Cookiecutter update, GIS testing adjustments

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "14cbc49f79a6bba2502c8b3a593ff0babaf661ed",
+  "commit": "b9bacb7ddbbfaa8eff8c3e0182ebf2e8a66d00c7",
   "context": {
     "cookiecutter": {
       "full_name": "David Huard",
@@ -22,7 +22,7 @@
       "generated_with_cruft": "y",
       "__gh_slug": "https://github.com/CSHS-CWRA/RavenPy",
       "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-      "_commit": "14cbc49f79a6bba2502c8b3a593ff0babaf661ed"
+      "_commit": "b9bacb7ddbbfaa8eff8c3e0182ebf2e8a66d00c7"
     }
   },
   "directory": null,

.github/workflows/bump-version.yml

@@ -21,6 +21,7 @@ on:
       - CHANGELOG.rst
       - CI/**.in
       - CI/**.txt
+      - CITATION.cff
       - CODE_OF_CONDUCT.md
       - CONTRIBUTING.rst
       - Makefile

.github/workflows/main.yml

@@ -63,7 +63,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ 'ubuntu-latest', "macos-latest" ]
-        python-version: [ "3.11", "3.12", "3.13" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
         include:
           - os: 'ubuntu-latest'
             python-version: '3.10'

.gitignore

@@ -1,4 +1,5 @@
 # RAVENPY-specific
+Raven_errors.txt
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.readthedocs.yml

@@ -32,5 +32,3 @@ python:
   install:
     - method: pip
       path: .
-      extra_requirements:
-        - docs

CHANGELOG.rst

@@ -7,13 +7,25 @@ Changelog
 
 Contributors: Trevor James Smith (:user:`Zeitsperre`).
 
-Changes
-^^^^^^^
+New features
+^^^^^^^^^^^^
 * `raven-hydro` minimum version updated from v0.5.0 to v4.12.1 (for more information, see: https://github.com/Ouranosinc/raven-hydro/pull/93). (PR #587)
-* Dependency updates. (PR #584):
+
+Breaking changes
+^^^^^^^^^^^^^^^^
+* Dependency updates. (PR #584, PR #589):
     * Updated required `xskillscore` (``>= 0.0.29``) and `climpred` (``>= 2.6.0``).
     * Removed version pins on `intake` and `intake-xarray`.
     * Minimum required `birdy` is now ``>= 0.9.1``.
+    * Minimum required `pytest` is now ``>=9.0``.
+* The development dependency recipes have been migrated to `dependency-groups` (PEP 735). Optional dsependency lists are now separated by features. (PR #589):
+    * `ravenpy[gis]`: GIS functionality.
+    * `ravenpy[plotting]`: Notebook interactivity.
+    * `ravenpy[raven-hydro]`: To compile and install the `raven-hydro` binary.
+* Many unnecessary/optional dependencies have been removed from the base library requirements. (PR #589):
+    * `dask`, `pydap`, `typing-extensions`, `xsdba`, `xskillscore` have been removed from install requirements.
+    * `affine` and `setuptools` are no longer listed in `gis` recipe requirements.
+    * `requests` is now explicitly listed in `gis` recipe requirements.
 
 Fixes
 ^^^^^
@@ -25,6 +37,12 @@ Internal changes
 * Added a Makefile recipe and a GitHub Workflow to run tests against the notebooks using ``pytest --nbval`` on changes as well as on a weekly schedule. (PR #584)
 * Fixed a bug in several workflows that was impeding triggers when Pull Requests are merged to `main`.  (PR #584)
 * The conda configurations (``environment-dev.yml`` and ``environment-docs.yml``) now specify the exact dependencies needed to run the development and documentation builds. (PR #584)
+* Tests reliant on GIS libraries can now be disabled using `pytest -m "not gis"`. Many tests that were previously skipped have been re-enabled with modified assertions reflecting changes to the model expected output. (PR #589)
+* The cookiecutter template has been updated. (PR #589):
+    * Enabled PEP 735 (`dependency-groups`) for development dependency management.
+    * Replaced `pre-commit` with `prek`.
+    * The Makefile now performs installation calls for recipes.
+    * `tox.toml` now uses `dependency-groups` and the new `optional-dependencies` lists for environment setup.
 
