissions: + contents: read + pages: write + id-token: write + +concurrency: + group: "pages" + cancel-in-progress: false + + +jobs: + deploy: + environment: + name: documenation + url: ${{steps.deployement.outputs.page_url}} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Configure Git Credentials + run: | + git config user.name github-actions[bot] + git config user.email 41898282+github-actions[bot]@users.noreply.github.com + - uses: actions/setup-python@v5 + with: + python-version: 3.x + - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV + - uses: actions/cache@v4 + with: + key: mkdocs-material-${{ env.cache_id }} + path: .cache + restore-keys: | + mkdocs-material- + + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v3 + with: + version: "latest" + enable-cache: true + cache-dependency-glob: "**/pyproject.toml" + + - name: Check if cache used + if: steps.setup-uv.outputs.cache-hit == 'true' + run: echo "Cache was restored" + + - run: uv sync --only-group docs + + - run: uv run mkdocs build --config-file config/mkdocs.yml + + # - run: uv run mkdocs gh-deploy --force --config-file config/mkdocs.yml + + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + # Upload entire repository + path: 'site/' + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/release_drafter.yml b/.github/workflows/release_drafter.yml new file mode 100644 index 00000000..93ad4284 --- /dev/null +++ b/.github/workflows/release_drafter.yml @@ -0,0 +1,42 @@ +name: Release Drafter + +on: + push: + # branches to consider in the event; optional, defaults to all + branches: + - main + - dev + # pull_request event is required only for autolabeler + pull_request: + # Only following types are handled by the action, but one can default to all as well + types: [opened, reopened, synchronize] + # pull_request_target event is required for autolabeler to support PRs from forks + # pull_request_target: + # types: [opened, reopened, synchronize] + +permissions: + contents: read + +jobs: + update_release_draft: + permissions: + # write permission is required to create a github release + contents: write + # write permission is required for autolabeler + # otherwise, read permission is required at least + pull-requests: write + runs-on: ubuntu-latest + steps: + # (Optional) GitHub Enterprise requires GHE_HOST variable set + #- name: Set GHE_HOST + # run: | + # echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV + + # Drafts your next Release notes as Pull Requests are merged into "master" + - uses: release-drafter/release-drafter@v6 + # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml + # with: + config-name: release_draft.yml + # disable-autolabeler: true + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 49ea5f3f..f974c59d 100644 --- a/.gitignore +++ b/.gitignore @@ -141,7 +141,6 @@ __MACOSX # Extra directories/files /**data*/ -!tests/*/* agml/_helios agml/helios_config.sh agml/train diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..ecceba16 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,74 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, gender identity and expression, level of experience, +nationality, personal appearance, race, religion, or sexual identity and +orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or +advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at <>. All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at [http://contributor-covenant.org/version/1/4][version] + +[homepage]: http://contributor-covenant.org +[version]: http://contributor-covenant.org/version/1/4/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3400045c..3b2be648 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -189,7 +189,12 @@ We will then review the changes and review next steps for adding the dataset int ### Installing uv +<<<<<<< HEAD + +Install uv follow the guidelines in https://docs.astral.sh/uv/getting-started/installation/, it is recommended to use the standalone installation. +======= Dependencies and admin actions are done using `uv`. To Install uv follow the guidelines in https://docs.astral.sh/uv/getting-started/installation/, it is recommended to use the standalone installation. +>>>>>>> dev ### Building Project diff --git a/README.md b/README.md index f2928ac2..946b079f 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@
- +
---- @@ -12,10 +12,10 @@ We're looking to hire a postdoc with both Python library development and ML expe ## Overview AgML is a comprehensive library for agricultural machine learning. Currently, AgML provides -access to a wealth of public agricultural datasets for common agricultural deep learning tasks. In the future, AgML will provide ag-specific ML functionality related to data, training, and evaluation. Here's a conceptual diagram of the overall framework. +access to a wealth of public agricultural datasets for common agricultural deep learning tasks. In the future, AgML will provide ag-specific ML functionality related to data, training, and evaluation. Here's a conceptual diagram of the overall framework.- +
