New data collected at 2024-12-23_00-02-02

github-actions/mapview/R-CMD-check.yaml

@@ -0,0 +1,53 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

github-actions/mapview/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

github-actions/mapview/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

github-actions/mlflow/advice.yml

@@ -23,4 +23,4 @@ jobs:
             const script = require(
               `${process.env.GITHUB_WORKSPACE}/.github/workflows/advice.js`
             );
-            script({ context, github });
+            await script({ context, github });

github-actions/mlflow/autoformat.yml

@@ -157,22 +157,37 @@ jobs:
     needs: [check-comment, format]
     if: ${{ needs.format.outputs.reformatted == 'true' }}
     permissions: {}
+    outputs:
+      head_sha: ${{ steps.push.outputs.head_sha }}
     steps:
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ secrets.APP_ID }}
+          # See https://docs.github.com/en/apps/creating-github-apps/authenticating-with-a-github-app/managing-private-keys-for-github-apps
+          # for how to rotate the private key
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
       - uses: actions/checkout@v4
         with:
           repository: ${{ needs.check-comment.outputs.repository }}
           ref: ${{ needs.check-comment.outputs.head_ref }}
           # Set fetch-depth to merge the base branch
           fetch-depth: 300
-          token: ${{ secrets.MLFLOW_AUTOMATION_TOKEN }}
+          # As reported in https://github.com/orgs/community/discussions/25702, if an action pushes
+          # code using `GITHUB_TOKEN`, that won't trigger new workflow runs on the PR.
+          # A personal access token is required to trigger new workflow runs.
+          token: ${{ steps.app-token.outputs.token }}
 
       - name: Merge base branch
+        env:
+          BASE_REPO: ${{ needs.check-comment.outputs.base_repo }}
+          BASE_REF: ${{ needs.check-comment.outputs.base_ref }}
         run: |
           git config user.name 'mlflow-automation'
           git config user.email '[email protected]'
-          git remote add base https://github.com/${{ needs.check-comment.outputs.base_repo }}.git
-          git fetch base ${{ needs.check-comment.outputs.base_ref }}
-          git merge base/${{ needs.check-comment.outputs.base_ref }}
+          git remote add base https://github.com/${BASE_REPO}.git
+          git fetch base $BASE_REF
+          git merge base/${BASE_REF}
 
       - name: Download patch
         uses: actions/download-artifact@v4
@@ -181,9 +196,14 @@ jobs:
           path: /tmp
 
       - name: Apply patch and push
+        id: push
+        env:
+          RUN_ID: ${{ github.run_id }}
+          REPOSITORY: ${{ github.repository }}
         run: |
-          git apply /tmp/${{ github.run_id }}.diff
-          git commit -sam "Autoformat: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"
+          git apply /tmp/${RUN_ID}.diff
+          git commit -sam "Autoformat: https://github.com/${REPOSITORY}/actions/runs/${RUN_ID}"
+          echo "head_sha=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT
           git push
 
   update-status:
@@ -192,7 +212,8 @@ jobs:
     needs: [check-comment, format, push]
     if: always() && needs.check-comment.outputs.should_autoformat == 'true'
     permissions:
-      statuses: write # autoformat.updateStatus
+      statuses: write # To update check statuses
+      actions: write # To approve workflow runs
     steps:
       - uses: actions/checkout@v4
         with:
@@ -205,4 +226,13 @@ jobs:
             const needs = ${{ toJson(needs) }};
             const head_sha = '${{ needs.check-comment.outputs.head_sha }}'
             const autoformat = require('./.github/workflows/autoformat.js');
+            // TODO: Remove try-catch block once we are confident that the code works fine.
+            try {
+              const push_head_sha = '${{ needs.push.outputs.head_sha }}';
+              if (push_head_sha) {
+                await autoformat.approveWorkflowRuns(context, github, push_head_sha);
+              }
+            } catch (error) {
+              core.warning(`Failed to approve workflow runs: ${error}`);
+            }
             await autoformat.updateStatus(context, github, head_sha, needs);

github-actions/mlflow/closing-pr.yml

@@ -28,4 +28,4 @@ jobs:
             const script = require(
               `${process.env.GITHUB_WORKSPACE}/.github/workflows/closing-pr.js`
             );
-            script({ context, github });
+            await script({ context, github });

github-actions/mlflow/devcontainer.yml

@@ -100,6 +100,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: devcontainer
     if: github.event_name == 'push'
+    timeout-minutes: 60
     permissions:
       packages: write # to push to ghcr.io
     steps:

github-actions/mlflow/js.yml

@@ -26,6 +26,7 @@ jobs:
   js:
     if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     permissions: {}
+    timeout-minutes: 30
     strategy:
       fail-fast: false
       matrix:

github-actions/mlflow/labeling.yml

@@ -19,14 +19,16 @@ jobs:
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     permissions:
-      pull-requests: write # harupy/auto-labeling
-      issues: write # harupy/auto-labeling
-    timeout-minutes: 120
+      pull-requests: write
+      issues: write
+    timeout-minutes: 5
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: recursive
-      - uses: harupy/auto-labeling@master
+          sparse-checkout: |
+            .github
+      - uses: actions/github-script@v7
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          label-pattern: '- \[(.*?)\] ?`(.+?)`'
+          script: |
+            const script = require('./.github/workflows/labeling.js');
+            await script({ github, context });

github-actions/mlflow/maintainer-approval.yml

@@ -6,6 +6,7 @@ on:
 jobs:
   check:
     runs-on: ubuntu-latest
+    timeout-minutes: 5
     permissions:
       pull-requests: read
     steps:

github-actions/mlflow/master.yml

@@ -112,11 +112,13 @@ jobs:
       - uses: ./.github/actions/cache-pip
       - name: Install dependencies
         run: |
+          source ./dev/install-common-deps.sh
           pip install .
       - uses: ./.github/actions/show-versions
       - name: Run tests
         run: |
           python -c "import sys; assert sys.version_info[:2] == (3, 10), sys.version_info"
+          pytest tests/types/test_type_hints.py
 
   database:
     if: github.event_name != 'pull_request' || github.event.pull_request.draft == false

github-actions/mlflow/recipe-template.yml

@@ -87,6 +87,7 @@ jobs:
           cd ${{ github.event.inputs.repository }} && pytest tests --rootdir .
   recipe-windows:
     runs-on: windows-latest
+    timeout-minutes: 120
     permissions: {}
     steps:
       - uses: actions/checkout@v4