Update to xclim 0.61, xsdba 0.6.1 and xscen 0.15

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.13" ]
+        python-version: [ "3.14" ]
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@fe104658747b27e96e4f7e80cd0a94068e53901d # v2.16.1
@@ -53,7 +53,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: [ "3.10", "3.11", "3.12" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@fe104658747b27e96e4f7e80cd0a94068e53901d # v2.16.1
@@ -69,11 +69,12 @@ jobs:
           cache-downloads: true
           cache-environment: true
           environment-file: environment.yml
+          environment-name: finch
           create-args: >-
             python=${{ matrix.python-version }}
       - name: Install finch-wps
         run: |
-          make develop
+          make install
       - name: Check versions
         run: |
           python -m pip check

.readthedocs.yml

@@ -21,7 +21,7 @@ build:
     python: "mambaforge-23.11"
 
 conda:
-  environment: environment-docs.yml
+  environment: environment.yml
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

Makefile

@@ -42,12 +42,13 @@ help: ## print this help message. (Default)
 .PHONY: install
 install: ## install finch application
 	@echo "Installing application ..."
-	@-bash -c 'pip install -e .'
+	@-bash -c 'python -m pip install --editable .'
 	@echo "\nStart service with \`make start\` and stop with \`make stop\`."
 
 develop: ## install finch application with development libraries
 	@echo "Installing development requirements for tests and docs ..."
-	@-bash -c 'pip install -e ".[dev]"'
+	@-bash -c 'test "${CONDA_PREFIX:-''} == $(dirname $(dirname $(which python)))" && echo "You are installing deps with pip inside a conda environment, this could lead to broken conda environments."'
+	@-bash -c 'python -m pip install --editable ".[dev]"'
 
 start: ## start finch service as daemon (background process)
 	@echo "Starting application ..."

docs/source/conf.py

@@ -53,51 +53,6 @@
     "sphinxcontrib.bibtex",
 ]
 
-# To avoid having to install these and burst memory limit on ReadTheDocs.
-# List of all tested working mock imports from all birds so new birds can
-# inherit without having to test which work which do not.
-if os.environ.get("READTHEDOCS") == "True":
-    autodoc_mock_imports = [
-        "affine",
-        "bottleneck",
-        "cairo",
-        "cartopy",
-        "cftime",
-        "cf_xarray",
-        "clisops",
-        "dask",
-        "fiona",
-        "gdal",
-        "geopandas",
-        "geos",
-        "geotiff",
-        "hdf4",
-        "hdf5",
-        "matplotlib",
-        "netCDF4",
-        "numba",
-        "numpy",
-        "ocgis",
-        "osgeo",
-        "pandas",
-        "parse",
-        "proj",
-        "pyproj",
-        "rasterio",
-        "rasterstats",
-        "scikit-learn",
-        "scipy",
-        "sentry_sdk",
-        "shapely",
-        "siphon",
-        "sklearn",
-        "slugify",
-        "spotpy",
-        "statsmodels",
-        "unidecode",
-        "xarray",
-        "zlib",
-    ]
 
 # Bibliography stuff, for correct xclim docstring formatting
 # We need to download the reference file from xclim for the correct version.
@@ -124,12 +79,7 @@
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
 }
 
-# Monkeypatch constant because the following are mock imports.
-# Only works if numpy is actually installed and at the same time being mocked.
-# import numpy
-# numpy.pi = 3.1416
-
-# We are using mock imports in readthedocs, so probably safer to not run the notebooks
+# Probably safer to not run the notebooks
 nbsphinx_execute = "never"
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/dev_guide.rst

@@ -14,11 +14,13 @@ Developer Guide
 Building the docs
 -----------------
 
-First install dependencies for the documentation:
+First install an environment with conda/mamba and finch within it.
 
 .. code-block:: shell
 
-   $ make develop
+   $ mamba env create -f environment.yml
+   $ mamba activate finch
+   $ pip install -e .
 
 Run the Sphinx docs generator:
 
@@ -33,14 +35,13 @@ Running tests
 
 Run tests using pytest_.
 
-First activate the ``finch`` Conda environment and install ``pytest``.
+First install an environment with conda/mamba and finch within it.
 
 .. code-block:: shell
 
-   $ source activate finch
-   $ pip install -e ".[dev]"  # if not already installed
-   # or
-   $ make develop
+   $ mamba env create -f environment.yml
+   $ mamba activate finch
+   $ pip install -e .
 
 Run quick tests (skip slow and online):
 
@@ -82,11 +83,11 @@ To update the `conda` specification file for building identical environments_ on
 
 .. code-block:: console
 
-   $ conda env create -f environment.yml
-   $ source activate finch
+   $ mamba env create -f environment.yml
+   $ mamba activate finch
    $ make clean
-   $ make install
-   $ conda list -n finch --explicit > spec-file.txt
+   $ pip install -e .
+   $ mamba list -n finch --explicit > spec-file.txt
 
 .. _environments: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments
 

docs/source/installation.rst

@@ -39,12 +39,12 @@ Check out code from the Finch GitHub repo and start the installation:
    $ git clone https://github.com/bird-house/finch.git
    $ cd finch
 
-Create Conda environment named `finch`:
+Create Conda environment named `finch` (including the development and documentation dependencies):
 
 .. code-block:: console
 
    $ conda env create -f environment.yml
-   $ source activate finch
+   $ conda activate finch
 
 Install `finch` app:
 
@@ -54,17 +54,10 @@ Install `finch` app:
    OR
    $ make install
 
-For development you can use this command:
-
-.. code-block:: console
-
-  $ pip install -e .[dev]
-  OR
-  $ make develop
 
 Install from Conda
 ------------------
 
 .. note::
 
-   `finch` is not yet available on conda-forge. But we are working on making this package available soon!
+   There are no plans to make `finch` available on conda-forge.

environment.yml

@@ -3,19 +3,18 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python >=3.10,<3.13
-  - pip >=25.3.0
+  - python >=3.11,<3.15
+  - pip >=26.1.0
   - anyascii >=0.3.0
   - cftime >=1.4.1
   - cf_xarray >=0.9.3
-  - click >=8.0.0
+  - click >=8.1.7
   - clisops >=0.16.2
-  - dask >=2023.5.1,<2025.3.0
+  - dask >=2023.5.1
   - distributed
   - geopandas >=1.0
   - jinja2 >=3.1.4
-  - netcdf4 <=1.7.2
-  - numcodecs <0.16.0
+  - netcdf4
   - numpy >=1.25.0
   - pandas >=2.2.0,<3.0
   - parse >=1.20
@@ -28,9 +27,38 @@ dependencies:
   - setuptools >=78.1.1
   - siphon >=0.10.0
   - werkzeug >=3.0.6
-  - xarray >=2023.11.0,<2025.03.0
-  - xclim =0.52.2  # remember to match xclim version in requirements_docs.txt as well
+  - xarray >=2023.11.0
+  - xclim >=0.61,<0.62 # remember to match xclim version in pyproject.toml as well
   - xesmf >=0.8.2,!=0.8.8
-  - xscen =0.10.0  # remember to match xscen version in environment.yml as well
+  - xsdba =0.6.1   # remember to match xsdba version in pyproject.toml as well
+  - xscen >=0.15,<0.16  # remember to match xscen version in pyproject.toml as well
   # Temporary fixes
   - fastprogress <1.1  # FIXME: Temporary fix following https://github.com/intake/intake-esm/pull/773. Remove when intake-esm is updated in xscen.
+  # Dev
+  - birdy >=0.8.1
+  - black >=26.1.0
+  - bump-my-version >=1.2.6
+  - coverage >=7.5.0
+  - cruft >=2.15.0
+  - flake8 >=7.3.0
+  - flake8-rst-docstrings >=0.4.0
+  - flit >=3.11.0,<4.0
+  - geojson
+  - lxml
+  - nbsphinx >=0.9.8
+  - nbval >=0.10.0
+  - owslib
+  - pip >=25.3.0
+  - pre-commit >=3.5.0
+  - pylint >=3.3.3
+  - pytest >=8.0.0
+  - pytest-cov >=5.0.0
+  - pytest-flake8
+  - ruff >=0.14.0
+  - watchdog >=4.0.0
+  - yamllint >=1.26.0
+  # Docs
+  - ipython >=8.5.0
+  - matplotlib-base >=3.5.0
+  - sphinx >=9.0.0
+  - sphinxcontrib-bibtex >=2.6.0