fix: isolate required and optional dependencies

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install uv
-          uv pip install . -r pyproject.toml --system --extra dev --resolution ${{ matrix.versions.resolution }}
+          uv pip install .[dev,io] -r pyproject.toml --system --resolution ${{ matrix.versions.resolution }}
 
       - name: Execute Tests
         run: |

docs/environment.yml

@@ -8,4 +8,4 @@ dependencies:
   - pandoc
   - pip
   - pip:
-    - -e ../.[docs]
+    - -e ../.[docs,io]

pyproject.toml

@@ -18,10 +18,8 @@ dependencies = [
   "tqdm>=4.64.0",
   "dask>=2023.0.1",
   "statsmodels>=0.14.0",
-  "netCDF4>=1.5.8",
   "numba>=0.57",
   "typing-extensions>=4.8.0",
-  "zarr>=2.14.0",
   "xarray-datatree>=0.0.12",
 ]
 
@@ -53,6 +51,11 @@ docs = [
   "ipython>=8.14",
   "ipykernel>=6.23",
 ]
+io = [
+  "h5netcdf>=1.0.0",
+  "netcdf4>=1.5.8",
+  "zarr>=2.14.0",
+]
 
 [project.urls]
 homepage = "https://github.com/xarray-contrib/xeofs"

tests/models/cross/test_cca.py

@@ -226,7 +226,7 @@ def test_predict():
     _ = cca.inverse_transform(Y=Ry_pred)
 
 
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(tmp_path, engine):
     """Test save/load methods in MCA class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/cross/test_cpcca.py

@@ -274,7 +274,7 @@ def test_predict():
     _ = cpcca.inverse_transform(Y=Ry_pred)
 
 
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 @pytest.mark.parametrize("alpha", [0.0, 0.5, 1.0])
 def test_save_load(tmp_path, engine, alpha):
     """Test save/load methods in MCA class, ensuring that we can
@@ -319,7 +319,7 @@ def test_save_load(tmp_path, engine, alpha):
     assert np.allclose(XYr_o[1], XYr_l[1])
 
 
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 @pytest.mark.parametrize("alpha", [0.0, 0.5, 1.0])
 def test_save_load_with_data(tmp_path, engine, alpha):
     """Test save/load methods in CPCCA class, ensuring that we can

tests/models/cross/test_mca.py

@@ -376,7 +376,7 @@ def test_compute(mock_dask_data_array, dim, compute):
         (("lon", "lat")),
     ],
 )
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(dim, mock_data_array, tmp_path, engine):
     """Test save/load methods in MCA class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/cross/test_mca_rotator.py

@@ -230,7 +230,7 @@ def test_compute(mca_model_delayed, compute):
         (("lon", "lat")),
     ],
 )
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(dim, mock_data_array, tmp_path, engine):
     """Test save/load methods in MCA class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/cross/test_rda.py

@@ -226,7 +226,7 @@ def test_predict():
     _ = rda.inverse_transform(Y=Ry_pred)
 
 
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(tmp_path, engine):
     """Test save/load methods in MCA class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/single/test_eof.py

@@ -494,7 +494,7 @@ def test_inverse_transform(dim, mock_data_array, normalized):
         (("lon", "lat")),
     ],
 )
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(dim, mock_data_array, tmp_path, engine):
     """Test save/load methods in EOF class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/single/test_eof_rotator.py

@@ -203,7 +203,7 @@ def test_compute(eof_model_delayed, compute):
         (("lon", "lat")),
     ],
 )
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(dim, mock_data_array, tmp_path, engine):
     """Test save/load methods in EOF class, ensuring that we can
     roundtrip the model and get the same results when transforming

tests/models/single/test_sparse_pca.py

@@ -483,7 +483,7 @@ def test_inverse_transform(dim, mock_data_array, normalized):
         (("lon", "lat")),
     ],
 )
-@pytest.mark.parametrize("engine", ["netcdf4", "zarr"])
+@pytest.mark.parametrize("engine", ["h5netcdf", "netcdf4", "zarr"])
 def test_save_load(dim, mock_data_array, tmp_path, engine):
     """Test save/load methods in SparsePCA class, ensuring that we can
     roundtrip the model and get the same results when transforming