Merge pull request #140 from jGaboardi/update_min_python

update min supported Python and testing workflow

.github/workflows/tests.yaml

@@ -18,15 +18,17 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         environment-file:
-          - ci/envs/38-minimal.yaml
-          - ci/envs/39-latest.yaml
+          - ci/envs/310-minimal.yaml
           - ci/envs/310-latest.yaml
           - ci/envs/311-latest.yaml
-          - ci/envs/311-dev.yaml
+          - ci/envs/312-latest.yaml
+          - ci/envs/312-dev.yaml
         include:
-          - environment-file: ci/envs/311-latest.yaml
-            os: macos-latest
-          - environment-file: ci/envs/311-latest.yaml
+          - environment-file: ci/envs/312-latest.yaml
+            os: macos-13 # Intel
+          - environment-file: ci/envs/312-latest.yaml
+            os: macos-14 # Apple Silicon
+          - environment-file: ci/envs/312-latest.yaml
             os: windows-latest
     defaults:
       run:
@@ -46,16 +48,6 @@ jobs:
 
       - name: Test pointpats
         run: |
-          pytest -v --color yes --cov pointpats --cov-config .coveragerc --cov-append --cov-report term-missing --cov-report xml .
+          pytest -v --color yes --cov pointpats --cov-append --cov-report term-missing --cov-report xml .
 
-      - uses: codecov/codecov-action@v3
-
-      - name: Generate and publish the report
-        if: |
-          failure()
-          && steps.status.outcome == 'failure'
-          && github.event_name == 'schedule'
-          && github.repository_owner == 'pysal'
-        uses: xarray-contrib/issue-from-pytest-log@v1
-        with:
-          log-path: pytest-log.jsonl
+      - uses: codecov/codecov-action@v4

ci/envs/310-latest.yaml

@@ -3,15 +3,15 @@ channels:
   - conda-forge
 dependencies:
   - python=3.10
-  - scipy
+  - geopandas
+  - libpysal
+  - matplotlib
   - numpy
   - pandas
-  - matplotlib
-  - libpysal
+  - scipy
+  - shapely
   # tests
   - scikit-learn
-  - shapely
-  - geopandas
   - statsmodels
   - pytest
   - pytest-cov

ci/envs/310-minimal.yaml

@@ -0,0 +1,18 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - geopandas=0.12
+  - libpysal=4.8
+  - matplotlib=3.6
+  - numpy=1.24
+  - pandas=1.4
+  - scipy=1.10
+  - shapely=2
+  # tests
+  - scikit-learn=1.2
+  - statsmodels
+  - pytest
+  - pytest-cov
+  - codecov

ci/envs/311-latest.yaml

@@ -3,25 +3,19 @@ channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - scipy
+  - geopandas
+  - libpysal
+  - matplotlib
   - numpy
   - pandas
-  - matplotlib
-  - libpysal
+  - scipy
+  - shapely
   # tests
   - scikit-learn
-  - shapely
-  - geopandas
   - statsmodels
   - pytest
   - pytest-cov
   - codecov
   - pip
   - pip:
       - KDEpy
-  # for docs build action (this env only)
-  - nbsphinx
-  - numpydoc
-  - sphinx
-  - sphinxcontrib-bibtex
-  - sphinx_bootstrap_theme

ci/envs/311-dev.yaml → ci/envs/312-dev.yaml

@@ -2,26 +2,26 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
-  - numpy
-  - pandas
-  - matplotlib
+  - python=3.12
+  - folium
   - libpysal
   - mapclassify
-  - folium
-  # tests
+  - matplotlib
+  - numpy
+  - pandas
   - shapely
-  - pyproj
+  # tests
+  - codecov
   - fiona
   - pytest
   - pytest-cov
-  - codecov
+  - pyproj
   - pip
   - pip:
       - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple
-      - git+https://github.com/geopandas/geopandas.git
-      - git+https://github.com/pysal/libpysal.git
+      - KDEpy
       - scipy
       - scikit-learn
       - statsmodels
-      - KDEpy
+      - git+https://github.com/pysal/libpysal.git
+      - git+https://github.com/geopandas/geopandas.git

ci/envs/39-latest.yaml → ci/envs/312-latest.yaml

@@ -2,20 +2,26 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
-  - scipy
+  - python=3.12
+  - geopandas
+  - libpysal
+  - matplotlib
   - numpy
   - pandas
-  - matplotlib
-  - libpysal
+  - scipy
+  - shapely
   # tests
   - scikit-learn
-  - shapely
-  - geopandas
   - statsmodels
   - pytest
   - pytest-cov
   - codecov
   - pip
   - pip:
       - KDEpy
+  # for docs build action (this env only)
+  - nbsphinx
+  - numpydoc
+  - sphinx
+  - sphinxcontrib-bibtex
+  - sphinx_bootstrap_theme

environment.yml

@@ -3,8 +3,11 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - pandas
+  - python
+  - geopandas
   - libpysal
   - matplotlib
+  - numpy
   - pandas
-  - scipy>=0.11
+  - scipy
+  - shapley

pointpats/tests/test_spacetime.py

@@ -335,7 +335,8 @@ def test_explore(self):
                 [0.0008675512091255166, 28.514975377735905],
             ],
         )
-        assert len(m.to_dict()["children"]) == 5
+        # old folium returns 5, new folium returns 3
+        assert len(m.to_dict()["children"]) >= 3
 
 
     def test_hotspots_without_neighbors(self):

pyproject.toml

@@ -25,14 +25,14 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: GIS",
 ]
-requires-python = ">=3.7"
+requires-python = ">=3.10"
 dependencies = [
-    "numpy",
-    "pandas",
-    "scipy >=1.8",
-    "libpysal >=4",
-    "matplotlib",
-    "geopandas",
+    "libpysal >=4.8",
+    "geopandas >= 0.12",
+    "matplotlib >=3.6",
+    "numpy >=1.24",
+    "pandas >=1.4, !=1.5.0",
+    "scipy >=1.10",
     "shapely >=2"
 ]
 
@@ -53,12 +53,13 @@ docs = [
     "myst-parser"
 ]
 tests = [
-    "geopandas",
     "codecov",
     "coverage",
     "pytest",
     "pytest-mpl",
     "pytest-cov",
+    "scikit-learn >=1.2",
+    "statsmodels",
     "watermark",
 ]
 
@@ -71,7 +72,6 @@ line-length = 88
 [tool.ruff]
 line-length = 88
 select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
-target-version = "py39"
 ignore = [
     "B006",
     "B008",