Merge remote-tracking branch 'upstream/main' into adopt_sphinx_design

* upstream/main: (59 commits)
  Updated environment lockfiles (SciTools#5211)
  update ci locks location (SciTools#5228)
  Fixes to _discontiguity_in_bounds (attempt 2) (SciTools#4975)
  Finalises Lazy Data documentation (SciTools#5137)
  Modernize and simplify iris.analysis._Groupby (SciTools#5015)
  clarity on whatsnew entry contributors (SciTools#5240)
  Handle derived coordinates correctly in `concatenate` (SciTools#5096)
  Use real array for data of of small netCDF variables. (SciTools#5229)
  Bump scitools/workflows from 2023.04.1 to 2023.04.2 (SciTools#5236)
  fixing whatsnew entry
  remove results creation commit from blame
  configure codecov
  adding a whatsnew entry
  Replacing numpy legacy printing with array2string and remaking results for dependent tests
  Adding a whatsnew entry for 5224 (SciTools#5234)
  Cf cell method (SciTools#5224)
  Bump scitools/workflows from 2023.03.3 to 2023.04.1 (SciTools#5231)
  [pre-commit.ci] pre-commit autoupdate (SciTools#5230)
  Bump scitools/workflows from 2023.03.2 to 2023.03.3 (SciTools#5227)
  raise dask min pin (SciTools#5225)
  ...

Author: tkknight

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Format: numpy array format (#5235)
+c18dcd8dafef0cc7bbbf80dfce66f76a46ce59c5

.github/workflows/benchmark.yml

@@ -21,21 +21,20 @@ jobs:
     env:
       IRIS_TEST_DATA_LOC_PATH: benchmarks
       IRIS_TEST_DATA_PATH: benchmarks/iris-test-data
-      IRIS_TEST_DATA_VERSION: "2.18"
+      IRIS_TEST_DATA_VERSION: "2.19"
       # Lets us manually bump the cache to rebuild
       ENV_CACHE_BUILD: "0"
       TEST_DATA_CACHE_BUILD: "2"
-      PY_VER: 3.8
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Install Nox
+      - name: Install ASV & Nox
         run: |
-          pip install nox
+          pip install asv nox
 
       - name: Cache environment directories
         id: cache-env-dir
@@ -78,7 +77,7 @@ jobs:
           
           if [ "$first_commit" != "" ]
           then
-            nox --session="benchmarks(overnight)" -- $first_commit
+            python benchmarks/bm_runner.py overnight $first_commit
           fi
 
       - name: Create issues for performance shifts

.github/workflows/ci-tests.yml

@@ -36,8 +36,12 @@ jobs:
       matrix:
         os: ["ubuntu-latest"]
         python-version: ["3.10"]
-        session: ["tests", "doctest", "gallery", "linkcheck"]
+        session: ["doctest", "gallery", "linkcheck"]
         include:
+          - os: "ubuntu-latest"
+            python-version: "3.10"
+            session: "tests"
+            coverage: "--coverage"
           - os: "ubuntu-latest"
             python-version: "3.9"
             session: "tests"
@@ -46,7 +50,7 @@ jobs:
             session: "tests"
 
     env:
-      IRIS_TEST_DATA_VERSION: "2.18"
+      IRIS_TEST_DATA_VERSION: "2.19"
       ENV_NAME: "ci-tests"
 
     steps:
@@ -59,7 +63,7 @@ jobs:
           CACHE_WEEKS: 2
         run: |
           echo "CACHE_PERIOD=$(date +%Y).$(expr $(date +%U) / ${CACHE_WEEKS})" >> ${GITHUB_ENV}
-          echo "LOCK_FILE=requirements/ci/nox.lock/py$(echo ${{ matrix.python-version }} | tr -d '.')-linux-64.lock" >> ${GITHUB_ENV}
+          echo "LOCK_FILE=requirements/locks/py$(echo ${{ matrix.python-version }} | tr -d '.')-linux-64.lock" >> ${GITHUB_ENV}
 
       - name: "data cache"
         uses: ./.github/workflows/composite/iris-data-cache
@@ -107,7 +111,7 @@ jobs:
       - name: "nox cache"
         uses: ./.github/workflows/composite/nox-cache
         with:
-          cache_build: 0
+          cache_build: 2
           env_name: ${{ env.ENV_NAME }}
           lock_file: ${{ env.LOCK_FILE }}
 
@@ -133,4 +137,8 @@ jobs:
         env:
           PY_VER: ${{ matrix.python-version }}
         run: |
-          nox --session ${{ matrix.session }} -- --verbose
+          nox --session ${{ matrix.session }} -- --verbose ${{ matrix.coverage }}
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v3
+        if: ${{ matrix.coverage }}

