Merge branch 'shapefile_masking' of https://github.com/acchamber/iris …

…into shapefile_masking

* 'shapefile_masking' of https://github.com/acchamber/iris: (102 commits)
  [pre-commit.ci] auto fixes from pre-commit.com hooks
  Update lib/iris/_shapefiles.py
  [pre-commit.ci] auto fixes from pre-commit.com hooks
  Numpydocs misc (SciTools#5728)
  Updated environment lockfiles (SciTools#5731)
  Bump codecov/codecov-action from 3 to 4 (SciTools#5727)
  DOCS: API docs ToC more levels (SciTools#5714)
  Bump scitools/workflows from 2024.01.0 to 2024.02.0 (SciTools#5726)
  DOCS: numpydocs 8 (SciTools#5722)
  DOCS: numpydocs 7 (SciTools#5720)
  DOCS: numpydocs 6 (SciTools#5718)
  fix docstring types and remove duplicate line. (SciTools#5719)
  Updated environment lockfiles (SciTools#5717)
  numpydocs (SciTools#5715)
  DOCS: numpydocs 4 (SciTools#5711)
  DOCS: Add ruff section to the dev guide docs (SciTools#5701)
  [pre-commit.ci] pre-commit autoupdate (SciTools#5709)
  Bump scitools/workflows from 2023.12.1 to 2024.01.0 (SciTools#5710)
  Faster trivial equality checks for coordinates and arrays (SciTools#5691)
  Make the Coord.cell method lazy (SciTools#5693)
  ...

.github/workflows/benchmarks_report.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Download artifact
         id: download-artifact
         # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#using-data-from-the-triggering-workflow
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -54,7 +54,7 @@ jobs:
           echo "reports_exist=$reports_exist" >> "$GITHUB_OUTPUT"
 
       - name: Store artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: benchmark_reports
           path: benchmark_reports
@@ -65,17 +65,17 @@ jobs:
     if: needs.download.outputs.reports_exist == 1
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Download artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: benchmark_reports
           path: .github/workflows/benchmark_reports
 
       - name: Set up Python
         # benchmarks/bm_runner.py only needs builtins to run.
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
 
       - name: Post reports
         env:

.github/workflows/benchmarks_run.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -46,7 +46,7 @@ jobs:
 
       - name: Cache environment directories
         id: cache-env-dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             .nox
@@ -56,7 +56,7 @@ jobs:
 
       - name: Cache test data directory
         id: cache-test-data
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ${{ env.IRIS_TEST_DATA_PATH }}
@@ -113,14 +113,14 @@ jobs:
 
       - name: Upload any benchmark reports
         if: success() || steps.overnight.outcome == 'failure'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: benchmark_reports
           path: .github/workflows/benchmark_reports
 
       - name: Archive asv results
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: asv-raw-results
           path: benchmarks/.asv/results

.github/workflows/ci-citation.yml

@@ -0,0 +1,30 @@
+name: ci-citation
+
+on:
+  pull_request:
+    paths:
+      - "CITATION.cff"
+
+  push:
+    paths:
+      - "CITATION.cff"
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: "check CITATION.cff"
+        uses: citation-file-format/cffconvert-github-action@4cf11baa70a673bfdf9dad0acc7ee33b3f4b6084
+        with:
+          args: "--validate"

.github/workflows/ci-manifest.yml

@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.10.0
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2024.02.0

.github/workflows/ci-tests.yml

@@ -55,7 +55,7 @@ jobs:
 
     steps:
       - name: "checkout"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "environment configure"
         env:
@@ -80,7 +80,7 @@ jobs:
           env_name: ${{ env.ENV_NAME }}
 
       - name: "conda install"
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
           channels: conda-forge,defaults
@@ -140,5 +140,5 @@ jobs:
           nox --session ${{ matrix.session }} -- --verbose ${{ matrix.coverage }}
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         if: ${{ matrix.coverage }}

.github/workflows/ci-wheels.yml

@@ -28,7 +28,7 @@ jobs:
     name: "build sdist & wheel"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -37,7 +37,7 @@ jobs:
       run: |
         pipx run build
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: pypi-artifacts
         path: ${{ github.workspace }}/dist/*
@@ -57,11 +57,11 @@ jobs:
     env:
       ENV_NAME: "ci-wheels"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: pypi-artifacts
         path: ${{ github.workspace }}/dist
@@ -82,7 +82,7 @@ jobs:
         env_name: ${{ env.ENV_NAME }}
 
     - name: "conda install"
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
         channels: conda-forge,defaults
@@ -116,7 +116,7 @@ jobs:
     name: "show artifacts"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: pypi-artifacts
         path: ${{ github.workspace }}/dist
@@ -133,7 +133,7 @@ jobs:
     # and check for the SciTools repo
     if: github.event_name == 'push' && github.event.ref == 'refs/heads/main' && github.repository_owner == 'SciTools'
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: pypi-artifacts
         path: ${{ github.workspace }}/dist
@@ -153,7 +153,7 @@ jobs:
     # upload to PyPI for every tag starting with 'v'
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') && github.repository_owner == 'SciTools'
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: pypi-artifacts
         path: ${{ github.workspace }}/dist

.github/workflows/refresh-lockfiles.yml

@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.10.0
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2024.02.0
     secrets: inherit

.github/workflows/stale.yml

@@ -14,7 +14,7 @@ jobs:
     if: "github.repository == 'SciTools/iris'"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/stale@v8
+      - uses: actions/stale@v9
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 

.gitignore

@@ -65,6 +65,7 @@ lib/iris/tests/results/imagerepo.lock
 # Auto generated documentation files
 docs/src/_build/*
 docs/src/generated
+docs/src/sg_execution_times.rst
 
 # Example test results
 docs/iris_image_test_output/

.pre-commit-config.yaml

@@ -28,33 +28,28 @@ repos:
         # Don't commit to main branch.
     -   id: no-commit-to-branch
 
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.14"
+    hooks:
+    -   id: ruff
+        types: [file, python]
+        args: [--fix, --show-fixes]
+    -   id: ruff-format
+        types: [file, python]
+
 -   repo: https://github.com/codespell-project/codespell
     rev: "v2.2.6"
     hooks:
     -   id: codespell
         types_or: [asciidoc, python, markdown, rst]
         additional_dependencies: [tomli]
 
--   repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-    -   id: black
-        pass_filenames: false
-        args: [--config=./pyproject.toml, .]
-
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
         types: [file, python]
 
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
-        types: [file, python]
-        args: [--filter-files]
-
 -   repo: https://github.com/asottile/blacken-docs
     rev: 1.16.0
     hooks:

.readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: "ubuntu-22.04"
   tools:
-    python: mambaforge-4.10
+    python: "mambaforge-22.9"
   jobs:
     post_checkout:
       # The SciTools/iris repository is shallow i.e., has a .git/shallow,