update cookiecutter template (#358)

### What kind of change does this PR introduce?

* Update cookiecutter to the latest commit
* Adds a few free grep-based hooks for finding unwanted artifacts in the
code base
* Updates `ruff` to v0.2.0 conventions, `black` to 24.2.0

### Does this PR introduce a breaking change?

No.

### Other information:

`cache-cleaner.yml` was missing the required permissions to run
properly. This has been corrected.

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/tjs/git/cookiecutter-pypackage",
-  "commit": "55001f0fb2b470d1be2e992bfb8e006b4bc3807c",
+  "commit": "f391bbd6ee14ab2478c64a1f78b74bd9903cae81",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/bump-version.yml

@@ -74,7 +74,7 @@ jobs:
       - name: Current Version
         run: |
           bump-my-version show current_version
-          CURRENT_VERSION="$(grep -E '__version__'  xscen/__init__.py | cut -d ' ' -f3)"
+          CURRENT_VERSION="$(grep -E '__version__' xscen/__init__.py | cut -d ' ' -f3)"
           echo "CURRENT_VERSION=${CURRENT_VERSION}" >> $GITHUB_ENV
       - name: Conditional Bump Version
         run: |

.github/workflows/cache-cleaner.yml

@@ -12,6 +12,8 @@ jobs:
   cleanup:
     name: Cleanup
     runs-on: ubuntu-latest
+    permissions:
+      actions: write
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@63c24ba6bd7ba022e95695ff85de572c04a18142 # v2.7.0

.github/workflows/publish-pypi.yml

@@ -20,7 +20,13 @@ jobs:
       - name: Harden Runner
         uses: step-security/harden-runner@63c24ba6bd7ba022e95695ff85de572c04a18142 # v2.7.0
         with:
-          egress-policy: audit
+          disable-sudo: true
+          egress-policy: block
+          allowed-endpoints: >
+            files.pythonhosted.org:443
+            github.com:443
+            pypi.org:443
+            upload.pypi.org:443
       - uses: actions/checkout@v4.1.1
       - name: Set up Python3
         uses: actions/setup-python@v5.0.0

.github/workflows/tag-testpypi.yml

@@ -44,7 +44,13 @@ jobs:
       - name: Harden Runner
         uses: step-security/harden-runner@63c24ba6bd7ba022e95695ff85de572c04a18142 # v2.7.0
         with:
-          egress-policy: audit
+          disable-sudo: true
+          egress-policy: block
+          allowed-endpoints: >
+            files.pythonhosted.org:443
+            github.com:443
+            pypi.org:443
+            test.pypi.org:443
       - uses: actions/checkout@v4.1.1
       - name: Set up Python3
         uses: actions/setup-python@v5.0.0
@@ -60,5 +66,5 @@ jobs:
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@v1.8.12
         with:
-          repository_url: https://test.pypi.org/legacy/
-          skip_existing: true
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true

.pre-commit-config.yaml

@@ -27,6 +27,11 @@ repos:
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
+      - id: python-check-blanket-noqa
+      - id: python-no-eval
+        exclude: biasadjust.py
+      - id: python-no-log-warn
+      - id: python-use-type-annotations
       - id: rst-inline-touching-normal
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.23.1
@@ -79,7 +84,7 @@ repos:
     hooks:
       - id: nbstripout
         files: ".ipynb"
-        args: [ '--extra-keys', 'metadata.kernelspec' ]
+        args: [ '--extra-keys=metadata.kernelspec' ]
   - repo: https://github.com/Yelp/detect-secrets
     rev: v1.4.0
     hooks:

CHANGES.rst

@@ -2,6 +2,17 @@
 Changelog
 =========
 
+v0.9.0 (unreleased)
+-------------------
+Contributors to this version: Trevor James Smith (:user:`Zeitsperre`).
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* Updated the `cookiecutter` template to the latest version. (:pull:`358`):
+    * Addresses a handful of misconfigurations in the GitHub Workflows.
+    * Added a few free `grep`-based hooks for finding unwanted artifacts in the code base.
+    * Updated `ruff` to v0.2.0 and `black` to v24.2.0.
+
 v0.8.3 (2024-02-28)
 -------------------
 Contributors to this version: Juliette Lavoie (:user:`juliettelavoie`), Trevor James Smith (:user:`Zeitsperre`), Gabriel Rondeau-Genesse (:user:`RondeauG`), Pascal Bourgault (:user:`aulemahal`).