.github/workflows/ci-wheels.yml

@@ -74,7 +74,7 @@ jobs:
           CACHE_WEEKS: 2
       run: |
         echo "CACHE_PERIOD=$(date +%Y).$(expr $(date +%U) / ${CACHE_WEEKS})" >> ${GITHUB_ENV}
-        echo "LOCK_FILE=requirements/ci/nox.lock/py$(echo ${{ matrix.python-version }} | tr -d '.')-linux-64.lock" >> ${GITHUB_ENV}
+        echo "LOCK_FILE=requirements/locks/py$(echo ${{ matrix.python-version }} | tr -d '.')-linux-64.lock" >> ${GITHUB_ENV}
 
     - name: "conda package cache"
       uses: ./.github/workflows/composite/conda-pkg-cache
@@ -103,7 +103,7 @@ jobs:
     - name: "nox cache"
       uses: ./.github/workflows/composite/nox-cache
       with:
-        cache_build: 0
+        cache_build: 1
         env_name: ${{ env.ENV_NAME }}
         lock_file: ${{ env.LOCK_FILE }}
 
@@ -132,7 +132,8 @@ jobs:
     name: "publish to test.pypi"
     runs-on: ubuntu-latest
     # upload to Test PyPI for every commit on main branch
-    if: github.event_name == 'push' && github.event.ref == 'refs/heads/main'
+    # 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
       with:
@@ -152,7 +153,7 @@ jobs:
     name: "publish to pypi"
     runs-on: ubuntu-latest
     # upload to PyPI for every tag starting with 'v'
-    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') && github.repository-owner == 'SciTools'
     steps:
     - uses: actions/download-artifact@v3
       with:

.github/workflows/refresh-lockfiles.yml

@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@main
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.04.2
     secrets: inherit

.github/workflows/stale.yml

@@ -14,7 +14,7 @@ jobs:
     if: "github.repository == 'SciTools/iris'"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@v8
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.3.0
     hooks:
     -   id: black
         pass_filenames: false
@@ -43,18 +43,17 @@ repos:
         args: [--config=./setup.cfg]
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
     -   id: isort
         types: [file, python]
         args: [--filter-files]
 
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.13.0
     hooks:
     -   id: blacken-docs
         types: [file, rst]
-        additional_dependencies: [black==21.6b0]
 
 -   repo: https://github.com/aio-libs/sort-all
     rev: v1.2.0

.readthedocs.yml

@@ -19,7 +19,7 @@ build:
       - git stash pop
 
 conda:
-  environment: requirements/ci/readthedocs.yml
+  environment: requirements/readthedocs.yml
 
 sphinx:
   configuration: docs/src/conf.py

Makefile

@@ -1,2 +1,2 @@
 lockfiles:
-	python tools/update_lockfiles.py -o requirements/ci/nox.lock requirements/ci/py*.yml
+	python tools/update_lockfiles.py -o requirements/locks requirements/py*.yml

README.md

@@ -19,6 +19,9 @@
 <a href="https://results.pre-commit.ci/latest/github/SciTools/iris/main">
 <img src="https://results.pre-commit.ci/badge/github/SciTools/iris/main.svg"
      alt="pre-commit.ci status"></a>
+<a href="https://codecov.io/gh/SciTools/iris">
+<img src="https://codecov.io/gh/SciTools/iris/branch/main/graph/badge.svg?token=0GeICSIF3g"
+     alt="code coverage"></a>
 </p>
 
 <p align="center">
@@ -54,3 +57,24 @@ For documentation see the
 developer version or the most recent released
 <a href="https://scitools-iris.readthedocs.io/en/stable/">stable</a> version.
 </p>
+
+## [#ShowYourStripes](https://showyourstripes.info/s/globe)
+
+<h4 align="center">
+  <a href="https://showyourstripes.info/s/globe">
+    <img src="https://raw.githubusercontent.com/ed-hawkins/show-your-stripes/master/2021/GLOBE---1850-2021-MO.png"
+         height="50" width="800"
+         alt="#showyourstripes Global 1850-2021"></a>
+</h4>
+
+**Graphics and Lead Scientist**: [Ed Hawkins](http://www.met.reading.ac.uk/~ed/home/index.php), National Centre for Atmospheric Science, University of Reading.
+
+**Data**: Berkeley Earth, NOAA, UK Met Office, MeteoSwiss, DWD, SMHI, UoR, Meteo France & ZAMG.
+
+<p>
+<a href="https://showyourstripes.info/s/globe">#ShowYourStripes</a> is distributed under a
+<a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>
+<a href="https://creativecommons.org/licenses/by/4.0/">
+  <img src="https://i.creativecommons.org/l/by/4.0/80x15.png" alt="creative-commons-by" style="border-width:0"></a>
+</p>
+