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

* upstream/main: moved latest warning banner logic to conf.py (SciTools#5508) updated layout of top navbar (SciTools#5505) Oblique and Rotated Mercator (SciTools#5548) [pre-commit.ci] pre-commit autoupdate (SciTools#5549) [pre-commit.ci] pre-commit autoupdate (SciTools#5527) Bump scitools/workflows from 2023.09.1 to 2023.10.0 (SciTools#5540) nep29 drop table schedule numpy>1.21 (SciTools#5525) Updated environment lockfiles (SciTools#5545) Replaced `NotImplementedError` with `NotImplemented` (SciTools#5544) Gallery: show colour bar stealing space from multiple axes (SciTools#5537) Updated environment lockfiles (SciTools#5524) Set some memory benchmarks to on-demand to reduce noise. (SciTools#5481) updating docs and stale comment (SciTools#5522) Ensure removal of release candidate from What's New title. (SciTools#5526) Updated environment lockfiles (SciTools#5513) Docs page on filtering warnings (SciTools#5509) Replaced pkg_resources version parser with packager version parser. (SciTools#5511) Categorise warnings (SciTools#5498) Updated all np.product calls to np.prod (SciTools#5493)
tkknight · Oct 26, 2023 · 3d7586b · 3d7586b
2 parents 7e7f9b2 + cc52dca
commit 3d7586b
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diff --git a/.github/workflows/benchmarks_run.yml b/.github/workflows/benchmarks_run.yml
@@ -29,7 +29,7 @@ jobs:
     env:
       IRIS_TEST_DATA_LOC_PATH: benchmarks
       IRIS_TEST_DATA_PATH: benchmarks/iris-test-data
-      IRIS_TEST_DATA_VERSION: "2.19"
+      IRIS_TEST_DATA_VERSION: "2.21"
       # Lets us manually bump the cache to rebuild
       ENV_CACHE_BUILD: "0"
       TEST_DATA_CACHE_BUILD: "2"

diff --git a/.github/workflows/ci-manifest.yml b/.github/workflows/ci-manifest.yml
@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.09.1
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.10.0
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -50,7 +50,7 @@ jobs:
             session: "tests"
 
     env:
-      IRIS_TEST_DATA_VERSION: "2.19"
+      IRIS_TEST_DATA_VERSION: "2.21"
       ENV_NAME: "ci-tests"
 
     steps:

diff --git a/.github/workflows/refresh-lockfiles.yml b/.github/workflows/refresh-lockfiles.yml
@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.09.1
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.10.0
     secrets: inherit
diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -46,7 +46,7 @@ jobs:
 
             If you still care about this issue, then please either:
               * Re-open this issue, if you have sufficient permissions, or
-              * Add a comment pinging `@SciTools/iris-devs` who will re-open on your behalf.
+              * Add a comment stating that this is still relevant and someone will re-open it on your behalf.
 
           # Comment on the staled prs while closed.
           close-pr-message: |

diff --git a/.pre-commit-config.yaml b/.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: v4.4.0
+    rev: v4.5.0
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
@@ -29,14 +29,14 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/codespell-project/codespell
-    rev: "v2.2.5"
+    rev: "v2.2.6"
     hooks:
     -   id: codespell
         types_or: [asciidoc, python, markdown, rst]
         additional_dependencies: [tomli]
 
 -   repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.0
     hooks:
     -   id: black
         pass_filenames: false

diff --git a/benchmarks/benchmarks/cperf/__init__.py b/benchmarks/benchmarks/cperf/__init__.py
@@ -53,7 +53,7 @@ def setup(self, file_type, three_d, three_times):
             if three_d:
                 create_kwargs["n_levels"] = 71
 
-            # Will re-use a file if already present.
+            # Will reuse a file if already present.
             file_path = make_cubesphere_testfile(**create_kwargs)
 
         else:

diff --git a/benchmarks/benchmarks/experimental/ugrid/regions_combine.py b/benchmarks/benchmarks/experimental/ugrid/regions_combine.py
@@ -23,7 +23,7 @@
 from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD
 from iris.experimental.ugrid.utils import recombine_submeshes
 
