Support raven-hydro 0.4.0 (#459)

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

* Updates `raven-hydro` to v0.4.0 (`RavenHydroFramework` v4.0.1)
* Updates and pins a few development dependencies
* Adds support for Python3.13
* Adds builds for macOS to the GitHub Workflows
* Unpins `netcdf4` (raises pin to v1.7.2)
* Progressively drops the coveralls Python package for conda builds
(unmaintained).

### Does this PR introduce a breaking change?

Possibly. Behaviour of `RavenHydroFramework` may affect output values.

Author: Zeitsperre

.github/workflows/main.yml

@@ -59,10 +59,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ 'ubuntu-latest' ]  # 'macos-latest' disabled until a new build of raven-hydro is available
-        python-version: [ "3.11", "3.12" ]
+        os: [ 'ubuntu-latest', "macos-latest" ]
+        python-version: [ "3.11", "3.12", "3.13" ]
         tox-env: [ 'false' ]
-          # - "3.13" # not yet supported by dependencies
         include:
           - os: 'ubuntu-latest'
             python-version: '3.10'
@@ -98,21 +97,18 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
 
-      - name: Install GDAL (Ubuntu)
+      - name: Install GDAL + Set GDAL_VERSION (Ubuntu)
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
           sudo apt-get install libgdal-dev
+          echo "GDAL_VERSION=$(gdal-config --version)" >> $GITHUB_ENV
       - name: Install GDAL (macOS)
         if: matrix.os == 'macos-latest'
         uses: tecolicom/actions-use-homebrew-tools@b9c066b79607fa3d71e0be05d7003bb75fd9ff34 # v1.3
         with:
           tools: gdal
           cache: "yes"
-      - name: Set GDAL_VERSION (Ubuntu)
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          echo "GDAL_VERSION=$(gdal-config --version)" >> $GITHUB_ENV
       - name: Set GDAL_VERSION (macOS)
         if: matrix.os == 'macos-latest'
         run: |
@@ -125,8 +121,10 @@ jobs:
         run: |
           if [ "${{ matrix.tox-env }}" != "false" ]; then
             python3 -m tox -e ${{ matrix.tox-env }}
-          else
+          elif [ "${{ matrix.python-version }}" != "3.13" ]; then
             python3 -m tox -e py${{ matrix.python-version }}-coveralls
+          else
+            python3 -m tox -e py${{ matrix.python-version }}
           fi
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -142,10 +140,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ "ubuntu-latest" ]
-          # - macos-latest  # disabled until a new build of raven-hydro is available
+        os: [ "ubuntu-latest", "macos-latest" ]
           # - windows-latest  # disabled until xesmf is available
-        python-version: [ "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.13" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -192,15 +189,12 @@ jobs:
           python -m pip check || true
       - name: Test RavenPy
         run: |
-          python -m pytest --cov --numprocesses=logical
-      - name: Report coverage
-        run: |
-          python -m coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-conda_${{ matrix.python-version }}_${{ matrix.os }}
-          COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
+          python -m pytest --numprocesses=logical --cov=src/ravenpy --cov-report=lcov
+      - name: Report Coverage
+        uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b # v2.3.6
+        with:
+          flag-name: run-conda_${{ matrix.python-version }}_${{ matrix.os }}
+          parallel: true
 
   finish:
     needs:

.gitignore

@@ -47,6 +47,7 @@ htmlcov/
 .coverage.*
 .cache
 nosetests.xml
+coverage.lcov
 coverage.xml
 *.cover
 .hypothesis/

.pre-commit-config.yaml

@@ -50,7 +50,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [ '--fix' ]
@@ -92,7 +92,7 @@ repos:
         additional_dependencies: [ 'black==25.1.0' ]
       - id: blackdoc-autoupdate-black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies: [ 'tomli' ]
@@ -108,7 +108,7 @@ repos:
       - id: check-github-workflows
       - id: check-readthedocs
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.3.0
+    rev: v1.3.1
     hooks:
       - id: zizmor
         args: [ '--config=.zizmor.yml' ]

CHANGELOG.rst

@@ -11,6 +11,10 @@ v0.18.0 (unreleased)
     * Removed several `type: ignore` statements.
     * Spelling errors in documentation have been addressed.
 * Fix bug in _MonthlyRecord class definition crashing the pydantic-autodoc serialization. (PR #458)
+* `ravenpy` now supports Python3.13. (PR #459)
+* Update `raven-hydro` to v0.4.0 (`RavenHydroFramework` v4.0.1). (PR #459)
+* Update `xclim` to v0.54.0, `pint` to v0.24.4, and `numpy` to v1.24.0 (no longer pinned below v2.0). (PR #459)
+* GitHub Workflows now test `ravenpy` using macOS as well as Python3.13. (PR #459)
 
 v0.17.0 (2025-01-27)
 --------------------

Makefile

@@ -54,12 +54,12 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 	rm -fr .pytest_cache
 
