Pytest merge conflicts

.github/dependabot.yml

@@ -6,10 +6,15 @@ version: 2
 updates:
 
   - package-ecosystem: "github-actions"
-    directory: "/"
+    directories:
+      - "/"
+      - "/.github/workflows/composite/*"
     schedule:
-      # Check for updates to GitHub Actions every weekday
-      interval: "daily"
+      # Check later in the week - the upstream dependabot check in `workflows` runs deliberately early in the week.
+      #  Therefore allowing time for the `workflows` update to be merged-and-released first.
+      interval: "weekly"
+      day: "thursday"
+      time: "01:00"
+      timezone: "Europe/London"
     labels:
-      - "New: Pull Request"
       - "Bot"

.github/labeler.yml

@@ -1,6 +1,9 @@
-# Make sure any dependency changes are benchmarked (only changes to the locks
-#  make a material difference - changes to the Conda YAML files are not
-#  benchmarked).
+# benchmark_this automatically triggers the benchmark workflow when added by
+#  a user. No triggering happens when GitHub Actions adds the label (this
+#  avoids security vulnerabilities), so alternative triggers for the below
+#  files are therefore included in workflows/benchmarks_run.yml. Automatic
+#  labelling is still included here to make it easier to search pull requests,
+#  and to reinforce the culture of using this label.
 benchmark_this:
 - changed-files:
-  - any-glob-to-any-file: 'requirements/locks/*.lock'
+  - any-glob-to-any-file: ['requirements/locks/*.lock', "setup.py"]

.github/pull_request_template.md

@@ -7,3 +7,8 @@
 
 ---
 [Consult Iris pull request check list]( https://scitools-iris.readthedocs.io/en/latest/developers_guide/contributing_pull_request_checklist.html)
+
+---
+Add any of the below labels to trigger actions on this PR:
+
+- https://github.com/SciTools/iris/labels/benchmark_this

.github/workflows/benchmarks_run.yml

@@ -16,20 +16,51 @@ on:
         required: false
         type: string
   pull_request:
-    types: [labeled]
+    # Add the `labeled` type to the default list.
+    types: [labeled, opened, synchronize, reopened]
 
 jobs:
+  pre-checks:
+    runs-on: ubuntu-latest
+    if: github.repository == 'SciTools/iris'
+    outputs:
+      overnight: ${{ steps.overnight.outputs.check }}
+      branch: ${{ steps.branch.outputs.check }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - id: files-changed
+        uses: marceloprado/has-changed-path@df1b7a3161b8fb9fd8c90403c66a9e66dfde50cb
+        with:
+          # SEE ALSO .github/labeler.yml .
+          paths: requirements/locks/*.lock setup.py
+      - id: overnight
+        if: github.event_name != 'pull_request'
+        run: echo "check=true" >> "$GITHUB_OUTPUT"
+      - id: branch
+        if: >
+          github.event_name == 'pull_request'
+          &&
+          (
+            steps.files-changed.outputs.changed == 'true'
+            ||
+            github.event.label.name == 'benchmark_this'
+          )
+        run: echo "check=true" >> "$GITHUB_OUTPUT"
+
+
   benchmark:
-    if: >
-      github.repository == 'SciTools/iris' && 
-      (github.event_name != 'pull_request' || 
-      github.event.label.name == 'benchmark_this')
     runs-on: ubuntu-latest
+    needs: pre-checks
+    if: >
+      needs.pre-checks.outputs.overnight == 'true' ||
+      needs.pre-checks.outputs.branch == 'true'
 
     env:
       IRIS_TEST_DATA_LOC_PATH: benchmarks
       IRIS_TEST_DATA_PATH: benchmarks/iris-test-data
-      IRIS_TEST_DATA_VERSION: "2.22"
+      IRIS_TEST_DATA_VERSION: "2.28"
       # Lets us manually bump the cache to rebuild
       ENV_CACHE_BUILD: "0"
       TEST_DATA_CACHE_BUILD: "2"
@@ -40,9 +71,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Install ASV & Nox
+      - name: Install Nox
         run: |
-          pip install "asv!=0.6.2" nox
+          pip install nox
 
       - name: Cache environment directories
         id: cache-env-dir
@@ -76,16 +107,16 @@ jobs:
           echo "OVERRIDE_TEST_DATA_REPOSITORY=${GITHUB_WORKSPACE}/${IRIS_TEST_DATA_PATH}/test_data" >> $GITHUB_ENV
 
       - name: Benchmark this pull request
-        if: ${{ github.event.label.name == 'benchmark_this' }}
+        if: needs.pre-checks.outputs.branch == 'true'
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PR_NUMBER: ${{ github.event.number }}
         run: |
-          python benchmarks/bm_runner.py branch origin/${{ github.base_ref }}
+          nox -s benchmarks -- branch origin/${{ github.base_ref }}
 
       - name: Run overnight benchmarks
         id: overnight
-        if: ${{ github.event_name != 'pull_request' }}
+        if: needs.pre-checks.outputs.overnight == 'true'
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -97,7 +128,7 @@ jobs:
 
           if [ "$first_commit" != "" ]
           then
-            python benchmarks/bm_runner.py overnight $first_commit
+            nox -s benchmarks -- overnight $first_commit
           fi
 
       - name: Warn of failure

.github/workflows/ci-manifest.yml

@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2024.02.1
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2024.10.2