 .. _changes_0.20.0:
 

CONTRIBUTING.rst

@@ -96,18 +96,19 @@ Ready to contribute? Here's how to set up `ravenpy` for local development.
 
         .. code-block:: console
 
-            python -m pip install -e .[dev]
-            pre-commit install
+            python -m pip install --group dev
+            python -m pip install --editable .
+            prek install
 
     This installs ``ravenpy`` in an "editable" state, meaning that changes to the code are immediately seen by the environment. To ensure a consistent coding style, `make dev` also installs the ``pre-commit`` hooks to your local clone.
 
-    On commit, ``pre-commit`` will check that ``flake8``, ``ruff``, ``numpydoc`` and other hooks are passing, perform automatic fixes if possible, and warn of violations that require intervention. If your commit fails the checks initially, simply fix the errors, re-add the files, and re-commit.
+    On commit, ``prek`` will will run ``pre-commit`` checks that ensure code quality checks are passing, perform automatic fixes if possible, and warn of violations that require intervention. If your commit fails the checks initially, simply fix the errors, re-add the files, and re-commit.
 
     You can also run the hooks manually with:
 
         .. code-block:: console
 
-            pre-commit run -a
+            prek run -a
 
     If you want to skip the ``pre-commit`` hooks temporarily, you can pass the `--no-verify` flag to `git commit`.
 
@@ -134,10 +135,10 @@ Ready to contribute? Here's how to set up `ravenpy` for local development.
     .. code-block:: console
 
         git add .
-        git commit -m "Your detailed description of your changes."
+        git commit -s -m "Your detailed description of your changes."
         git push origin name-of-your-bugfix-or-feature
 
-    If ``pre-commit`` hooks fail, try fixing the issues, re-staging the files to be committed, and re-committing your changes (or, if need be, you can skip them with `git commit --no-verify`).
+    If ``pre-commit`` hooks fail, try fixing the issues, re-staging the files to be committed, and re-committing your changes (or, if need be, you can skip them with `--no-verify` flag).
 
 #. Submit a `Pull Request <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request>`_ through the GitHub website.
 
@@ -195,6 +196,14 @@ Before you submit a pull request, check that it meets these guidelines:
 
 #. The pull request should work for all currently supported Python versions. Check the `pyproject.toml` or `tox.ini` files for the list of supported versions.
 
+#. If you haven't already, ensure that you have read and agreed to the `Developer Certificate of Origin (DCO) <https://developercertificate.org/>`_, and that you have signed your commits using:
+
+    .. code-block:: bash
+
+          git commit -s/--signoff
+
+    This will add a `Signed-off-by:` line to your commit message, which indicates that you agree to the DCO.
+
 Tips
 ----
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean clean-build clean-pyc clean-test coverage dist docs help install lint lint/flake8
+.PHONY: clean clean-build clean-pyc clean-test coverage development dist docs help install lint release test
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -49,27 +49,41 @@ clean-pyc: ## remove Python file artifacts
 	find . -name '__pycache__' -exec rm -fr {} +
 
 clean-test: ## remove test and coverage artifacts
-	rm -fr .tox/
 	rm -f .coverage
-	rm -fr htmlcov/
 	rm -fr .pytest_cache
+	rm -fr .tox/
+	rm -fr htmlcov/
+
+install-lint: ## install dependencies needed for linting
+	python -m pip install --quiet --group lint
+
+install-docs: ## install dependencies needed for building the docs
+	python -m pip install --quiet --group docs
+
+install-test: ## install dependencies needed for standard testing
+	python -m pip install --quiet --group test
+
+install-tox: ## install base dependencies needed for running tox
+	python -m pip install --quiet --group tox
 
 ## Testing targets:
 
-lint/flake8: ## check style with flake8
+lint: install-lint ## check style
 	python -m ruff check src/ravenpy tests
 	python -m flake8 --config=.flake8 src/ravenpy tests
 	python -m numpydoc lint src/ravenpy/**.py
+	python -m vulture src/ravenpy tests
+	codespell src/ravenpy tests docs
+	python -m deptry src
+	python -m yamllint --config-file=.yamllint.yaml src/ravenpy
 
