Fix CSV formatting by adding missing commas in package_list.csv #66
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| # Start with a list of packages in packages.csv, and get external data about them (e.g. last commit date) to generate an HTML page with the package information. This workflow is triggered manually from the Actions tab. | |
| # Olly Butters | |
| # 1/5/26 | |
| name: Package list | |
| # Controls when the workflow will run | |
| on: | |
| schedule: | |
| - cron: '30 5 * * 0' | |
| timezone: "Europe/London" | |
| push: | |
| branches: [ "main" ] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-slim | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| # Parse the package list, get the external data, and write to a new CSV file | |
| - name: Build package data | |
| run: | | |
| echo $GITHUB_WORKSPACE | |
| ls $GITHUB_WORKSPACE | |
| # Create new output file | |
| echo "Name,Description,CRAN link,CRAN version, CRAN license,Last commit,GitHub version,GitHub license,Github owner,Status" > output.csv | |
| while IFS="," read -r name description gh_link cran_link status | |
| do | |
| echo "-----------------------------------" | |
| echo "name: $name" | |
| echo "desc: $description" | |
| echo "github_link: $gh_link" | |
| echo "cran_link: $cran_link" | |
| echo "status: $status" | |
| echo "" | |
| ##### GitHub info | |
| echo -e "\nGitHub repo information" | |
| # Extract the repo name from the GitHub link | |
| gh_repo_name=$(echo $gh_link | awk -F/ '{print $NF}') | |
| echo $gh_repo_name | |
| # clone the repo | |
| git clone $gh_link | |
| cd $gh_repo_name | |
| # Last commit date of repo | |
| gh_last_commit=$(git log -1 --format=%cs) | |
| echo "last commit: $gh_last_commit" | |
| # Last release | |
| if [ $(git rev-list --tags --max-count=1) ]; then | |
| gh_last_release=$(git describe --tags $(git rev-list --tags --max-count=1)) | |
| else | |
| gh_last_release="" | |
| fi | |
| echo "last GitHub release: $gh_last_release" | |
| # Use the GitHub API to pull in info about the repoisitory | |
| echo "\nGitHub API information" | |
| gh repo view --json codeOfConduct,description,homepageUrl,licenseInfo,owner,parent,updatedAt > gh_repo_info.json | |
| echo "API response:" | |
| cat gh_repo_info.json | |
| # Get the license as it appears in GitHub | |
| gh_license=$(cat gh_repo_info.json | jq '.licenseInfo.nickname') | |
| if [ -z "${gh_license}" ] || [ "${gh_license}" = '""' ]; then | |
| gh_license=$(cat gh_repo_info.json | jq '.licenseInfo.name') | |
| fi | |
| # If the license is "Other", check for a LICENSE.md file and see if it contains actual license | |
| if [ "${gh_license}" = '"Other"' ]; then | |
| if [ -f "LICENSE.md" ]; then | |
| echo "License file found: LICENSE.md" | |
| if $(grep -q "MIT License" LICENSE.md); then | |
| gh_license="MIT License" | |
| fi | |
| fi | |
| fi | |
| echo "GitHub license: $gh_license" | |
| gh_owner=$(cat gh_repo_info.json | jq '.owner.login') | |
| echo "GitHub owner: $gh_owner" | |
| gh_code_of_conduct=$(cat gh_repo_info.json | jq '.codeOfConduct.name') | |
| echo "GitHub code of conduct: $gh_code_of_conduct" | |
| # Tidy up | |
| cd .. | |
| rm -rf $gh_repo_name | |
| ##### CRAN info | |
| echo "CRAN information" | |
| if [ -z "${cran_link}" ]; then | |
| cran_version="" | |
| cran_license="" | |
| else | |
| # Get CRAN package name from cran_link | |
| CRAN_package_name=$(echo $cran_link | awk -F= '{print $NF}') | |
| echo "CRAN package name: $CRAN_package_name" | |
| # Get the version number from CRAN | |
| # This is overkill really, it takes ages to install all the R dependencies. Could just parse the CRAN DESCRIPTION file. | |
| #version=$(Rscript --vanilla -e 'print(subset(tools::CRAN_package_db(), Package == "dsBase")[["Version"]], row.names=FALSE)') | |
| #echo "version: $version" | |
| cran_description_file_link="https://cran.r-project.org/web/packages/${CRAN_package_name}/DESCRIPTION" | |
| wget --content-on-error $cran_description_file_link | |
| # might not be on the CRAN | |
| if [ -f DESCRIPTION ]; then | |
| cran_version=$(grep -oP '^Version:\s*\K([a-zA-Z0-9\. _-]+)\s*$' DESCRIPTION) | |
| cran_license=$(grep -oP '^License:\s*\K([a-zA-Z0-9\. _\-\(\)><=\+]+)\s*$' DESCRIPTION) | |
| # tidy up | |
| rm DESCRIPTION | |
| else | |
| cran_version="" | |
| cran_license="" | |
| fi | |
| fi | |
| echo "CRAN version: $cran_version" | |
| echo "CRAN license: $cran_license" | |
| # write to file | |
| echo "$name,$description,$cran_link,$cran_version,$cran_license,$gh_link,$gh_last_commit,$gh_last_release,$gh_license,$gh_owner,$status" >> output.csv | |
| echo "-----------------------------------" | |
| done < <(tail -n +2 package_list.csv) | |
| mkdir gh-pages | |
| cp output.csv gh-pages/ | |
| cat output.csv | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Parse the output CSV file and generate an HTML page | |
| - name: build html page | |
| run: | | |
| python3 web_pages/build_packages_page.py | |
| mv output/* gh-pages/ | |
| - name: Upload static files as artifact | |
| id: deployment | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: gh-pages | |
| # Deployment job | |
| deploy: | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-slim | |
| permissions: | |
| pages: write | |
| id-token: write | |
| needs: build | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |