Update project configuration

Author: btschwertfeger

.github/workflows/_codecov.yaml

@@ -47,7 +47,7 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Install package
-        run: python -m pip install ".[dev,test]"
+        run: python -m pip install . -r requirements-dev.txt
 
       - name: Generate coverage report
         run: pytest --retries 1 --cov --cov-report=xml

.github/workflows/_codeql.yaml

@@ -30,10 +30,10 @@ jobs:
       contents: read
       security-events: write
 
-    # strategy:
-    #   fail-fast: false
-    #   matrix:
-    #     language: ["python"]
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ["python"]
     # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
     # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 

.github/workflows/_test.yaml

@@ -38,7 +38,7 @@ jobs:
         run: python -m pip install --user --upgrade pip
 
       - name: Install package
-        run: python -m pip install --user ".[dev,test]"
+        run: python -m pip install --user . -r requirements-dev.txt
 
       - name: Run unit tests
         run: pytest -vv --retries 1 tests

CHANGELOG.md

@@ -2,7 +2,19 @@
 
 ## [Unreleased](https://github.com/btschwertfeger/python-cmethods/tree/HEAD)
 
-[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.3.0...HEAD)
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.3.1...HEAD)
+
+**Merged pull requests:**
+
+- Bump github/codeql-action from 3.29.2 to 3.29.5 in the all group [\#171](https://github.com/btschwertfeger/python-cmethods/pull/171) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump github/codeql-action from 3.28.18 to 3.29.2 in the all group [\#170](https://github.com/btschwertfeger/python-cmethods/pull/170) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Update project settings [\#169](https://github.com/btschwertfeger/python-cmethods/pull/169) ([btschwertfeger](https://github.com/btschwertfeger))
+- Bump the all group with 4 updates [\#168](https://github.com/btschwertfeger/python-cmethods/pull/168) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump the all group with 3 updates [\#167](https://github.com/btschwertfeger/python-cmethods/pull/167) ([dependabot[bot]](https://github.com/apps/dependabot))
+
+## [v2.3.1](https://github.com/btschwertfeger/python-cmethods/tree/v2.3.1) (2025-04-01)
+
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.3.0...v2.3.1)
 
 **Fixed bugs:**
 
@@ -11,10 +23,16 @@
 **Closed issues:**
 
 - Create Jupyter Notebooks for possible strategies [\#135](https://github.com/btschwertfeger/python-cmethods/issues/135)
+- Parts of the pyproject.toml are deprecated [\#164](https://github.com/btschwertfeger/python-cmethods/issues/164)
 
 **Merged pull requests:**
 
+- Bump the all group with 2 updates [\#166](https://github.com/btschwertfeger/python-cmethods/pull/166) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump the all group with 3 updates [\#162](https://github.com/btschwertfeger/python-cmethods/pull/162) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump github/codeql-action from 3.28.8 to 3.28.9 in the all group [\#161](https://github.com/btschwertfeger/python-cmethods/pull/161) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump dependabot/fetch-metadata from 2.2.0 to 2.3.0 [\#159](https://github.com/btschwertfeger/python-cmethods/pull/159) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump codecov/codecov-action from 5.1.2 to 5.3.1 [\#158](https://github.com/btschwertfeger/python-cmethods/pull/158) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump github/codeql-action from 3.28.1 to 3.28.8 [\#157](https://github.com/btschwertfeger/python-cmethods/pull/157) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump actions/setup-python from 5.3.0 to 5.4.0 [\#156](https://github.com/btschwertfeger/python-cmethods/pull/156) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.28.0 to 3.28.1 [\#152](https://github.com/btschwertfeger/python-cmethods/pull/152) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Add `release.yaml` [\#151](https://github.com/btschwertfeger/python-cmethods/pull/151) ([btschwertfeger](https://github.com/btschwertfeger))
@@ -23,20 +41,15 @@
 - Bump github/codeql-action from 3.27.6 to 3.27.9 [\#148](https://github.com/btschwertfeger/python-cmethods/pull/148) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump codecov/codecov-action from 4.6.0 to 5.1.1 [\#147](https://github.com/btschwertfeger/python-cmethods/pull/147) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.27.4 to 3.27.6 [\#146](https://github.com/btschwertfeger/python-cmethods/pull/146) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Do not rely on trusted publishing for PyPI upload [\#145](https://github.com/btschwertfeger/python-cmethods/pull/145) ([btschwertfeger](https://github.com/btschwertfeger))
 - Bump github/codeql-action from 3.27.1 to 3.27.4 [\#141](https://github.com/btschwertfeger/python-cmethods/pull/141) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.27.0 to 3.27.1 [\#140](https://github.com/btschwertfeger/python-cmethods/pull/140) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump actions/checkout from 4.2.1 to 4.2.2 [\#138](https://github.com/btschwertfeger/python-cmethods/pull/138) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump actions/setup-python from 5.2.0 to 5.3.0 [\#137](https://github.com/btschwertfeger/python-cmethods/pull/137) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.26.13 to 3.27.0 [\#136](https://github.com/btschwertfeger/python-cmethods/pull/136) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Update and apply Pre-Commit hooks [\#134](https://github.com/btschwertfeger/python-cmethods/pull/134) ([btschwertfeger](https://github.com/btschwertfeger))
 - Bump actions/checkout from 4.1.7 to 4.2.1 [\#132](https://github.com/btschwertfeger/python-cmethods/pull/132) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.26.11 to 3.26.13 [\#131](https://github.com/btschwertfeger/python-cmethods/pull/131) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump codecov/codecov-action from 4.5.0 to 4.6.0 [\#130](https://github.com/btschwertfeger/python-cmethods/pull/130) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.26.8 to 3.26.11 [\#129](https://github.com/btschwertfeger/python-cmethods/pull/129) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Move CITATION file to top-level [\#126](https://github.com/btschwertfeger/python-cmethods/pull/126) ([btschwertfeger](https://github.com/btschwertfeger))
-- Add CITATION file [\#125](https://github.com/btschwertfeger/python-cmethods/pull/125) ([btschwertfeger](https://github.com/btschwertfeger))
-- Update project settings [\#124](https://github.com/btschwertfeger/python-cmethods/pull/124) ([btschwertfeger](https://github.com/btschwertfeger))
 - Bump github/codeql-action from 3.26.7 to 3.26.8 [\#123](https://github.com/btschwertfeger/python-cmethods/pull/123) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump github/codeql-action from 3.26.6 to 3.26.7 [\#122](https://github.com/btschwertfeger/python-cmethods/pull/122) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump actions/setup-python from 5.1.1 to 5.2.0 [\#121](https://github.com/btschwertfeger/python-cmethods/pull/121) ([dependabot[bot]](https://github.com/apps/dependabot))
@@ -49,6 +62,14 @@
 - Bump actions/setup-python from 5.1.0 to 5.1.1 [\#114](https://github.com/btschwertfeger/python-cmethods/pull/114) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump dependabot/fetch-metadata from 2.1.0 to 2.2.0 [\#113](https://github.com/btschwertfeger/python-cmethods/pull/113) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Bump actions/checkout from 4.1.6 to 4.1.7 [\#110](https://github.com/btschwertfeger/python-cmethods/pull/110) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Resolve "Parts of the pyproject.toml are deprecated" [\#165](https://github.com/btschwertfeger/python-cmethods/pull/165) ([btschwertfeger](https://github.com/btschwertfeger))
+- Fix the documentation build [\#163](https://github.com/btschwertfeger/python-cmethods/pull/163) ([btschwertfeger](https://github.com/btschwertfeger))
+- Update copyright headers [\#160](https://github.com/btschwertfeger/python-cmethods/pull/160) ([btschwertfeger](https://github.com/btschwertfeger))
+- Do not rely on trusted publishing for PyPI upload [\#145](https://github.com/btschwertfeger/python-cmethods/pull/145) ([btschwertfeger](https://github.com/btschwertfeger))
+- Update and apply Pre-Commit hooks [\#134](https://github.com/btschwertfeger/python-cmethods/pull/134) ([btschwertfeger](https://github.com/btschwertfeger))
+- Move CITATION file to top-level [\#126](https://github.com/btschwertfeger/python-cmethods/pull/126) ([btschwertfeger](https://github.com/btschwertfeger))
+- Add CITATION file [\#125](https://github.com/btschwertfeger/python-cmethods/pull/125) ([btschwertfeger](https://github.com/btschwertfeger))
+- Update project settings [\#124](https://github.com/btschwertfeger/python-cmethods/pull/124) ([btschwertfeger](https://github.com/btschwertfeger))
 
