gpd & shp as hard reqs -- no optional testing -- #763 (#764)

* RLS: v1.7.5.post1

* update pre-commit

* remove no-optional -- add GPD & SHP are hard reqs

* minor ruff linting

* GPD/SHP hard req in README

* forgot to remove no-opt yaml - proper shp pin

* proper gpd pin

* polish required imports

.github/workflows/testing.yml

@@ -26,7 +26,6 @@
          os: [ubuntu-latest]
          environment-file:
            - ci/310-oldest.yaml
-           - ci/310-no-optional.yaml
            - ci/310-latest.yaml
            - ci/311-latest.yaml
            - ci/312-latest.yaml
@@ -59,9 +58,8 @@
            micromamba info
            micromamba list
        
-       - name: spatial versions (if geopandas is installed)
+       - name: spatial versions
          run: 'python -c "import geopandas; geopandas.show_versions();"'
-         if: contains(matrix.environment-file, 'no-optional') != true
 
        - name: run tests
          run: |

.pre-commit-config.yaml

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

README.md

@@ -64,15 +64,12 @@ $ pip install git+https://github.com/pysal/spaghetti
 ## Requirements
 
 - [`esda`](https://pysal.org/esda/)
+- [`geopandas`](https://geopandas.org/en/stable/)
 - [`libpysal`](https://pysal.org/libpysal/)
 - [`libspatialindex`](https://libspatialindex.org/en/stable/)
 - [`numpy`](https://numpy.org/devdocs/)
 - [`rtree`](https://rtree.readthedocs.io/en/stable/)
 - [`scipy`](http://scipy.github.io/devdocs/)
-
-## Soft Dependencies
-
-- [`geopandas`](https://geopandas.org/en/stable/)
 - [`shapely`](https://shapely.readthedocs.io/en/stable/)
 
 ## History

ci/310-latest.yaml

@@ -5,12 +5,14 @@ dependencies:
   - python=3.10
   # required
   - esda
+  - geopandas
   - libpysal
   - numpy
   - pandas
   - pip
   - rtree
   - scipy
+  - shapely
   - watermark
   # testing
   - codecov

ci/310-oldest.yaml

@@ -5,18 +5,17 @@ dependencies:
   - python=3.10
   # required
   - esda=2.1
+  - geopandas=0.12
   - libpysal=4.6
   - numpy=1.22
   - pandas=1.4
   - pip
   - rtree=1.0
   - scipy=1.8
+  - shapely=2.0
   # testing
   - codecov
   - pytest
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
-  # optional
-  - geopandas=0.12
-  - shapely=2.0

ci/311-latest.yaml

@@ -5,12 +5,14 @@ dependencies:
   - python=3.11
   # required
   - esda
+  - geopandas
   - libpysal
   - numpy
   - pandas
   - pip
   - rtree
   - scipy
+  - shapely
   - watermark
   # testing
   - codecov

ci/312-latest.yaml

@@ -5,12 +5,14 @@ dependencies:
   - python=3.12
   # required
   - esda
+  - geopandas
   - libpysal
   - numpy
   - pandas
   - pip
   - rtree
   - scipy
+  - shapely
   - watermark
   # testing
   - codecov

pyproject.toml

@@ -24,11 +24,13 @@ classifiers = [
 requires-python = ">=3.10"
 dependencies = [
     "esda>=2.1",
+    "geopandas>=0.12",
     "libpysal>=4.6",
     "numpy>=1.22",
     "pandas>=1.4,!=1.5.0",
     "rtree>=1.0",
     "scipy>=1.8",
+    "shapely>=2.0.1",
 ]
 
 [project.urls]
@@ -47,10 +49,6 @@ docs = [
     "sphinxcontrib-bibtex",
     "sphinx_bootstrap_theme",
 ]
-plus = [
-    "geopandas>=0.12",
-    "shapely>=2.0",
-]
 tests = [
     "pytest",
     "pytest-cov",
@@ -82,9 +80,10 @@ include = [
 