CONTRIBUTING.rst

@@ -47,7 +47,7 @@ If you are proposing a feature:
 * Explain in detail how it would work.
 * Keep the scope as narrow as possible, to make it easier to implement.
 * Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+  are welcome. :)
 
 Get Started!
 ------------
@@ -204,7 +204,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 #. The pull request should not break the templates.
 
-#. The pull request should work for Python 3.9, 3.10, and 3.11. Check that the tests pass for all supported Python versions.
+#. The pull request should work for Python 3.9, 3.10, 3.11, and 3.12. Check that the tests pass for all supported Python versions.
 
 Tips
 ----

docs/conf.py

@@ -26,13 +26,13 @@
 
 sys.path.insert(0, os.path.abspath(".."))
 if os.environ.get("READTHEDOCS") and "ESMFMKFILE" not in os.environ:
-    # RTD doesn't activate the env, and esmpy depends on a env var set there
+    # RTD doesn't activate the env, and esmpy depends on an env var set there
     # We assume the `os` package is in {ENV}/lib/pythonX.X/os.py
     # See conda-forge/esmf-feedstock#91 and readthedocs/readthedocs.org#4067
     os.environ["ESMFMKFILE"] = str(Path(os.__file__).parent.parent / "esmf.mk")
 
-import xscen  # noqa
-import xarray  # noqa
+import xscen  # noqa: E402,F401
+import xarray  # noqa: E402
 
 xarray.DataArray.__module__ = "xarray"
 xarray.Dataset.__module__ = "xarray"

environment-dev.yml

@@ -38,9 +38,9 @@ dependencies:
   - pyarrow >=1.0.0
   # Dev
   - babel
-  - black ==24.1.1
+  - black ==24.2.0
   - blackdoc ==0.3.9
-  - bump-my-version >=0.17.1
+  - bump-my-version >=0.18.3
 #  - coverage>=6.2.2,<7.0.0
 #  - coveralls>=3.3.1
   - flake8 >=6.1.0

pyproject.toml

@@ -73,7 +73,7 @@ dev = [
   "pip >=23.3.0",
   "black ==24.2.0",
   "blackdoc ==0.3.9",
-  "bump-my-version >=0.17.1",
+  "bump-my-version >=0.18.3",
   "coverage >=6.2.2,<8.0.0",
   "coveralls >=3.3.1",
   "flake8-alphabetize >=0.0.21",
@@ -193,7 +193,7 @@ testpaths = "tests"
 markers = ["requires_netcdf: marks tests that require netcdf files to run"]
 
 [tool.ruff]
-src = [""]
+src = ["xscen"]
 line-length = 150
 target-version = "py39"
 exclude = [
@@ -215,30 +215,30 @@ select = [
   "W"
 ]
 
-[tool.ruff.flake8-bandit]
-check-typed-exception = true
-
 [tool.ruff.format]
 line-ending = "auto"
 
-[tool.ruff.isort]
+[tool.ruff.lint.flake8-bandit]
+check-typed-exception = true
+
+[tool.ruff.lint.isort]
 known-first-party = ["xscen"]
 case-sensitive = true
 detect-same-package = false
 lines-after-imports = 1
 no-lines-before = ["future", "standard-library"]
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 15
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "xscen/**/__init__.py" = ["F401", "F403"]
 "tests/**/*.py" = ["D100", "D101", "D102", "D103"]
 
-[tool.ruff.pycodestyle]
+[tool.ruff.lint.pycodestyle]
 max-doc-length = 180
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
 [tool.setuptools]

tox.ini

@@ -19,12 +19,12 @@ download = true
 conda_channels =
 conda_env =
 deps =
-    black ==24.1.1
+    black ==24.2.0
     blackdoc ==0.3.9
     isort ==5.13.2
     flake8
     flake8-rst-docstrings
-    ruff
+    ruff >=0.2.0
 commands_pre =
     pip list
 commands =

