Merge branch 'main' into cla_v5

.github/labeler.yml

@@ -0,0 +1,6 @@
+# Make sure any dependency changes are benchmarked (only changes to the locks
+#  make a material difference - changes to the Conda YAML files are not
+#  benchmarked).
+benchmark_this:
+- changed-files:
+  - any-glob-to-any-file: 'requirements/locks/*.lock'

.github/workflows/benchmarks_run.yml

@@ -42,11 +42,11 @@ jobs:
 
       - name: Install ASV & Nox
         run: |
-          pip install asv nox
+          pip install "asv!=0.6.2" nox
 
       - name: Cache environment directories
         id: cache-env-dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             .nox
@@ -56,7 +56,7 @@ jobs:
 
       - name: Cache test data directory
         id: cache-test-data
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ${{ env.IRIS_TEST_DATA_PATH }}

.github/workflows/ci-citation.yml

@@ -0,0 +1,30 @@
+name: ci-citation
+
+on:
+  pull_request:
+    paths:
+      - "CITATION.cff"
+
+  push:
+    paths:
+      - "CITATION.cff"
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: "check CITATION.cff"
+        uses: citation-file-format/cffconvert-github-action@4cf11baa70a673bfdf9dad0acc7ee33b3f4b6084
+        with:
+          args: "--validate"

.github/workflows/ci-manifest.yml

@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.12.1
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2024.02.0

.github/workflows/ci-tests.yml

@@ -140,5 +140,5 @@ jobs:
           nox --session ${{ matrix.session }} -- --verbose ${{ matrix.coverage }}
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         if: ${{ matrix.coverage }}

.github/workflows/labeler.yml

@@ -0,0 +1,15 @@
+# Reference
+#   - https://github.com/actions/labeler
+
+name: "Pull Request Labeler"
+on:
+- pull_request_target
+
+jobs:
+  labeler:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@v5

.github/workflows/refresh-lockfiles.yml

@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.12.1
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2024.02.0
     secrets: inherit

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.8"
+    rev: "v0.2.1"
     hooks:
     -   id: ruff
         types: [file, python]
@@ -45,7 +45,7 @@ repos:
         additional_dependencies: [tomli]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
         types: [file, python]

.readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: "ubuntu-22.04"
   tools:
-    python: mambaforge-4.10
+    python: "mambaforge-22.9"
   jobs:
     post_checkout:
       # The SciTools/iris repository is shallow i.e., has a .git/shallow,

.ruff.toml

@@ -11,7 +11,6 @@ lint.ignore = [
     # pycodestyle (E, W)
     # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
     "E",
-    "W",
 
     # mccabe (C90)
     # https://docs.astral.sh/ruff/rules/#mccabe-c90
@@ -26,22 +25,10 @@ lint.ignore = [
     # (D-1) Permanent
     "D105",  # Missing docstring in magic method
     # (D-2) Temporary, to be removed when we are more compliant. Rare cases mmove  to (1).
-    "D417",  # Missing argument descriptions in the docstring
     "D101",  # Missing docstring in public class
     "D102",  # Missing docstring in public method
-    "D104",  # Missing docstring in public package
-    "D106",  # Missing docstring in public nested class
-    # (D-3) Temporary, before an initial review, either fix ocurrenvces or move to (2).
-    "D100",  # Missing docstring in public module
+    # (D-3) Temporary, before an initial review, either fix ocurrences or move to (2).
     "D103",  # Missing docstring in public function
-    "D200",  # One-line docstring should fit on one line
-    "D202",  # No blank lines allowed after function docstring
-    "D205",  # 1 blank line required between summary line and description
-    "D401",  # First line of docstring should be in imperative mood: ...
-    "D404",  # First word of the docstring should not be "This"
-    "D405",  # Section name should be properly capitalized
-    "D406",  # Section name should end with a newline
-    "D407",  # Missing dashed underline after section
 
