Merge pull request #2 from phobson/ruff-gha

ruff config

.github/workflows/python-ruff.yml

@@ -0,0 +1,19 @@
+name: ruff 'n' stuff
+on: [pull_request]
+
+jobs:
+    build:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v3
+        - name: Install Python
+          uses: actions/setup-python@v4
+          with:
+            python-version: "3.12"
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install ruff
+        # Update output format to enable automatic inline annotations.
+        - name: Run Ruff
+          run: ruff check --output-format=github .

.github/workflows/python-run-tests.yml

@@ -5,9 +5,9 @@ name: Run basic unit tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [ master ]
   pull_request:
-    branches: [ main ]
+    branches: [ master ]
 
 jobs:
   build:
@@ -26,14 +26,21 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
           gridgen
-          numpy
+          shapely
+          fiona
+          geopandas
+          scipy
           matplotlib
-          pyproj
+          ipywidgets
           pytest
+          pytest-mpl
+          pytest-cov
+          pytest-pep8
           coverage
           docopt
           requests
           pyyaml
+          pygridgen
         init-shell: bash
         cache-environment: true
         post-cleanup: 'all'

check_pygridtools.py

@@ -5,7 +5,7 @@
 matplotlib.use('agg')
 style.use('classic')
 
-import pygridtools
+import pygridtools  #  noqa: E402
 
 
 if '--strict' in sys.argv:

pygridtools/__init__.py

@@ -1,7 +1,7 @@
-from .misc import *
-from .core import *
-from . import iotools
-from . import viz
-from . import validate
+from .misc import *  # noqa: F403
+from .core import *  # noqa: F403
+from . import iotools  # noqa: F401
+from . import viz  # noqa: F401
+from . import validate  # noqa: F401
 
-from .tests import test, teststrict
+from .tests import test, teststrict  # noqa: F401

pygridtools/core.py

@@ -1,4 +1,3 @@
-from __future__ import division
 
 import warnings
 from copy import deepcopy
@@ -198,7 +197,7 @@ def extract(nodes, jstart=None, istart=None, jend=None, iend=None):
     return deepcopy(nodes[jstart:jend, istart:iend])
 
 
-class ModelGrid(object):
+class ModelGrid:
     """
     Container for a curvilinear-orthogonal grid. Provides convenient
     access to masking, manipulation, and visualization methods.
@@ -745,12 +744,15 @@ def mask_centroids(self, inside=None, outside=None, use_existing=True):
         cell_mask = numpy.bitwise_or(inside_cell_mask, outside_cell_mask)
         return self.update_cell_mask(mask=cell_mask, merge_existing=use_existing)
 
-    @numpy.deprecate(message='use mask_nodes or mask_centroids')
     def mask_cells_with_polygon(self, polyverts, use_centroids=True, **kwargs):
-        if use_centroids:
-            return self.mask_centroids(polyverts, **kwargs)
-        else:
-            return self.mask_nodes(polyverts, **kwargs)
+        with warnings.warn(
+            ".mask_cells_with_polygon is deprecated. Use .mask_nodes or .mask_centroids",
+            DeprecationWarning
+        ):
+            if use_centroids:
+                return self.mask_centroids(polyverts, **kwargs)
+            else:
+                return self.mask_nodes(polyverts, **kwargs)
 
     def plot_cells(self, engine='mpl', ax=None, usemask=True, showisland=True,
                    cell_kws=None, domain_kws=None, extent_kws=None,
@@ -822,10 +824,7 @@ def to_point_geodataframe(self, which='nodes', usemask=True, elev=None):
 
     def to_polygon_geodataframe(self, usemask=True, elev=None):
         x, y = self._get_x_y(which='nodes', usemask=False)
-        if usemask:
-            mask = self.cell_mask.copy()
-        else:
-            mask = None
+        mask = self.cell_mask.copy() if usemask else None
 
         return misc.gdf_of_cells(x, y, mask, crs=self.crs, elev=elev, triangles=False)
 

pygridtools/gefdc.py

@@ -7,8 +7,6 @@
 from shapely.geometry import Point
 import geopandas
 
-from pygridtools import iotools
-from pygridtools import misc
 from pygridtools import validate
 