- lint/flake8: ## check style with flake8
+lint/flake8: ## check style with flake8
 	python -m ruff check src/ravenpy tests
 	python -m flake8 --config=.flake8 src/ravenpy tests
 	python -m numpydoc lint src/ravenpy/**.py
 
- lint/black: ## check style with black
+lint/black: ## check style with black
 	python -m black --check src/ravenpy tests
 	python -m blackdoc --check src/ravenpy docs
 	python -m isort --check src/ravenpy tests

environment-dev.yml

@@ -2,53 +2,52 @@ name: ravenpy-dev
 channels:
   - conda-forge
 dependencies:
-  - python >=3.9,<3.13
-  - raven-hydro >=0.3.1,<1.0
-  - libgcc  # for mixing raven-hydro from PyPI with conda environments
+  - python >=3.10,<3.14
+  - raven-hydro >=0.4.0,<1.0
+  # - libgcc  # for mixing raven-hydro from PyPI with conda environments
   - affine >=2.4.0
   - cftime >=1.4.1
   - cf_xarray >=0.9.3
   - click >=8.0.0
   - climpred >=2.4.0
-  - dask >=2024.4.0
+  - dask >=2024.8.1
   - fiona >=1.9.0
   - gdal >=3.1
   - geopandas >=1.0
   - h5netcdf >=1.3.0
   - haversine >=2.8.0
   - matplotlib-base >=3.6.0
-  - netcdf4 <=1.6.5
-  - numpy >=1.23.0,<2.0
+  - netcdf4 >=1.7.2
+  - numpy >=1.24.0
   - owslib >=0.29.1
   - pandas >=2.2.0
-  - pint >=0.20,<0.24
-  - platformdirs
+  - pint >=0.24.4
+  - platformdirs >=4.3.6
   - pydantic >=2.0
   - pydap >=3.4.0
   - pymetalink >=6.5.2
   - pymbolic >=2024.2
   - pyproj >=3.3.0
   - rasterio
   - rioxarray
-  - scipy >=1.10.0
+  - scipy >=1.11.0
   - shapely >=2.0.0
   - spotpy >=1.6.1
   - statsmodels >=0.14.2
   - typing_extensions
-  - xarray >=2023.11.0
-  - xclim >=0.50.0
+  - xarray >=2023.11.0,!=2024.10.0
+  - xclim >=0.54.0
   - xesmf
   - xskillscore
   - zarr >=2.13,<3.0 # FIXME: zarr v3 does not support FSMap like before: https://github.com/zarr-developers/zarr-python/issues/2706
   # Dev tools and testing
   - pip >=25.0
   - black ==25.1.0
   - blackdoc ==0.3.9
-  - bump-my-version >=0.30.1
+  - bump-my-version >=0.32.1
   - click >=8.1.7
   - coverage >=7.5.0
-  - coveralls >=4.0.0
-  - filelock
+  - filelock >=3.14.0
   - flake8 >=7.1.1
   - flake8-rst-docstrings >=0.3.0
   - flit >=3.10.1,<4.0
@@ -58,6 +57,7 @@ dependencies:
   - mypy >=1.14.1
   - numpydoc >=1.8.0
   - pre-commit >=3.5.0
+  - pylint >=3.3.0
   - pytest >=8.2.2
   - pytest-cov >=5.0.0
   - pytest-xdist >=3.2.0

environment-docs.yml

@@ -1,18 +1,18 @@
 name: ravenpy-docs
 channels:
-- conda-forge
-- defaults
+  - conda-forge
 dependencies:
   - python >=3.12,<3.13
-  - raven-hydro >=0.3.1,<1.0
-  - autodoc-pydantic
+  - raven-hydro >=0.4.0,<1.0
+  - autodoc-pydantic >=2.1.0
   - birdy
   - cairosvg >=2.6.0
   - cartopy >=0.23.0
   - click >=8.0.0
-  - clisops >=0.13.0
+  - clisops >=0.15.0
   - gcsfs
   - gdal >=3.1
+  - h5netcdf >=1.3.0
 # Needed for notebooks/HydroShare_integration.ipynb
 # See: https://github.com/CSHS-CWRA/RavenPy/pull/326
 #  - "hsclient",
@@ -27,9 +27,9 @@ dependencies:
   - jupytext
   - matplotlib-base >=3.6.0
   - myst-nb
-  - nbsphinx
-  - netCDF4 <=1.6.5
-  - numpy >=1.23.0,<2.0.0
+  - nbsphinx >=0.9.5
+  - netCDF4 >=1.7.2
+  - numpy >=1.24.0
   - notebook
   - pydantic >=2.0
   - pymetalink >=6.5.2
@@ -43,6 +43,6 @@ dependencies:
   - sphinx-rtd-theme >=1.0
   - sphinxcontrib-svg2pdfconverter >=1.2.3
   - typing_extensions
-  - xarray >=2023.11.0
+  - xarray >=2023.11.0,!=2024.10.0
 #  - xesmf  # mocked
   - zarr >=2.13,<3.0 # FIXME: zarr v3 does not support FSMap like before: https://github.com/zarr-developers/zarr-python/issues/2706