AgML supports both the [TensorFlow](https://www.tensorflow.org/) and [PyTorch](https://pytorch.org/) machine learning frameworks. @@ -45,7 +45,7 @@ loader = agml.data.AgMLDataLoader('apple_flower_segmentation') ``` You can then use the in-built processing methods to get the loader ready for your training and evaluation pipelines. This includes, but -is not limited to, batching data, shuffling data, splitting data into training, validation, and test sets, and applying transforms. +is not limited to, batching data, shuffling data, splitting data into training, validation, and test sets, and applying transforms. ```python import albumentations as A @@ -125,35 +125,35 @@ model.run_training(loader) | Dataset | Task | Number of Images | | :--- | ---: |-----------------:| -[bean_disease_uganda](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/bean_disease_uganda.md) | Image Classification | 1295 | -[carrot_weeds_germany](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/carrot_weeds_germany.md) | Semantic Segmentation | 60 | -[plant_seedlings_aarhus](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_seedlings_aarhus.md) | Image Classification | 5539 | -[soybean_weed_uav_brazil](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/soybean_weed_uav_brazil.md) | Image Classification | 15336 | -[sugarcane_damage_usa](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/sugarcane_damage_usa.md) | Image Classification | 153 | -[crop_weeds_greece](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/crop_weeds_greece.md) | Image Classification | 508 | -[sugarbeet_weed_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/sugarbeet_weed_segmentation.md) | Semantic Segmentation | 1931 | -[rangeland_weeds_australia](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/rangeland_weeds_australia.md) | Image Classification | 17509 | -[fruit_detection_worldwide](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/fruit_detection_worldwide.md) | Object Detection | 565 | -[leaf_counting_denmark](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/leaf_counting_denmark.md) | Image Classification | 9372 | -[apple_detection_usa](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_usa.md) | Object Detection | 2290 | -[mango_detection_australia](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/mango_detection_australia.md) | Object Detection | 1730 | -[apple_flower_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_flower_segmentation.md) | Semantic Segmentation | 148 | -[apple_segmentation_minnesota](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_segmentation_minnesota.md) | Semantic Segmentation | 670 | -[rice_seedling_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/rice_seedling_segmentation.md) | Semantic Segmentation | 224 | -[plant_village_classification](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_village_classification.md) | Image Classification | 55448 | -[autonomous_greenhouse_regression](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/autonomous_greenhouse_regression.md) | Image Regression | 389 | -[grape_detection_syntheticday](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_syntheticday.md) | Object Detection | 448 | -[grape_detection_californiaday](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_californiaday.md) | Object Detection | 126 | -[grape_detection_californianight](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_californianight.md) | Object Detection | 150 | -[guava_disease_pakistan](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/guava_disease_pakistan.md) | Image Classification | 306 | -[apple_detection_spain](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_spain.md) | Object Detection | 967 | -[apple_detection_drone_brazil](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_drone_brazil.md) | Object Detection | 689 | -[plant_doc_classification](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_doc_classification.md) | Image Classification | 2598 | -[plant_doc_detection](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/plant_doc_detection.md) | Object Detection | 2346 | -[wheat_head_counting](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/wheat_head_counting.md) | Object Detection | 6512 | -[peachpear_flower_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/peachpear_flower_segmentation.md) | Semantic Segmentation | 42 | -[red_grapes_and_leaves_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/red_grapes_and_leaves_segmentation.md) | Semantic Segmentation | 258 | -[white_grapes_and_leaves_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/white_grapes_and_leaves_segmentation.md) | Semantic Segmentation | 273 | +[bean_disease_uganda](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/bean_disease_uganda.md) | Image Classification | 1295 | +[carrot_weeds_germany](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/carrot_weeds_germany.md) | Semantic Segmentation | 60 | +[plant_seedlings_aarhus](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_seedlings_aarhus.md) | Image