-lint: lint/flake8 ## check style
-
-test: ## run tests quickly with the default Python
+test: install-test ## run tests quickly with the default Python
 	python -m pytest
 
-test-all: ## run tests on every Python version with tox
+test-all: install-tox ## run tests on every Python version with tox
 	python -m tox
 
-coverage: ## check code coverage quickly with the default Python
+coverage: install-test ## check code coverage quickly with the default Python
 	python -m coverage run --source src/ravenpy -m pytest
 	python -m coverage report -m
 	python -m coverage html
@@ -82,10 +96,10 @@ test-notebooks: ## test all notebooks under docs/notebooks
 
 ## Sphinx targets:
 
-autodoc: clean-docs ## create sphinx-apidoc files
+autodoc: install-docs clean-docs ## create sphinx-apidoc files
 	sphinx-apidoc -o docs/apidoc --private --module-first src/ravenpy
 
-autodoc-custom-index: clean-docs ## create sphinx-apidoc files but with special index handling for indices and indicators
+autodoc-custom-index: install-docs clean-docs ## create sphinx-apidoc files but with special index handling for indices and indicators
 	env SPHINX_APIDOC_OPTIONS="members,undoc-members,show-inheritance,noindex" sphinx-apidoc -o docs/apidoc --private --module-first src/ravenpy
 
 linkcheck: autodoc ## run checks over all external links found throughout the documentation
@@ -96,17 +110,19 @@ initialize-translations: autodoc-custom-index ## initialize translations, ignori
 	sphinx-intl update -p docs/_build/gettext -d docs/locales -l fr
 	rm -fr docs/locales/fr/LC_MESSAGES/apidoc
 
-docs: autodoc-custom-index ## generate Sphinx HTML documentation, including API docs
+build-docs: autodoc-custom-index ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html BUILDDIR="_build/html/en"
 ifneq ("$(wildcard $(LOCALES))","")
 	${MAKE} -C docs gettext
 	$(MAKE) -C docs html BUILDDIR="_build/html/fr" SPHINXOPTS="-D language='fr'"
 endif
+
+docs: build-docs  ## open the built documentation in a web browser
 ifndef READTHEDOCS
 	$(BROWSER) docs/_build/html/en/html/index.html
 endif
 
-servedocs: docs ## compile the docs watching for changes
+servedocs: autodoc-custom-index ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
 ## Development targets:
@@ -121,6 +137,7 @@ release: dist ## package and upload a release
 install: clean ## install the package to the active Python's site-packages
 	python -m pip install --no-user .
 
-develop: clean ## install the package and development dependencies in editable mode to the active Python's site-packages
-	python -m pip install --no-user --editable ".[all]"
-	pre-commit install
+development: clean ## install the package to the active Python's site-packages
+	python -m pip install --group dev
+	python -m pip install --no-user --editable .[extras]
+	prek install

README.rst

@@ -9,7 +9,7 @@ RavenPy |logo|
 +----------------------------+-----------------------------------------------------+
 | Open Source                | |license| |ossf-score| |zenodo|                     |
 +----------------------------+-----------------------------------------------------+
-| Coding Standards           | |ruff| |ossf-bp| |pre-commit|                       |
+| Coding Standards           | |ruff| |ossf-bp| |prek| |pre-commit-ci|             |
 +----------------------------+-----------------------------------------------------+
 | Development Status         | |status| |build| |coveralls|                        |
 +----------------------------+-----------------------------------------------------+
@@ -91,10 +91,14 @@ This package was created with Cookiecutter_ and the `Ouranosinc/cookiecutter-pyp
         :target: https://securityscorecards.dev/viewer/?uri=github.com/CSHS-CWRA/RavenPy
         :alt: OpenSSF Scorecard
 
