Help tests pass (#165)

* Py source consistency using isort and pyupgrade tools, rm unused imports

Also remove unused shebangs on non-executable module and test files

* Add fix for GitHub dependency graph

* Make pretty

* Set 'en' for default language

* Use Makefile docs target to also build API docs

* Roll back numpy, scipy, and shapely versions for compatibility

* Try Mambaforge for CI

* Use Mambaforge for CI

---------

Co-authored-by: Mike Taves <[email protected]>

.github/workflows/docs.yml

@@ -37,11 +37,9 @@ jobs:
           - uses: actions/checkout@v2
           - uses: conda-incubator/setup-miniconda@v2
             with:
-              auto-update-conda: true
+              miniforge-variant: Mambaforge
+              miniforge-version: latest
               python-version: 3.8
-              mamba-version: "*"
-              channels: conda-forge,defaults
-              channel-priority: true
 
           - name: Show conda installation info
             run: |
@@ -54,4 +52,4 @@ jobs:
               pip install -e .
 
           - name: Build documentation
-            run: make -C docs clean html
+            run: make docs

.github/workflows/test-notebooks.yml

@@ -27,11 +27,9 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          auto-update-conda: true
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge
-          channel-priority: true
 
       - name: Show conda installation info
         run: |

.github/workflows/test.yml

@@ -27,11 +27,9 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          auto-update-conda: true
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
 
       - name: Show conda installation info
         run: |

docs/conf.py

@@ -85,7 +85,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

pymt/component/model.py

@@ -134,7 +134,7 @@ def load(cls, source):
             source, with_connectivities=True
         )
 
-        for (name, component) in components.items():
+        for name, component in components.items():
             for port in connectivities[name]:
                 mapping = get_exchange_item_mapping(port["exchange_items"])
                 component.connect(

pymt/errors.py

@@ -1,5 +1,4 @@
 class PymtError(Exception):
-
     pass
 
 

pymt/events/manager.py

@@ -111,7 +111,7 @@ def initialize(self):
         """
         if not self._initializing:
             self._initializing = True
-            for (event, _) in self._order:
+            for event, _ in self._order:
                 try:
                     event.initialize()
                 except Exception:
@@ -154,7 +154,7 @@ def finalize(self):
             if not self._finalizing:
                 self._finalizing = True
                 # for event in self._timeline.events:
-                for (event, _) in self._order[::-1]:
+                for event, _ in self._order[::-1]:
                     event.finalize()
             self._initialized = False
 

pymt/events/port.py

@@ -138,7 +138,7 @@ def initialize(self):
 
     def run(self, stop_time):
         """Map values from one port to another."""
-        for (dst_name, src_name) in self._vars_to_map:
+        for dst_name, src_name in self._vars_to_map:
             src_values = self._src.get_value(
                 src_name, units=self._dst.get_var_units(dst_name)
             )

pymt/framework/timeinterp.py

@@ -15,7 +15,6 @@
 
 
 class TimeInterpolator:
-
     METHODS = (
         "linear",
         "nearest",

pymt/grids/connectivity.py

@@ -96,7 +96,7 @@ def _get_offsets(shape, ordering="cw", dtype=int):
         offsets = np.array([0, 1], dtype=dtype)
 
     strides = np.cumprod(list(shape[-1:0:-1]))
-    for (dim, stride) in enumerate(strides):
+    for dim, stride in enumerate(strides):
         new_offsets = offsets + stride
         if ordered and dim % 2 == 0:
             offsets = np.append(offsets, new_offsets[::-1])
@@ -220,7 +220,7 @@ def get_connectivity(shape, **kwds):
             c.append(np.array(cell, dtype=kwds["dtype"]))
     else:
         c = np.empty((c0.size * points_per_cell,), dtype=kwds["dtype"])
-        for (i, offset) in enumerate(offsets):
+        for i, offset in enumerate(offsets):
             c[i::points_per_cell] = c0 + offset
 
     if with_offsets:

pymt/grids/map.py

@@ -65,7 +65,7 @@ def __init__(self, *args, **kwargs):
 
         self._point = {}
         last_offset = 0
-        for (cell_id, offset) in enumerate(self._offset):
+        for cell_id, offset in enumerate(self._offset):
             cell = self._connectivity[last_offset:offset]
             last_offset = offset
 