 
@@ -93,7 +91,7 @@ def write_cellinp(cell_array, outputfile='cell.inp', mode='w',
     nrows, ncols = cell_array.shape
 
     rowfmt = '{0:3d}  {1:s}\n'
-    colfmt = f'{{:0{_n_digits(ncols)}d}}'
+    # colfmt = f'{{:0{_n_digits(ncols)}d}}'
 
     if cell_array.shape[1] > maxcols:
         first_array = cell_array[:, :maxcols]
@@ -108,7 +106,7 @@ def write_cellinp(cell_array, outputfile='cell.inp', mode='w',
 
     else:
         columns = numpy.arange(1, maxcols + 1, dtype=int)
-        colstr = [list('{:04d}'.format(c)) for c in columns]
+        colstr = [list(f'{c:04d}') for c in columns]
         hundreds = ''.join([c[1] for c in colstr])
         tens = ''.join([c[2] for c in colstr])
         ones = ''.join([c[3] for c in colstr])
@@ -117,19 +115,16 @@ def write_cellinp(cell_array, outputfile='cell.inp', mode='w',
             if writeheader:
                 title = 'C -- cell.inp for EFDC model by pygridtools\n'
                 outfile.write(title)
-                outfile.write('C    {}\n'.format(hundreds[:ncols]))
-                outfile.write('C    {}\n'.format(tens[:ncols]))
-                outfile.write('C    {}\n'.format(ones[:ncols]))
+                outfile.write(f'C    {hundreds[:ncols]}\n')
+                outfile.write(f'C    {tens[:ncols]}\n')
+                outfile.write(f'C    {ones[:ncols]}\n')
 
             for n, row in enumerate(cell_array):
                 row_number = nrows - n
                 row_strings = row.astype(str)
                 cell_text = ''.join(row_strings.tolist())
-                if rowlabels:
-                    rowheader = ''
-                    row_text = rowfmt.format(int(row_number), cell_text)
-                else:
-                    row_text = '     {0:s}\n'.format(cell_text)
+
+                row_text = rowfmt.format(int(row_number), cell_text) if rowlabels else f'     {cell_text:s}\n'
 
                 outfile.write(row_text)
 
@@ -153,7 +148,7 @@ def write_gridout_file(xcoords, ycoords, outfile):
     })
 
     with Path(outfile).open('w') as f:
-        f.write('## {:d} x {:d}\n'.format(nx, ny))
+        f.write(f'## {nx:d} x {ny:d}\n')
 
     # XXX: https://github.com/pandas-dev/pandas/issues/21882
     with Path(outfile).open('a') as f:
@@ -295,8 +290,8 @@ def make_gefdc_cells(node_mask, cell_mask=None, triangles=False):
             if total == bank_cell * shift**2:
                 cells[cj, ci] = land_cell
 
-    nrows = cells.shape[0]
-    ncols = cells.shape[1]
+    # nrows = cells.shape[0]
+    # ncols = cells.shape[1]
 
     # nchunks = numpy.ceil(ncols / maxcols)
     # if ncols > maxcols:

pygridtools/iotools.py

@@ -1,12 +1,7 @@
-import os
-from collections import OrderedDict
-from textwrap import dedent
 import warnings
 
 import numpy
-import pandas
 from matplotlib import pyplot
-from shapely.geometry import Point, Polygon
 import geopandas
 
 try:
@@ -17,8 +12,6 @@
 from pygridgen.tests import requires
 import pygridgen as pgg
 
-from pygridtools import misc
-from pygridtools import validate
 from pygridtools import viz
 
 
@@ -218,7 +211,7 @@ def interactive_grid_shape(grid, max_n=200, plotfxn=None, **kwargs):
     ... ( 0,  0,  1.00), ( 0, 15,  0.50), ( 8, 15, -0.25),
     ... (11, 13, -0.25)])
     >>> g = grid.Gridgen(d[:, 0], d[:, 1], d[:, 2], (75, 75), ul_idx=1, focus=None)
-    >>> new_grid, widget = iotools.interactive_grid_shape(g, plotfxn=plot_grid)
+    >>> new_grid, widget = iotools.interactive_grid_shape(g, plotfxn=plot_grid)  # doctest: +SKIP
     """
 
     if not plotfxn:
@@ -235,7 +228,7 @@ def interactive_grid_shape(grid, max_n=200, plotfxn=None, **kwargs):
     )
 
 
-class _FocusProperties():
+class _FocusProperties:
     """A dummy class to hold the properties of the grid._FocusPoint() object.
     This class is required so that multiple ipywidgets.interactive widgets
     can interact on the same plot.
@@ -399,7 +392,7 @@ def interactive_grid_focus(g, n_points, plotfxn=None, **kwargs):
     ... (11, 13, -0.25)])
     >>> g = grid.Gridgen(d[:, 0], d[:, 1], d[:, 2], (75, 75), ul_idx=1, focus=None)
     >>> n = 4 # number of focus objects
-    >>> new_grid, widget = iotools.interactive_grid_focus(g, n)
+    >>> new_grid, widget = iotools.interactive_grid_focus(g, n)  # doctest: +SKIP
     """
 
     if not plotfxn:
@@ -437,6 +430,6 @@ def interactive_grid_focus(g, n_points, plotfxn=None, **kwargs):
     tab_nest = ipywidgets.Tab()
     tab_nest.children = widgets
     for n in range(len(widgets)):
-        tab_nest.set_title(n, 'Focus {}'.format(n + 1))
+        tab_nest.set_title(n, f'Focus {n + 1}')
 
     return focus_points, tab_nest

pygridtools/misc.py

@@ -1,10 +1,10 @@
 from collections import OrderedDict
 from shapely.geometry import Point, Polygon
+import importlib
 
 import numpy
 import matplotlib.path as mpath
 import pandas
-from shapely import geometry
 import geopandas
 from pygridgen import csa
 