Classification | 5539 | +[soybean_weed_uav_brazil](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/soybean_weed_uav_brazil.md) | Image Classification | 15336 | +[sugarcane_damage_usa](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/sugarcane_damage_usa.md) | Image Classification | 153 | +[crop_weeds_greece](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/crop_weeds_greece.md) | Image Classification | 508 | +[sugarbeet_weed_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/sugarbeet_weed_segmentation.md) | Semantic Segmentation | 1931 | +[rangeland_weeds_australia](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/rangeland_weeds_australia.md) | Image Classification | 17509 | +[fruit_detection_worldwide](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/fruit_detection_worldwide.md) | Object Detection | 565 | +[leaf_counting_denmark](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/leaf_counting_denmark.md) | Image Classification | 9372 | +[apple_detection_usa](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_usa.md) | Object Detection | 2290 | +[mango_detection_australia](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/mango_detection_australia.md) | Object Detection | 1730 | +[apple_flower_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_flower_segmentation.md) | Semantic Segmentation | 148 | +[apple_segmentation_minnesota](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_segmentation_minnesota.md) | Semantic Segmentation | 670 | +[rice_seedling_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/rice_seedling_segmentation.md) | Semantic Segmentation | 224 | +[plant_village_classification](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_village_classification.md) | Image Classification | 55448 | +[autonomous_greenhouse_regression](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/autonomous_greenhouse_regression.md) | Image Regression | 389 | +[grape_detection_syntheticday](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_syntheticday.md) | Object Detection | 448 | +[grape_detection_californiaday](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_californiaday.md) | Object Detection | 126 | +[grape_detection_californianight](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/grape_detection_californianight.md) | Object Detection | 150 | +[guava_disease_pakistan](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/guava_disease_pakistan.md) | Image Classification | 306 | +[apple_detection_spain](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_spain.md) | Object Detection | 967 | +[apple_detection_drone_brazil](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/apple_detection_drone_brazil.md) | Object Detection | 689 | +[plant_doc_classification](https://github.com/Project-AgML/AgML/blob/dev/docs/datasets/plant_doc_classification.md) | Image Classification | 2598 | +[plant_doc_detection](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/plant_doc_detection.md) | Object Detection | 2346 | +[wheat_head_counting](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/wheat_head_counting.md) | Object Detection | 6512 | +[peachpear_flower_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/peachpear_flower_segmentation.md) | Semantic Segmentation | 42 | +[red_grapes_and_leaves_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/red_grapes_and_leaves_segmentation.md) | Semantic Segmentation | 258 | +[white_grapes_and_leaves_segmentation](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/white_grapes_and_leaves_segmentation.md) | Semantic Segmentation | 273 | [ghai_romaine_detection](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/ghai_romaine_detection.md) | Object Detection | 500 | [ghai_green_cabbage_detection](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/ghai_green_cabbage_detection.md) | Object Detection | 500 | [ghai_iceberg_lettuce_detection](https://github.com/Project-AgML/AgML/blob/main/docs/datasets/ghai_iceberg_lettuce_detection.md) | Object Detection | 500 | @@ -170,13 +170,13 @@ model.run_training(loader) ### Using Public Agricultural Data -AgML aims to provide easy access to a range of existing public agricultural datasets The core of AgML's public data pipeline is -[`AgMLDataLoader`](/agml/data/loader.py). You can use the `AgMLDataLoader` or `agml.data.download_public_dataset()` to download -the dataset locally from which point it will be automatically loaded from the disk on future runs. +AgML aims to provide easy access to a range of existing public agricultural datasets The core of AgML's public data pipeline is +[`AgMLDataLoader`](/agml/data/loader.py). You can use the `AgMLDataLoader` or `agml.data.download_public_dataset()` to download +the dataset locally from which point it will be automatically loaded from the disk on future runs. From this point, the data within the loader can be split into train/val/test sets, batched, have augmentations and transforms applied, and be converted into a