Merge remote-tracking branch 'upstream/main' into cmake-build

Author: WillAyd

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,72 @@
+name: Feature Request
+description: Suggest an idea for pandas
+title: "ENH: "
+labels: [Enhancement, Needs Triage]
+
+body:
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Feature Type
+      description: Please check what type of feature request you would like to propose.
+      options:
+        - label: >
+            Adding new functionality to pandas
+        - label: >
+            Changing existing functionality in pandas
+        - label: >
+            Removing existing functionality in pandas
+  - type: textarea
+    id: description
+    attributes:
+      label: Problem Description
+      description: >
+        Please describe what problem the feature would solve, e.g. "I wish I could use pandas to ..."
+      placeholder: >
+        I wish I could use pandas to return a Series from a DataFrame when possible.
+    validations:
+      required: true
+  - type: textarea
+    id: feature
+    attributes:
+      label: Feature Description
+      description: >
+        Please describe how the new feature would be implemented, using psudocode if relevant.
+      placeholder: >
+        Add a new parameter to DataFrame, to_series, to return a Series if possible.
+
+        def __init__(self, ..., to_series: bool=False):
+            """
+            Parameters
+            ----------
+            ...
+
+            to_series : bool, default False
+                Return a Series if possible
+            """
+            if to_series:
+                return Series(data)
+    validations:
+      required: true
+  - type: textarea
+    id: alternative
+    attributes:
+      label: Alternative Solutions
+      description: >
+        Please describe any alternative solution (existing functionality, 3rd party package, etc.)
+        that would satisfy the feature request.
+      placeholder: >
+        Write a custom function to return a Series when possible.
+
+        def to_series(...)
+           result = pd.DataFrame(...)
+           ...
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: >
+        Please provide any relevant Github issues, code examples or references that help describe and support
+        the feature request.

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -6,8 +6,8 @@ runs:
 
     - name: Environment Detail
       run: |
-        conda info
-        conda list
+        micromamba info
+        micromamba list
       shell: bash -el {0}
 
     - name: Build Pandas

.github/actions/build_pandas/action.yml

@@ -6,8 +6,8 @@ inputs:
   environment-name:
     description: Name to use for the Conda environment
     default: test
-  python-version:
-    description: Python version to install
+  extra-specs:
+    description: Extra packages to install
     required: false
   pyarrow-version:
     description: If set, overrides the PyArrow version in the Conda environment to the given string.
@@ -24,14 +24,13 @@ runs:
       if: ${{ inputs.pyarrow-version }}
 
     - name: Install ${{ inputs.environment-file }}
-      uses: conda-incubator/[email protected]
+      uses: mamba-org/provision-with-micromamba@v12
       with:
         environment-file: ${{ inputs.environment-file }}
-        activate-environment: ${{ inputs.environment-name }}
-        python-version: ${{ inputs.python-version }}
-        channel-priority: ${{ runner.os == 'macOS' && 'flexible' || 'strict' }}
+        environment-name: ${{ inputs.environment-name }}
+        extra-specs: ${{ inputs.extra-specs }}
         channels: conda-forge
-        mamba-version: "0.24"
-        use-mamba: true
-        use-only-tar-bz2: true
+        channel-priority: ${{ runner.os == 'macOS' && 'flexible' || 'strict' }}
         condarc-file: ci/condarc.yml
+        cache-env: true
+        cache-downloads: true

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

@@ -12,6 +12,9 @@ on:
     paths-ignore:
       - "doc/**"
 
+permissions:
+  contents: read
+
 jobs:
   pytest:
     runs-on: ubuntu-latest

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

@@ -3,8 +3,14 @@ on:
   issue_comment:
     types: created
 
+permissions:
+  contents: read
+
 jobs:
   issue_assign:
+    permissions:
+      issues: write
+      pull-requests: write
     runs-on: ubuntu-latest
     steps:
     - if: github.event.comment.body == 'take'

.github/workflows/assign.yml

@@ -9,8 +9,15 @@ env:
   ENV_FILE: environment.yml
   COMMENT: ${{github.event.comment.body}}
 
+permissions:
+  contents: read
+
 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')
@@ -33,12 +40,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Cache conda
-        uses: actions/cache@v3
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ hashFiles('${{ env.ENV_FILE }}') }}
-
         # Although asv sets up its own env, deps are still needed
         # during discovery process
       - name: Set up Conda

