-
Notifications
You must be signed in to change notification settings - Fork 97
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'develop' of https://github.com/talmolab/sleap into eliz…
…abeth/update-python-and-dependencies
- Loading branch information
Showing
11 changed files
with
611 additions
and
237 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,179 @@ | ||
| # Run tests using built conda packages. | ||
| name: Build Conda CI (no upload) | ||
|
|
||
| # Run when changes to pip wheel | ||
| on: | ||
| push: | ||
| paths: | ||
| - ".conda/meta.yaml" | ||
| - ".conda_mac/meta.yaml" | ||
| - "setup.py" | ||
| - "requirements.txt" | ||
| - "dev_requirements.txt" | ||
| - "environment_build.yml" | ||
| - ".github/workflows/build_conda_ci.yml" | ||
|
|
||
| # If RUN_BUILD_JOB is set to true, then RUN_ID will be overwritten to the current run id | ||
| env: | ||
| RUN_BUILD_JOB: true | ||
| RUN_ID: 10713717594 # Only used if RUN_BUILD_JOB is false (to dowload build artifact) | ||
|
|
||
| jobs: | ||
| build: | ||
| name: Build package from push (${{ matrix.os }}) | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: ["windows-2022", "ubuntu-22.04", "macos-14"] | ||
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategymatrixinclude | ||
| include: | ||
| # Use these variables as defaults | ||
| - condarc: .conda/condarc.yaml | ||
| - conda-folder: .conda | ||
| - pyver: "3.10" | ||
| - build-prefix: win | ||
| - os: "ubuntu-22.04" | ||
| build-prefix: linux | ||
| # Use special condarc if macos | ||
| - os: "macos-14" | ||
| condarc: .conda_mac/condarc.yaml | ||
| conda-folder: .conda_mac | ||
| build-prefix: osx | ||
|
|
||
| steps: | ||
| # Setup | ||
| - name: Checkout | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Setup Miniconda | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| uses: conda-incubator/[email protected] | ||
| with: | ||
| miniforge-version: latest | ||
| condarc-file: ${{ matrix.condarc }} | ||
| python-version: ${{ matrix.pyver }} | ||
| environment-file: environment_build.yml | ||
| activate-environment: sleap_ci | ||
| conda-solver: "libmamba" | ||
|
|
||
| - name: Print build environment info | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| shell: bash -l {0} | ||
| run: | | ||
| which python | ||
| conda list | ||
| pip freeze | ||
| # Build conda package | ||
| - name: Build conda package | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda build ${{ matrix.conda-folder }} --output-folder build | ||
| # Upload artifact "tests" can use it | ||
| - name: Upload conda package artifact | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: sleap-build-${{ matrix.build-prefix }} | ||
| path: build # Upload entire build directory | ||
| retention-days: 1 | ||
| overwrite: true | ||
|
|
||
| tests: | ||
| name: Run tests using package (${{ matrix.os }}) | ||
| runs-on: ${{ matrix.os }} | ||
| needs: build # Ensure the build job has completed before starting this job. | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: ["windows-2022", "ubuntu-22.04", "macos-14"] | ||
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategymatrixinclude | ||
| include: | ||
| # Default values | ||
| - build-prefix: win | ||
| - build-suffix: 64 | ||
| - test_args: pytest --durations=-1 tests/ | ||
| - condarc: .conda/condarc.yaml | ||
| - pyver: "3.10" | ||
| - conda-channels: -c conda-forge -c nvidia -c anaconda | ||
| # Ubuntu specific values | ||
| - os: ubuntu-22.04 | ||
| build-prefix: linux | ||
| # Otherwise core dumped in github actions | ||
| test_args: | | ||
| sudo apt install xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 | ||
| sudo Xvfb :1 -screen 0 1024x768x24 </dev/null & | ||
| export DISPLAY=":1" | ||
| pytest tests -k 'not exclude_from_linux_pip_test' | ||
| # Use special condarc if macos | ||
| - os: "macos-14" | ||
| build-prefix: osx | ||
| build-suffix: arm64 | ||
| condarc: .conda_mac/condarc.yaml | ||
| conda-channels: -c conda-forge -c anaconda | ||
|
|
||
| steps: | ||
| - name: Checkout repo | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.pyver }} | ||
|
|
||
| - name: Use current run id for conda package download | ||
| shell: bash -l {0} | ||
| if: env.RUN_BUILD_JOB == 'true' | ||
