Regular maintenance

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.11', '3.12', '3.13']
 
     steps:
     - name: Checkout code
@@ -31,6 +31,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install setuptools
         pip install -r requirements-test.txt
         pip install -r requirements.txt
     - name: Install pyDeltaRCM
@@ -52,7 +53,7 @@ jobs:
 
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.10'
+      PYTHON: '3.13'
 
     steps:
     - uses: actions/checkout@v4
@@ -63,6 +64,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install setuptools
         pip install pytest pytest-cov pytest-mpl coveralls
         pip install -r requirements.txt
     - name: Install pyDeltaRCM
@@ -95,10 +97,11 @@ jobs:
     - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install setuptools
         pip install -r requirements.txt
         pip install -r requirements-docs.txt
         sudo apt update -y && sudo apt install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng
@@ -109,7 +112,7 @@ jobs:
       run: |
         (cd docs && make docs)
     - name: Upload log file
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: log-file

.github/workflows/deploy.yml

@@ -18,7 +18,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

pyDeltaRCM/_version.py

@@ -3,4 +3,4 @@ def __version__() -> str:
     Private version declaration, gets assigned to pyDeltaRCM.__version__
     during import
     """
-    return "2.1.5"
+    return "2.1.6"

pyDeltaRCM/shared_tools.py

@@ -272,6 +272,7 @@ def custom_unravel(i: int, shape: Tuple[int, int]) -> Tuple[int, int]:
         from pyDeltaRCM.shared_tools import custom_unravel
 
     .. doctest::
+        :skip:
 
         >>> _shape = (100, 200)  # e.g., delta.eta.shape
 
@@ -318,6 +319,7 @@ def custom_ravel(tup: Tuple[int, int], shape: Tuple[int, int]) -> int:
         from pyDeltaRCM.shared_tools import custom_ravel
 
     .. doctest::
+        :skip:
 
         >>> _shape = (100, 200)  # e.g., delta.eta.shape
 
@@ -368,6 +370,7 @@ def custom_pad(arr: np.ndarray) -> np.ndarray:
     Consider a model domain of size `(4, 8)`
 
     .. doctest::
+        :skip:
 
         >>> arr = np.arange(32).reshape(4, 8)
 
@@ -382,6 +385,7 @@ def custom_pad(arr: np.ndarray) -> np.ndarray:
     sliced:
 
     .. doctest::
+        :skip:
 
         >>> for i in range(4):
         ...     for j in range(8):

tests/integration/test_timing_triggers.py

@@ -11,11 +11,9 @@
 
 
 class TestTimingOutputData:
-
     def test_update_make_record(self, tmp_path: Path) -> None:
         # create a delta with default settings
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_checkpoint': True})
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml", {"save_checkpoint": True})
         _delta = DeltaModel(input_file=p)
 
         # modify the save interval to be twice dt
@@ -89,7 +87,7 @@ def test_update_make_record(self, tmp_path: Path) -> None:
     def test_update_saving_intervals_on_cycle(self, tmp_path: Path) -> None:
         """dt == 300; save_dt == 600"""
         # create a delta with default settings
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml')
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml")
         _delta = DeltaModel(input_file=p)
 
         # modify the timestep and save interval to be twice dt
@@ -141,7 +139,7 @@ def test_update_saving_intervals_on_cycle(self, tmp_path: Path) -> None:
     def test_update_saving_intervals_short(self, tmp_path: Path) -> None:
         """dt == 300; save_dt == 100"""
         # create a delta with default settings
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml')
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml")
         _delta = DeltaModel(input_file=p)
 
         # modify the timestep and save interval to be twice dt
@@ -182,10 +180,12 @@ def test_update_saving_intervals_short(self, tmp_path: Path) -> None:
         assert _delta.save_iter == 4  # once during init
         assert _delta.time == 900
 
-    def test_update_saving_intervals_offset_long_not_double(self, tmp_path: Path) -> None:
+    def test_update_saving_intervals_offset_long_not_double(
+        self, tmp_path: Path
+    ) -> None:
         """dt == 300; save_dt == 500"""
         # create a delta with default settings
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml')
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml")
         _delta = DeltaModel(input_file=p)
 
         # modify the timestep and save interval to be twice dt
@@ -223,10 +223,12 @@ def test_update_saving_intervals_offset_long_not_double(self, tmp_path: Path) ->
         assert _delta.time == 3600
         assert _delta.save_grids_and_figs.call_count == 6
 
-    def test_update_saving_intervals_offset_long_over_double(self, tmp_path: Path) -> None:
+    def test_update_saving_intervals_offset_long_over_double(
+        self, tmp_path: Path
+    ) -> None:
         """dt == 300; save_dt == 1000"""
         # create a delta with default settings
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml')
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml")
         _delta = DeltaModel(input_file=p)
 
         # modify the timestep and save interval to be twice dt
@@ -280,7 +282,7 @@ def test_update_saving_intervals_offset_long_over_double(self, tmp_path: Path) -
         assert _delta._is_finalized is False
 
     def test_finalize_updated(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml')
+        p = utilities.yaml_from_dict(tmp_path, "input.yaml")
         _delta = DeltaModel(input_file=p)
 