@@ -81,7 +81,7 @@ def make_record(ID, coords, geomtype, props):
     """
 
     if geomtype not in ['Point', 'LineString', 'Polygon']:
-        raise ValueError('Geometry {} not suppered'.format(geomtype))
+        raise ValueError(f'Geometry {geomtype} not suppered')
 
     if isinstance(coords, numpy.ma.MaskedArray):
         coords = coords.data
@@ -123,10 +123,9 @@ def interpolate_bathymetry(bathy, x_points, y_points, xcol='x', ycol='y', zcol='
 
     """
 
-    try:
-        import pygridgen
-    except ImportError:  # pragma: no cover
-        raise ImportError("`pygridgen` not installed. Cannot interpolate bathymetry.")
+    HASPGG = bool(importlib.util.find_spec("pygridgen"))
+    if not HASPGG:
+        raise RuntimeError("`pygridgen` not installed. Cannot interpolate bathymetry.")
 
     if bathy is None:
         elev = numpy.zeros(x_points.shape)
@@ -372,7 +371,7 @@ def gdf_of_cells(X, Y, mask, crs, elev=None, triangles=False):
                 # build the attributes
                 record = OrderedDict(
                     id=row, ii=ii + 2, jj=jj + 2, elev=Z,
-                    ii_jj='{:02d}_{:02d}'.format(ii + 2, jj + 2),
+                    ii_jj=f'{ii + 2:02d}_{jj + 2:02d}',
                     geometry=Polygon(shell=coords)
                 )
 
@@ -428,7 +427,7 @@ def gdf_of_points(X, Y, crs, elev=None):
                 record = OrderedDict(
                     id=int(row), ii=int(ii + 2), jj=int(jj + 2),
                     elev=float(elev[jj, ii]),
-                    ii_jj='{:02d}_{:02d}'.format(ii + 2, jj + 2),
+                    ii_jj=f'{ii + 2:02d}_{jj + 2:02d}',
                     geometry=Point(coords)
                 )
 

pygridtools/tests/__init__.py

@@ -1,6 +1,5 @@
 from importlib import resources
 
-import pygridtools
 from pygridgen.tests import requires
 
 try:
@@ -11,15 +10,15 @@
 
 @requires(pytest, 'pytest')
 def test(*args):
-    options = [resources('pygridtools', '')]
+    options = [str(resources.files("pygridtools"))]
     options.extend(list(args))
     return pytest.main(options)
 
 
 @requires(pytest, 'pytest')
 def teststrict(*args):
     options = list(set([
-        resources('pygridtools', ''),
+        str(resources.files("pygridtools")),
         '--mpl',
         '--doctest-modules'
     ] + list(args)))

pygridtools/tests/conftest.py

@@ -10,7 +10,7 @@
 from pygridtools.iotools import _FocusProperties
 
 
-class FakeGrid(object):
+class FakeGrid:
     def __init__(self, boundary):
         self.x, self.y = simple_nodes()
         self.xn, self.yn = simple_nodes()

pygridtools/tests/test_core.py

@@ -1,7 +1,4 @@
-import os
-import warnings
 from pkg_resources import resource_filename
-import tempfile
 
 import numpy
 from numpy import nan
@@ -282,7 +279,7 @@ def polyverts():
 def test_ModelGrid_bad_shapes(simple_cells):
     xc, yc = simple_cells
     with raises(ValueError):
-        mg = core.ModelGrid(xc, yc[2:, 2:])
+        core.ModelGrid(xc, yc[2:, 2:])
 
 
 def test_ModelGrid_nodes_and_cells(g1, simple_cells):
@@ -665,7 +662,10 @@ def test_masks_no_polys(mg):
 
 def test_ModelGrid_to_point_geodataframe(g1):
     expectedfile = resource_filename('pygridtools.tests.baseline_files',  'mgshp_nomask_nodes_points.shp')
-    expected = geopandas.read_file(expectedfile)
+    expected = geopandas.read_file(expectedfile).assign(
+        ii=lambda df: df["ii"].astype("int64"),
+        jj=lambda df: df["jj"].astype("int64"),
+    )
     result = g1.to_point_geodataframe(which='nodes', usemask=False)
     utils.assert_gdfs_equal(expected.drop(columns=['river', 'reach']), result)