| run: echo "RUN_ID=${{ github.run_id }}" >> $GITHUB_ENV | ||
|
|
||
| # https://github.com/actions/download-artifact?tab=readme-ov-file#usage | ||
| - name: Download conda package artifact | ||
| uses: actions/download-artifact@v4 | ||
| id: download | ||
| with: | ||
| name: sleap-build-${{ matrix.build-prefix }} | ||
| path: build | ||
| run-id: ${{ env.RUN_ID }} | ||
| github-token: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| - name: List items in current directory | ||
| run: | | ||
| ls . | ||
| ls -R build | ||
| - name: Setup Miniconda | ||
| uses: conda-incubator/[email protected] | ||
| with: | ||
| miniforge-version: latest | ||
| condarc-file: ${{ matrix.condarc }} | ||
| python-version: ${{ matrix.pyver }} | ||
| conda-solver: "libmamba" | ||
|
|
||
| - name: Create conda environment | ||
| shell: bash -l {0} | ||
| run: conda create sleap -y -n sleap_ci -c ./build ${{ matrix.conda-channels }} | ||
|
|
||
| - name: Install packages for testing | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda activate sleap_ci | ||
| pip install -r "dev_requirements.txt" | ||
| # Note: "conda activate" does not persist across steps | ||
| - name: Print environment info | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda activate sleap_ci | ||
| conda info | ||
| conda list | ||
| pip freeze | ||
| - name: Test package | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda activate sleap_ci | ||
| ${{ matrix.test_args}} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| name: Reusable Comment Workflow | ||
|
|
||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| subject_id: | ||
| required: true | ||
| type: string | ||
| body_prefix: | ||
| required: true | ||
| type: string | ||
| comment_type: | ||
| required: true | ||
| type: string | ||
|
|
||
| jobs: | ||
| comment: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Post a comment | ||
| uses: actions/github-script@v6 | ||
| with: | ||
| script: | | ||
| const { owner, repo } = context.repo; | ||
| const subject_id = '${{ inputs.subject_id }}'; | ||
| const comment_type = '${{ inputs.comment_type }}'; | ||
| const baseBody = ` | ||
| We appreciate your input and will review it soon. | ||
| > [!WARNING] | ||
| > A friendly reminder that this is a public forum. Please be cautious when clicking links, downloading files, or running scripts posted by others. | ||
| > | ||
| > - Always verify the credibility of links and code. | ||
| > - Avoid running scripts or installing files from untrusted sources. | ||
| > - If you're unsure, ask for clarification before proceeding. | ||
| Stay safe and happy SLEAPing! | ||
| Best regards, | ||
| The Team | ||
| `; | ||
| const body = `${{ inputs.body_prefix }}\n\n${baseBody}`; | ||
| const mutation = comment_type === 'discussion' | ||
| ? ` | ||
| mutation($discussionId: ID!, $body: String!) { | ||
| addDiscussionComment(input: {discussionId: $discussionId, body: $body}) { | ||
| comment { | ||
| id | ||
| } | ||
| } | ||
| } | ||
| ` | ||
| : ` | ||
| mutation($issueId: ID!, $body: String!) { | ||
| addComment(input: {subjectId: $issueId, body: $body}) { | ||
| commentEdge { | ||
| node { | ||
| id | ||
| body | ||
| } | ||
| } | ||
| } | ||
| } | ||
| `; | ||
| const variables = comment_type === 'discussion' | ||
| ? { discussionId: subject_id, body: body.trim() } | ||
| : { issueId: subject_id, body: body.trim() }; | ||
| await github.graphql(mutation, variables); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: Comment on New Discussions and Issues | ||
|
|
||
| on: | ||
| discussion: | ||
| types: [created] | ||
| issues: | ||
| types: [opened] | ||
|
|
||
| jobs: | ||
| comment_on_discussion: | ||
| if: github.event_name == 'discussion' | ||
| uses: ./.github/workflows/comment-template.yml | ||
| with: | ||
| subject_id: ${{ github.event.discussion.node_id }} | ||
| body_prefix: "Thank you for starting a new discussion!" | ||
| comment_type: "discussion" | ||
|
|
||
| comment_on_issue: | ||
| if: github.event_name == 'issues' | ||
| uses: ./.github/workflows/comment-template.yml | ||
| with: | ||
| subject_id: ${{ github.event.issue.node_id }} | ||
| body_prefix: "Thank you for opening a new issue!" | ||
| comment_type: "issue" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.