Merge pull request #444 from jGaboardi/GH438_lint_format_maint

re- lint & re-format repo – #438

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 files: "spopt\/"
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.9"
+    rev: "v0.3.3"
     hooks:
       - id: ruff
       - id: ruff-format

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -9,7 +8,6 @@
 # import your package to obtain the version info to display on the docs website
 import spopt
 
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -46,7 +44,7 @@
 
 # General information about the project.
 project = "spopt"
-copyright = "2020-, pysal developers"
+copyright = "2020-, pysal developers"  # noqa: A001
 author = "pysal developers"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -85,7 +83,8 @@
 html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 html_title = f"{project} v{version} Manual"
 
-# (Optional) Logo of your package. Should be small enough to fit the navbar (ideally 24x24).
+# (Optional) Logo of your package.
+# Should be small enough to fit the navbar (ideally 24x24).
 # Path should be relative to the ``_static`` files directory.
 # html_logo = "_static/images/package_logo.jpg"
 
@@ -299,7 +298,7 @@ def setup(app):
     \nbsphinxstartnotebook{\scriptsize\noindent\strut
     \textcolor{gray}{The following section was generated from
     \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
-"""
+"""  # noqa: E501
 
 # This is processed by Jinja2 and inserted after each notebook
 nbsphinx_epilog = r"""

pyproject.toml

@@ -81,10 +81,9 @@ include = ["spopt", "spopt.*"]
 
 [tool.ruff]
 line-length = 88
-select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
-exclude = ["spopt/tests/*", "docs/*"]
+lint.select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
  "*__init__.py" = [
      "F401",  # imported but unused
      "F403",  # star import; unable to detect undefined names

spopt/region/components.py

@@ -1,6 +1,7 @@
 """
 Checking for connected components in a graph.
 """
+
 __author__ = "Sergio J. Rey <srey@asu.edu>"
 
 

spopt/region/csgraph_utils.py

@@ -4,6 +4,7 @@
 [compressed sparse graph routines](
 https://docs.scipy.org/doc/scipy/reference/sparse.csgraph.html).
 """
+
 import numpy as np
 from scipy.sparse import csgraph as csg
 from scipy.sparse import csr_matrix

spopt/tests/conftest.py

@@ -1,8 +1,8 @@
-import pytest
 import warnings
 
 import geopandas
 import numpy
+import pytest
 import shapely
 
 from spopt.locate.util import simulated_geo_points

spopt/tests/test_azp.py

@@ -1,7 +1,6 @@
-import libpysal
 import geopandas
+import libpysal
 import numpy
-
 from packaging.version import Version
 
 from spopt.region import AZP

spopt/tests/test_c_p_median.py

@@ -1,19 +1,14 @@
-from spopt.locate.base import (
-    FacilityModelBuilder,
-    LocateSolver,
-    T_FacModel,
-    SpecificationError,
-)
+import os
+
 import numpy
 import pandas
-import geopandas
 import pulp
-import spaghetti
+import pytest
 
 from spopt.locate import PMedian
-from spopt.locate.util import simulated_geo_points
-import pytest
-import os
+from spopt.locate.base import (
+    SpecificationError,
+)
 
