Update NIRCam PSF photometry notebook #138
Workflow file for this run
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| name: notebook-pep8-check | |
| on: | |
| # use pull_request_target instead of pull_request to allow pushes to PR branch | |
| pull_request_target: | |
| branches: | |
| - main | |
| paths: | |
| - 'notebooks/*/*.ipynb' | |
| types: [ labeled, opened, synchronize, reopened ] | |
| # looks like either each folder needs its own job or pull requests need to be | |
| # limited to one folder at a time, otherwise requirements files will be mixed. | |
| env: | |
| pep8_script: '.github/helpers/pep8_nb_checker.py' | |
| magic_cells: '.github/helpers/nb_flake8_magic.json' | |
| instruct_post: '.github/helpers/tech_review_instructions.md' | |
| flake8_config: '.flake8' | |
| bot_name: 'github-actions[bot]' | |
| bot_email: '41898282+github-actions[bot]@users.noreply.github.com' | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| # GITHUB_TOKEN cannot push to PR branch without these permissions | |
| jobs: | |
| do-notebook-pep8-check: | |
| if: | | |
| contains(github.event.pull_request.labels.*.name, 'Technical Review') && | |
| github.event.pull_request.head.user.login != 'github-actions[bot]' && | |
| github.event.pull_request.draft == false && | |
| github.event.pull_request.state == 'open' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Event familiarization | |
| run: | | |
| echo "---github.event.pull_request.draft---" | |
| echo ${{ github.event.pull_request.draft }} | |
| echo "---github.event.pull_request.state---" | |
| echo ${{ github.event.pull_request.state }} | |
| echo "---contains(github.event.pull_request.labels.*.name, 'Technical Review')---" | |
| echo ${{ contains(github.event.pull_request.labels.*.name, 'Technical Review') }} | |
| echo "---github.event.pull_request.user.login---" | |
| echo ${{ github.event.pull_request.user.login }} | |
| echo "---github.event.pull_request.author_association---" | |
| echo ${{ github.event.pull_request.author_association }} | |
| echo "---github.event.pull_request.head.ref---" | |
| echo ${{ github.event.pull_request.head.ref }} | |
| echo "---github.event.pull_request.head.sha---" | |
| echo ${{ github.event.pull_request.head.sha }} | |
| echo "---github.event.pull_request.base.ref---" | |
| echo ${{ github.event.pull_request.base.ref }} | |
| echo "---github.event.pull_request.base.sha---" | |
| echo ${{ github.event.pull_request.base.sha }} | |
| # this is the latest commit on the base/target branch; NOT | |
| # (necessarily) the commit from which the PR diverges! | |
| echo "---github.event.action---" | |
| echo ${{ github.event.action }} | |
| echo "---github.event.sender.login---" | |
| echo ${{ github.event.sender.login }} | |
| - name: Check out PR branch | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 0 | |
| # (0 fetches all branches even with ref specified... don't love | |
| # fetching everything, but don't see how else to pull base + PR) | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Get changed files | |
| run: | | |
| # for clarity, add an upstream remote and fetch the base/target branch | |
| # ('origin' after checkout step is the PR branch's remote. | |
| # if the PR branch is from a fork, 'upstream' is needed to fetch the | |
| # base branch. if the PR and base branches share a remote, 'origin' | |
| # and 'upstream' will point to the same repository, which is fine.) | |
| echo "---add upstream remote---"; | |
| git remote add upstream "https://github.com/${{ github.event.pull_request.base.user.login }}/${{ github.event.repository.name }}.git"; | |
| git remote -v | |
| echo "---fetch upstream base branch---"; | |
| git fetch upstream ${{ github.event.pull_request.base.ref }} | |
| # find last common ancestor commit between target and PR branches | |
| last_common=$(git merge-base upstream/${{ github.event.pull_request.base.ref }} ${{ github.event.pull_request.head.ref }}) | |
| echo "last_common" | |
| echo $last_common | |
| # make an array of all notebooks added/copied/modified in PR branch | |
| git_diff=$(git diff --name-only --diff-filter=ACM $last_common ${{ github.event.pull_request.head.sha }} *ipynb) | |
| echo "git_diff" | |
| echo $git_diff | |
| # (yes to added, copied, modified and NO to renamed, deleted, type | |
| # changed, unmerged, or unknown seems reasonable.) | |
| changed_files=($(printf '%s\n' $git_diff)) | |
| echo "changed_files" | |
| echo "${changed_files[@]}" | |
| echo "changed_files=${changed_files[@]}" >> $GITHUB_ENV | |
