Update to Python 3.12 (#43)

* Add Python 3.12 to GHA pytest-with-coverage workflow

This lets us use the workflow to test whether all the packages NEMO-Cmd depends
on have been updated to support Python 3.12.

* Add workflow_dispatch trigger to GHA CI workflow

Enables workflow to be triggered from GitHub CLI, browser, or via API.

This is primarily to allow the workflow to be run via
    gh workflow run pytest-with-coverage --ref py312
during the conda-forge Python 3.12 migration to test if the environment is
solvable yet.

* Update pkgs & versions used in recent dev env

* Change dev & rtd envs to Python 3.12

* Drop TROVE classifiers

They are now just outdated maintenance overhead.

* Change sphinx-linkcheck workflow to Python 3.12

* Change to Python 3.12 for development

* Drop support for Python 3.8, 3.9 & 3.10

* Update bbox assertion in test_random_oil_spills

Update shapely testing function re: "ShapelyDeprecationWarning: The
'almost_equals()' method is deprecated and will be removed in Shapely 2.1".

.github/workflows/pytest-with-coverage.yaml

@@ -3,6 +3,9 @@ name: pytest-with-coverage
 on:
   push:
     branches: [ '*' ]
+  # Enable workflow to be triggered from GitHub CLI, browser, or via API
+  # primarily for testing conda env solution for new Python versions
+  workflow_dispatch:
 
 jobs:
   pytest-with-coverage:
@@ -12,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.11', '3.12']
     uses: UBC-MOAD/gha-workflows/.github/workflows/pytest-with-coverage.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

.github/workflows/sphinx-linkcheck.yaml

@@ -15,7 +15,7 @@ jobs:
       matrix:
         # Need to specify Python version here because we use test env which gets its
         # Python version via matrix
-        python-version: [ '3.10' ]
+        python-version: [ '3.12' ]
     uses: UBC-MOAD/gha-workflows/.github/workflows/sphinx-linkcheck.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

README.rst

@@ -7,8 +7,8 @@ UBC EOAS MOAD Group Tools Package
 .. image:: https://img.shields.io/badge/license-Apache%202-cb2533.svg
     :target: https://www.apache.org/licenses/LICENSE-2.0
     :alt: Licensed under the Apache License, Version 2.0
-.. image:: https://img.shields.io/badge/python-3.8+-blue.svg
-    :target: https://docs.python.org/3.10/
+.. image:: https://img.shields.io/badge/Python-3.11%20%7C%203.12-blue?logo=python&label=Python&logoColor=gold
+    :target: https://docs.python.org/3.12/
     :alt: Python Version
 .. image:: https://img.shields.io/badge/version%20control-git-blue.svg?logo=github
     :target: https://github.com/UBC-MOAD/moad_tools

envs/environment-dev.yaml

@@ -28,7 +28,7 @@ dependencies:
   - pandas
   - pip
   - pytables
-  - python=3.10
+  - python=3.12
   - pyyaml
   - rasterio
   - scipy

envs/environment-rtd.yaml

@@ -8,7 +8,7 @@ channels:
   - nodefaults
 
 dependencies:
-  - python=3.10
+  - python=3.12
 
   # RTD packages
   - mock

envs/requirements.txt

@@ -5,103 +5,100 @@
 # to create an isolated development environment.
 #
 # Create/update this file with:
-#   (moad-tools)$ python3 -m pip list --format=freeze >> envs/requirements.txt
+#   (moad-tools)$ python -m pip list --format=freeze >> envs/requirements.txt
 
