Merge pull request #228 from jGaboardi/GH225_CI_maint

update CI - minimum versions, naming, etc.

.github/workflows/build_docs.yml

@@ -19,7 +19,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/311.yaml]
+         environment-file: [ci/312-latest.yaml]
          experimental: [false]
      defaults:
        run:

.github/workflows/tests.yml

@@ -28,16 +28,17 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         environment-file:
-          - ci/39-MIN.yaml
-          - ci/310.yaml
-          - ci/311.yaml
-          - ci/311-DEV.yaml
+          - ci/310-oldest.yaml
+          - ci/310-latest.yaml
+          - ci/311-latest.yaml
+          - ci/312-latest.yaml
+          - ci/312-dev.yaml
         include:
-          - environment-file: ci/311.yaml
+          - environment-file: ci/312-latest.yaml
             os: macos-13 # Intel
-          - environment-file: ci/311.yaml
+          - environment-file: ci/312-latest.yaml
             os: macos-14 # Apple Silicon
-          - environment-file: ci/311.yaml
+          - environment-file: ci/312-latest.yaml
             os: windows-latest
       fail-fast: false
 
@@ -51,15 +52,6 @@ jobs:
           environment-file: ${{ matrix.environment-file }}
           micromamba-version: 'latest'
 
-      - name: install bleeding edge libpysal, esda, mapclassify & splot (Ubuntu / Python 3.11)
-        shell: bash -l {0}
-        run: |
-          pip install git+https://github.com/pysal/libpysal.git@main
-          pip install git+https://github.com/pysal/esda.git@main
-          pip install git+https://github.com/pysal/mapclassify.git@main
-          pip install git+https://github.com/pysal/splot.git@main
-        if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
-
       - name: environment info
         shell: bash -l {0}
         run: |
@@ -69,13 +61,13 @@ jobs:
       - 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')
+        if: contains(matrix.environment-file, 'dev')
 
       - name: run pytest
         run: pytest giddy -r a -v -n auto --cov giddy --cov-report xml --color yes --cov-append --cov-report term-missing
 
       - name: run docstring tests
-        if: contains(matrix.environment-file, '311-DEV') && contains(matrix.os, 'ubuntu')
+        if: contains(matrix.environment-file, '312-dev') && contains(matrix.os, 'ubuntu')
         run: |
           pytest \
           -v \

README.md

@@ -3,7 +3,7 @@ PySAL-giddy for exploratory spatiotemporal data analysis
 
 [![Continuous Integration](https://github.com/pysal/giddy/actions/workflows/tests.yml/badge.svg)](https://github.com/pysal/giddy/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/pysal/giddy/branch/main/graph/badge.svg)](https://codecov.io/gh/pysal/giddy)
-[![Gitter room](https://badges.gitter.im/pysal/giddy.svg)](https://gitter.im/pysal/giddy)
+[![Discord](https://img.shields.io/badge/Discord-join%20chat-7289da?style=flat&logo=discord&logoColor=cccccc&link=https://discord.gg/qUvMmdEmnp)](https://discord.gg/qUvMmdEmnp)
 [![PyPI version](https://badge.fury.io/py/giddy.svg)](https://badge.fury.io/py/giddy)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1322825.svg)](https://doi.org/10.5281/zenodo.1322825)
 [![badge](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pysal/giddy/main)
@@ -73,11 +73,11 @@ pip install git+https://github.com/pysal/giddy
 
 #### Requirements
 
-- scipy>=1.3.0
-- libpysal>=4.0.1
-- mapclassify>=2.1.1
-- esda>=2.1.1
-- quantecon>=0.4.7
+- scipy>=1.8
+- libpysal>=4.8
+- mapclassify>=2.5
+- esda>=2.4
+- quantecon>=0.7
 
 Contribute
 --------------
@@ -89,7 +89,7 @@ If you have any suggestion, feature request, or bug report, please open a new [i
 Support
 -----------
 
-If you are having issues, please talk to us in the [gitter room](https://gitter.im/pysal/giddy).
+If you are having issues, please talk to us in the [discord channel](https://discord.gg/qUvMmdEmnp).
 
 License
 ----------

ci/310.yaml → ci/310-latest.yaml

@@ -4,11 +4,11 @@ channels:
 dependencies:
   - python=3.10
   # required
-  - esda>=2.1.1
-  - libpysal>=4.0.1
-  - mapclassify>=2.1.1
-  - quantecon>=0.4.7
-  - scipy>=1.3.0
+  - esda
+  - libpysal
+  - mapclassify
+  - quantecon
+  - scipy
   - splot
   # testing
   - codecov

ci/39-MIN.yaml → ci/310-oldest.yaml

@@ -2,13 +2,13 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.10
   # required
-  - esda>=2.1.1
-  - libpysal>=4.0.1
-  - mapclassify>=2.1.1
-  - quantecon>=0.4.7
-  - scipy>=1.3.0
+  - esda=2.4
+  - libpysal=4.8
+  - mapclassify=2.5
+  - quantecon=0.7
+  - scipy=1.8
   - splot
   # testing
   - codecov

ci/311.yaml → ci/311-latest.yaml

@@ -4,11 +4,11 @@ channels:
 dependencies:
   - python=3.11
   # required
-  - esda>=2.1.1
-  - libpysal>=4.0.1
-  - mapclassify>=2.1.1
-  - quantecon>=0.4.7
-  - scipy>=1.3.0
+  - esda
+  - libpysal
+  - mapclassify
+  - quantecon
+  - scipy
   - splot
   # testing
   - codecov