-from ... import TrackAddedMemoryAllocation
+from ... import TrackAddedMemoryAllocation, on_demand_benchmark
 from ...generate_data.ugrid import make_cube_like_2d_cubesphere
 
 
@@ -200,6 +200,8 @@ class CombineRegionsComputeRealData(MixinCombineRegions):
     def time_compute_data(self, n_cubesphere):
         _ = self.recombined_cube.data
 
+    # Vulnerable to noise, so disabled by default.
+    @on_demand_benchmark
     @TrackAddedMemoryAllocation.decorator
     def track_addedmem_compute_data(self, n_cubesphere):
         _ = self.recombined_cube.data
@@ -217,6 +219,8 @@ def time_save(self, n_cubesphere):
         # Save to disk, which must compute data + stream it to file.
         save(self.recombined_cube, "tmp.nc")
 
+    # Vulnerable to noise, so disabled by default.
+    @on_demand_benchmark
     @TrackAddedMemoryAllocation.decorator
     def track_addedmem_save(self, n_cubesphere):
         save(self.recombined_cube, "tmp.nc")
@@ -245,6 +249,8 @@ def time_stream_file2file(self, n_cubesphere):
         # Save to disk, which must compute data + stream it to file.
         save(self.recombined_cube, "tmp.nc")
 
+    # Vulnerable to noise, so disabled by default.
+    @on_demand_benchmark
     @TrackAddedMemoryAllocation.decorator
     def track_addedmem_stream_file2file(self, n_cubesphere):
         save(self.recombined_cube, "tmp.nc")
diff --git a/benchmarks/benchmarks/generate_data/stock.py b/benchmarks/benchmarks/generate_data/stock.py
@@ -39,7 +39,7 @@ def _external(func_name_, temp_file_dir, **kwargs_):
     )
     if not REUSE_DATA or not save_path.is_file():
         # The xios functions take control of save location so need to move to
-        #  a more specific name that allows re-use.
+        #  a more specific name that allows reuse.
         actual_path = run_function_elsewhere(
             _external,
             func_name_=func_name,

diff --git a/benchmarks/benchmarks/load/__init__.py b/benchmarks/benchmarks/load/__init__.py
@@ -69,7 +69,7 @@ def time_realise(self, _, __, ___, ____) -> None:
 
 
 class STASHConstraint:
-    # xyz sizes mimic LoadAndRealise to maximise file re-use.
+    # xyz sizes mimic LoadAndRealise to maximise file reuse.
     params = [[(2, 2, 2), (1280, 960, 5), (2, 2, 1000)], ["FF", "PP"]]
     param_names = ["xyz", "file_format"]
 

diff --git a/benchmarks/benchmarks/save.py b/benchmarks/benchmarks/save.py
@@ -16,7 +16,7 @@
 from iris import save
 from iris.experimental.ugrid import save_mesh
 
-from . import TrackAddedMemoryAllocation
+from . import TrackAddedMemoryAllocation, on_demand_benchmark
 from .generate_data.ugrid import make_cube_like_2d_cubesphere
 
 
@@ -47,6 +47,8 @@ def time_netcdf_save_mesh(self, n_cubesphere, is_unstructured):
         if is_unstructured:
             self._save_mesh(self.cube)
 
+    # Vulnerable to noise, so disabled by default.
+    @on_demand_benchmark
     @TrackAddedMemoryAllocation.decorator
     def track_addedmem_netcdf_save(self, n_cubesphere, is_unstructured):
         # Don't need to copy the cube here since track_ benchmarks don't

diff --git a/benchmarks/bm_runner.py b/benchmarks/bm_runner.py
@@ -82,7 +82,7 @@ def _prep_data_gen_env() -> None:
     else:
         echo("Setting up the data generation environment ...")
         # Get Nox to build an environment for the `tests` session, but don't
-        #  run the session. Will re-use a cached environment if appropriate.
+        #  run the session. Will reuse a cached environment if appropriate.
         _subprocess_runner(
             [
                 "nox",

diff --git a/docs/gallery_code/meteorology/plot_COP_1d.py b/docs/gallery_code/meteorology/plot_COP_1d.py
@@ -54,7 +54,7 @@ def main():
     )
 
