Merge pull request #685 from jGaboardi/try_py311

1st attempt for Python 3.11 testing

.github/workflows/build_docs.yml

@@ -19,7 +19,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/310.yaml]
+         environment-file: [ci/311.yaml]
          experimental: [false]
      defaults:
        run:

.github/workflows/testing.yml

@@ -27,25 +27,27 @@
    testing:
      needs: linting
      env:
-       RUN_TEST: pytest -v -n auto spaghetti --cov spaghetti --doctest-modules --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing --timeout 60
+       RUN_TEST: pytest spaghetti -v -r a -n auto --cov spaghetti --doctest-modules --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing --timeout 60
      name: ${{ matrix.os }}, ${{ matrix.environment-file }}
      runs-on: ${{ matrix.os }}
      timeout-minutes: 30
      strategy:
        matrix:
          os: [ubuntu-latest]
          environment-file:
-           - ci/38.yaml
-           - ci/39.yaml
-           - ci/310.yaml
+           - ci/38-BASE.yaml
+           - ci/39-BASE.yaml
            - ci/310-BASE.yaml
-           - ci/310-DEV.yaml
            - ci/310-DEV_shapely_dev.yaml
+           - ci/311-BARE.yaml
+           - ci/311-BASE.yaml
+           - ci/311-DEV.yaml
          include:
-           - environment-file: ci/310.yaml
+           - environment-file: ci/311-BASE.yaml
              os: macos-latest
-           - environment-file: ci/310.yaml
+           - environment-file: ci/311-BASE.yaml
              os: windows-latest
+       fail-fast: false
 
      steps:
        - name: checkout repo
@@ -58,13 +60,24 @@
            micromamba-version: 'latest'
            channel-priority: 'flexible'
 
-       - name: install bleeding edge libpysal & esda (Ubuntu / Python 3.10)
+       - name: install bleeding edge libpysal & esda (Ubuntu / Python 3.11)
          shell: bash -l {0}
          run: |
            pip install git+https://github.com/pysal/libpysal.git@master
            pip install git+https://github.com/pysal/esda.git@master
          if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
 
+       - name: environment info
+         shell: bash -l {0}
+         run: |
+           micromamba info
+           micromamba list
+       
+       - name: spatial versions (if geopandas is installed)
+         shell: bash -l {0}
+         run: 'python -c "import geopandas; geopandas.show_versions();"'
+         if: contains(matrix.environment-file, 'DEV') || contains(matrix.environment-file, 'BASE')
+
        - name: run tests - bash
          shell: bash -l {0}
          run: ${{ env.RUN_TEST }}

README.md

@@ -31,7 +31,7 @@ The following are a selection of some examples that can be launched individually
 
 ## Installation
 
-Python [3.8](https://docs.python.org/3.8/), [3.9](https://docs.python.org/3.9/), and [3.10](https://docs.python.org/3.10/) are tested for support by `spaghetti`. Please make sure that you are operating in a Python >= 3.8 environment.
+Python [3.8](https://docs.python.org/3.8/), [3.9](https://docs.python.org/3.9/), [3.10](https://docs.python.org/3.10/), and [3.11](https://docs.python.org/3.11/) are tested for support by `spaghetti`. Please make sure that you are operating in a Python >= 3.8 environment.
 
 **Installing with `conda` via [`conda-forge`](https://github.com/conda-forge/spaghetti-feedstock) (highly recommended)**
 

ci/310-BASE.yaml

@@ -19,3 +19,5 @@ dependencies:
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
+  # optional
+  - geopandas>=0.7.0

ci/311-BARE.yaml

@@ -0,0 +1,21 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  # required
+  - esda
+  - libpysal
+  - numpy
+  - pandas>=1.0
+  - pip
+  - rtree
+  - scipy>=1.0
+  - watermark
+  # testing/formatting
+  - black
+  - codecov
+  - pytest
+  - pytest-cov
+  - pytest-timeout
+  - pytest-xdist

ci/310.yaml → ci/311-BASE.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   # required
   - esda
   - libpysal

ci/310-DEV.yaml → ci/311-DEV.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   # required
   - numpy
   - pandas>=1.0

docs/installation.rst

@@ -1,6 +1,6 @@
 .. Installation
 
-Python 3.8_, 3.9_, and 3.10_ are tested for support by `spaghetti`. Please make sure that you are operating in a Python >= 3.8 environment.
+Python 3.8_, 3.9_, 3.10_, and 3.11_ are tested for support by `spaghetti`. Please make sure that you are operating in a Python >= 3.8 environment.
 