 
 class TestSyntheticLocate:
@@ -160,9 +155,12 @@ def test_infeasibility_predefined_facilities_fulfillment_error(self):
         schools_priority_3_arr = numpy.array(schools_priority_3)
         with pytest.raises(
             SpecificationError,
-            match="Problem is infeasible. The predefined facilities can't be fulfilled, ",
+            match=(
+                "Problem is infeasible. "
+                "The predefined facilities can't be fulfilled, "
+            ),
         ):
-            pmedian = PMedian.from_cost_matrix(
+            PMedian.from_cost_matrix(
                 self.cost_matrix,
                 self.demand,
                 self.p_facility,
@@ -174,9 +172,12 @@ def test_infeasibility_predefined_facilities_fulfillment_error(self):
     def test_no_capacity_data_predefined_facilities_error(self):
         with pytest.raises(
             SpecificationError,
-            match="Data on the capacity of the facility is missing, so the model cannot be calculated.",
+            match=(
+                "Data on the capacity of the facility is missing, "
+                "so the model cannot be calculated."
+            ),
         ):
-            pmedian = PMedian.from_cost_matrix(
+            PMedian.from_cost_matrix(
                 self.cost_matrix,
                 self.demand,
                 self.p_facility,
@@ -190,7 +191,7 @@ def test_infeasibility_capacity_smaller_than_demand_error(self):
             SpecificationError,
             match="Problem is infeasible. The highest possible capacity",
         ):
-            pmedian = PMedian.from_cost_matrix(
+            PMedian.from_cost_matrix(
                 self.cost_matrix,
                 demand_test,
                 self.p_facility,

spopt/tests/test_clscp-so.py

@@ -1,11 +1,10 @@
+# ruff: noqa: N999
+
 import numpy
-import geopandas
 import pulp
-import spaghetti
+import pytest
 
 from spopt.locate import LSCP
-from spopt.locate.util import simulated_geo_points
-import pytest
 
 
 class TestSyntheticLocate:

spopt/tests/test_knearest_p_median.py

@@ -1,16 +1,11 @@
-import numpy
 import geopandas
-import pandas
+import numpy
 import pulp
+import pytest
 from shapely.geometry import Point
 
-from spopt.locate.p_median import KNearestPMedian
 from spopt.locate.base import SpecificationError
-import os
-import pickle
-import platform
-import pytest
-import warnings
+from spopt.locate.p_median import KNearestPMedian
 
 
 class TestKNearestPMedian:
@@ -50,11 +45,11 @@ def test_knearest_p_median_from_geodataframe_no_results(self):
         assert isinstance(result, KNearestPMedian)
 
         with pytest.raises(AttributeError):
-            result.cli2fac
+            result.cli2fac  # noqa: B018
         with pytest.raises(AttributeError):
-            result.fac2cli
+            result.fac2cli  # noqa: B018
         with pytest.raises(AttributeError):
-            result.mean_dist
+            result.mean_dist  # noqa: B018
 
     def test_solve(self):
         self.k_nearest_pmedian.solve(self.solver)

spopt/tests/test_locate_util.py

@@ -1,5 +1,5 @@
 import pytest
-import spaghetti
+
 from spopt.locate.util import simulated_geo_points
 
 

spopt/tests/test_lscp.py

@@ -1,24 +1,19 @@
-from spopt.locate.base import FacilityModelBuilder
-import numpy
+import os
+import pickle
+import platform
+import warnings
+
 import geopandas
+import numpy
 import pandas
 import pulp
-import spaghetti
+import pytest
 from shapely.geometry import Point, Polygon
 
 from spopt.locate import LSCP
-from spopt.locate.util import simulated_geo_points
-import os
-import pickle
-import platform
-import pytest
-import warnings
+from spopt.locate.base import FacilityModelBuilder
 
-operating_system = platform.platform()[:7].lower()
-if operating_system == "windows":
-    WINDOWS = True
-else:
-    WINDOWS = False
+WINDOWS = platform.platform()[:7].lower() == "windows"
 
 
 class TestSyntheticLocate:
@@ -44,9 +39,9 @@ def test_lscp_from_cost_matrix_no_results(self):
         assert isinstance(result, LSCP)
 
         with pytest.raises(AttributeError):
-            result.cli2fac
+            result.cli2fac  # noqa: B018
         with pytest.raises(AttributeError):
-            result.fac2cli
+            result.fac2cli  # noqa: B018
 
     def test_lscp_facility_client_array_from_cost_matrix(self):
         with open(self.dirpath + "lscp_fac2cli.pkl", "rb") as f:
@@ -254,13 +249,15 @@ def test_attribute_error_add_set_covering_constraint(self):
             )
 
