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Dynamic Foraging test suite

fixes nan bias value #386

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fixes nan bias value

fixes nan bias value #386

Workflow file for this run

.github/workflows/dynamic-foraging-cicd.yml at 1e79074
name: Dynamic Foraging test suite
on:
pull_request:
push:
branches:
- main
- dev*
- release*
release:
types: [published]
workflow_dispatch:
jobs:
# ╔──────────────────────────╗
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tests:
runs-on: windows-latest
name: Dynamic Foraging unit tests
steps:
- uses: actions/checkout@v6
- uses: astral-sh/setup-uv@v8.1.0
with:
enable-cache: true
- name: Install python dependencies
run: uv sync --all-packages
- name: Run ruff format
run: uv run ruff format --check
- name: Run ruff check
run: uv run ruff check
- name: Run codespell
run: uv run codespell
- name: Setup .NET Core SDK
uses: actions/setup-dotnet@v5
with:
dotnet-version: 8.x
- name: Restore dotnet tools
run: dotnet tool restore
- name: Setup Bonsai environment
working-directory: ./.bonsai
run: ./setup.ps1
- name: Run python unit tests
run: uv run python -m unittest
- name: Regenerate all schemas
run: |
uv run dynamic-foraging regenerate
uv run --package aind-behavior-dynamic-foraging-curricula python -m aind_behavior_dynamic_foraging_curricula._schema
- name: Build all packages
run: uv build --all-packages
- name: Check for uncommitted changes
shell: bash
run: |
git config --global core.safecrlf false
git diff --exit-code || (echo "Untracked changes found" && exit 1)
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# │ | __/| |_| | |_) | | | (__ | _ < __/ | __/ (_| \__ \ __/ │
# │ |_| \__,_|_.__/|_|_|\___| |_| \_\___|_|\___|\__,_|___/\___| │
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# ╚─────────────────────────────────────────────────────────────────╝
prepare-release:
runs-on: windows-latest
name: Set version and regenerate schemas
needs: tests
if: github.event_name == 'release' && github.event.action == 'published'
outputs:
version: ${{ steps.get_version.outputs.version }}
steps:
- uses: actions/checkout@v5
with:
fetch-depth: 0
ref: main
# PAT from an admin account so the version-bump commit and tag
# push below can bypass the branch ruleset protecting `main`.
token: ${{ secrets.RELEASE_PAT }}
- uses: astral-sh/setup-uv@v8.1.0
with:
enable-cache: true
- name: Extract version from tag
id: get_version
shell: bash
run: |
version=$(echo "${{ github.event.release.tag_name }}" | sed 's/^v//')
echo "version=$version" >> $GITHUB_OUTPUT
echo "Setting version to: $version"
- name: Validate version for all packages
shell: bash
run: |
for pkg in aind-behavior-dynamic-foraging aind-behavior-dynamic-foraging-curricula; do
uv version ${{ steps.get_version.outputs.version }} --package $pkg --dry-run
done
- name: Set version for all packages
shell: bash
run: |
for pkg in aind-behavior-dynamic-foraging aind-behavior-dynamic-foraging-curricula; do
uv version ${{ steps.get_version.outputs.version }} --package $pkg
done
- name: Regenerate all schemas
run: |
uv run dynamic-foraging regenerate
uv run --package aind-behavior-dynamic-foraging-curricula python -m aind_behavior_dynamic_foraging_curricula._schema
- name: Build all packages
run: uv build --all-packages
- name: Upload wheels as artifact
uses: actions/upload-artifact@v4
with:
name: dist
path: dist/
retention-days: 1
- name: Commit version and schema changes
shell: bash
run: |
git config --global user.name "github-actions[bot]"
git config --global user.email "github-actions[bot]@users.noreply.github.com"
git add .
git diff --cached --quiet && echo "No changes to commit" && exit 0
git commit -m "Set version ${{ steps.get_version.outputs.version }} and regenerate schemas [skip ci]"
git push origin main
# Move the release tag to point to this new commit
git tag -fa "${{ github.event.release.tag_name }}" -m "${{ github.event.release.tag_name }}"
git push origin "${{ github.event.release.tag_name }}" --force
# ╔────────────────────────────────────────╗
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# │ |_| \__,_|_.__/|_|_|___/_| |_| │
# │ │
# ╚────────────────────────────────────────╝
publish-to-pypi:
runs-on: ubuntu-latest
name: Publish to PyPI
needs: prepare-release
# disabled for now
if: false
steps:
- name: Download wheels artifact
uses: actions/download-artifact@v4
with:
name: dist
path: dist/
- uses: astral-sh/setup-uv@v8.1.0
with:
enable-cache: true
- name: Publish to PyPI
run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}
- name: Upload wheels to GitHub release
uses: softprops/action-gh-release@v2
with:
files: dist/*
# ╔─────────────────────────╗
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# ╚─────────────────────────╝
build-docs:
name: Build and deploy documentation to GitHub Pages
runs-on: ubuntu-latest
needs: [tests, prepare-release]
if: |
always()
&& needs.tests.result == 'success'
&& (needs.prepare-release.result == 'success' || needs.prepare-release.result == 'skipped')
&& (
(github.event_name == 'release' && !github.event.release.prerelease)
|| github.event_name == 'workflow_dispatch'
)
steps:
- name: Checkout repository
uses: actions/checkout@v6
with:
ref: main
- name: Install uv
uses: astral-sh/setup-uv@v8.1.0
with:
enable-cache: true
- name: Setup Graphviz
uses: ts-graphviz/setup-graphviz@v2
- name: Install docs group of dependencies
run: uv sync --group docs
- name: Build Sphinx documentation
working-directory: docs
run: uv run sphinx-build -b html . ../_build/html
- name: Deploy to GitHub Pages
uses: peaceiris/actions-gh-pages@v4
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: _build/html
force_orphan: true