training-ready dataset (including batching, tensor conversion, and image formatting). -To see the various ways in which you can use AgML datasets in your training pipelines, check out +To see the various ways in which you can use AgML datasets in your training pipelines, check out the [example notebook](/examples/AgML-Data.ipynb). ## Annotation Formats diff --git a/agml/data/loader.py b/agml/data/loader.py index bbf6f8d6..b0143acd 100644 --- a/agml/data/loader.py +++ b/agml/data/loader.py @@ -23,14 +23,24 @@ import numpy as np -from agml.backend.config import SUPER_BASE_DIR, data_save_path, synthetic_data_save_path +from agml.framework import AgMLSerializable +from agml.data.manager import DataManager +from agml.data.builder import DataBuilder +from agml.data.metadata import DatasetMetadata, make_metadata +from agml.data.exporters.yolo import export_yolo +from agml.utils.logging import log +from agml.utils.io import get_file_list, get_dir_list +from agml.utils.data import load_public_sources +from agml.utils.general import NoArgument, resolve_list_value +from agml.utils.random import inject_random_state +from agml.backend.config import data_save_path, synthetic_data_save_path, SUPER_BASE_DIR from agml.backend.experimental import AgMLExperimentalFeatureWrapper from agml.backend.tftorch import ( - StrictBackendError, - _add_dataset_to_mro, # noqa get_backend, set_backend, user_changed_backend, + StrictBackendError, + _add_dataset_to_mro, # noqa ) from agml.data.builder import DataBuilder from agml.data.exporters.yolo import export_yolo diff --git a/config/mkdocs.yml b/config/mkdocs.yml new file mode 100644 index 00000000..146afaf7 --- /dev/null +++ b/config/mkdocs.yml @@ -0,0 +1,189 @@ +site_name: "AgML" +site_description: "A comprehensive library for agricultural deep learning" +site_url: "" + +repo_url: "https://github.com/Project-AgML/AgML" +repo_name: "AgML" + +watch: + [ + ../config/mkdocs.yml, + ../README.md, + ../LICENSE, + ../CODE_OF_CONDUCT.md, + ../CONTRIBUTING.md, + ../agml, + ../docs, + ] + +copyright: Copyright © 2024 +edit_uri: edit/main/docs/ + +docs_dir: ../docs +site_dir: ../site + +use_directory_urls: false +validation: + omitted_files: warn + absolute_links: warn + unrecognized_links: warn + +nav: + - Home: + - Overview: index.md + - Changelog: changelog.md + - Credits: credits.md + - License: license.md + - Datasets: + - Dataset Listing: dataset_listing.md + - Datasets: datasets/ + # defer to gen-files + literate-nav + - API reference: + - AgML: reference/ + - Development: + - Contributing: development.md + - Code of Conduct: code_of_conduct.md + - Coverage report: coverage.md + +theme: + name: material + logo: assets/agml-logo.png + custom_dir: ../docs/overrides + features: + - announce.dismiss + - content.action.edit + - content.action.view + - content.code.annotate + - content.code.copy + - content.tooltips + - navigation.footer + - navigation.indexes + - navigation.sections + - navigation.tabs + - navigation.tabs.sticky + - navigation.top + - search.highlight + - search.suggest + - toc.follow + palette: + - media: "(prefers-color-scheme)" + toggle: + icon: material/brightness-auto + name: Switch to light mode + - media: "(prefers-color-scheme: light)" + scheme: default + primary: teal + accent: purple + toggle: + icon: material/weather-sunny + name: Switch to dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: black + accent: lime + toggle: + icon: material/weather-night + name: Switch to system preference + +extra_css: + - css/material.css + - css/mkdocstrings.css + +extra_javascript: + - js/feedback.js + +markdown_extensions: + - attr_list + - admonition + - callouts + - footnotes + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + - pymdownx.magiclink + - pymdownx.snippets: + base_path: + [ + !relative $config_dir, + README.md, + LICENSE, + CONTRIBUTING.md, + CODE_OF_CONDUCT.md, + scripts, + pyproject.toml, + ] + check_paths: true + + - pymdownx.superfences + - pymdownx.tabbed: + alternate_style: true + slugify: !!python/object/apply:pymdownx.slugs.slugify + kwds: + case: lower + - pymdownx.tasklist: + custom_checkbox: true + - toc: + permalink: true + +plugins: + - search + - markdown-exec + - gen-files: + scripts: + - ../scripts/docs/gen_ref_nav.py + - literate-nav: + nav_file: SUMMARY.md + - coverage + - mkdocstrings: + handlers: + python: + import: + - https://docs.python.org/3/objects.inv + paths: [../agml] + options: + docstring_options: + ignore_init_summary: true + docstring_section_style: list + filters: ["!