| # use arrays to check that changed notebooks are in the same directory | |
| # (note that xargs dirname can only be used in this way on Linux) | |
| # (https://unix.stackexchange.com/a/377820 for unique check) | |
| changed_dirs_all=( $(printf '%s\n' "${changed_files[@]}" | xargs dirname) ) | |
| echo "changed_dirs_all" | |
| echo "${changed_dirs_all[@]}" | |
| changed_dirs_uniq=( $(printf '%s\n' "${changed_dirs_all[@]}" | sort -u) ) | |
| echo "changed_dirs_uniq" | |
| echo "${changed_dirs_uniq[@]}" | |
| if [ "${#changed_dirs_uniq[@]}" != 1 ]; then echo "one_dir=no" >> $GITHUB_ENV; fi | |
| - name: Auto-fail if changed files are not in same directory | |
| if: env.one_dir | |
| uses: actions/github-script@v5 | |
| with: | |
| script: | | |
| core.setFailed('All changed files are not in the same directory.') | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 # JDAT recommends 3.8.10 | |
| - name: Install flake8 and script dependencies | |
| if: steps.cache-step.outputs.cache-hit != 'true' | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 numpy pytz | |
| - name: Run the PEP8 check's Python script | |
| run: | | |
| # ensure script's helper files come from the base branch, not the PR | |
| # (checkout also works, though you have to unstage the file afterward) | |
| git restore --source=upstream/${{ github.event.pull_request.base.ref }} --worktree $pep8_script $magic_cells $instruct_post $flake8_config | |
| # isolate changed notebooks in order to run PEP8 check | |
| for ff in ${{ env.changed_files }}; do | |
| # https://stackoverflow.com/a/6397979 | |
| if [[ $ff == *".ipynb" ]]; then | |
| python ${{ env.pep8_script }} -f $ff; | |
| fi | |
| done | |
| # check for changes to the notebooks in this local branch | |
| if [[ `git status --porcelain --untracked-files=no` ]]; then echo "push=yes" >> $GITHUB_ENV; fi | |
| shell: bash | |
| # if env.push is empty, the next steps are skipped and the job should pass | |
| - name: Push any changes to PR | |
| if: env.push | |
| run: | | |
| # verify identity to allow a push to which other workflows can respond | |
| git config --local user.email $bot_email | |
| git config --local user.name $bot_name | |
| # add the changed notebook(s) | |
| git add --update *.ipynb | |
| git status | |
| # (script output files should be untracked) | |
| # list changed notebooks in commit message; push the changes | |
| git_diff_new=($(git diff --name-only --diff-filter=M *ipynb)) | |
| git commit -m "[BOT] Left PEP8 feedback on PR ${{ github.event.number }}'s notebooks" -m "Files: $(printf '%s\n' $git_diff_new)" | |
| # (is tagging the PR for the best here?) | |
| git push origin "HEAD:${{ github.event.pull_request.head.ref }}" | |
| - name: Write instructional message (if new branch) | |
| if: env.push | |
| uses: actions/github-script@v5 | |
| with: | |
| script: | | |
| async function scanAndPost() | |
| { | |
| const template = "${{ env.instruct_post }}"; | |
| const branch = "${{ github.event.pull_request.head.ref }}"; | |
| const creator = "${{ github.event.pull_request.user.login }}"; | |
| const issueno = context.issue.number | |
| const { owner, repo } = context.repo; | |
| // scan PR comments (expecting JS array of JS lists) | |
| const comments = await github.rest.issues.listComments({ | |
| owner: owner, // as in account that owns the repo | |
| repo: repo, | |
| issue_number: issueno | |
| }); | |
| console.log("imported comments") | |
| //console.log(comments.data[0].user); | |
| // see how many were written by the bot | |
| const botPosts = comments.data.filter(post => post.user.login === "${{ env.bot_name }}").length; | |
| // if any, terminate early | |
| if (botPosts != 0) { console.log("Already commented!"); return; } | |
| // else, read text from template file | |
| const fs = require("fs").promises; | |
| const message = await fs.readFile(template, "utf8"); | |
| console.log("read file"); | |
| // format message with user and PR info | |
| const util = require("util"); | |
| const injectedMsg = util.format(message, creator, branch, | |
| branch, creator, repo); | |
| console.log("formatted message"); | |
| // create the comment | |
| github.rest.issues.createComment({ | |
| issue_number: issueno, | |
| owner: owner, | |
| repo: repo, | |
| body: injectedMsg | |
| }); | |
| // could label with github.rest.issues.addLabels... | |
| } | |
| scanAndPost(); | |
| - name: Auto-fail if changes were pushed | |
| if: env.push | |
| uses: actions/github-script@v5 | |
| with: | |
| script: core.setFailed('Notebook(s) failed PEP8 tests.') |