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

* upstream/main: (29 commits)
  review actions
  update .git-blame-ignore-revs
  adopt codespell
  Adopt sphinx design (SciTools#5127)
  Bump scitools/workflows from 2023.04.2 to 2023.04.3 (SciTools#5253)
  refresh manual pypi publish instructions (SciTools#5252)
  Updated environment lockfiles (SciTools#5250)
  removed bugfix section
  Make bm_runner location agnostic and include debugging. (SciTools#5247)
  Restore latest Whats New files.
  SciTools#5220 typo github.repository_owner. (SciTools#5248)
  Whats new updates for v3.5.0rc0. (SciTools#5246)
  libnetcdf <4.9 pin (SciTools#5242)
  update cf standard units (SciTools#5244)
  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)
  ...

Author: tkknight

.git-blame-ignore-revs

@@ -0,0 +1,20 @@
+# Format: numpy array format (#5235)
+c18dcd8dafef0cc7bbbf80dfce66f76a46ce59c5
+
+# style: flake8 (#3755)
+7c86bc0168684345dc475457b1a77dadc77ce9bb
+
+# style: black (#3518)
+ffcfad475e0593e1e40895453cf1df154e5f6f2c
+
+# style: isort (#4174)
+15bbcc5ac3d539cb6e820148b66e7cf55d91c5d2
+
+# style: blacken-docs (#4205)
+1572e180243e492d8ff76fa8cdefb82ef6f90415
+
+# style: sort-all (#4353)
+64705dbc40881233aae45f051d96049150369e53
+
+# style: codespell (#5186)
+417aa6bbd9b10d25cad7def54d47ef4d718bc38d

.github/workflows/ci-tests.yml

@@ -63,7 +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
@@ -111,7 +111,7 @@ jobs:
       - name: "nox cache"
         uses: ./.github/workflows/composite/nox-cache
         with:
-          cache_build: 1
+          cache_build: 2
           env_name: ${{ env.ENV_NAME }}
           lock_file: ${{ env.LOCK_FILE }}
 

.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 }}
 
@@ -133,7 +133,7 @@ jobs:
     runs-on: ubuntu-latest
     # upload to Test PyPI for every commit on main branch
     # and check for the SciTools repo
-    if: github.event_name == 'push' && github.event.ref == 'refs/heads/main' && github.repository-owner == 'SciTools'
+    if: github.event_name == 'push' && github.event.ref == 'refs/heads/main' && github.repository_owner == 'SciTools'
     steps:
     - uses: actions/download-artifact@v3
       with:
@@ -153,7 +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') && github.repository-owner == 'SciTools'
+    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@2023.04.1
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.04.3
     secrets: inherit

.pre-commit-config.yaml

@@ -28,6 +28,13 @@ repos:
         # Don't commit to main branch.
     -   id: no-commit-to-branch
 
+-   repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.2"
+    hooks:
+    -   id: codespell
+        types_or: [asciidoc, python, markdown, rst]
+        additional_dependencies: [tomli]
+
 -   repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:

benchmarks/benchmarks/experimental/ugrid/regions_combine.py

@@ -50,7 +50,7 @@ def _make_region_cubes(self, full_mesh_cube):
         i_faces = np.concatenate([i_faces[:, 2:], i_faces[:, :2]], axis=1)
         # flatten to get [2 3 4 0 1 (-) 8 9 10 6 7 (-) 13 14 15 11 12 ...]
         i_faces = i_faces.flatten()
-        # reduce back to orignal length, wrap any overflows into valid range
+        # reduce back to original length, wrap any overflows into valid range
         i_faces = i_faces[:n_faces] % n_faces
 
         # Divide into regions -- always slightly uneven, since 7 doesn't divide

benchmarks/benchmarks/sperf/combine_regions.py

@@ -46,7 +46,7 @@ def _make_region_cubes(self, full_mesh_cube):
         i_faces = np.concatenate([i_faces[:, 2:], i_faces[:, :2]], axis=1)
         # flatten to get [2 3 4 0 1 (-) 8 9 10 6 7 (-) 13 14 15 11 12 ...]
         i_faces = i_faces.flatten()
-        # reduce back to orignal length, wrap any overflows into valid range
+        # reduce back to original length, wrap any overflows into valid range
         i_faces = i_faces[:n_faces] % n_faces
 
         # Divide into regions -- always slightly uneven, since 7 doesn't divide

benchmarks/bm_runner.py

@@ -23,14 +23,26 @@
 #  for more.
 COMPARE_FACTOR = 1.2
 
+BENCHMARKS_DIR = Path(__file__).parent
 
 # Common ASV arguments for all run_types except `custom`.
 ASV_HARNESS = (
-    "asv run {posargs} --attribute rounds=4 --interleave-rounds --strict "
+    "run {posargs} --attribute rounds=4 --interleave-rounds --strict "
     "--show-stderr"
 )
 
 
+def _subprocess_run_print(args, **kwargs):
+    print(f"BM_RUNNER DEBUG: {' '.join(args)}")
+    return subprocess.run(args, **kwargs)
+
+
+def _subprocess_run_asv(args, **kwargs):
+    args.insert(0, "asv")
+    kwargs["cwd"] = BENCHMARKS_DIR
+    return _subprocess_run_print(args, **kwargs)
+
+
 def _check_requirements(package: str) -> None:
     try:
         import_module(package)
@@ -47,7 +59,7 @@ def _prep_data_gen_env() -> None:
     Create/access a separate, unchanging environment for generating test data.
     """
 