         # mock the top-level
@@ -311,9 +313,9 @@ def test_finalize_updated(self, tmp_path: Path) -> None:
         assert _delta._is_finalized is True
 
     def test_save_one_fig_no_grids(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_dt': 1,
-                                      'save_eta_figs': True})
+        p = utilities.yaml_from_dict(
+            tmp_path, "input.yaml", {"save_dt": 1, "save_eta_figs": True}
+        )
         _delta = DeltaModel(input_file=p)
 
         # mock the timestep computations
@@ -324,8 +326,8 @@ def test_save_one_fig_no_grids(self, tmp_path: Path) -> None:
         _delta.output_checkpoint = mock.MagicMock()
 
         # check one set images created during init
-        img_glob = glob.glob(os.path.join(_delta.prefix, '*.png'))
-        nc_glob = glob.glob(os.path.join(_delta.prefix, '*.nc'))
+        img_glob = glob.glob(os.path.join(_delta.prefix, "*.png"))
+        nc_glob = glob.glob(os.path.join(_delta.prefix, "*.nc"))
         assert len(img_glob) == 1
         assert len(nc_glob) == 0
 
@@ -337,23 +339,23 @@ def test_save_one_fig_no_grids(self, tmp_path: Path) -> None:
         _delta.solve_water_and_sediment_timestep.call_count == 2
 
         # check for output eta files
-        exp_path_nc = os.path.join(
-            tmp_path / 'out_dir', 'pyDeltaRCM_output.nc')
-        exp_path_png0 = os.path.join(tmp_path / 'out_dir', 'eta_00000.png')
-        exp_path_png1 = os.path.join(tmp_path / 'out_dir', 'eta_00001.png')
-        exp_path_png2 = os.path.join(tmp_path / 'out_dir', 'eta_00002.png')
-        exp_path_png3 = os.path.join(tmp_path / 'out_dir', 'eta_00003.png')
+        exp_path_nc = os.path.join(tmp_path / "out_dir", "pyDeltaRCM_output.nc")
+        exp_path_png0 = os.path.join(tmp_path / "out_dir", "eta_00000.png")
+        exp_path_png1 = os.path.join(tmp_path / "out_dir", "eta_00001.png")
+        exp_path_png2 = os.path.join(tmp_path / "out_dir", "eta_00002.png")
+        exp_path_png3 = os.path.join(tmp_path / "out_dir", "eta_00003.png")
         assert not os.path.isfile(exp_path_nc)
         assert os.path.isfile(exp_path_png0)
         assert os.path.isfile(exp_path_png1)
         assert os.path.isfile(exp_path_png2)
         assert not os.path.isfile(exp_path_png3)
 
     def test_save_one_fig_one_grid(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_dt': 1,
-                                      'save_eta_grids': True,
-                                      'save_discharge_figs': True})
+        p = utilities.yaml_from_dict(
+            tmp_path,
+            "input.yaml",
+            {"save_dt": 1, "save_eta_grids": True, "save_discharge_figs": True},
+        )
         _delta = DeltaModel(input_file=p)
 
         # mock the timestep computations
@@ -363,8 +365,7 @@ def test_save_one_fig_one_grid(self, tmp_path: Path) -> None:
         _delta.log_model_time = mock.MagicMock()
         _delta.output_checkpoint = mock.MagicMock()
 
-        exp_path_nc = os.path.join(
-            tmp_path / 'out_dir', 'pyDeltaRCM_output.nc')
+        exp_path_nc = os.path.join(tmp_path / "out_dir", "pyDeltaRCM_output.nc")
         assert os.path.isfile(exp_path_nc)
         nc_size_before = os.path.getsize(exp_path_nc)
         assert nc_size_before > 0
@@ -385,9 +386,9 @@ def test_save_one_fig_one_grid(self, tmp_path: Path) -> None:
         assert nc_size_after > nc_size_before
 
     def test_save_metadata_no_grids(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_dt': 1,
-                                      'save_metadata': True})
+        p = utilities.yaml_from_dict(
+            tmp_path, "input.yaml", {"save_dt": 1, "save_metadata": True}
+        )
         _delta = DeltaModel(input_file=p)
 
         # mock the timestep computations
@@ -397,8 +398,7 @@ def test_save_metadata_no_grids(self, tmp_path: Path) -> None:
         _delta.log_model_time = mock.MagicMock()
         _delta.output_checkpoint = mock.MagicMock()
 
