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[CI] GitHub Actions workflows and GitLab CI example script
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| Original file line number | Diff line number | Diff line change |
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| ## Disclaimer - This GitHub Actions workflow runs all the tests for changed pipelines. | ||
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| # Name the workflow | ||
| name: pipeline_tests | ||
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| # Define when it runs (on PR when code for a pipeline changes) | ||
| on: | ||
| pull_request: | ||
| paths: | ||
| - 'narps_open/pipelines/**' | ||
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| # Jobs that define the workflow | ||
| jobs: | ||
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| # A job to list the tests to be run | ||
| identify-tests: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| tests: ${{ steps.identify.outputs.tests }} | ||
| steps: | ||
| - name: Checkout main branch for comparison | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: main | ||
| fetch-depth: 0 | ||
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| - name: Checkout current branch | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
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| - name: Create a list of tests for changed pipelines | ||
| id: identify | ||
| run: | | ||
| # Loop through modified files | ||
| for file in $(git diff --name-only remotes/origin/main...$GITHUB_SHA) | ||
| do | ||
| # List team id corresponding to team_* files | ||
| if [[ "$file" =~ .*"narps_open/pipelines/team_".* ]]; then | ||
| echo "Modified pipeline = $file" | ||
| tmp=${file#*"team_"} # remove prefix ending in "team_" | ||
| team_id=${tmp%".py"*} # remove suffix starting with ".py" | ||
| # Populate the list of test files | ||
| test_files="$test_files tests/pipelines/test_team_$team_id.py" | ||
| fi | ||
| done | ||
| # Send the test list as job output | ||
| echo "tests=$test_files" >> $GITHUB_OUTPUT | ||
| # A job to run the identified tests | ||
| pytest: | ||
| needs: identify-tests | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Set up Python 3.9 | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: 3.9 | ||
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| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pytest | ||
| pip install . | ||
| - name: Collect tests with pytest | ||
| run: pytest --collect-only -q ${{ needs.identify-tests.outputs.tests }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| ## Disclaimer - This GitHub Actions workflow runs all the changed tests for the project. | ||
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| # Name the workflow | ||
| name: test_changes | ||
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| # Define when it runs (on PR when a test changes) | ||
| on: | ||
| pull_request: | ||
| paths: | ||
| - 'tests/**' | ||
|
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| # Jobs that define the workflow | ||
| jobs: | ||
|
|
||
| # A job to list the tests to be run | ||
| pytest: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout main branch for comparison | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: main | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Checkout current branch | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Create a list of tests for changed tests | ||
| id: identify | ||
| run: | | ||
| echo "tests=$(git diff --name-only remotes/origin/main...$GITHUB_SHA)" >> $GITHUB_OUTPUT | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pytest | ||
| pip install . | ||
| - name: Collect tests with pytest | ||
| run: pytest --collect-only -q ${{ steps.identify.outputs.tests }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| ## Disclaimer - This GitHub Actions workflow runs all the unit tests for the project. | ||
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| # Name the workflow | ||
| name: unit_testing | ||
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| # Define when it runs (on PR when narps_open files change) | ||
| on: | ||
| pull_request: | ||
| paths: | ||
| - 'narps_open/**' | ||
| - '!narps_open/pipelines/**' | ||
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| # Jobs that define the workflow | ||
| jobs: | ||
| # Name of the job running unit tests | ||
| pytest: | ||
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| # Define the runner for this job | ||
| runs-on: ubuntu-latest | ||
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| # Steps that define the job | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Set up Python 3.9 | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: 3.9 | ||
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| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pytest | ||
| pip install . | ||
| - name: Collect tests with pytest | ||
| run: | | ||
| pytest --collect-only -q --ignore=tests/pipelines/ tests/ |
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| Original file line number | Diff line number | Diff line change |
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| ## Disclaimer - This GitLab CI script allow contributors to perform CI on | ||
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| # We assume the runner uses Docker as executor | ||
| # We assume that the following images are available on the system : | ||