xscen/__init__.py

@@ -25,19 +25,19 @@
 # Import top-level functions
 from .aggregate import *
 from .biasadjust import *
-from .catalog import DataCatalog, ProjectCatalog  # noqa
+from .catalog import DataCatalog, ProjectCatalog
 from .catutils import build_path, parse_directory
-from .config import CONFIG, load_config  # noqa
+from .config import CONFIG, load_config
 from .diagnostics import properties_and_measures
 from .ensembles import *
-from .extract import (  # noqa
+from .extract import (
     extract_dataset,
     get_warming_level,
     search_data_catalogs,
     subset_warming_level,
 )
-from .indicators import compute_indicators  # noqa
-from .io import save_to_netcdf, save_to_table, save_to_zarr  # noqa
+from .indicators import compute_indicators
+from .io import save_to_netcdf, save_to_table, save_to_zarr
 from .reduce import build_reduction_data, reduce_ensemble
 from .regrid import *
 from .scripting import (
@@ -58,7 +58,7 @@
 
 def warning_on_one_line(
     message: str, category: Warning, filename: str, lineno: int, file=None, line=None
-):  # noqa: D103
+):
     """Monkeypatch Reformat warning so that `warnings.warn` doesn't mention itself."""
     return f"{filename}:{lineno}: {category.__name__}: {message}\n"
 
@@ -72,7 +72,8 @@ def warning_on_one_line(
     category=FutureWarning,
     module="intake_esm",
     message="The default of observed=False is deprecated and will be changed to True in a future version of pandas. "
-    "Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.",
+    "Pass observed=False to retain current behavior or observed=True to adopt the future default "
+    "and silence this warning.",
 )
 warnings.filterwarnings(
     "ignore",

xscen/catalog.py

@@ -22,8 +22,7 @@
 from intake_esm.cat import ESMCatalogModel
 
 from .config import CONFIG, args_as_str, recursive_update
-from .utils import (  # noqa
-    CV,
+from .utils import (
     date_parser,
     ensure_correct_time,
     ensure_new_xrfreq,
@@ -42,6 +41,7 @@
     "ProjectCatalog",
     "concat_data_catalogs",
     "generate_id",
+    "subset_file_coverage",
     "unstack_id",
 ]
 

xscen/catutils.py

@@ -30,14 +30,7 @@
 from .catalog import COLUMNS, DataCatalog, generate_id
 from .config import parse_config
 from .io import get_engine
-from .utils import (  # noqa
-    CV,
-    date_parser,
-    ensure_correct_time,
-    ensure_new_xrfreq,
-    get_cat_attrs,
-    standardize_periods,
-)
+from .utils import CV, date_parser, ensure_new_xrfreq, get_cat_attrs
 
 logger = logging.getLogger(__name__)
 
@@ -434,7 +427,7 @@ def _parse_first_ds(
 
 
 @parse_config
-def parse_directory(  # noqa:C901
+def parse_directory(  # noqa: C901
     directories: list[Union[str, os.PathLike]],
     patterns: list[str],
     *,

xscen/extract.py

@@ -18,8 +18,13 @@
 from intake_esm.derived import DerivedVariableRegistry
 from xclim.core.calendar import compare_offsets
 
-from .catalog import DataCatalog  # noqa
-from .catalog import ID_COLUMNS, concat_data_catalogs, generate_id, subset_file_coverage
+from .catalog import (
+    ID_COLUMNS,
+    DataCatalog,
+    concat_data_catalogs,
+    generate_id,
+    subset_file_coverage,
+)
 from .catutils import parse_from_ds
 from .config import parse_config
 from .indicators import load_xclim_module, registry_from_module

xscen/indicators.py

@@ -21,7 +21,7 @@
 
 logger = logging.getLogger(__name__)
 
-__all__ = ["compute_indicators", "load_xclim_module"]
+__all__ = ["compute_indicators", "load_xclim_module", "registry_from_module"]
 
 
 def load_xclim_module(

xscen/utils.py

@@ -33,10 +33,13 @@
 logger = logging.getLogger(__name__)
 
 __all__ = [
+    "CV",
     "add_attr",
     "change_units",
     "clean_up",
     "date_parser",
+    "ensure_correct_time",
+    "ensure_new_xrfreq",
     "get_cat_attrs",
     "maybe_unstack",
     "minimum_calendar",
@@ -48,6 +51,7 @@
     "unstack_dates",
     "unstack_fill_nan",
     "update_attr",
+    "xrfreq_to_timedelta",
 ]
 
 TRANSLATOR = defaultdict(lambda: lambda s: s)