Merge branch 'main' into dev/to_excel

Author: rmhowe425

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
       image: ubuntu-2004:2022.04.1
     resource_class: arm.large
     environment:
-      ENV_FILE: ci/deps/circle-38-arm64.yaml
+      ENV_FILE: ci/deps/circle-39-arm64.yaml
       PYTEST_WORKERS: auto
       PATTERN: "not single_cpu and not slow and not network and not clipboard and not arm_slow and not db"
       PYTEST_TARGET: "pandas"
@@ -92,4 +92,4 @@ workflows:
               only: /^v.*/
           matrix:
             parameters:
-              cibw-build: ["cp38-manylinux_aarch64", "cp39-manylinux_aarch64", "cp310-manylinux_aarch64", "cp311-manylinux_aarch64"]
+              cibw-build: ["cp39-manylinux_aarch64", "cp310-manylinux_aarch64", "cp311-manylinux_aarch64"]

.circleci/setup_env.sh

@@ -54,10 +54,7 @@ if pip list | grep -q ^pandas; then
     pip uninstall -y pandas || true
 fi
 
-echo "Build extensions"
-python setup.py build_ext -q -j4
-
 echo "Install pandas"
-python -m pip install --no-build-isolation --no-use-pep517 -e .
+python -m pip install --no-build-isolation -ve .
 
 echo "done"

.github/actions/build_pandas/action.yml

@@ -1,5 +1,9 @@
 name: Build pandas
 description: Rebuilds the C extensions and installs pandas
+inputs:
+  editable:
+    description: Whether to build pandas in editable mode (default true)
+    default: true
 runs:
   using: composite
   steps:
@@ -12,9 +16,9 @@ runs:
 
     - name: Build Pandas
       run: |
-        python setup.py build_ext -j $N_JOBS
-        python -m pip install -e . --no-build-isolation --no-use-pep517 --no-index
+        if [[ ${{ inputs.editable }} == "true" ]]; then
+          pip install -e . --no-build-isolation -v
+        else
+          pip install . --no-build-isolation -v
+        fi
       shell: bash -el {0}
-      env:
-        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
-        N_JOBS: ${{ runner.os == 'macOS' && 3 || 2 }}

.github/actions/run-tests/action.yml

@@ -7,7 +7,7 @@ runs:
       shell: bash -el {0}
 
     - name: Publish test results
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: Test results
         path: test-data.xml
@@ -19,7 +19,7 @@ runs:
       if: failure()
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         flags: unittests
         name: codecov-pandas

.github/actions/setup-conda/action.yml

@@ -3,23 +3,14 @@ inputs:
   environment-file:
     description: Conda environment file to use.
     default: environment.yml
-  environment-name:
-    description: Name to use for the Conda environment
-    default: test
-  extra-specs:
-    description: Extra packages to install
-    required: false
 runs:
   using: composite
   steps:
     - name: Install ${{ inputs.environment-file }}
-      uses: mamba-org/provision-with-micromamba@v12
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: ${{ inputs.environment-file }}
-        environment-name: ${{ inputs.environment-name }}
-        extra-specs: ${{ inputs.extra-specs }}
-        channels: conda-forge
-        channel-priority: 'strict'
+        environment-name: test
         condarc-file: ci/condarc.yml
-        cache-env: true
+        cache-environment: true
         cache-downloads: true

.github/workflows/32-bit-linux.yml

@@ -63,8 +63,24 @@ jobs:
     - name: Build Pandas
       id: build
       uses: ./.github/actions/build_pandas
+      with:
+        editable: false
 
