fix: Update bibliography records #631
Workflow file for this run
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| name: 'PR-Checks' | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| branches: | |
| - master | |
| concurrency: | |
| group: prCheck-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| # Validate YAML | |
| Validate-YAML: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Install tools | |
| run: | | |
| sudo apt -y update | |
| sudo apt install -y yamllint | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.yml | |
| - name: Validate any YAML files | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| if yamllint $file; then | |
| echo "YAML $file is valid" | |
| else | |
| echo "YAML $file is invalid" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| # Validate XML | |
| Validate-XML: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Install tools | |
| run: | | |
| sudo apt -y update | |
| sudo apt install -y libxml2-utils | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.xml | |
| - name: Validate any XML files | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| echo "Validating XML file: $file" | |
| if xmllint --noout $file; then | |
| echo "XML $file is valid" | |
| else | |
| echo "XML $file is invalid" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| # Validate Perl scripts | |
| Validate-Perl-Scripts: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/galacticusorg/buildenv:latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check out repository analysis-perl | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: galacticusorg/analysis-perl | |
| path: analysis-perl | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| echo "GALACTICUS_ANALYSIS_PERL_PATH=$GITHUB_WORKSPACE/analysis-perl" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Get changed scripts | |
| id: changed-scripts | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.pl | |
| - name: Install tools | |
| run: | | |
| apt -y update | |
| apt install -y libxml-simple-perl | |
| - name: Validate any Perl scripts | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-scripts.outputs.all_changed_files }}; do | |
| if perl -c $file; then | |
| echo "Perl script $file compiles correctly" | |
| else | |
| echo "Perl script $file fails to compile" | |
| status=1 | |
| fi | |
| if [[ -x $file ]]; then | |
| echo "Perl script $file is executable" | |
| else | |
| echo "Perl script $file is not executable" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| # Validate Perl modules | |
| Validate-Perl-Modules: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/galacticusorg/buildenv:latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Get changed modules | |
| id: changed-modules | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.pm | |
| - name: Install tools | |
| run: | | |
| apt -y update | |
| apt install -y libxml-simple-perl | |
| - name: Validate any Perl modules | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-modules.outputs.all_changed_files }}; do | |
| if perl -c $file; then | |
| echo "Perl module $file compiles correctly" | |
| else | |
| echo "Perl module $file fails to compile" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| # Fortran static analysis | |
| Fortran-Static-Analysis: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/galacticusorg/buildenv:latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.F90 | |
| - name: Perform static analysis on Fortran files | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| if ./scripts/aux/staticAnalyzer.pl $file; then | |
| echo "Fortran file $file passes analysis" | |
| else | |
| echo "Fortran file $file fails analysis" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| # Embedded XML and LaTeX checks | |
| Embedded-XML-LaTeX: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/galacticusorg/buildenv:latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| echo "DICTIONARY=en_US" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Install tools | |
| run: | | |
| apt -y update | |
| apt install -y texlive texlive-latex-extra texlive-science texlive-extra-utils hunspell hunspell-en-us libxml-simple-perl libregexp-common-perl libfile-temp-perl | |
| - name: Build class information | |
| run: | | |
| cd $GALACTICUS_EXEC_PATH | |
| make -j2 work/build/stateStorables.xml | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.F90 | |
| **/*.Inc | |
| - name: Perform checks of embedded XML and LaTeX | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| if ./scripts/aux/embeddedAnalyzer.pl $file warnings.md; then | |
| echo "Embedded XML/LaTeX in file $file passes analysis" | |
| else | |
| echo "Embedded XML/LaTeX in file $file fails analysis" | |
| status=1 | |
| fi | |
| done | |
| exit $status | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v3 | |
| with: | |
| files: warnings.md | |
| - name: Output to a job summary | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| cat warnings.md >> $GITHUB_STEP_SUMMARY | |
| - name: Comment on the PR if any warnings were found | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| continue-on-error: true | |
| uses: thollander/actions-comment-pull-request@v3 | |
| with: | |
| file-path: warnings.md | |
| # Spell check LaTeX files | |
| Spell-Check-LaTeX: | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/galacticusorg/buildenv:latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: "Set environmental variables" | |
| run: | | |
| echo "GALACTICUS_EXEC_PATH=$GITHUB_WORKSPACE" >> $GITHUB_ENV | |
| echo "DICTIONARY=en_US" >> $GITHUB_ENV | |
| - name: Mark directory safe | |
| run: | | |
| git config --global --add safe.directory $GALACTICUS_EXEC_PATH | |
| - name: Install tools | |
| run: | | |
| apt -y update | |
| apt install -y texlive texlive-latex-extra texlive-science texlive-extra-utils hunspell hunspell-en-us libxml-simple-perl libregexp-common-perl libfile-temp-perl | |
| - name: Build class information | |
| run: | | |
| cd $GALACTICUS_EXEC_PATH | |
| make -j2 work/build/stateStorables.xml | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v45 | |
| with: | |
| files: | | |
| **/*.tex | |
| - name: Perform checks of LaTeX files | |
| run: | | |
| status=0 | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| ./scripts/aux/spellChecker.pl $file warnings.md | |
| done | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v3 | |
| with: | |
| files: warnings.md | |
| - name: Comment on the PR if any warnings were found | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| uses: thollander/actions-comment-pull-request@v3 | |
| with: | |
| file-path: warnings.md |