 ## [v2.3.0](https://github.com/btschwertfeger/python-cmethods/tree/v2.3.0) (2024-06-19)
 

Makefile

@@ -44,7 +44,7 @@ install: check-uv
 .PHONY: dev
 dev:
 	@git lfs install
-	$(UV) pip install -e ".[dev,test,jupyter,examples]" -r doc/requirements.txt
+	$(UV) pip install -e . -r doc/requirements.txt -r requirements-dev.txt
 
 ## ======= T E S T I N G =======================================================
 ## test		Run the unit tests
@@ -124,9 +124,9 @@ changelog:
 clean:
 	rm -rf .mypy_cache .pytest_cache .cache \
 		build/ dist/ python_cmethods.egg-info \
-		docs/_build \
 		examples/.ipynb_checkpoints .ipynb_checkpoints \
-		doc/_build
+		doc/_build \
+		.coverage* pytest.xml
 
 	rm -f .coverage cmethods/_version.py
 

README.md

@@ -26,7 +26,7 @@ efficiency, python-cmethods offers a comprehensive suite of functions tailored
 for applying bias correction methods to climate model simulations and
 observational datasets via command-line interface and API.
 
-Please cite this project as described in
+If you use this project, cite it as described in
 https://zenodo.org/doi/10.5281/zenodo.7652755.
 
 ## Table of Contents

pyproject.toml

@@ -75,7 +75,7 @@ include = ["cmethods*"]
 exclude = ["doc*", "tests*", "examples*", ".env", ".venv"]
 
 [tool.setuptools_scm]
-write_to = "cmethods/_version.py"
+version_file = "cmethods/_version.py"
 version_scheme = "guess-next-dev"
 local_scheme = "no-local-version"
 
@@ -100,31 +100,6 @@ concurrency = ["multiprocessing"]
 exclude_lines = ["coverage: disable", "if TYPE_CHECKING:"]
 skip_empty = true
 
-[project.optional-dependencies]
-jupyter = ["venv-kernel"]
-dev = [
-  # building
-  "setuptools_scm",
-  "build",
-  # linting
-  "pylint",
-  "flake8",
-  "ruff",
-  # typing
-  "mypy",
-]
-test = [
-  # testing
-  "pytest",
-  "pytest-cov",
-  "pytest-retry",
-  "zarr",
-  "dask[distributed]",
-  "scikit-learn",
-  "scipy",
-]
-examples = ["matplotlib"]
-
 [tool.codespell]
 check-filenames = true
 

requirements-dev.txt

@@ -0,0 +1,8 @@
+dask[distributed]
+pytest
+pytest-cov
+pytest-retry
+scikit-learn
+scipy
+venv-kernel
+zarr