| # - elodiegermani/open_pipeline | ||
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| default: | ||
| # Run all scripts in a docker container based on this image | ||
| image: elodiegermani/open_pipeline | ||
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| before_script: | ||
| # Activate conda virtual environment | ||
| - source activate neuro | ||
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| # Install the narps_open python package from the source code | ||
| - pip install . | ||
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| stages: | ||
| - code_quality | ||
| - testing | ||
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| # Static analysis of the project's code | ||
| pylint_job: | ||
| stage: code_quality | ||
| script: | ||
| # Install pylint | ||
| - pip install pylint | ||
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| # Run pylint | ||
| - pylint --exit-zero narps_open > pylint_report_narps_open.txt | ||
| - pylint --exit-zero tests > pylint_report_tests.txt | ||
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| artifacts: | ||
| when: always | ||
| paths: | ||
| - pylint_report_narps_open.txt | ||
| - pylint_report_tests.txt | ||
| - todos_narps_open.txt | ||
| - todos_tests.txt | ||
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| # Running tests for narps_open (except pipelines) | ||
| unit_tests-job: | ||
| stage: testing | ||
| script: | ||
| # Install pytest & coverage | ||
| - pip install pytest pytest-cov | ||
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| # Run tests and produce reports | ||
| - coverage run -m pytest --junit-xml=pytest_report.xml --ignore=tests/pipelines/ tests/ | ||
| - coverage report | ||
| - coverage xml | ||
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| artifacts: | ||
| when: on_success | ||
| reports: | ||
| junit: pytest_report.xml | ||
| coverage_report: | ||
| coverage_format: cobertura | ||
| path: coverage.xml | ||
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| rules: | ||
| # If something changed in narps_open (except in narps_open/pipelines) | ||
| - if: $CI_COMMIT_BRANCH | ||
| changes: | ||
| compare_to: 'refs/heads/main' | ||
| paths: | ||
| - 'narps_open/(?!pipelines)*' | ||
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| # Running tests for pipelines | ||
| pipeline_tests-job: | ||
| stage: testing | ||
| variables: | ||
| PIPELINES_TEST_FILES : "" | ||
| #GIT_STRATEGY: clone # So that we can access the main branch for git diff purpose | ||
| script: | ||
| # Install pytest & coverage | ||
| - pip install pytest pytest-cov | ||
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| - git switch main | ||
| - git switch $CI_COMMIT_BRANCH | ||
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| # List test files corresponding to modified files | ||
| - | | ||
| for file in $(git diff --name-only origin/main...$CI_COMMIT_BRANCH) | ||
| do | ||
| if [[ "$file" =~ .*"pipeline".* ]]; then | ||
| echo "Modified pipeline = $file" | ||
| tmp=${file#*"team_"} # remove prefix ending in "team_" | ||
| team_id=${tmp%".py"*} # remove suffix starting with ".py" | ||
| PIPELINES_TEST_FILES="$PIPELINES_TEST_FILES tests/pipelines/test_team_$team_id.py" | ||
| fi | ||
| done | ||
| - echo "$PIPELINES_TEST_FILES" | ||
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| # Run tests and produce reports | ||
| - coverage run -m pytest --junit-xml=pytest_report.xml "$PIPELINES_TEST_FILES" | ||
| - coverage report | ||
| - coverage xml | ||
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| artifacts: | ||
| when: on_success | ||
| reports: | ||
| junit: pytest_report.xml | ||
| coverage_report: | ||
| coverage_format: cobertura | ||
| path: coverage.xml | ||
|
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| rules: | ||
| # If something changed in narps_open/pipelines | ||
| - if: $CI_COMMIT_BRANCH | ||
| changes: | ||
| compare_to: 'refs/heads/main' | ||
| paths: | ||
| - 'narps_open/pipelines*' | ||
|
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| # Running tests that changed | ||
| test_changes-job: | ||
| stage: testing | ||
| variables: | ||
| TEST_FILES : "" | ||
| #GIT_STRATEGY: clone # So that we can access the main branch for git diff purpose | ||
| script: | ||
| # Install pytest & coverage | ||
| - pip install pytest pytest-cov | ||
|
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| - git switch main | ||
| - git switch $CI_COMMIT_BRANCH | ||
|
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| # List test files corresponding to modified files | ||
| - TEST_FILES=$(git diff --name-only origin/main...$CI_COMMIT_BRANCH) | ||
|
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| # Run tests and produce reports | ||
| - coverage run -m pytest --junit-xml=pytest_report.xml "$TEST_FILES" | ||
| - coverage report | ||
| - coverage xml | ||
|
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| artifacts: | ||
| when: on_success | ||
| reports: | ||
| junit: pytest_report.xml | ||
| coverage_report: | ||
| coverage_format: cobertura | ||
| path: coverage.xml | ||
|
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| rules: | ||
| # If something changed in narps_open/pipelines | ||
| - if: $CI_COMMIT_BRANCH | ||
| changes: | ||
| compare_to: 'refs/heads/main' | ||
| paths: | ||
| - 'tests/*' |
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