     # The following checks are independent of each other and should still be run if one fails
+
+    # TODO: The doctests have to be run first right now, since the Cython doctests only work
+    # with pandas installed in non-editable mode
+    # This can be removed once pytest-cython doesn't require C extensions to be installed inplace
+    - name: Run doctests
+      run: cd ci && ./code_checks.sh doctests
+      if: ${{ steps.build.outcome == 'success' && always() }}
+
+    - name: Install pandas in editable mode
+      id: build-editable
+      uses: ./.github/actions/build_pandas
+      with:
+        editable: true
+
     - name: Check for no warnings when building single-page docs
       run: ci/code_checks.sh single-docs
       if: ${{ steps.build.outcome == 'success' && always() }}
@@ -73,10 +89,6 @@ jobs:
       run: ci/code_checks.sh code
       if: ${{ steps.build.outcome == 'success' && always() }}
 
-    - name: Run doctests
-      run: ci/code_checks.sh doctests
-      if: ${{ steps.build.outcome == 'success' && always() }}
-
     - name: Run docstring validation
       run: ci/code_checks.sh docstrings
       if: ${{ steps.build.outcome == 'success' && always() }}
@@ -179,7 +191,7 @@ jobs:
         id: setup_python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.10'
           cache: 'pip'
           cache-dependency-path: 'requirements-dev.txt'
 

.github/workflows/assign.yml

@@ -18,6 +18,7 @@ jobs:
       actions: read
       contents: read
       security-events: write
+    if: github.repository_owner == 'pandas-dev'
 
     strategy:
       fail-fast: false

.github/workflows/code-checks.yml

@@ -1,30 +1,45 @@
-name: "ASV Bot"
-
+name: Comment Commands
 on:
-  issue_comment: # Pull requests are issues
-    types:
-      - created
-
-env:
-  ENV_FILE: environment.yml
-  COMMENT: ${{github.event.comment.body}}
+  issue_comment:
+    types: created
 
 permissions:
   contents: read
+  issues: write
+  pull-requests: write
 
 jobs:
-  autotune:
-    permissions:
-      contents: read
-      issues: write
-      pull-requests: write
-    name: "Run benchmarks"
-    # TODO: Support more benchmarking options later, against different branches, against self, etc
-    if: startsWith(github.event.comment.body, '@github-actions benchmark')
+  issue_assign:
+    runs-on: ubuntu-22.04
+    if: (!github.event.issue.pull_request) && github.event.comment.body == 'take'
+    concurrency:
+      group: ${{ github.actor }}-issue-assign
+    steps:
+      - run: |
+          echo "Assigning issue ${{ github.event.issue.number }} to ${{ github.event.comment.user.login }}"
+          curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"assignees": ["${{ github.event.comment.user.login }}"]}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/assignees
+  preview_docs:
     runs-on: ubuntu-22.04
+    if: github.event.issue.pull_request && github.event.comment.body == '/preview'
+    concurrency:
+      group: ${{ github.actor }}-preview-docs
+    steps:
+      - run: |
+          if curl --output /dev/null --silent --head --fail "https://pandas.pydata.org/preview/${{ github.event.issue.number }}/"; then
+            curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"body": "Website preview of this PR available at: https://pandas.pydata.org/preview/${{ github.event.issue.number }}/"}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments
+          else
+            curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"body": "No preview found for PR #${{ github.event.issue.number }}. Did the docs build complete?"}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments
+          fi
+  asv_run:
+    runs-on: ubuntu-22.04
+    # TODO: Support more benchmarking options later, against different branches, against self, etc
+    if: github.event.issue.pull_request && startsWith(github.event.comment.body, '@github-actions benchmark')
     defaults:
       run:
         shell: bash -el {0}
+    env:
+      ENV_FILE: environment.yml
+      COMMENT: ${{github.event.comment.body}}
 
     concurrency:
       # Set concurrency to prevent abuse(full runs are ~5.5 hours !!!)
@@ -47,7 +62,7 @@ jobs:
 
       - name: Run benchmarks
         id: bench
-        continue-on-error: true # This is a fake failure, asv will exit code 1 for regressions
+        continue-on-error: true # asv will exit code 1 for regressions
         run: |
           # extracting the regex, see https://stackoverflow.com/a/36798723
           REGEX=$(echo "$COMMENT" | sed -n "s/^.*-b\s*\(\S*\).*$/\1/p")