@@ -78,7 +78,7 @@ def __init__(self, *args, **kwargs):
         (point_x, point_y) = (self.get_x(), self.get_y())
         self._polys = []
         last_offset = 0
-        for (cell_id, offset) in enumerate(self._offset):
+        for cell_id, offset in enumerate(self._offset):
             cell = self._connectivity[last_offset:offset]
             last_offset = offset
 

pymt/grids/raster.py

@@ -99,7 +99,7 @@ def __init__(self, shape, spacing, origin, **kwds):
         kwds.setdefault("set_connectivity", False)
 
         xi = []
-        for (nx, dx, x0) in zip(shape, spacing, origin):
+        for nx, dx, x0 in zip(shape, spacing, origin):
             xi.append(np.arange(nx, dtype=np.float64) * dx + x0)
 
         self._spacing = np.array(spacing, dtype=np.float64)

pymt/grids/unstructured.py

@@ -169,7 +169,7 @@ def get_connectivity_as_matrix(self, fill_val=MAXSIZE):
         offset = self._offset[0]
         matrix[0, :offset] = self._connectivity[:offset]
         matrix[0, offset:] = fill_val
-        for (cell, offset) in enumerate(self._offset[:-1]):
+        for cell, offset in enumerate(self._offset[:-1]):
             n_vertices = nodes_per_cell[cell]
             matrix[cell + 1, :n_vertices] = self._connectivity[
                 offset : offset + n_vertices

pymt/grids/utils.py

@@ -39,7 +39,7 @@ def coordinates_to_numpy_matrix(*args):
     assert_arrays_are_equal_size(*args)
 
     coords = np.empty((len(args), len(args[0])), dtype=float)
-    for (dim, arg) in enumerate(args):
+    for dim, arg in enumerate(args):
         coords[dim][:] = arg.flatten()
     return coords
 
@@ -95,7 +95,7 @@ def _find_first(array, value):
 
 def connectivity_matrix_as_array(face_nodes, bad_val):
     nodes_per_face = np.empty(face_nodes.shape[0], dtype=int)
-    for (face_id, face) in enumerate(face_nodes):
+    for face_id, face in enumerate(face_nodes):
         nnodes = _find_first(face, bad_val)
         if nnodes > 0:
             nodes_per_face[face_id] = _find_first(face, bad_val)
@@ -105,7 +105,7 @@ def connectivity_matrix_as_array(face_nodes, bad_val):
 
     connectivity = np.empty(offsets[-1], dtype=int)
     offset = 0
-    for (n_nodes, face) in zip(nodes_per_face, face_nodes):
+    for n_nodes, face in zip(nodes_per_face, face_nodes):
         connectivity[offset : offset + n_nodes] = face[:n_nodes]
         offset += n_nodes
 

pymt/mappers/celltopoint.py

@@ -12,7 +12,7 @@ def map_points_to_cells(coords, src_grid, src_point_ids, bad_val=-1):
     point_to_cell_id = np.empty(len(dst_x), dtype=int)
     point_to_cell_id.fill(bad_val)
 
-    for (j, point_id) in enumerate(src_point_ids):
+    for j, point_id in enumerate(src_point_ids):
         for cell_id in src_grid.get_shared_cells(point_id):
             if src_grid.is_in_cell(dst_x[j], dst_y[j], cell_id):
                 point_to_cell_id[j] = cell_id
@@ -21,7 +21,6 @@ def map_points_to_cells(coords, src_grid, src_point_ids, bad_val=-1):
 
 
 class CellToPoint(IGridMapper):
-
     _name = "CellToPoint"
 
     def initialize(self, dest_grid, src_grid, **kwds):

pymt/mappers/esmp.py

@@ -16,7 +16,6 @@
 
 
 class EsmpMapper(IGridMapper):
-
     _name = None
 
     @property
@@ -99,7 +98,6 @@ def get_dest_data(self):
 
 
 class EsmpCellToCell(EsmpMapper):
-
     _name = "CellToCell"
 
     def init_fields(self):
@@ -117,7 +115,6 @@ def test(dst_grid, src_grid):
 
 
 class EsmpPointToPoint(EsmpMapper):
-
     _name = "PointToPoint"
 
     def init_fields(self):

pymt/mappers/pointtocell.py

@@ -12,7 +12,7 @@ def map_cells_to_points(coords, dst_grid, dst_point_ids, bad_val=-1):
     src_x, src_y = coords
 
     cell_to_point_id = defaultdict(list)
-    for (j, point_id) in enumerate(dst_point_ids):
+    for j, point_id in enumerate(dst_point_ids):
         for cell_id in dst_grid.get_shared_cells(point_id):
             if dst_grid.is_in_cell(src_x[j], src_y[j], cell_id):
                 cell_to_point_id[cell_id].append(j)
@@ -21,7 +21,6 @@ def map_cells_to_points(coords, dst_grid, dst_point_ids, bad_val=-1):
 
 
 class PointToCell(IGridMapper):
-
     _name = "PointToCell"
 
     def initialize(self, dest_grid, src_grid, **kwds):
@@ -53,7 +52,7 @@ def run(self, src_values, **kwds):
         if dst_vals.size != self._dst_cell_count:
             raise ValueError("size mismatch between destination and cell count")
 