pyproject.toml

@@ -27,7 +27,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
-  # "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: Implementation :: CPython",
   "Topic :: Scientific/Engineering :: Atmospheric Science",
   "Topic :: Scientific/Engineering :: GIS",
@@ -40,26 +40,25 @@ dependencies = [
   "cf-xarray >=0.9.3",
   "click >=8.0.0",
   "climpred >=2.4.0",
-  "dask>=2024.4.0",
+  "dask >=2024.8.1",
   "h5netcdf >=1.3.0",
   "haversine >=2.8.0",
   "matplotlib >=3.6.0",
-  "netCDF4 <=1.6.5",
-  "numpy >=1.23,<2.0.0",
+  "numpy >=1.24.0",
   "owslib >=0.29.1",
   "pandas >=2.2.0",
-  "pint >=0.20,<0.24",
-  "platformdirs",
+  "pint >=0.24.4",
+  "platformdirs >=4.3.6",
   "pydantic >=2.0",
   "pydap >=3.4.0",
   "pymbolic >=2024.2",
-  "raven-hydro >=0.3.1,<1.0",
-  "scipy >=1.9.0",
+  "raven-hydro >=0.4.0,<1.0",
+  "scipy >=1.11.0",
   "spotpy >=1.6.1",
   "statsmodels >=0.14.2",
   "typing-extensions",
-  "xarray >=2023.11.0",
-  "xclim >=0.50.0",
+  "xarray >=2023.11.0,!=2024.10.0",
+  "xclim >=0.54.0",
   "xskillscore"
 ]
 
@@ -68,9 +67,9 @@ dev = [
   # Dev tools and testing
   "black ==25.1.0",
   "blackdoc ==0.3.9",
-  "bump-my-version >=0.30.1",
+  "bump-my-version >=0.32.1",
   "coverage >=7.5.0",
-  "filelock",
+  "filelock >=3.14.0",
   "flake8 >=7.1.1",
   "flake8-rst-docstrings >=0.3.0",
   "flit >=3.10.1,<4.0",
@@ -82,7 +81,7 @@ dev = [
   "numpydoc >=1.8.0",
   "pip >=25.0",
   "pre-commit >=3.5.0",
-  "pylint",
+  "pylint >=3.3.0",
   "pytest >=8.3.2",
   "pytest-cov >=5.0.0",
   "pytest-xdist >=3.2.0",
@@ -91,11 +90,11 @@ dev = [
   "watchdog >=4.0.0"
 ]
 docs = [
-  "autodoc-pydantic",
+  "autodoc-pydantic >=2.1.0",
   "birdhouse-birdy",
   "cairosvg >=2.6.0",
   "cartopy >=0.23.0",
-  "clisops >=0.13.0",
+  "clisops >=0.15.0",
   "gcsfs",
   # Needed for notebooks/HydroShare_integration.ipynb
   # See: https://github.com/CSHS-CWRA/RavenPy/pull/326
@@ -117,13 +116,11 @@ docs = [
   "s3fs",
   "salib",
   "sphinx >=7.1.0",
-  "sphinx-autoapi",
   "sphinx-click",
   "sphinx-codeautolink >=0.16.2",
   "sphinx-copybutton",
   "sphinx-rtd-theme >=1.0",
   "sphinxcontrib-svg2pdfconverter >=1.2.3",
-  "typing-extensions",
   "xesmf",
   "zarr >=2.10.0,<3.0" # FIXME: zarr v3 does not support FSMap like before: https://github.com/zarr-developers/zarr-python/issues/2706
 ]
@@ -133,6 +130,7 @@ gis = [
   "geopandas >=1.0",
   "gdal >=3.1",
   "lxml",
+  "netcdf4 >=1.7.2",
   "pyproj >=3.3.0",
   "rasterio",
   "rioxarray",
@@ -325,23 +323,31 @@ warn_required_dynamic_aliases = true
 warn_untyped_fields = true
 
 [tool.pytest.ini_options]
+minversion = "7.0"
 addopts = [
   "--verbose",
   "--color=yes",
+  "--strict-config",
   "--strict-markers",
   "--tb=native",
   "--numprocesses=0",
   "--maxprocesses=8",
   "--dist=worksteal"
 ]
 python_files = "test_*.py"
-norecursedirs = ["src", ".git", "bin"]
+norecursedirs = ["docs/notebooks"]
 filterwarnings = ["ignore::UserWarning"]
-testpaths = "tests"
+testpaths = [
+  "tests"
+]
+pythonpath = [
+  "src"
+]
 markers = [
   "slow: marks tests as slow (deselect with '-m \"not slow\"')",
   "online: mark tests that require external services (deselect with '-m \"not online\"')"
 ]
+xfail_strict = true
 
 [tool.ruff]
 src = ["ravenpy"]