     # pyupgrade (UP)
     # https://docs.astral.sh/ruff/rules/#pyupgrade-up
@@ -71,10 +58,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
     "A",
 
-    # flake8-copyright (CPY)
-    # https://docs.astral.sh/ruff/rules/#flake8-copyright-cpy
-    "CPY",
-
     # flake8-comprehensions (C4)
     # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
     "C4",
@@ -91,10 +74,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
     "FA",
 
-    # flake8-implicit-str-concat (ISC)
-    # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
-    "ISC",
-
     # flake8-logging-format (G)
     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
     "G",
@@ -187,10 +166,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flynt-fly
     "FLY",
 
-    # Airflow (AIR)
-    # https://docs.astral.sh/ruff/rules/#airflow-air
-    "AIR",
-
     # Perflint (PERF)
     # https://docs.astral.sh/ruff/rules/#perflint-perf
     "PERF",

CITATION.cff

@@ -0,0 +1,23 @@
+cff-version: 1.2.0
+message: "If Iris played an important part in your research then please add us to your reference list by using the references below."
+title: "Iris"
+keywords:
+  - "cf-metadata"
+  - "data-analysis"
+  - "earth-science"
+  - "grib"
+  - "netcdf"
+  - "meteorology"
+  - "oceanography"
+  - "space-weather"
+  - "ugrid"
+  - "visualisation"
+authors:
+    - name: "Iris contributors"
+abstract: "A powerful, format-agnostic, and community-driven Python package for analysing and visualising Earth science data"
+license: "BSD-3-Clause"
+license-url: "https://spdx.org/licenses/BSD-3-Clause.html"
+doi: "10.5281/zenodo.595182"
+url: "http://scitools.org.uk/"
+repository-code: "https://github.com/SciTools/iris"
+type: "software"

MANIFEST.in

@@ -18,6 +18,9 @@ exclude .ruff.toml
 exclude CHANGES
 exclude CODE_OF_CONDUCT.md
 exclude codecov.yml
+include COPYING
+include COPYING.LESSER
+include CITATION.cff
 include LICENSE
 exclude Makefile
 exclude noxfile.py

benchmarks/asv_delegated_conda.py

@@ -2,8 +2,9 @@
 #
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-"""ASV plug-in providing an alternative :class:`asv.plugins.conda.Conda`
-subclass that manages the Conda environment via custom user scripts.
+"""ASV plug-in providing an alternative :class:`asv.plugins.conda.Conda` subclass.
+
+Manages the Conda environment via custom user scripts.
 
 """
 
@@ -42,7 +43,9 @@ def __init__(
         requirements: dict,
         tagged_env_vars: dict,
     ) -> None:
-        """Parameters
+        """__init__.
+
+        Parameters
         ----------
         conf : Config instance
 

benchmarks/benchmarks/__init__.py

@@ -10,7 +10,7 @@
 
 
 def disable_repeat_between_setup(benchmark_object):
-    """Decorator for benchmarks where object persistence would be inappropriate.
+    """Benchmarks where object persistence would be inappropriate (decorator).
 
     E.g:
         * Benchmarking data realisation
@@ -36,7 +36,9 @@ def disable_repeat_between_setup(benchmark_object):
 
 
 class TrackAddedMemoryAllocation:
-    """Context manager which measures by how much process resident memory grew,
+    """Measures by how much process resident memory grew, during execution.
+
+    Context manager which measures by how much process resident memory grew,
     during execution of its enclosed code block.
 
     Obviously limited as to what it actually measures : Relies on the current
@@ -84,7 +86,7 @@ def addedmem_mb(self):
 
     @staticmethod
     def decorator(decorated_func):
-        """Decorates this benchmark to track growth in resident memory during execution.
+        """Benchmark to track growth in resident memory during execution.
 
