Python protein translation #779
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| --- | |
| # | |
| # .github/workflows/python.yml | |
| # | |
| name: Python Workflow 4.0 | |
| on: # yamllint disable-line rule:truthy | |
| pull_request: | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| stage1: | |
| name: Change Check | |
| runs-on: 'ubuntu-latest' | |
| outputs: | |
| docs_changed: ${{ steps.check_file_changed.outputs.docs_changed }} | |
| matrix_exercise: ${{ steps.check_file_changed.outputs.matrix_exercise }} | |
| exercise_count: ${{ steps.check_file_changed.outputs.exercise_count }} | |
| steps: | |
| - name: Check GitHub Vars | |
| id: github-vars | |
| run: set | grep -e ^CI -e ^GITHUB_ -e ^RUNNER_ | |
| - name: Checkout Repo | |
| id: checkout-repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.ref }} | |
| submodules: recursive | |
| - name: Get Change List | |
| id: check_file_changed | |
| run: | | |
| { | |
| printf "Workflow: %s\n\n" "${GITHUB_WORKFLOW}" | |
| printf "Runner: name[%s] arch[%s]\n" "${RUNNER_NAME}" "${RUNNER_ARCH}" | |
| printf "Repo: %s\n" "${GITHUB_REPOSITORY}" | |
| printf "User: %s\n" "${GITHUB_TRIGGERING_ACTOR}" | |
| printf "\n" | |
| } | tee -a "${GITHUB_STEP_SUMMARY}" | |
| # Diff HEAD with the previous commit then output to stdout. | |
| GIT_DIFF="$(git diff --name-only HEAD^ HEAD | tee /tmp/changed_files.txt)" | |
| { | |
| printf "=== Which files changed? ===\n" | |
| printf "\`\`\`text\n" | |
| printf "%s\n" "${GIT_DIFF}" | |
| printf "\`\`\`\n" | |
| } | tee -a "${GITHUB_STEP_SUMMARY}" | |
| HAS_WF_DIFF=false | |
| HAS_EX_DIFF=false | |
| if printf "%s\n" "${GIT_DIFF}" | grep -E '^(.github/workflows/python.yml|.github/citools/python/)$'; then | |
| HAS_WF_DIFF=true | |
| fi | |
| if printf "%s\n" "${GIT_DIFF}" | grep -E '^python/.*[.]py$'; then | |
| HAS_EX_DIFF=true | |
| fi | |
| printf "\n" | |
| printf "=== Did WF/CI change without exercise changes? ===\n" | |
| CI_FORCE_FULL=false | |
| if ${HAS_WF_DIFF} && ! ${HAS_EX_DIFF}; then | |
| CI_FORCE_FULL=true | |
| printf "%s\n" "${CI_FORCE_FULL}" | |
| fi | |
| printf "\n" | |
| # Get changed exercise list. | |
| if [[ ${GITHUB_EVENT_NAME} == pull_request ]] && ! ${CI_FORCE_FULL}; then | |
| printf "Generating pull request changed exercise list.\n" | |
| grep -E '^python/[-a-z0-9]+./.*$' /tmp/changed_files.txt | cut -f1,2 -d/ | sort -Vu | tee /tmp/exercises.txt || true | |
| else | |
| printf "Generating complete exercise list.\n" | |
| find ./python/ -type d -print | grep -v -E '^[.]/python/(|[.].*)$' | sed -r -e 's:[.]/(python/[-a-z0-9]+)/?.*$:\1:g' | sort -Vu | tee /tmp/exercises.txt || true | |
| HAS_DIFF=true | |
| fi | |
| printf "\n" | |
| # Check if the files are present in the changed file list (added, modified, deleted) then output to stdout. | |
| HAS_DIFF="${HAS_DIFF:-false}" | |
| printf "=== Which Python files changed? ===\n" | |
| if printf "%s\n" "${GIT_DIFF}" | grep -E '^(python/.*[.]py|.github/workflows/python.yml)'; then | |
| HAS_DIFF=true | |
| printf "%s\n" "${HAS_DIFF}" | |
| fi | |
| printf "\n" | |
| # Did Python files change? | |
| printf "=== Did Python files change? ===\n" | |
| printf "%s\n" "${HAS_DIFF}" | |
| printf "\n" | |
| # Generate exercise job matrix from changed files list. | |
| printf "=== Generating matrix exercise list. ===\n" | |
| declare -i last=0 | |
| declare -i count=0 | |
| last=$(wc -l /tmp/exercises.txt | cut -f1 -d\ ) | |
| ((last -= 1)) || true | |
| entries="" | |
| while read -r line; do | |
| if [[ ! ${count} -lt ${last} ]]; then | |
| comma="" | |
| else | |
| comma="," | |
| fi | |
| printf -v entry "\"%s\"%s\n" "${line}" "${comma}" | |
| ((count += 1)) | |
| entries+="${entry}" | |
| done < <(sort -V /tmp/exercises.txt) | |
| jq --sort-keys . >/tmp/exercises.json <<EOF | |
| [ ${entries} ] | |
| EOF | |
| exercise_count="$(jq '. | length' /tmp/exercises.json)" | |