     # Generate area-weights array. As e1 and a1b are on the same grid we can
-    # do this just once and re-use. This method requires bounds on lat/lon
+    # do this just once and reuse. This method requires bounds on lat/lon
     # coords, so let's add some in sensible locations using the "guess_bounds"
     # method.
     e1.coord("latitude").guess_bounds()

diff --git a/docs/gallery_code/meteorology/plot_COP_maps.py b/docs/gallery_code/meteorology/plot_COP_maps.py
@@ -171,23 +171,13 @@ def main():
         )
         plt.gca().coastlines()
 
-    # Now add a colourbar who's leftmost point is the same as the leftmost
-    # point of the left hand plot and rightmost point is the rightmost
-    # point of the right hand plot.
-
-    # Get the positions of the 2nd plot and the left position of the 1st plot.
-    left, bottom, width, height = ax_array[1].get_position().bounds
-    first_plot_left = ax_array[0].get_position().bounds[0]
-
-    # The width of the colorbar should now be simple.
-    width = left - first_plot_left + width
-
-    # Add axes to the figure, to place the colour bar.
-    colorbar_axes = fig.add_axes([first_plot_left, 0.18, width, 0.03])
-
-    # Add the colour bar.
+    # Now add a colour bar which spans the two plots.  Here we pass Figure.axes
+    # which is a list of all (two) axes currently on the figure.  Note that
+    # these are different to the contents of ax_array, because those were
+    # standard Matplotlib Axes that Iris automatically replaced with Cartopy
+    # GeoAxes.
     cbar = plt.colorbar(
-        contour_result, colorbar_axes, orientation="horizontal"
+        contour_result, ax=fig.axes, aspect=60, orientation="horizontal"
     )
 
     # Label the colour bar and add ticks.

diff --git a/docs/src/_templates/layout.html b/docs/src/_templates/layout.html
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -294,7 +294,9 @@ def _dotv(version):
     "collapse_navigation": True,
     "navigation_depth": 3,
     "show_prev_next": True,
-    "navbar_align": "left",
+    "navbar_align": "content",
+    # removes the search box from the top bar
+    "navbar_persistent": [],
     # TODO: review if 6 links is too crowded.
     "header_links_before_dropdown": 6,
     "github_url": "https://github.com/SciTools/iris",
@@ -329,6 +331,16 @@ def _dotv(version):
     },
 }
 
+# if we are building via Read The Docs and it is the latest (not stable)
+if on_rtd and rtd_version == "latest":
+    html_theme_options[
+        "announcement"
+    ] = f"""
+        You are viewing the <b>latest</b> unreleased documentation
+        <strong>{version}</strong>. You can switch to a
+        <a href="https://scitools-iris.readthedocs.io/en/stable/">stable</a>
+        version."""
+
 rev_parse = run(["git", "rev-parse", "--short", "HEAD"], capture_output=True)
 commit_sha = rev_parse.stdout.decode().strip()
 

diff --git a/docs/src/developers_guide/contributing_documentation_easy.rst b/docs/src/developers_guide/contributing_documentation_easy.rst
@@ -81,9 +81,9 @@ Describing what you've changed and why will help the person who reviews your cha
 .. tip::
 
    If you're not sure that you're making your pull request right, or have a
-   question, then make it anyway! You can then comment on it tagging
-   ``@SciTools/iris-devs`` to ask your question (then edit your pull request if
-   you need to).
+   question, then make it anyway! You can then comment on it to ask your
+   question, then someone from the dev team will be happy to help you out (then
+   edit your pull request if you need to).
 
 What Happens Next?
 ^^^^^^^^^^^^^^^^^^