 [tool.ruff]
 line-length = 88
-select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
+lint.select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
 exclude = ["spaghetti/tests/*", "docs/*"]
-[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

spaghetti/network.py

@@ -11,7 +11,6 @@
 import esda
 import numpy
 from libpysal import cg, weights
-from libpysal.common import requires
 
 from . import util
 from .analysis import GlobalAutoK
@@ -2636,7 +2635,7 @@ def Moran(self, pp_name, permutations=999, graph=False):  # noqa N802
         counts = self.count_per_link(pointpat.obs_to_arc, graph=graph)
 
         # Build the y vector
-        y = [counts[i] if i in counts else 0.0 for i in w.neighbors]
+        y = [counts.get(i, 0.0) for i in w.neighbors]
 
         # Moran's I
         moran = esda.moran.Moran(y, w, permutations=permutations)
@@ -3044,7 +3043,6 @@ def mst_weighted_sort(net, maximum, net_kws):
     return spanning_tree
 
 
-@requires("geopandas", "shapely")
 def element_as_gdf(
     net,
     vertices=False,
@@ -3119,7 +3117,6 @@ def element_as_gdf(
 
     When both network vertices and arcs are desired, the variable
     declaration must be in the order: <vertices>, <arcs>.
-    This function requires ``geopandas``.
 
     See also
     --------

spaghetti/util.py

@@ -1,21 +1,10 @@
-from warnings import warn
-
+import geopandas
 import numpy
+import pandas
+import shapely
 from libpysal import cg
-from libpysal.common import requires
 from rtree import Rtree
-
-try:
-    import geopandas
-    import pandas
-    import shapely
-    from shapely.geometry import LineString
-except ImportError:
-    warn(
-        "geopandas/shapely not available. Some functionality will be disabled.",
-        UserWarning,
-        stacklevel=1,
-    )
+from shapely.geometry import LineString
 
 
 def compute_length(v0, v1):
@@ -654,7 +643,6 @@ def build_chains(space_h, space_v, exterior, bounds, h=True):
     return chains
 
 
-@requires("geopandas", "shapely")
 def _points_as_gdf(net, vertices, vertices_for_arcs, pp_name, snapped, id_col=None):
     """Internal function for returning a point ``geopandas.GeoDataFrame``
     called from within ``spaghetti.element_as_gdf()``.
@@ -686,8 +674,7 @@ def _points_as_gdf(net, vertices, vertices_for_arcs, pp_name, snapped, id_col=No
     Notes
     -----
 
-    1. See ``spaghetti.element_as_gdf()`` for description of arguments.
-    2. This function requires ``geopandas``.
+    See ``spaghetti.element_as_gdf()`` for description of arguments.
 
     """
 
@@ -736,7 +723,6 @@ def _points_as_gdf(net, vertices, vertices_for_arcs, pp_name, snapped, id_col=No
     return points
 
 
-@requires("geopandas", "shapely")
 def _arcs_as_gdf(net, points, id_col=None):
     """Internal function for returning an arc ``geopandas.GeoDataFrame``
     called from within ``spaghetti.element_as_gdf()``.
@@ -751,8 +737,7 @@ def _arcs_as_gdf(net, points, id_col=None):
     Notes
     -----
 
-    1. See ``spaghetti.element_as_gdf()`` for description of arguments.
-    2. This function requires ``geopandas``.
+    See ``spaghetti.element_as_gdf()`` for description of arguments.
 
     """
 
@@ -776,7 +761,6 @@ def _line_coords(loc):
     return arcs
 
 
-@requires("geopandas", "shapely")
 def _routes_as_gdf(paths, id_col):
     """Internal function for returning a shortest paths
     ``geopandas.GeoDataFrame`` called from within
@@ -793,8 +777,7 @@ def _routes_as_gdf(paths, id_col):
     Notes
     -----
 
-    1. See ``spaghetti.element_as_gdf()`` for description of arguments.
-    2. This function requires ``geopandas``.
+    See ``spaghetti.element_as_gdf()`` for description of arguments.
 
     """