-        exp_path_nc = os.path.join(
-            tmp_path / 'out_dir', 'pyDeltaRCM_output.nc')
+        exp_path_nc = os.path.join(tmp_path / "out_dir", "pyDeltaRCM_output.nc")
         assert os.path.isfile(exp_path_nc)
 
         for _ in range(0, 2):
@@ -410,17 +410,22 @@ def test_save_metadata_no_grids(self, tmp_path: Path) -> None:
         _delta.finalize()
 
         ds = netCDF4.Dataset(exp_path_nc, "r", format="NETCDF4")
-        assert not ('eta' in ds.variables)
-        assert ds['meta']['H_SL'].shape[0] == 3
-        assert ds['meta']['L0'][:] == 3
+        assert not ("eta" in ds.variables)
+        assert ds["meta"]["H_SL"].shape[0] == 3
+        assert ds["meta"]["L0"][:] == 3
 
     def test_save_subsidence_metadata_no_grids(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_dt': 1,
-                                      'toggle_subsidence': True,
-                                      'start_subsidence': 0,
-                                      'subsidence_rate': 1,
-                                      'save_metadata': True})
+        p = utilities.yaml_from_dict(
+            tmp_path,
+            "input.yaml",
+            {
+                "save_dt": 1,
+                "toggle_subsidence": True,
+                "start_subsidence": 0,
+                "subsidence_rate": 1,
+                "save_metadata": True,
+            },
+        )
         _delta = DeltaModel(input_file=p)
 
         # mock the timestep computations
@@ -430,8 +435,7 @@ def test_save_subsidence_metadata_no_grids(self, tmp_path: Path) -> None:
         _delta.log_model_time = mock.MagicMock()
         _delta.output_checkpoint = mock.MagicMock()
 
-        exp_path_nc = os.path.join(
-            tmp_path / 'out_dir', 'pyDeltaRCM_output.nc')
+        exp_path_nc = os.path.join(tmp_path / "out_dir", "pyDeltaRCM_output.nc")
         assert os.path.isfile(exp_path_nc)
 
         for _ in range(0, 2):
@@ -443,19 +447,24 @@ def test_save_subsidence_metadata_no_grids(self, tmp_path: Path) -> None:
         _delta.finalize()
 
         ds = netCDF4.Dataset(exp_path_nc, "r", format="NETCDF4")
-        assert not ('eta' in ds.variables)
-        assert ds['meta']['H_SL'].shape[0] == 3
-        assert ds['meta']['L0'][:] == 3
-        assert ds['meta']['sigma'].shape == _delta.sigma.shape
-        assert np.all(ds['meta']['sigma'] == _delta.sigma)
-        assert ds['meta']['start_subsidence'][:] == 0
+        assert not ("eta" in ds.variables)
+        assert ds["meta"]["H_SL"].shape[0] == 3
+        assert ds["meta"]["L0"][:] == 3
+        assert ds["meta"]["sigma"].shape == _delta.sigma.shape
+        assert np.all(ds["meta"]["sigma"] == _delta.sigma)
+        assert ds["meta"]["start_subsidence"][:] == 0
 
     def test_save_one_grid_metadata_by_default(self, tmp_path: Path) -> None:
-        p = utilities.yaml_from_dict(tmp_path, 'input.yaml',
-                                     {'save_dt': 1,
-                                      'save_metadata': False,
-                                      'save_eta_grids': True,
-                                      'C0_percent': 0.2})
+        p = utilities.yaml_from_dict(
+            tmp_path,
+            "input.yaml",
+            {
+                "save_dt": 1,
+                "save_metadata": False,
+                "save_eta_grids": True,
+                "C0_percent": 0.2,
+            },
+        )
         _delta = DeltaModel(input_file=p)
 
         # mock the timestep computations
@@ -465,8 +474,7 @@ def test_save_one_grid_metadata_by_default(self, tmp_path: Path) -> None:
         _delta.log_model_time = mock.MagicMock()
         _delta.output_checkpoint = mock.MagicMock()
 
-        exp_path_nc = os.path.join(
-            tmp_path / 'out_dir', 'pyDeltaRCM_output.nc')
+        exp_path_nc = os.path.join(tmp_path / "out_dir", "pyDeltaRCM_output.nc")
         assert os.path.isfile(exp_path_nc)
 
         for _ in range(0, 6):
@@ -477,10 +485,10 @@ def test_save_one_grid_metadata_by_default(self, tmp_path: Path) -> None:
 
         _delta.finalize()
         ds = netCDF4.Dataset(exp_path_nc, "r", format="NETCDF4")
-        _arr = ds.variables['eta']
+        _arr = ds.variables["eta"]
         assert _arr.shape[1] == _delta.eta.shape[0]
         assert _arr.shape[2] == _delta.eta.shape[1]
-        assert ('meta' in ds.groups)  # if any grids, save meta too
-        assert ds.groups['meta']['H_SL'].shape[0] == _arr.shape[0]
-        assert np.all(ds.groups['meta']['C0_percent'][:] == 0.2)
-        assert np.all(ds.groups['meta']['f_bedload'][:] == 0.5)
+        assert "meta" in ds.groups  # if any grids, save meta too
+        assert ds.groups["meta"]["H_SL"].shape[0] == _arr.shape[0]
+        assert np.all(ds.groups["meta"]["C0_percent"][:].data == 0.2)
+        assert np.all(ds.groups["meta"]["f_bedload"][:].data == 0.5)