-    root_dir = Path(__file__).parents[1]
+    root_dir = BENCHMARKS_DIR.parent
     python_version = "3.10"
     data_gen_var = "DATA_GEN_PYTHON"
     if data_gen_var in environ:
@@ -56,7 +68,7 @@ def _prep_data_gen_env() -> None:
         print("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.
-        subprocess.run(
+        _subprocess_run_print(
             [
                 "nox",
                 f"--noxfile={root_dir / 'noxfile.py'}",
@@ -75,15 +87,15 @@ def _prep_data_gen_env() -> None:
         print("Installing Mule into data generation environment ...")
         mule_dir = data_gen_python.parents[1] / "resources" / "mule"
         if not mule_dir.is_dir():
-            subprocess.run(
+            _subprocess_run_print(
                 [
                     "git",
                     "clone",
                     "https://github.com/metomi/mule.git",
                     str(mule_dir),
                 ]
             )
-        subprocess.run(
+        _subprocess_run_print(
             [
                 str(data_gen_python),
                 "-m",
@@ -103,28 +115,28 @@ def _setup_common() -> None:
     _prep_data_gen_env()
 
     print("Setting up ASV ...")
-    subprocess.run(["asv", "machine", "--yes"])
+    _subprocess_run_asv(["machine", "--yes"])
 
     print("Setup complete.")
 
 
 def _asv_compare(*commits: str, overnight_mode: bool = False) -> None:
     """Run through a list of commits comparing each one to the next."""
     commits = [commit[:8] for commit in commits]
-    shifts_dir = Path(".asv") / "performance-shifts"
+    shifts_dir = BENCHMARKS_DIR / ".asv" / "performance-shifts"
     for i in range(len(commits) - 1):
         before = commits[i]
         after = commits[i + 1]
         asv_command = (
-            f"asv compare {before} {after} --factor={COMPARE_FACTOR} --split"
+            f"compare {before} {after} --factor={COMPARE_FACTOR} --split"
         )
-        subprocess.run(asv_command.split(" "))
+        _subprocess_run_asv(asv_command.split(" "))
 
         if overnight_mode:
             # Record performance shifts.
             # Run the command again but limited to only showing performance
             #  shifts.
-            shifts = subprocess.run(
+            shifts = _subprocess_run_asv(
                 [*asv_command.split(" "), "--only-changed"],
                 capture_output=True,
                 text=True,
@@ -207,11 +219,11 @@ def func(args: argparse.Namespace) -> None:
 
         commit_range = f"{args.first_commit}^^.."
         asv_command = ASV_HARNESS.format(posargs=commit_range)
-        subprocess.run([*asv_command.split(" "), *args.asv_args])
+        _subprocess_run_asv([*asv_command.split(" "), *args.asv_args])
 
         # git rev-list --first-parent is the command ASV uses.
         git_command = f"git rev-list --first-parent {commit_range}"
-        commit_string = subprocess.run(
+        commit_string = _subprocess_run_print(
             git_command.split(" "), capture_output=True, text=True
         ).stdout
         commit_list = commit_string.rstrip().split("\n")
@@ -246,7 +258,7 @@ def func(args: argparse.Namespace) -> None:
         _setup_common()
 
         git_command = f"git merge-base HEAD {args.base_branch}"
-        merge_base = subprocess.run(
+        merge_base = _subprocess_run_print(
             git_command.split(" "), capture_output=True, text=True
         ).stdout[:8]
 
@@ -255,7 +267,7 @@ def func(args: argparse.Namespace) -> None:
             hashfile.flush()
             commit_range = f"HASHFILE:{hashfile.name}"
             asv_command = ASV_HARNESS.format(posargs=commit_range)
-            subprocess.run([*asv_command.split(" "), *args.asv_args])
+            _subprocess_run_asv([*asv_command.split(" "), *args.asv_args])
 
         _asv_compare(merge_base, "HEAD")
 
@@ -312,13 +324,13 @@ def csperf(
         asv_command = asv_command.replace(" --strict", "")
         # Only do a single round.
         asv_command = re.sub(r"rounds=\d", "rounds=1", asv_command)
-        subprocess.run([*asv_command.split(" "), *args.asv_args])
+        _subprocess_run_asv([*asv_command.split(" "), *args.asv_args])
 
-        asv_command = f"asv publish {commit_range} --html-dir={publish_subdir}"
-        subprocess.run(asv_command.split(" "))
+        asv_command = f"publish {commit_range} --html-dir={publish_subdir}"
+        _subprocess_run_asv(asv_command.split(" "))
 
         # Print completion message.
-        location = Path().cwd() / ".asv"
+        location = BENCHMARKS_DIR / ".asv"
         print(
             f'New ASV results for "{run_type}".\n'
             f'See "{publish_subdir}",'
@@ -366,7 +378,7 @@ def add_arguments(self) -> None:
     @staticmethod
     def func(args: argparse.Namespace) -> None:
         _setup_common()
-        subprocess.run(["asv", args.asv_sub_command, *args.asv_args])
+        _subprocess_run_asv([args.asv_sub_command, *args.asv_args])
 
 
 def main():

codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  # see https://docs.codecov.com/docs/commit-status
+  status:
+    project:
+      default:
+        target: auto
+        # coverage can drop by up to <threshold>% while still posting success
+        threshold: 3%
+    patch: off

docs/gallery_code/general/plot_projections_and_annotations.py

@@ -78,7 +78,7 @@ def make_plot(projection_name, projection_crs):
     y_points = y_lower + y_delta * np.concatenate(
         (zeros, steps, ones, steps[::-1])
     )
-    # Get the Iris coordinate sytem of the X coordinate (Y should be the same).
+    # Get the Iris coordinate system of the X coordinate (Y should be the same).
     cs_data1 = x_coord.coord_system
     # Construct an equivalent Cartopy coordinate reference system ("crs").
     crs_data1 = cs_data1.as_cartopy_crs()