.github/workflows/ci-tests.yml

@@ -35,22 +35,23 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         session: ["doctest", "gallery", "linkcheck"]
         include:
           - os: "ubuntu-latest"
-            python-version: "3.11"
+            python-version: "3.12"
             session: "tests"
             coverage: "--coverage"
           - os: "ubuntu-latest"
-            python-version: "3.10"
+            python-version: "3.11"
             session: "tests"
           - os: "ubuntu-latest"
-            python-version: "3.9"
+            python-version: "3.10"
             session: "tests"
 
     env:
-      IRIS_TEST_DATA_VERSION: "2.22"
+      # NOTE: IRIS_TEST_DATA_VERSION is also set in benchmarks_run.yml
+      IRIS_TEST_DATA_VERSION: "2.28"
       ENV_NAME: "ci-tests"
 
     steps:
@@ -68,30 +69,29 @@ jobs:
       - name: "data cache"
         uses: ./.github/workflows/composite/iris-data-cache
         with:
-          cache_build: 0
+          cache_build: 6
           env_name: ${{ env.ENV_NAME }}
           version: ${{ env.IRIS_TEST_DATA_VERSION }}
 
       - name: "conda package cache"
         uses: ./.github/workflows/composite/conda-pkg-cache
         with:
-          cache_build: 0
+          cache_build: 6
           cache_period: ${{ env.CACHE_PERIOD }}
           env_name: ${{ env.ENV_NAME }}
 
       - name: "conda install"
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          channels: conda-forge,defaults
+          channels: conda-forge
           activate-environment: ${{ env.ENV_NAME }}
           auto-update-conda: false
-          use-only-tar-bz2: true
 
       - name: "conda environment cache"
         uses: ./.github/workflows/composite/conda-env-cache
         with:
-          cache_build: 0
+          cache_build: 6
           cache_period: ${{ env.CACHE_PERIOD }}
           env_name: ${{ env.ENV_NAME }}
           install_packages: "cartopy nox pip"
@@ -104,14 +104,14 @@ jobs:
       - name: "cartopy cache"
         uses: ./.github/workflows/composite/cartopy-cache
         with:
-          cache_build: 0
+          cache_build: 6
           cache_period: ${{ env.CACHE_PERIOD }}
           env_name: ${{ env.ENV_NAME }}
 
       - name: "nox cache"
         uses: ./.github/workflows/composite/nox-cache
         with:
-          cache_build: 2
+          cache_build: 6
           env_name: ${{ env.ENV_NAME }}
           lock_file: ${{ env.LOCK_FILE }}
 
@@ -136,9 +136,13 @@ jobs:
       - name: "iris ${{ matrix.session }}"
         env:
           PY_VER: ${{ matrix.python-version }}
+          # Force coloured output on GitHub Actions.
+          PY_COLORS: "1"
         run: |
           nox --session ${{ matrix.session }} -- --verbose ${{ matrix.coverage }}
 
-      - name: Upload coverage report
-        uses: codecov/codecov-action@v4
+      - name: "upload coverage report"
         if: ${{ matrix.coverage }}
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci-wheels.yml

@@ -52,7 +52,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         session: ["wheel"]
     env:
       ENV_NAME: "ci-wheels"

.github/workflows/composite/cartopy-cache/action.yml

@@ -20,7 +20,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: cartopy-cache
       with:
         path: ~/.local/share/cartopy

.github/workflows/composite/conda-env-cache/action.yml

@@ -23,7 +23,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: conda-env-cache
       with:
         path: ${{ env.CONDA }}/envs/${{ inputs.env_name }}

.github/workflows/composite/conda-pkg-cache/action.yml

@@ -16,7 +16,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         path: ~/conda_pkgs_dir
         key: ${{ runner.os }}-conda-pkgs-${{ inputs.env_name }}-p${{ inputs.cache_period }}-b${{ inputs.cache_build }}

.github/workflows/composite/iris-data-cache/action.yml

@@ -16,7 +16,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: data-cache
       with:
         path: ~/iris-test-data

.github/workflows/composite/nox-cache/action.yml

@@ -16,7 +16,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         path: ${{ github.workspace }}/.nox
         key: ${{ runner.os }}-nox-${{ inputs.env_name }}-s${{ matrix.session }}-py${{ matrix.python-version }}-b${{ inputs.cache_build }}-${{ hashFiles(inputs.lock_file) }}

.github/workflows/refresh-lockfiles.yml

@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2024.02.1
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2024.10.2
     secrets: inherit

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ minimum_pre_commit_version: 1.21.0
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.2.1"
+    rev: "v0.7.1"
     hooks:
     -   id: ruff
         types: [file, python]
@@ -38,20 +38,20 @@ repos:
         types: [file, python]
 
 -   repo: https://github.com/codespell-project/codespell
-    rev: "v2.2.6"
+    rev: "v2.3.0"
     hooks:
     -   id: codespell
         types_or: [asciidoc, python, markdown, rst]
         additional_dependencies: [tomli]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
         types: [file, python]
 
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
         types: [file, rst]
@@ -61,3 +61,18 @@ repos:
     hooks:
     -   id: sort-all
         types: [file, python]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.13.0'
+    hooks:
+    -   id: mypy
+        additional_dependencies:
+            - 'types-requests'
+        exclude: 'noxfile\.py|docs/src/conf\.py'
+
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+      - id: numpydoc-validation
+        exclude: "^lib/iris/tests/|docs/gallery_code/"
+        types: [file, python]