ci/312-dev.yaml

@@ -0,0 +1,31 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  # required
+  - pip
+  # testing
+  - codecov
+  - ipywidgets
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - pytest-doctestplus
+  - pip:
+    # dev versions of packages
+    - --pre \
+      --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple  \
+      --extra-index-url https://pypi.org/simple
+    - numpy
+    - pandas
+    - scipy
+    - git+https://github.com/pysal/esda.git@main
+    - git+https://github.com/geopandas/geopandas.git@main
+    - git+https://github.com/pysal/libpysal.git@main
+    - git+https://github.com/pysal/mapclassify.git@main
+    - git+https://github.com/QuantEcon/QuantEcon.py.git@main
+    - git+https://github.com/pysal/splot.git@main
+
+

ci/312-latest.yaml

@@ -0,0 +1,19 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  # required
+  - esda
+  - libpysal
+  - mapclassify
+  - quantecon
+  - scipy
+  - splot
+  # testing
+  - codecov
+  - ipywidgets
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist

docs/installation.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-giddy currently supports python `3.9`_, `3.10`_, and `3.11`_.
+giddy currently supports python `3.10`_, `3.11`_, and `3.12`_.
 Please make sure that you are operating in a python 3 environment.
 
 Installing released version
@@ -41,9 +41,9 @@ your fork. By making changes
 to your local clone and submitting a pull request to `pysal/giddy`_, you can
 contribute to the giddy development.
 
-.. _3.9: https://docs.python.org/3.9/
 .. _3.10: https://docs.python.org/3.10/
 .. _3.11: https://docs.python.org/3.11/
+.. _3.12: https://docs.python.org/3.12/
 .. _Python Package Index: https://pypi.org/project/giddy/
 .. _pysal/giddy: https://github.com/pysal/giddy
 .. _fork: https://help.github.com/articles/fork-a-repo/

environment.yml

@@ -3,12 +3,11 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - jupyterlab
   - esda
+  - geopandas
+  - jupyterlab
   - libpysal
+  - mapclassify
   - quantecon
   - scipy
-  - geopandas
   - splot
-  - pip
-

giddy/directional.py

@@ -360,7 +360,7 @@ def plot_origin(self):  # TODO add attribute option to color vectors
 
         xlim = [self._dx.min(), self._dx.max()]
         ylim = [self._dy.min(), self._dy.max()]
-        for x, y in zip(self._dx, self._dy):
+        for x, y in zip(self._dx, self._dy, strict=False):
             xs = [0, x]
             ys = [0, y]
             plt.plot(xs, ys, "-b")  # TODO change this to scale with attribute

giddy/markov.py

@@ -817,7 +817,7 @@ def __init__(
             self.classes = classes
             self.k = len(classes)
             self.m = self.k
-            label_dict = dict(zip(classes, range(self.k)))
+            label_dict = dict(zip(classes, range(self.k), strict=False))
             y_int = []
             for yi in y:
                 y_int.append(list(map(label_dict.get, yi)))

giddy/sequence.py

@@ -185,7 +185,7 @@ def __init__(self, y, subs_mat=None, dist_type=None, indel=None, cluster_type=No
         self.indel = indel
         self.subs_mat = subs_mat
         self.cluster_type = cluster_type
-        self.label_dict = dict(zip(self.classes, range(self.k)))
+        self.label_dict = dict(zip(self.classes, range(self.k), strict=False))
 
         y_int = []
         for yi in y:
@@ -267,7 +267,11 @@ def __init__(self, y, subs_mat=None, dist_type=None, indel=None, cluster_type=No
                     y_tran_index = np.zeros_like(y_int)
                     y_tran = []
                     for i in range(y_int.shape[1]):
-                        y_tran.append(list(zip(y_int_ext[:, i], y_int_ext[:, i + 1])))
+                        y_tran.append(
+                            list(
+                                zip(y_int_ext[:, i], y_int_ext[:, i + 1], strict=False)
+                            )
+                        )
                     for i in range(y_int.shape[0]):
                         for j in range(y_int.shape[1]):
                             y_tran_index[i, j] = dict_trans_state[y_tran[j][i]]
@@ -337,7 +341,7 @@ def _om_dist(self, y_int):
         moves_str, unique_indices = np.unique(y_str, axis=0, return_index=True)
         moves_int = y_int[unique_indices]
         uni_num = len(moves_str)
-        dict_move_index = dict(zip(map(tuple, moves_int), range(uni_num)))
+        dict_move_index = dict(zip(map(tuple, moves_int), range(uni_num), strict=False))
 
         # dict_move_index = dict(zip(map(tuple, moves_str), range(uni_num)))
 

giddy/util.py

@@ -179,7 +179,7 @@ def _fill_empty_diagonal_3d(p):
     p0 = p_temp.sum(axis=2) == 0
     if p0.sum() > 0:
         rows, cols = np.where(p0)
-        row_zero_i = list(zip(rows, cols))
+        row_zero_i = list(zip(rows, cols, strict=False))
         for row in row_zero_i:
             i, j = row
             p_temp[i, j, j] = 1

pyproject.toml

@@ -16,20 +16,18 @@ keywords = ["spatial statistics", "spatiotemporal analysis"]
 readme = "README.md"
 classifiers = [
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: GIS",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
-    "esda>=2.1.1",
-    "libpysal>=4.0.1",
-    "quantecon>=0.4.7",
-    "scipy>=1.3",
+    "esda>=2.4",
+    "libpysal>=4.8",
+    "mapclassify>=2.5",
+    "quantecon>=0.7",
+    "scipy>=1.8",
 ]
 
 [project.urls]