| printf "%s=%s\n" "exercise_count" "${exercise_count}" | tee -a "${GITHUB_OUTPUT}" | |
| matrix_exercise="$(jq --compact-output --sort-keys . /tmp/exercises.json)" | |
| printf "%s=%s\n" "matrix_exercise" "${matrix_exercise}" | tee -a "${GITHUB_OUTPUT}" | |
| printf "\n" | |
| cat "${GITHUB_OUTPUT}" | |
| # Don't run stage 2 if PR mode doesn't have testable changes. | |
| if [[ ${GITHUB_EVENT_NAME} == pull_request ]] && [[ -z ${entries} ]]; then | |
| printf "In PR mode with no testable changes, disabling stage 2.\n" | |
| HAS_DIFF=false | |
| fi | |
| # Set the output named "docs_changed" | |
| printf "%s=%s\n" "docs_changed" "${HAS_DIFF}" >> "${GITHUB_OUTPUT}" | |
| check-matrix: | |
| runs-on: ubuntu-latest | |
| needs: stage1 | |
| steps: | |
| - name: Install json2yaml | |
| run: sudo npm install -g json2yaml | |
| - name: Check matrix::exercises | |
| run: | | |
| exercise_count='${{ needs.stage1.outputs.exercise_count }}' | |
| matrix_exercise='${{ needs.stage1.outputs.matrix_exercise }}' | |
| { | |
| printf "\`\`\`text\n" | |
| printf "exercise_count=%s\n" "${exercise_count}" | |
| printf "matrix_exercise=%s\n" "${matrix_exercise}" | |
| printf "\`\`\`\n" | |
| printf "json:\n" | |
| printf "\`\`\`text\n" | |
| printf "%s" "${matrix_exercise}" | jq . | |
| printf "\`\`\`\n" | |
| } | tee -a "${GITHUB_STEP_SUMMARY}" | |
| { | |
| printf "yaml:\n" | |
| printf "\`\`\`text\n" | |
| printf "{ \"matrix\": { \"exercise\": %s } }" "${matrix_exercise}" | json2yaml | |
| printf "\`\`\`\n" | |
| } | tee -a "${GITHUB_STEP_SUMMARY}" | |
| stage2: | |
| name: Python Checks | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest", "windows-latest", "macos-latest"] | |
| exclude: | |
| - os: "macos-latest" | |
| - os: "windows-latest" | |
| exercise: ${{fromJson(needs.stage1.outputs.matrix_exercise)}} | |
| runs-on: "${{ matrix.os }}" | |
| container: | |
| image: vpayno/ci-generic-debian:latest | |
| needs: [stage1] | |
| if: needs.stage1.outputs.docs_changed == 'true' | |
| steps: | |
| - name: Checkout Repo [${{ matrix.exercise }}] | |
| id: checkout-repo | |
| uses: actions/checkout@v3 | |
| - name: Config Python Tools [${{ matrix.exercise }}] | |
| id: config-python-tools | |
| run: |- | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-setup-config | |
| - name: Verify Python Tools [${{ matrix.exercise }}] | |
| id: verify-python-tools | |
| run: |- | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-setup-verify | |
| - name: Show Python version [${{ matrix.exercise }}] | |
| id: python-version | |
| run: | | |
| python --version | |
| pyenv --version | |
| pip --version | |
| - name: Analysing the code with pylint [${{ matrix.exercise }}] | |
| id: pylint | |
| run: | | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-lint-pylint | |
| - name: Analysing the code with ruff [${{ matrix.exercise }}] | |
| id: ruff | |
| run: | | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-lint-ruff | |
| - name: Analysing the code with pyright [${{ matrix.exercise }}] | |
| id: pyright | |
| run: | | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-lint-pyright | |
| - name: Analysing the code with bandit [${{ matrix.exercise }}] | |
| id: bandit | |
| run: | | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-lint-bandit | |
| - name: Analysing the code with refurb [${{ matrix.exercise }}] | |
| id: refurb | |
| run: | | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-lint-refurb || true | |
| - name: Testing with doctests [${{ matrix.exercise }}] | |
| id: pytest-doctest-run | |
| run: |- | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-test-with-doctests | |
| - name: Testing with pytest [${{ matrix.exercise }}] | |
| id: pytest-pytest-run | |
| run: |- | |
| ./.github/citools/common/run_wrapper_script "./${{ matrix.exercise }}" ../../.github/citools/python/python-test-with-coverage |