     def test_error_lscp_different_crs(self):
-        with pytest.warns(
-            UserWarning, match="Facility geodataframe contains mixed type"
+        with (
+            pytest.warns(
+                UserWarning, match="Facility geodataframe contains mixed type"
+            ),
+            pytest.raises(ValueError, match="Geodataframes crs are different: "),
         ):
-            with pytest.raises(ValueError, match="Geodataframes crs are different: "):
-                LSCP.from_geodataframe(
-                    self.gdf_dem_crs, self.gdf_fac, "geometry", "geometry", 10
-                )
+            LSCP.from_geodataframe(
+                self.gdf_dem_crs, self.gdf_fac, "geometry", "geometry", 10
+            )
 
     def test_warning_lscp_demand_geodataframe(self):
         with pytest.warns(UserWarning, match="Demand geodataframe contains mixed type"):

spopt/tests/test_lscpb.py

@@ -1,18 +1,16 @@
-import numpy
+import os
+import pickle
+import warnings
+
 import geopandas
+import numpy
 import pandas
 import pulp
-import spaghetti
+import pytest
 from shapely.geometry import Point, Polygon
 
 from spopt.locate import LSCPB
 from spopt.locate.base import FacilityModelBuilder
-from spopt.locate.util import simulated_geo_points
-
-import os
-import pickle
-import warnings
-import pytest
 
 
 class TestSyntheticLocate:
@@ -47,11 +45,11 @@ def test_lscpb_from_cost_matrix_no_results(self):
         assert isinstance(result, LSCPB)
 
         with pytest.raises(AttributeError):
-            result.cli2fac
+            result.cli2fac  # noqa: B018
         with pytest.raises(AttributeError):
-            result.fac2cli
+            result.fac2cli  # noqa: B018
         with pytest.raises(AttributeError):
-            result.backup_perc
+            result.backup_perc  # noqa: B018
 
     def test_lscpb_facility_client_array_from_cost_matrix(self):
         with open(self.dirpath + "lscpb_fac2cli.pkl", "rb") as f:
@@ -278,18 +276,20 @@ def setup_method(self) -> None:
             self.gdf_dem_buffered["geometry"] = self.gdf_dem.buffer(2)
 
     def test_error_lscpb_different_crs(self):
-        with pytest.warns(
-            UserWarning, match="Facility geodataframe contains mixed type"
+        with (
+            pytest.warns(
+                UserWarning, match="Facility geodataframe contains mixed type"
+            ),
+            pytest.raises(ValueError, match="Geodataframes crs are different: "),
         ):
-            with pytest.raises(ValueError, match="Geodataframes crs are different: "):
-                LSCPB.from_geodataframe(
-                    self.gdf_dem_crs,
-                    self.gdf_fac,
-                    "geometry",
-                    "geometry",
-                    10,
-                    pulp.PULP_CBC_CMD(msg=False),
-                )
+            LSCPB.from_geodataframe(
+                self.gdf_dem_crs,
+                self.gdf_fac,
+                "geometry",
+                "geometry",
+                10,
+                pulp.PULP_CBC_CMD(msg=False),
+            )
 
     def test_warning_lscpb_demand_geodataframe(self):
         with pytest.warns(UserWarning, match="Demand geodataframe contains mixed type"):

spopt/tests/test_maxp.py

@@ -2,7 +2,9 @@
 import libpysal
 import numpy
 import pytest
+from packaging.version import Version
 from shapely.geometry import box
+
 from spopt.region import MaxPHeuristic
 from spopt.region.base import (
     form_single_component,
@@ -11,9 +13,6 @@
     plot_components,
 )
 
-from packaging.version import Version
-
-
 # see gh:spopt#437
 LIBPYSAL_GE_48 = Version(libpysal.__version__) >= Version("4.8.0")
 w_kwargs = {"use_index": True} if LIBPYSAL_GE_48 else {}