-.. |pre-commit| image:: https://results.pre-commit.ci/badge/github/CSHS-CWRA/RavenPy/master.svg
+.. |pre-commit-ci| image:: https://results.pre-commit.ci/badge/github/CSHS-CWRA/RavenPy/master.svg
         :target: https://results.pre-commit.ci/latest/github/CSHS-CWRA/RavenPy/master
         :alt: pre-commit.ci status
 
+.. |prek| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/j178/prek/master/docs/assets/badge-v0.json
+        :target: https://github.com/j178/prek
+        :alt: prek
+
 .. |pypi| image:: https://img.shields.io/pypi/v/RavenPy.svg
         :target: https://pypi.python.org/pypi/RavenPy
         :alt: PyPI

docs/conf.py

@@ -118,7 +118,6 @@ def rebuild_readme():
 
 # To avoid having to install these and burst memory limit on ReadTheDocs.
 autodoc_mock_imports = [
-  "affine",
   "fiona",
   "geopandas",
   "holoviews",

docs/index.rst

@@ -35,6 +35,11 @@ Welcome to RavenPy's documentation!
 
    apidoc/modules
 
+.. toctree::
+   :caption: GitHub Repository
+
+   CSHS-CWRA/RavenPy <https://github.com/CSHS-CWRA/RavenPy>
+
 Indices and tables
 ==================
 * :ref:`genindex`

environment-dev.yml

@@ -1,6 +1,7 @@
 name: ravenpy-dev
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - python >=3.10,<3.15
   - raven-hydro >=4.12.1,<5.0
@@ -31,29 +32,30 @@ dependencies:
   - xskillscore >=0.0.29
   - zarr
   # Dev tools and testing
-  - pip >=25.2
-  - bump-my-version >=1.2.3
-  - click >=8.2.0
+  - pip >=26.0.1
+  - bump-my-version >=1.2.6
+  - click >=8.3.1
+  - codespell >=2.4.1
   - coverage >=7.5.0
-  - deptry >=0.23.0
+  - deptry >=0.24.0
   - filelock >=3.14.0
   - flake8 >=7.3.0
   - flake8-rst-docstrings >=0.4.0
   - flit >=3.11.0,<4.0
-  - mypy >=1.18.2
-  - numpydoc >=1.9.0
+  - mypy >=1.19.1
+  - numpydoc >=1.10.0
   - pooch >=1.8.0
-  - pre-commit >=3.5.0
-  - pylint >=3.3.0
-  - pytest >=8.2.3
-  - pytest-cov >=5.0.0
+  - prek >=0.3.0
+  - pylint >=4.0.4
+  - pytest >=9.0.2
+  - pytest-cov >=7.0.0
   - pytest-xdist >=3.2.0
-  - ruff >=0.13.3
-  - tox >=4.30.3
+  - ruff >=0.15.0
+  - tox >=4.41.0
+  - tox-gh >=1.6.1
   - vulture >=2.14
-  - watchdog >=4.0.0
+  - watchdog >=6.0.0
   # GIS support
-  - affine >=2.4.0
   - fiona >=1.9.0
   - gdal >=3.1
   - geopandas >=1.0
@@ -62,7 +64,6 @@ dependencies:
   - pyproj >=3.3.0
   - rasterio
   - rioxarray
-  - setuptools >=71.0
   - shapely >=2.0.0
   # Notebook support
   - birdy >=0.9.1

environment-docs.yml

@@ -1,12 +1,13 @@
 name: ravenpy-docs
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - python >=3.13,<3.14
   - raven-hydro >=4.12.1,<5.0
   - cftime >=1.4.1
   - cf-xarray >=0.9.3
-  - click >=8.2.0
+  - click >=8.3.1
   - climpred >=2.6.0
   - dask >=2024.8.1
   - h5netcdf >=1.5.0
@@ -38,6 +39,6 @@ dependencies:
   - sphinx >=8.2.0
   - sphinx-click
   - sphinx-codeautolink >=0.16.2
-  - sphinx-copybutton
+  - sphinx-copybutton >=0.5.2
   - sphinx-rtd-theme >=1.0
   - sphinxcontrib-svg2pdfconverter >=1.2.3