.github/workflows/asv-bot.yml

@@ -5,8 +5,14 @@ on:
     - cron: "0 7 1 * *" # At 07:00 on 1st of every month.
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   update-pre-commit:
+    permissions:
+      contents: write  # for technote-space/create-pr-action to push code
+      pull-requests: write  # for technote-space/create-pr-action to create a PR
     if: github.repository_owner == 'pandas-dev'
     name: Autoupdate pre-commit config
     runs-on: ubuntu-latest

.github/workflows/autoupdate-pre-commit-config.yml

@@ -14,6 +14,9 @@ env:
   ENV_FILE: environment.yml
   PANDAS_CI: 1
 
+permissions:
+  contents: read
+
 jobs:
   pre_commit:
     name: pre-commit
@@ -52,50 +55,46 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Cache conda
-      uses: actions/cache@v3
-      with:
-        path: ~/conda_pkgs_dir
-        key: ${{ runner.os }}-conda-${{ hashFiles('${{ env.ENV_FILE }}') }}
-
     - name: Set up Conda
       uses: ./.github/actions/setup-conda
 
     - name: Build Pandas
       id: build
       uses: ./.github/actions/build_pandas
 
+    # The following checks are independent of each other and should still be run if one fails
     - name: Check for no warnings when building single-page docs
       run: ci/code_checks.sh single-docs
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Run checks on imported code
       run: ci/code_checks.sh code
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Run doctests
       run: ci/code_checks.sh doctests
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Run docstring validation
       run: ci/code_checks.sh docstrings
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Use existing environment for type checking
       run: |
         echo $PATH >> $GITHUB_PATH
         echo "PYTHONHOME=$PYTHONHOME" >> $GITHUB_ENV
         echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Typing
       uses: pre-commit/[email protected]
       with:
         extra_args: --hook-stage manual --all-files
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Run docstring validation script tests
       run: pytest scripts
-      if: ${{ steps.build.outcome == 'success' }}
+      if: ${{ steps.build.outcome == 'success' && always() }}
 
   asv-benchmarks:
     name: ASV Benchmarks
@@ -115,12 +114,6 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Cache conda
-      uses: actions/cache@v3
-      with:
-        path: ~/conda_pkgs_dir
-        key: ${{ runner.os }}-conda-${{ hashFiles('${{ env.ENV_FILE }}') }}
-
     - name: Set up Conda
       uses: ./.github/actions/setup-conda
 

.github/workflows/code-checks.yml

@@ -0,0 +1,31 @@
+name: CodeQL
+on:
+  schedule:
+    # every day at midnight
+    - cron: "0 0 * * *"
+
+concurrency:
+  group: ${{ github.repository }}-${{ github.head_ref || github.sha }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language:
+          - python
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+      - uses: github/codeql-action/autobuild@v2
+      - uses: github/codeql-action/analyze@v2

.github/workflows/codeql.yml

@@ -14,6 +14,9 @@ env:
   ENV_FILE: environment.yml
   PANDAS_CI: 1
 
+permissions:
+  contents: read
+
 jobs:
   web_and_docs:
     name: Doc Build and Upload
@@ -46,6 +49,11 @@ jobs:
     - name: Build documentation
       run: doc/make.py --warnings-are-errors
 
+    - name: Build the interactive terminal
+      run: |
+        cd web/interactive_terminal
+        jupyter lite build
+
     - name: Install ssh key
       run: |
         mkdir -m 700 -p ~/.ssh

.github/workflows/docbuild-and-upload.yml

@@ -18,12 +18,15 @@ env:
   PATTERN: "not slow and not db and not network and not single_cpu"
 
 
+permissions:
+  contents: read
+
 jobs:
   pytest:
     defaults:
       run:
         shell: bash -el {0}
-    timeout-minutes: 90
+    timeout-minutes: 120
     strategy:
       matrix:
         os: [macos-latest, windows-latest]

.github/workflows/macos-windows.yml

@@ -27,6 +27,9 @@ env:
   COVERAGE: true
   PYTEST_TARGET: pandas
 
+permissions:
+  contents: read
+
 jobs:
   build:
     if: false # Comment this line out to "unfreeze"