 
 Installation
@@ -51,6 +51,7 @@ You can  also fork_ the `pysal/spaghetti`_ repo and create a local clone of your
 .. _3.8: https://docs.python.org/3.8/
 .. _3.9: https://docs.python.org/3.9/
 .. _3.10: https://docs.python.org/3.10/
+.. _3.11: https://docs.python.org/3.11/
 .. _spaghetti-feedstock: https://github.com/conda-forge/spaghetti-feedstock
 .. _a nice example: https://geopandas.readthedocs.io/en/latest/getting_started/install.html#creating-a-new-environment
 .. _conda: https://docs.conda.io/en/latest/

environment.yml

@@ -2,7 +2,7 @@ name: notebooks-environment
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   - esda
   - geopandas>=0.9.0
   - libspatialindex

setup.py

@@ -78,6 +78,7 @@ def setup_package():
             "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
             "Programming Language :: Python :: 3.10",
+            "Programming Language :: Python :: 3.11",
         ],
         license="3-Clause BSD",
         packages=[package],

spaghetti/network.py

@@ -1010,19 +1010,29 @@ def distancebandweights(self, threshold, n_processes=1, gen_tree=False):
 
         >>> import spaghetti
         >>> from libpysal import examples
+        >>> import warnings
         >>> streets_file = examples.get_path("streets.shp")
         >>> ntw = spaghetti.Network(in_data=streets_file)
 
         Create a contiguity-based ``W`` object based on network distance, ``500``
         US feet in this case.
 
-        >>> w = ntw.distancebandweights(threshold=500)
+        >>> with warnings.catch_warnings():
+        ...     warnings.filterwarnings(
+        ...         "ignore", "The weights matrix is not fully connected", UserWarning
+        ...     )
+        ...     w = ntw.distancebandweights(threshold=500)
 
         Show the number of units in the ``W`` object.
 
         >>> w.n
         230
 
+        There are 7 components in the ``W`` object.
+
+        >>> w.n_components
+        7
+
         There are ``8`` units with ``3`` neighbors in the ``W`` object.
 
         >>> w.histogram[-1]
@@ -2329,15 +2339,15 @@ def int_coord(c):
             return int(c) if (type(c) == float and c.is_integer()) else c
 
         # catch invalid split types
-        split_by = split_by.lower()
+        _split_by = split_by.lower()
         valid_split_types = ["distance", "count"]
-        if split_by not in valid_split_types:
+        if _split_by not in valid_split_types:
             msg = f"'{split_by}' is not a valid value for 'split_by'. "
             msg += f"Valid arguments include: {valid_split_types}."
             raise ValueError(msg)
 
         # catch invalid count params
-        if split_by == "count":
+        if _split_by == "count":
             if split_param <= 1:
                 msg = "Splitting arcs by 1 or less is not possible. "
                 msg += f"Currently 'split_param' is set to {split_param}."
@@ -2376,7 +2386,7 @@ def int_coord(c):
             length = split_network.arc_lengths[arc]
 
             # set initial segmentation interval
-            if split_by == "distance":
+            if _split_by == "distance":
                 interval = split_param
             else:
                 interval = length / float(split_param)
@@ -2757,8 +2767,13 @@ def extract_component(net, component_id, weightings=None):
 
     >>> from libpysal import examples
     >>> import spaghetti
+    >>> import warnings
     >>> snow_net = examples.get_path("Soho_Network.shp")
-    >>> ntw = spaghetti.Network(in_data=snow_net, extractgraph=False)
+    >>> with warnings.catch_warnings():
+    ...     warnings.filterwarnings(
+    ...         "ignore", "The weights matrix is not fully connected", UserWarning
+    ...     )
+    ...     ntw = spaghetti.Network(in_data=snow_net, extractgraph=False)
 
     The network is not fully connected.
 
@@ -3009,7 +3024,7 @@ def spanning_tree(net, method="sort", maximum=False, silence_warnings=True):
         if method.lower() == "sort":
             spanning_tree = mst_weighted_sort(net, maximum, net_kws)
         else:
-            msg = "'%s' not a valid method for minimum spanning tree creation"
+            msg = "'%s' not a valid method for minimum spanning tree creation."
             raise ValueError(msg % method)
 
         # instantiate the spanning tree as a network object