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) ...
tkknight · Mar 11, 2023 · c1e6e47 · c1e6e47
2 parents 163b56f + e2dc89c
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diff --git a/.github/workflows/ci-tests.yml b/.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 }}
diff --git a/.pre-commit-config.yaml b/.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

diff --git a/README.md b/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>
+
diff --git a/benchmarks/benchmarks/experimental/ugrid/__init__.py b/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):

diff --git a/docs/Makefile b/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..."; \

diff --git a/docs/gallery_code/general/plot_custom_aggregation.py b/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.

diff --git a/docs/gallery_code/general/plot_lineplot_with_legend.py b/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]
 

diff --git a/docs/gallery_code/general/plot_projections_and_annotations.py b/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()
 

diff --git a/docs/gallery_code/general/plot_zonal_means.py b/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)

diff --git a/docs/gallery_code/meteorology/plot_lagged_ensemble.py b/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]
 

diff --git a/docs/src/Makefile b/docs/src/Makefile
@@ -62,11 +62,6 @@ html-quick:
 	@echo
 	@echo "Build finished. The HTML (no gallery or api docs) pages are in $(BUILDDIR)/html"
 
-spelling:
-	$(SPHINXBUILD) -b spelling $(SRCDIR) $(BUILDDIR)
-	@echo
-	@echo "Build finished. The HTML (no gallery) pages are in $(BUILDDIR)/html"
-
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
@@ -156,4 +151,5 @@ doctest:
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
 show:
-	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(shell pwd)/$(BUILDDIR)/html/index.html')"
+	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(shell pwd)/$(BUILDDIR)/html/index.html')"
+
diff --git a/docs/src/common_links.inc b/docs/src/common_links.inc
@@ -9,7 +9,7 @@
 .. _conda: https://docs.conda.io/en/latest/
 .. _contributor: https://github.com/SciTools/scitools.org.uk/blob/master/contributors.json
 .. _core developers: https://github.com/SciTools/scitools.org.uk/blob/master/contributors.json
-.. _generating sss keys for GitHub: https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account
+.. _generating ssh keys for GitHub: https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account
 .. _GitHub Actions: https://docs.github.com/en/actions
 .. _GitHub Help Documentation: https://docs.github.com/en/github
 .. _GitHub Discussions: https://github.com/SciTools/iris/discussions
@@ -40,22 +40,26 @@
 .. _CF-UGRID: https://ugrid-conventions.github.io/ugrid-conventions/
 .. _issues on GitHub: https://github.com/SciTools/iris/issues?q=is%3Aopen+is%3Aissue+sort%3Areactions-%2B1-desc
 .. _python-stratify: https://github.com/SciTools/python-stratify
+.. _iris-esmf-regrid: https://github.com/SciTools-incubator/iris-esmf-regrid
+.. _netCDF4: https://github.com/Unidata/netcdf4-python
 
 
 .. comment
-    Core developers (@github names) in alphabetical order:
+    Core developers and prolific contributors (@github names) in alphabetical order:
 
 .. _@abooton: https://github.com/abooton
 .. _@alastair-gemmell: https://github.com/alastair-gemmell
 .. _@ajdawson: https://github.com/ajdawson
 .. _@bjlittle: https://github.com/bjlittle
 .. _@bouweandela: https://github.com/bouweandela
+.. _@bsherratt: https://github.com/bsherratt
 .. _@corinnebosley: https://github.com/corinnebosley
 .. _@cpelley: https://github.com/cpelley
 .. _@djkirkham: https://github.com/djkirkham
 .. _@DPeterK: https://github.com/DPeterK
 .. _@ESadek-MO: https://github.com/ESadek-MO
 .. _@esc24: https://github.com/esc24
+.. _@HGWright: https://github.com/HGWright
 .. _@jamesp: https://github.com/jamesp
 .. _@jonseddon: https://github.com/jonseddon
 .. _@jvegasbsc: https://github.com/jvegasbsc

diff --git a/docs/src/community/index.rst b/docs/src/community/index.rst
@@ -0,0 +1,58 @@
+.. include:: ../common_links.inc
+
+.. todo:
+    consider scientific-python.org
+    consider scientific-python.org/specs/
+
+Iris in the Community
+=====================
+
+Iris aims to be a valuable member of the open source scientific Python
+community.
+
+We listen out for developments in our dependencies and neighbouring projects,
+and we reach out to them when we can solve problems together; please feel free
+to reach out to us!
+
+We are aware of our place in the user's wider 'toolbox' - offering unique
+functionality and interoperating smoothly with other packages.
+
+We welcome contributions from all; whether that's an opinion, a 1-line
+clarification, or a whole new feature 🙂
+
+Quick Links
+-----------
+
+* `GitHub Discussions`_
+* :ref:`Getting involved<development_where_to_start>`
+* `Twitter <https://twitter.com/scitools_iris>`_
+
+Interoperability
+----------------
+
+There's a big choice of Python tools out there! Each one has strengths and
+weaknesses in different areas, so we don't want to force a single choice for your
+whole workflow - we'd much rather make it easy for you to choose the right tool
+for the moment, switching whenever you need. Below are our ongoing efforts at
+smoother interoperability:
+
+.. not using toctree due to combination of child pages and cross-references.
+
+* The :mod:`iris.pandas` module
+* :doc:`iris_xarray`
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+
+   iris_xarray
+
+Plugins
+-------
+
+Iris can be extended with **plugins**!  See below for further information:
+
+.. toctree::
+   :maxdepth: 2
+
+   plugins