         Intended for use on ASV ``track_`` benchmarks. Applies the
         :class:`TrackAddedMemoryAllocation` context manager to the benchmark
@@ -105,7 +107,9 @@ def _wrapper(*args, **kwargs):
 
 
 def on_demand_benchmark(benchmark_object):
-    """Decorator. Disables these benchmark(s) unless ON_DEMAND_BENCHARKS env var is set.
+    """Disables these benchmark(s) unless ON_DEMAND_BENCHARKS env var is set.
+
+    This is a decorator.
 
     For benchmarks that, for whatever reason, should not be run by default.
     E.g:

benchmarks/benchmarks/aux_factory.py

@@ -2,9 +2,7 @@
 #
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-"""AuxFactory benchmark tests.
-
-"""
+"""AuxFactory benchmark tests."""
 
 import numpy as np
 
@@ -18,7 +16,9 @@ class FactoryCommon:
     #       * make class an ABC
     #       * remove NotImplementedError
     #       * combine setup_common into setup
-    """A base class running a generalised suite of benchmarks for any factory.
+    """Run a generalised suite of benchmarks for any factory.
+
+    A base class running a generalised suite of benchmarks for any factory.
     Factory to be specified in a subclass.
 
     ASV will run the benchmarks within this class for any subclasses.

benchmarks/benchmarks/coords.py

@@ -2,9 +2,7 @@
 #
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-"""Coord benchmark tests.
-
-"""
+"""Coord benchmark tests."""
 
 import numpy as np
 
@@ -25,7 +23,9 @@ class CoordCommon:
     #       * make class an ABC
     #       * remove NotImplementedError
     #       * combine setup_common into setup
-    """A base class running a generalised suite of benchmarks for any coord.
+    """Run a generalised suite of benchmarks for any coord.
+
+    A base class running a generalised suite of benchmarks for any coord.
     Coord to be specified in a subclass.
 
     ASV will run the benchmarks within this class for any subclasses.

benchmarks/benchmarks/cperf/equality.py

@@ -2,15 +2,17 @@
 #
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-"""Equality benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""Equality benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import SingleDiagnosticMixin
 
 
 class EqualityMixin(SingleDiagnosticMixin):
-    r"""Uses :class:`SingleDiagnosticMixin` as the realistic case will be comparing
+    r"""Use :class:`SingleDiagnosticMixin` as the realistic case.
+
+    Uses :class:`SingleDiagnosticMixin` as the realistic case will be comparing
     :class:`~iris.cube.Cube`\\ s that have been loaded from file.
+
     """
 
     # Cut down the parent parameters.
@@ -24,9 +26,7 @@ def setup(self, file_type, three_d=False, three_times=False):
 
 @on_demand_benchmark
 class CubeEquality(EqualityMixin):
-    r"""Benchmark time and memory costs of comparing LFRic and UM
-    :class:`~iris.cube.Cube`\\ s.
-    """
+    r"""Benchmark time & memory costs of comparing LFRic & UM :class:`~iris.cube.Cube`\\ s."""
 
     def _comparison(self):
         _ = self.cube == self.other_cube

benchmarks/benchmarks/cperf/load.py

@@ -2,16 +2,16 @@
 #
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-"""File loading benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""File loading benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import SingleDiagnosticMixin
 
 
 @on_demand_benchmark
 class SingleDiagnosticLoad(SingleDiagnosticMixin):
     def time_load(self, _, __, ___):
-        """The 'real world comparison'
+        """Perform a 'real world comparison'.
+
         * UM coords are always realised (DimCoords).
         * LFRic coords are not realised by default (MeshCoords).
 
@@ -26,7 +26,7 @@ def time_load(self, _, __, ___):
             assert coord.has_lazy_bounds() == expecting_lazy_coords
 
     def time_load_w_realised_coords(self, _, __, ___):
-        """A valuable extra comparison where both UM and LFRic coords are realised."""
+        """Valuable extra comparison where both UM and LFRic coords are realised."""
         cube = self.load()
         for coord_name in "longitude", "latitude":
             coord = cube.coord(coord_name)