^_"] + heading_level: 1 + inherited_members: true + merge_init_into_class: true + separate_signature: true + show_root_heading: true + show_root_full_path: false + show_signature_annotations: true + show_source: true + show_symbol_type_heading: true + show_symbol_type_toc: true + signature_crossrefs: true + summary: true + - git-revision-date-localized: + enabled: !ENV [DEPLOY, false] + enable_creation_date: true + type: timeago + - minify: + minify_html: !ENV [DEPLOY, false] + - group: + enabled: !ENV [MATERIAL_INSIDERS, false] + plugins: + - typeset + +extra: + social: + - icon: fontawesome/brands/github + link: https://github.com/Project-AgML/AgML + - icon: fontawesome/brands/python + link: https://pypi.org/project/agml/ + + analytics: + feedback: + title: Was this page helpful? + ratings: + - icon: material/emoticon-happy-outline + name: This page was helpful + data: 1 + note: Thanks for your feedback! + - icon: material/emoticon-sad-outline + name: This page could be improved + data: 0 + note: Let us know how we can improve this page. diff --git a/config/release_draft.yml b/config/release_draft.yml new file mode 100644 index 00000000..92f676d5 --- /dev/null +++ b/config/release_draft.yml @@ -0,0 +1,55 @@ +name-template: "v$RESOLVED_VERSION" +tag-template: "v$RESOLVED_VERSION" +change-template: "- $TITLE #$NUMBER [@$AUTHOR]" +change-template: '- $TITLE @$AUTHOR (#$NUMBER)' +change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks. + + +categories: + - title: "✨ Features" + labels: + - "feature" + - "enhancement" + - "✨" + - "⚡️" + - title: "🐛 Bug Fixes" + labels: + - "fix" + - "bugfix" + - "bug" + - "🐛" + - title: "📚 Documentation" + labels: + - "documentation" + - "docs" + - "📚" + - title: " 🚨 Continous Integration" + labels: + - "testing" + - "test" + - title: " 🔨 Maintance" + labels: + - "Maintenance" + +exclude-labels: + - "changelog: skip" + +version-resolver: + major: + labels: + - "major" + minor: + labels: + - "minor" + patch: + labels: + - "patch" + default: patch + +template: | + + ## AgML release v$RESOLVED_VERSION + + This version include the following changes + + $CHANGES diff --git a/figures/agml-framework.png b/docs/assets/agml-framework.png similarity index 100% rename from figures/agml-framework.png rename to docs/assets/agml-framework.png diff --git a/figures/agml-logo-wide.png b/docs/assets/agml-logo-wide.png similarity index 100% rename from figures/agml-logo-wide.png rename to docs/assets/agml-logo-wide.png diff --git a/figures/agml-logo.png b/docs/assets/agml-logo.png similarity index 100% rename from figures/agml-logo.png rename to docs/assets/agml-logo.png diff --git a/docs/code_of_conduct.md b/docs/code_of_conduct.md new file mode 100644 index 00000000..22f934ef --- /dev/null +++ b/docs/code_of_conduct.md @@ -0,0 +1,8 @@ +--- +hide: +- feedback +--- + +# Code of Conduct + +--8<-- "CODE_OF_CONDUCT.md" diff --git a/docs/credits.md b/docs/credits.md new file mode 100644 index 00000000..9322404b --- /dev/null +++ b/docs/credits.md @@ -0,0 +1,10 @@ +--- +hide: +- toc +--- + + +```python exec="yes" +--8<-- "docs/gen_credits.py" +``` + diff --git a/docs/css/material.css b/docs/css/material.css new file mode 100644 index 00000000..9e8c14a6 --- /dev/null +++ b/docs/css/material.css @@ -0,0 +1,4 @@ +/* More space at the bottom of the page. */ +.md-main__inner { + margin-bottom: 1.5rem; +} diff --git a/docs/css/mkdocstrings.css b/docs/css/mkdocstrings.css new file mode 100644 index 00000000..88c73575 --- /dev/null +++ b/docs/css/mkdocstrings.css @@ -0,0 +1,27 @@ +/* Indentation. */ +div.doc-contents:not(.first) { + padding-left: 25px; + border-left: .05rem solid var(--md-typeset-table-color); +} + +/* Mark external links as such. */ +a.external::after, +a.autorefs-external::after { + /* https://primer.style/octicons/arrow-up-right-24 */ + mask-image: url('data:image/svg+xml,'); + -webkit-mask-image: url('data:image/svg+xml,'); + content: ' '; + + display: inline-block; + vertical-align: middle; + position: relative; + + height: 1em; + width: 1em; + background-color: currentColor; +} + +a.external:hover::after, +a.autorefs-external:hover::after { + background-color: var(--md-accent-fg-color); +} \ No newline at end of file diff --git a/docs/dataset_listing.md b/docs/dataset_listing.md new file mode 100644 index 00000000..af6a1b58 --- /dev/null +++ b/docs/dataset_listing.md @@ -0,0 +1,10 @@ +--- +hide: +- toc +--- + + +```python exec="yes" +--8<-- "docs/gen_dataset_list.py" +``` + diff --git a/docs/datasets/apple_detection_drone_brazil.md b/docs/datasets/apple_detection_drone_brazil.md index ae81ad94..cd43b6ec 100644 --- a/docs/datasets/apple_detection_drone_brazil.md +++ b/docs/datasets/apple_detection_drone_brazil.md @@ -21,4 +21,4 @@ ## Examples -![Example Images for apple_detection_drone_brazil](https://github.com/Project-AgML/AgML/blob/main/docs/sample_images/apple_detection_drone_brazil_examples.png) \ No newline at end of file +![Example Images for apple_detection_drone_brazil](../sample_images/apple_detection_drone_brazil_examples.png) \ No newline at end of file diff --git a/docs/datasets/apple_detection_spain.md b/docs/datasets/apple_detection_spain.md index cda3e0a8..6f7a58cc 100644 --- a/docs/datasets/apple_detection_spain.md +++ b/docs/datasets/apple_detection_spain.md @@ -21,4 +21,4 @@ ## Examples -![Example Images for apple_detection_spain](https://github.com/Project-AgML/AgML/blob/main/docs/sample_images/apple_detection_spain_examples.png) \ No newline at end of file +![Example Images for apple_detection_spain](../sample_images/apple_detection_spain_examples.png) \ No newline at end of file diff --git a/docs/development.md b/docs/development.md new file mode 100644 index 00000000..7cea1648 --- /dev/null +++ b/docs/development.md @@ -0,0 +1,3 @@ + + +--8<-- "CONTRIBUTING.md" diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..8e6f2fb4 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,6 @@ +--- +hide: +- feedback +--- + +--8<-- "README.md" diff --git a/docs/js/feedback.js b/docs/js/feedback.js new file mode 100644 index 00000000..f97321a5 --- /dev/null +++ b/docs/js/feedback.js @@ -0,0 +1,14 @@ +const feedback = document.forms.feedback; +feedback.hidden = false; + +feedback.addEventListener("submit", function(ev) { + ev.preventDefault(); + const commentElement = document.getElementById("feedback"); + commentElement.style.display = "block"; + feedback.firstElementChild.disabled = true; + const data = ev.submitter.getAttribute("data-md-value"); + const note = feedback.querySelector(".md-feedback__note [data-md-value='" + data + "']"); + if (note) { + note.hidden = false; + } +}) diff --git a/docs/license.md b/docs/license.md new file mode 100644 index 00000000..cbc38905 --- /dev/null +++ b/docs/license.md @@ -0,0 +1,8 @@ +--- +hide: +- feedback +--- + +# License + +--8<-- "LICENSE" diff --git a/docs/overrides/partials/comments.html b/docs/overrides/partials/comments.html new file mode 100644 index 00000000..1be8df33 --- /dev/null +++ b/docs/overrides/partials/comments.html @@ -0,0 +1,57 @@ + + + \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 19e707f4..df3d07f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,3 +70,19 @@ dev-dependencies = [ "coverage>=7.6.1", "interrogate>=1.7.0", ] + +[dependency-groups] +docs = [ + "markdown-callouts>=0.4.0", + "markdown-exec>=1.9.3", + "mkdocs-coverage>=1.1.0", + "mkdocs-gen-files>=0.5.0", + "mkdocs-git-revision-date-localized-plugin>=1.3.0", + "mkdocs-literate-nav>=0.6.1", + "mkdocs-material>=9.5.45", + "mkdocs-minify-plugin>=0.8.0", + "pymdown-extensions>=10.12", + "mkdocs-jupyter>=0.24.8", + "mkdocs>=1.6.1", + "mkdocstrings[python]>=0.26.1", +] diff --git a/scripts/docs/gen_credits.py b/scripts/docs/gen_credits.py new file mode 100644 index 00000000..e61d92fd --- /dev/null +++ b/scripts/docs/gen_credits.py @@ -0,0 +1,177 @@ +"""Script to generate the project's credits.""" + +from __future__ import annotations + +import os +import sys +from collections import defaultdict +from importlib.metadata import distributions +from itertools import chain +from pathlib import Path +from textwrap import dedent +from typing import Dict, Iterable, Union + +from jinja2 import StrictUndefined +from jinja2.sandbox import SandboxedEnvironment +from packaging.requirements import Requirement + +# TODO: Remove once support for Python 3.10 is dropped. +if sys.version_info >= (3, 11): + import tomllib +else: + import tomli as tomllib + +project_dir = Path(os.getenv("MKDOCS_CONFIG_DIR", ".")) +with project_dir.joinpath("../pyproject.toml").open("rb") as pyproject_file: + pyproject = tomllib.load(pyproject_file) +project = pyproject["project"] +project_name = project["name"] +devdeps = [dep for dep in pyproject["tool"]["uv"]["dev-dependencies"] if not dep.startswith("-e")] + +PackageMetadata = Dict[str, Union[str, Iterable[str]]] +Metadata = Dict[str, PackageMetadata] + + +def _merge_fields(metadata: dict) -> PackageMetadata: + fields = defaultdict(list) + for header, value in metadata.items(): + fields[header.lower()].append(value.strip()) + return { + field: value if len(value) > 1 or field in ("classifier", "requires-dist") else value[0] + for field, value in fields.items() + } + + +def _norm_name(name: str) -> str: + return name.replace("_", "-").replace(".", "-").lower() + + +def _requirements(deps: list[str]) -> dict[str, Requirement]: + return {_norm_name((req := Requirement(dep)).name): req for dep in deps} + + +def _extra_marker(req: Requirement) -> str | None: + if not req.marker: + return None + try: + return next(marker[2].value for marker in req.marker._markers if getattr(marker[0], "value", None) == "extra") + except StopIteration: + return None + + +def _get_metadata() -> Metadata: + metadata = {} + for pkg in distributions(): + name = _norm_name(pkg.name) # type: ignore[attr-defined,unused-ignore] + metadata[name] = _merge_fields(pkg.metadata) # type: ignore[arg-type] + metadata[name]["spec"] = set() + metadata[name]["extras"] = set() + metadata[name].setdefault("summary", "") + _set_license(metadata[name]) + return metadata + + +def _set_license(metadata: PackageMetadata) -> None: + license_field = metadata.get("license-expression", metadata.get("license", "")) + license_name = license_field if isinstance(license_field, str) else " + ".join(license_field) + check_classifiers = license_name in ("UNKNOWN", "Dual License", "") or license_name.count("\n") + if check_classifiers: + license_names = [] + for classifier in metadata["classifier"]: + if classifier.startswith("License ::"): + license_names.append(classifier.rsplit("::", 1)[1].strip()) + license_name = " + ".join(license_names) + metadata["license"] = license_name or "?" + + +def _get_deps(base_deps: dict[str, Requirement], metadata: Metadata) -> Metadata: + deps = {} + for dep_name, dep_req in base_deps.items(): + if dep_name not in metadata or dep_name == "agml": + continue + metadata[dep_name]["spec"] |= {str(spec) for spec in dep_req.specifier} # type: ignore[operator] + metadata[dep_name]["extras"] |= dep_req.extras # type: ignore[operator] + deps[dep_name] = metadata[dep_name] + + again = True + while again: + again = False + for pkg_name in metadata: + if pkg_name in deps: + for pkg_dependency in metadata[pkg_name].get("requires-dist", []): + requirement = Requirement(pkg_dependency) + dep_name = _norm_name(requirement.name) + extra_marker = _extra_marker(requirement) + if ( + dep_name in metadata + and dep_name not in deps + and dep_name != project["name"] + and (not extra_marker or extra_marker in deps[pkg_name]["extras"]) + ): + metadata[dep_name]["spec"] |= {str(spec) for spec in requirement.specifier} # type: ignore[operator] + deps[dep_name] = metadata[dep_name] + again = True + + return deps + + +def _render_credits() -> str: + metadata = _get_metadata() + dev_dependencies = _get_deps(_requirements(devdeps), metadata) + prod_dependencies = _get_deps( + _requirements( + chain( # type: ignore[arg-type] + project.get("dependencies", []), + chain(*project.get("optional-dependencies", {}).values()), + ), + ), + metadata, + ) + + template_data = { + "project_name": project_name, + "prod_dependencies": sorted(prod_dependencies.values(), key=lambda dep: str(dep["name"]).lower()), + "dev_dependencies": sorted(dev_dependencies.values(), key=lambda dep: str(dep["name"]).lower()), + "more_credits": "", + } + template_text = dedent( + """ + # Credits + + These projects were used to build *{{ project_name }}*. **Thank you!** + + [Python](https://www.python.org/) | + [uv](https://github.com/astral-sh/uv) | + + {% macro dep_line(dep) -%} + [{{ dep.name }}](https://pypi.org/project/{{ dep.name }}/) | {{ dep.summary }} | {{ ("`" ~ dep.spec|sort(reverse=True)|join(", ") ~ "`") if dep.spec else "" }} | `{{ dep.version }}` | {{ dep.license }} + {%- endmacro %} + + {% if prod_dependencies -%} + ### Runtime dependencies + + Project | Summary | Version (accepted) | Version (last resolved) | License + ------- | ------- | ------------------ | ----------------------- | ------- + {% for dep in prod_dependencies -%} + {{ dep_line(dep) }} + {% endfor %} + + {% endif -%} + {% if dev_dependencies -%} + ### Development dependencies + + Project | Summary | Version (accepted) | Version (last resolved) | License + ------- | ------- | ------------------ | ----------------------- | ------- + {% for dep in dev_dependencies -%} + {{ dep_line(dep) }} + {% endfor %} + + {% endif -%} + {% if more_credits %}**[More credits from the author]({{ more_credits }})**{% endif %} + """, + ) + jinja_env = SandboxedEnvironment(undefined=StrictUndefined) + return jinja_env.from_string(template_text).render(**template_data) + + +print(_render_credits()) diff --git a/scripts/docs/gen_dataset_list.py b/scripts/docs/gen_dataset_list.py new file mode 100644 index 00000000..7ee76830 --- /dev/null +++ b/scripts/docs/gen_dataset_list.py @@ -0,0 +1,47 @@ +import json +from textwrap import dedent +from importlib import resources + + +from jinja2.sandbox import SandboxedEnvironment +from jinja2 import StrictUndefined +# Check whether any dataset has been added that needs information updated (we do this +# by checking for any datasets in the `public_datasources.json` file that don't have +# corresponding information for the dataset statistics or other properties like shape). + + +def _render_dataset() -> str: + public_datasets = json.load(resources.files("agml._assets").joinpath("public_datasources.json").open("r")) + + public_datasets = { + "datasets": sorted( + [(value | {"dataset_name": key}) for key, value in public_datasets.items()], + key=lambda dep: str(dep["dataset_name"]).lower(), + ) + } + # return public_datasets + + template_datasets = dedent( + """ + + {% macro dat_line(dat) -%} + [{{dat.dataset_name}}](datasets/{{dat.dataset_name}}.html) | {{ dat.ml_task }} | {{ dat.n_images }} | {{ dat.docs_url }} | + {%- endmacro %} + + {% if datasets -%} + + ## Public Dataset Listing + + | Dataset | Task | Number of Images | Documentation| + | :--- | :---: |-----------:| :----| + {% for dataset in datasets -%} + {{ dat_line(dataset) }} + {% endfor %} + {% endif %} + """, + ) + jinja_env = SandboxedEnvironment(undefined=StrictUndefined) + return jinja_env.from_string(template_datasets).render(**public_datasets) + + +print(_render_dataset()) diff --git a/scripts/docs/gen_ref_nav.py b/scripts/docs/gen_ref_nav.py new file mode 100644 index 00000000..6939e864 --- /dev/null +++ b/scripts/docs/gen_ref_nav.py @@ -0,0 +1,37 @@ +"""Generate the code reference pages and navigation.""" + +from pathlib import Path + +import mkdocs_gen_files + +nav = mkdocs_gen_files.Nav() +mod_symbol = '
'
+
+root = Path(__file__).parent.parent