 affine==2.4.0
 alabaster==0.7.13
-arrow==1.2.3
+arrow==1.3.0
 attrs==23.1.0
-Babel==2.12.1
-black==23.7.0
-branca==0.6.0
-Brotli==1.0.9
-certifi==2023.7.22
-cftime==1.6.2
-charset-normalizer==3.2.0
+Babel==2.14.0
+black==23.11.0
+branca==0.7.0
+Brotli==1.1.0
+certifi==2023.11.17
+cftime==1.6.3
+charset-normalizer==3.3.2
 click==8.1.7
 click-plugins==1.1.1
 cligj==0.7.2
 colorama==0.4.6
-contourpy==1.1.0
-coverage==7.3.0
-cycler==0.11.0
-docutils==0.18.1
-exceptiongroup==1.1.3
-Fiona==1.9.4
-folium==0.14.0
-fonttools==4.42.1
-GDAL==3.7.1
-geopandas==0.13.2
-idna==3.4
+contourpy==1.2.0
+coverage==7.3.3
+cycler==0.12.1
+docutils==0.20.1
+exceptiongroup==1.2.0
+fiona==1.9.5
+folium==0.15.1
+fonttools==4.46.0
+GDAL==3.8.1
+geopandas==0.14.1
+idna==3.6
 imagesize==1.4.1
-importlib-metadata==6.8.0
+importlib-metadata==7.0.0
 iniconfig==2.0.0
 Jinja2==3.1.2
 joblib==1.3.2
 kiwisolver==1.4.5
-mapclassify==2.5.0
+mapclassify==2.6.1
 MarkupSafe==2.1.3
-matplotlib==3.7.2
-munch==4.0.0
+matplotlib==3.8.2
 munkres==1.1.4
 mypy-extensions==1.0.0
-netCDF4==1.6.4
-networkx==3.1
-numexpr==2.8.4
-numpy==1.25.2
-packaging==23.1
-pandas==2.0.3
-pathspec==0.11.2
-Pillow==10.0.1
-pip==23.3
-platformdirs==3.10.0
+netCDF4==1.6.5
+networkx==3.2.1
+numexpr==2.8.7
+numpy==1.26.2
+packaging==23.2
+pandas==2.1.4
+pathspec==0.12.1
+Pillow==10.1.0
+pip==23.3.2
+platformdirs==4.1.0
 pluggy==1.3.0
 ply==3.11
-pooch==1.7.0
 py-cpuinfo==9.0.0
-Pygments==2.16.1
-pyparsing==3.0.9
-pyproj==3.6.0
+Pygments==2.17.2
+pyparsing==3.1.1
+pyproj==3.6.1
 PyQt5==5.15.9
 PyQt5-sip==12.12.2
 PySocks==1.7.1
-pytest==7.4.0
+pytest==7.4.3
 pytest-cov==4.1.0
 pytest-randomly==3.15.0
 python-dateutil==2.8.2
-pytz==2023.3
+pytz==2023.3.post1
 PyYAML==6.0.1
-rasterio==1.3.8
+rasterio==1.3.9
 requests==2.31.0
-Rtree==1.0.1
-scikit-learn==1.3.0
-scipy==1.11.2
-setuptools==68.1.2
-shapely==2.0.1
-sip==6.7.11
+Rtree==1.1.0
+scikit-learn==1.3.2
+SciPy==1.11.4
+setuptools==68.2.2
+shapely==2.0.2
+sip==6.7.12
 six==1.16.0
 snowballstemmer==2.2.0
 snuggs==1.4.7
-Sphinx==7.2.4
-sphinx-notfound-page==0.8.3
-sphinx-rtd-theme==1.3.0
+Sphinx==7.2.6
+sphinx-notfound-page==1.0.0
+sphinx-rtd-theme==2.0.0
 sphinxcontrib-applehelp==1.0.7
 sphinxcontrib-devhelp==1.0.5
 sphinxcontrib-htmlhelp==2.0.4
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.6
 sphinxcontrib-serializinghtml==1.1.9
-tables==3.8.0
+tables==3.9.2
 threadpoolctl==3.2.0
 toml==0.10.2
 tomli==2.0.1
 tornado==6.3.3
-typing_extensions==4.7.1
+types-python-dateutil==2.8.19.14
 tzdata==2023.3
-unicodedata2==15.0.0
-urllib3==2.0.7
-wheel==0.41.2
-xarray==2023.8.0
-xyzservices==2023.7.0
-zipp==3.16.2
+urllib3==2.1.0
+wheel==0.42.0
+xarray==2023.12.0
+xyzservices==2023.10.1
+zipp==3.17.0

setup.cfg

@@ -26,26 +26,12 @@ url = https://ubc-moad-tools.readthedocs.org/en/latest/
 long_description = file: README.rst
 license = Apache License, Version 2.0
 platform = Linux
-classifiers =
-    Development Status :: 5 - Production
-    License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: Implementation :: CPython
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Operating System :: POSIX :: Linux
-    Operating System :: Unix
-    Environment :: Console
-    Intended Audience :: Science/Research
-    Intended Audience :: Education
-    Intended Audience :: Developers
 
 [options]
 zip_safe = False
 include_package_data = True
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.11
 install_requires =
     # see envs/environment-dev.yaml for conda environment dev installation
     # see envs/requirements.txt for versions most recently used in development
@@ -62,7 +48,6 @@ install_requires =
     # PyTables
     tables
     xarray
-    # moad_tools  # use python3 -m pip install --editable moad_tools/
 
 [options.entry_points]
 console_scripts =

tests/test_random_oil_spills.py

@@ -28,6 +28,7 @@
 import pandas
 import pytest
 import shapely.geometry
+import shapely.testing
 import xarray
 import yaml
 
@@ -270,7 +271,7 @@ def test_get_lat_lon_indices(self, config_file):
         assert lon == pytest.approx(expected.lon)
         assert geotiff_x_index == expected.geotiff_x_index
         assert geotiff_y_index == expected.geotiff_y_index
-        assert geotiff_bbox.almost_equals(expected.geotiff_bbox)
+        shapely.testing.assert_geometries_equal(geotiff_bbox, expected.geotiff_bbox, tolerance=1e-6)
 
 
 class TestGetVesselType: