Fix CI

.github/workflows/master.yml

@@ -20,22 +20,23 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.12", "3.13", "3.14", "3.x"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
+        sudo apt-get -y install libhdf5-dev
     - name: Install package
       run: |
-        pip install -e .[calc,tests]
+        pip install -e .[calc,tests] --no-binary h5netcdf --no-binary h5py
+        pip install git+https://github.com/dschwoerer/xarray@netcdf4-locking-closing
     - name: Test with pytest
       run: |
         pytest -vv --long --cov
@@ -48,7 +49,7 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.12"]
       fail-fast: false
 
     steps:
@@ -59,12 +60,13 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install xarray~=2023.1.0 pandas~=1.4.0
+        sudo apt-get -y install libhdf5-dev
+        pip install xarray~=2023.12.0 pandas~=2.2.0
     - name: Install package
       run: |
-        pip install -e .[tests]
+        pip install -e .[tests] --no-binary h5netcdf --no-binary h5py
+        pip install git+https://github.com/dschwoerer/xarray@netcdf4-locking-closing
     - name: Test with pytest
       run: |
         pytest -vv --long --cov

.github/workflows/pythonpackage.yml

@@ -20,21 +20,23 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.x"]
+        python-version: ["3.12", "3.13", "3.14", "3.x"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        sudo apt-get -y install libhdf5-dev
     - name: Install package
       run: |
-        pip install -e .[calc,tests]
+        pip install -e .[calc,tests] --no-binary h5netcdf --no-binary h5py
+        pip install git+https://github.com/dschwoerer/xarray@netcdf4-locking-closing
     - name: Test with pytest
       run: |
         pytest -vv --long --cov
@@ -47,7 +49,7 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.12"]
       fail-fast: false
 
     steps:
@@ -59,10 +61,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install xarray~=2023.1.0 pandas~=1.4.0
+        sudo apt-get -y install libhdf5-dev
+        pip install xarray~=2023.12.0 pandas~=2.2.0
     - name: Install package
       run: |
-        pip install -e .[tests]
+        pip install -e .[tests] --no-binary h5netcdf --no-binary h5py
+        pip install git+https://github.com/dschwoerer/xarray@netcdf4-locking-closing
     - name: Test with pytest
       run: |
         pytest -vv --long --cov

pyproject.toml

@@ -40,7 +40,7 @@ dependencies = [
     "natsort>=5.5.0",
     "matplotlib>=3.1.1,!=3.3.0,!=3.3.1,!=3.3.2",
     "animatplot-ng>=0.4.2",
-    "netcdf4>=1.4.0",
+    "h5netcdf",
     "Pillow>=6.1.0",
 ]
 

requirements.txt

@@ -4,7 +4,7 @@ dask[array]>=2.10.0
 natsort>=5.5.0
 matplotlib>=3.1.1,!=3.3.0,!=3.3.1,!=3.3.2
 animatplot>=0.4.2
-netcdf4>=1.4.0
+h5netcdf
 Pillow>=6.1.0
 
 # Not required for Python>=3.8, but included because conda does not support

xbout/tests/conftest.py

@@ -165,7 +165,7 @@ def create_example_grid_file_fci(tmp_path_factory):
 
     # Save
     filepath = save_dir.joinpath("fci.nc")
-    grid.to_netcdf(filepath, engine="netcdf4")
+    grid.to_netcdf(filepath, engine="h5netcdf")
 
     return filepath
 

xbout/tests/test_grid.py

@@ -27,7 +27,7 @@ def create_example_grid_file(tmp_path_factory):
 
     # Save
     filepath = save_dir.joinpath("grid.nc")
-    grid.to_netcdf(filepath, engine="netcdf4")
+    grid.to_netcdf(filepath, engine="h5netcdf")
 
     return filepath
 
@@ -52,7 +52,7 @@ def test_open_grid_extra_dims(self, create_example_grid_file, tmp_path_factory):
 
         dodgy_grid_directory = tmp_path_factory.mktemp("dodgy_grid")
         dodgy_grid_path = dodgy_grid_directory.joinpath("dodgy_grid.nc")
-        merge([example_grid, new_var]).to_netcdf(dodgy_grid_path, engine="netcdf4")
+        merge([example_grid, new_var]).to_netcdf(dodgy_grid_path, engine="h5netcdf")
 
         with pytest.warns(
             UserWarning, match="drop all variables containing " "the dimensions 'w'"

xbout/tests/test_load.py

@@ -43,7 +43,7 @@ def test_check_extensions(tmp_path):
     example_nc_file.write_text("content_nc")
 
     filetype = _check_filetype(example_nc_file)
-    assert filetype == "netcdf4"
+    assert filetype == "h5netcdf"
 
     example_hdf5_file = files_dir.joinpath("example.h5netcdf")
     example_hdf5_file.write_text("content_hdf5")

xbout/utils.py

@@ -31,7 +31,7 @@ def _add_attrs_to_var(ds, varname, copy=False):
 
 def _check_filetype(path):
     if path.suffix == ".nc":
-        filetype = "netcdf4"
+        filetype = "h5netcdf"
     elif path.suffix == ".h5netcdf":
         filetype = "h5netcdf"
     elif path.suffix == ".bp":