+src = root / "src"
+
+for path in sorted(src.rglob("*.py")):
+ module_path = path.relative_to(src).with_suffix("")
+ doc_path = path.relative_to(src).with_suffix(".md")
+ full_doc_path = Path("reference", doc_path)
+
+ parts = tuple(module_path.parts)
+
+ if parts[-1] == "__init__":
+ parts = parts[:-1]
+ doc_path = doc_path.with_name("index.md")
+ full_doc_path = full_doc_path.with_name("index.md")
+ elif parts[-1].startswith("_"):
+ continue
+
+ nav_parts = [f"{mod_symbol} {part}" for part in parts]
+ nav[tuple(nav_parts)] = doc_path.as_posix()
+
+ with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+ ident = ".".join(parts)
+ fd.write(f"---\ntitle: {ident}\n---\n\n::: {ident}")
+
+ mkdocs_gen_files.set_edit_path(full_doc_path, ".." / path.relative_to(root))
+
+with mkdocs_gen_files.open("reference/SUMMARY.md", "w") as nav_file:
+ nav_file.writelines(nav.build_literate_nav())
diff --git a/uv.lock b/uv.lock
index d2b2ff8c..95a3e9e3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -47,6 +47,20 @@ dev = [
{ name = "scikit-image" },
{ name = "shapely" },
]
+docs = [
+ { name = "markdown-callouts" },
+ { name = "markdown-exec" },
+ { name = "mkdocs" },
+ { name = "mkdocs-coverage" },
+ { name = "mkdocs-gen-files" },
+ { name = "mkdocs-git-revision-date-localized-plugin" },
+ { name = "mkdocs-jupyter" },
+ { name = "mkdocs-literate-nav" },
+ { name = "mkdocs-material" },
+ { name = "mkdocs-minify-plugin" },
+ { name = "mkdocstrings", extra = ["python"] },
+ { name = "pymdown-extensions" },
+]
[package.metadata]
requires-dist = [
@@ -77,6 +91,20 @@ dev = [
{ name = "scikit-image", specifier = ">=0.21.0" },
{ name = "shapely", specifier = ">=2.0.6" },
]
+docs = [
+ { name = "markdown-callouts", specifier = ">=0.4.0" },
+ { name = "markdown-exec", specifier = ">=1.9.3" },
+ { name = "mkdocs", specifier = ">=1.6.1" },
+ { name = "mkdocs-coverage", specifier = ">=1.1.0" },
+ { name = "mkdocs-gen-files", specifier = ">=0.5.0" },
+ { name = "mkdocs-git-revision-date-localized-plugin", specifier = ">=1.3.0" },
+ { name = "mkdocs-jupyter", specifier = ">=0.24.8" },
+ { name = "mkdocs-literate-nav", specifier = ">=0.6.1" },
+ { name = "mkdocs-material", specifier = ">=9.5.45" },
+ { name = "mkdocs-minify-plugin", specifier = ">=0.8.0" },
+ { name = "mkdocstrings", extras = ["python"], specifier = ">=0.26.1" },
+ { name = "pymdown-extensions", specifier = ">=10.12" },
+]
[[package]]
name = "albucore"
@@ -124,6 +152,40 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643 },
]
+[[package]]
+name = "appnope"
+version = "0.1.4"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/35/5d/752690df9ef5b76e169e68d6a129fa6d08a7100ca7f754c89495db3c6019/appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee", size = 4170 }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/81/29/5ecc3a15d5a33e31b26c11426c45c501e439cb865d0bff96315d86443b78/appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c", size = 4321 },
+]
+
+[[package]]
+name = "asttokens"
+version = "2.4.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "six" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/45/1d/f03bcb60c4a3212e15f99a56085d93093a497718adf828d050b9d675da81/asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0", size = 62284 }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/45/86/4736ac618d82a20d87d2f92ae19441ebc7ac9e7a581d7e58bbe79233b24a/asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24", size = 27764 },
+]
+
+[[package]]
+name = "astunparse"
+version = "1.6.3"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "six", marker = "python_full_version < '3.9'" },
+ { name = "wheel", marker = "python_full_version < '3.9'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/f3/af/4182184d3c338792894f34a62672919db7ca008c89abee9b564dd34d8029/astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872", size = 18290 }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/2b/03/13dde6512ad7b4557eb792fbcf0c653af6076b81e5941d36ec61f7ce6028/astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8", size = 12732 },
+]
+
[[package]]
name = "attrs"
version = "24.2.0"
@@ -133,6 +195,52 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/6a/21/5b6702a7f963e95456c0de2d495f67bf5fd62840ac655dc451586d23d39a/attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2", size = 63001 },
]
+[[package]]
+name = "babel"
+version = "2.16.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "pytz", marker = "python_full_version < '3.9'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/2a/74/f1bc80f23eeba13393b7222b11d95ca3af2c1e28edca18af487137eefed9/babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316", size = 9348104 }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/ed/20/bc79bc575ba2e2a7f70e8a1155618bb1301eaa5132a8271373a6903f73f8/babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b", size = 9587599 },
+]
+
+[[package]]
+name = "backcall"
+version = "0.2.0"
+source = { registry = "https://pypi.org/simple" }
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