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

* upstream/main: (23 commits)
  Lockfiles and pydata-sphinx-theme fix (SciTools#5188)
  Allow smarter weights (cubes, coordinates, cell measures, or ancillary variables) for aggregation (SciTools#5084)
  removed cell measure mask check and error (SciTools#5181)
  Updated environment lockfiles (SciTools#5177)
  Lazy weighted RMS calculation (SciTools#5017)
  Add coverage badge to README.md (SciTools#5176)
  Add coverage testing (SciTools#4765)
  Whats new updates for v3.4.1 .
  NetCDF thread safety take two (SciTools#5095)
  Updated environment lockfiles (SciTools#5163)
  Plugin support (SciTools#5144)
  Expand scope of common contributor links (SciTools#5159)
  Replace apparently retired UDUNITS documentation link. (SciTools#5153)
  [pre-commit.ci] pre-commit autoupdate (SciTools#5150)
  Fixing typo's in Gitwash. (SciTools#5145)
  add readme #showyourstripes (SciTools#5141)
  [pre-commit.ci] pre-commit autoupdate (SciTools#5143)
  Iris ❤ Xarray docs page. (SciTools#5025)
  [pre-commit.ci] pre-commit autoupdate (SciTools#5136)
  Updated citation (SciTools#5116)
  ...

Author: tkknight

.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"
@@ -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 }}

.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: 23.1.0
     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

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>
+

benchmarks/benchmarks/experimental/ugrid/__init__.py

@@ -50,7 +50,7 @@ def time_create(self, *params):
 
 class Connectivity(UGridCommon):
     def setup(self, n_faces):
-        self.array = np.zeros([n_faces, 3], dtype=np.int)
+        self.array = np.zeros([n_faces, 3], dtype=int)
         super().setup(n_faces)
 
     def create(self):

docs/Makefile

@@ -20,11 +20,6 @@ html-quick:
         echo "make html-quick in $$i..."; \
         (cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) html-quick); done
 
-spelling:
-	@for i in $(SUBDIRS); do \
-        echo "make spelling in $$i..."; \
-        (cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) spelling); done
-
 all:
 	@for i in $(SUBDIRS); do \
 		echo "make all in $$i..."; \

docs/gallery_code/general/plot_custom_aggregation.py

@@ -72,7 +72,7 @@ def main():
 
     # Make an aggregator from the user function.
     SPELL_COUNT = Aggregator(
-        "spell_count", count_spells, units_func=lambda units: 1
+        "spell_count", count_spells, units_func=lambda units, **kwargs: 1
     )
 
     # Define the parameters of the test.

docs/gallery_code/general/plot_lineplot_with_legend.py

@@ -24,7 +24,6 @@ def main():
     )
 
     for cube in temperature.slices("longitude"):
-
         # Create a string label to identify this cube (i.e. latitude: value).
         cube_label = "latitude: %s" % cube.coord("latitude").points[0]
 

docs/gallery_code/general/plot_projections_and_annotations.py

@@ -26,7 +26,6 @@
 
 
 def make_plot(projection_name, projection_crs):
-
     # Create a matplotlib Figure.
     plt.figure()
 

docs/gallery_code/general/plot_zonal_means.py

@@ -16,7 +16,6 @@
 
 
 def main():
-
     # Loads air_temp.pp and "collapses" longitude into a single, average value.
     fname = iris.sample_data_path("air_temp.pp")
     temperature = iris.load_cube(fname)

docs/gallery_code/meteorology/plot_lagged_ensemble.py

@@ -86,7 +86,6 @@ def main():
 
     # Iterate over all possible latitude longitude slices.
     for cube in last_timestep.slices(["latitude", "longitude"]):
-
         # Get the ensemble member number from the ensemble coordinate.
         ens_member = cube.coord("realization").points[0]