-        for (cell_id, point_ids) in self._map.items():
+        for cell_id, point_ids in self._map.items():
             if all(src_values[point_ids] > bad_val):
                 dst_vals[cell_id] = method(src_values[point_ids])
 

pymt/printers/nc/ugrid.py

@@ -140,7 +140,7 @@ def set_variable(self, name, *args, **kwds):
         attrs = kwds.pop("attrs", {})
 
         variable = self.data_variable(name)
-        for (attr, value) in attrs.items():
+        for attr, value in attrs.items():
             variable.setncattr(attr, value)
 
         if len(args) > 0:
@@ -206,7 +206,7 @@ def _set_variable_data(self):
 
     def _set_node_variable_data(self):
         point_fields = self.field.get_point_fields()
-        for (var_name, array) in point_fields.items():
+        for var_name, array in point_fields.items():
             self.create_variable(
                 var_name,
                 _NP_TO_NC_TYPE[str(array.dtype)],
@@ -226,7 +226,7 @@ def _set_node_variable_data(self):
 
     def _set_face_variable_data(self):
         face_fields = self.field.get_cell_fields()
-        for (var_name, array) in face_fields.items():
+        for var_name, array in face_fields.items():
             self.create_variable(
                 var_name,
                 _NP_TO_NC_TYPE[str(array.dtype)],
@@ -271,11 +271,11 @@ def axis_coordinates(self):
 
     def _set_mesh_dimensions(self):
         field_shape = self.field.get_shape()
-        for (name, axis) in zip(self.axis_coordinates, self.field_axes):
+        for name, axis in zip(self.axis_coordinates, self.field_axes):
             self.create_dimension(name, field_shape[axis])
 
     def _set_mesh_coordinate_data(self):
-        for (name, axis) in zip(self.axis_coordinates, self.field_axes):
+        for name, axis in zip(self.axis_coordinates, self.field_axes):
             self.create_variable(name, "f8", (name,))
             self.set_variable(
                 name,
@@ -313,7 +313,7 @@ def _set_mesh_dimensions(self):
     def _set_mesh_coordinate_data(self):
         dims = self.node_data_dimensions
         # for (name, axis) in zip(self.node_coordinates, self.field_axes):
-        for (name, axis) in zip(self.node_data_dimensions, self.field_axes):
+        for name, axis in zip(self.node_data_dimensions, self.field_axes):
             self.create_variable(name, "f8", dims)
             self.set_variable(
                 name,
@@ -367,7 +367,7 @@ def _set_mesh_coordinate_data(self):
         dims = self.node_data_dimensions
         # for (name, axis) in zip(self.node_data_dimensions, self.field_axes):
         # for (name, axis) in zip(self.node_coordinates, self.field_axes):
-        for (axis, name) in enumerate(self.node_coordinates):
+        for axis, name in enumerate(self.node_coordinates):
             self.create_variable(name, "f8", dims)
             self.set_variable(
                 name,

pymt/services/constant/constant.py

@@ -17,7 +17,7 @@ def initialize(self, filename):
             scalar_vars = yaml.safe_load(opened.read())
 
         self._vars = {}
-        for (name, value) in scalar_vars.items():
+        for name, value in scalar_vars.items():
             self._vars[name] = np.array(value, dtype=float)
 
         self._shape = (1,)

pymt/services/gridreader/interpolate.py

@@ -10,7 +10,7 @@ def get_time_series_values(field, ordering="ascending", prefix=""):
 
     names = sort_time_series_names(field, ordering=ordering, prefix=prefix)
 
-    for (var_name, ordered_names) in names.items():
+    for var_name, ordered_names in names.items():
         for name in ordered_names:
             values[var_name].append(field.get_values(name))
 
@@ -29,7 +29,7 @@ def create_interpolators(times, fields, prefix="", kind="linear"):
 
     names = sort_time_series_names(fields.keys(), prefix=prefix, ordering="ascending")
 
-    for (var_name, ordered_names) in names.items():
+    for var_name, ordered_names in names.items():
         interpolators[var_name] = create_interpolator(
             fields, zip(ordered_names, times), kind=kind
         )

pymt/services/gridreader/time_series_names.py

@@ -77,7 +77,7 @@ def sort_time_series_names(names, ordering="ascending", prefix=""):
     time_stamps = extract_time_stamps_from_names(
         names, ordering=ordering, prefix=prefix
     )
-    for (name, stamps) in time_stamps.items():
+    for name, stamps in time_stamps.items():
         ordered_names[name] = [unsplit(name, stamp) for stamp in stamps]
 
     return ordered_names

pymt/timeline.py

@@ -240,7 +240,7 @@ def add_recurring_events(self, events):
         except AttributeError:
             event_items = events
 
-        for (event, interval) in event_items:
+        for event, interval in event_items:
             self.add_recurring_event(event, interval)
 
     def add_recurring_event(self, event, interval):

requirements.txt

@@ -5,10 +5,10 @@ landlab>=2
 matplotlib
 model_metadata>=0.7
 netcdf4
-numpy
+numpy<1.24  # for Ku
 pyyaml
-scipy
-shapely
+scipy<1.9  # see #162
+shapely<2  # see #164
 xarray
 # cfunits
 # esmpy

setup.py

@@ -1,3 +1,5 @@
 from setuptools import setup
 
-setup()
+setup(
+    name="pymt",  # for GitHub dependency graph
+)