Merge pull request #46 from felixriese/prep-python312

Prepare for Python 3.12 support

.github/workflows/tests_and_linting.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         # Python versions need to be strings (otherwise: 3.10 -> 3.1)
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -32,31 +32,31 @@ jobs:
       run: |
         pip list
     - name: Lint with flake8 (with stopping)
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.12' }}
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Lint with flake8 (without stopping)
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.12' }}
       run: |
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Check formatting (black, isort)
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.12' }}
       run: |
         black --check .
         isort --check .
     - name: Test with pytest
-      if: ${{ matrix.python-version != '3.10' }}
+      if: ${{ matrix.python-version != '3.12' }}
       run: |
         pytest --nbval
     - name: Test with pytest and Codecov
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.12' }}
       run: |
         pip install pytest-cov
         pytest --nbval  --cov=susi --cov-report=xml --cov-config .coveragerc
     - name: Upload coverage to Codecov
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.12' }}
       uses: codecov/codecov-action@v1
       with:
         verbose: true

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ default_language_version:
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: no-commit-to-branch
       args: ['--branch', 'main']
@@ -14,17 +14,17 @@ repos:
     - id: detect-private-key
     - id: check-merge-conflict
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 24.3.0
   hooks:
     - id: black
-      language_version: python3.10
+      language_version: python3.11
       args: [--config=pyproject.toml]
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
     - id: isort
 - repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     args: ["--ignore=E501,W503"]

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Change Log
 ==========
 
+[1.4.0] - 2024-XX-XX
+--------------------
+- [ADDED] Official support for Python 3.12.
+- [REMOVED] Official support for Python 3.8 (will be deprecated in 10/2024). It might
+  still work, but will not be maintained on this version.
+
 [1.3.0] - 2023-07-08
 --------------------
 - [ADDED] Official support for Python 3.11.

dev-requirements.txt

@@ -2,11 +2,11 @@
 -r test-requirements.txt
 
 # for the documentation
-sphinx==7.0.1
-sphinx-autobuild>=0.7.1
-numpydoc==1.5.0
-sphinx_rtd_theme==1.2.2
+sphinx==7.2.6
+sphinx-autobuild>=2024.2.4
+numpydoc==1.6.0
+sphinx_rtd_theme==2.0.0
 
 # for linting
-mypy==1.4.1
-pre-commit==3.3.3
+mypy==1.9.0
+pre-commit==3.6.2

meta.yaml

@@ -18,11 +18,11 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.8
+    - python >=3.9
   run:
     - joblib >=0.13.0
     - numpy >=1.18.5
-    - python >=3.8
+    - python >=3.9
     - scikit-learn >=0.21.1
     - scipy >=1.3.1
     - tqdm >=4.45.0

setup.py

@@ -40,10 +40,10 @@
     packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Environment :: Console",
         "Intended Audience :: Developers",
         "Intended Audience :: Education",

susi/SOMClassifier.py

@@ -1,4 +1,5 @@
 """SOMClassifier class."""
+
 from typing import Optional, Sequence, Tuple, Union
 
 import numpy as np

susi/SOMUtils.py

@@ -1,4 +1,5 @@
 """SOMUtils functions."""
+
 from typing import Sequence, Tuple
 
 import numpy as np

susi/__init__.py

@@ -4,6 +4,7 @@
 self-organizing maps (SOM).
 
 """
+
 __version__ = "1.3.0"
 
 from .SOMClassifier import SOMClassifier

test-requirements.txt

@@ -1,9 +1,9 @@
-black==23.7.0
-codecov>=2.1.10
-coverage>=5.3
-flake8==6.0.0
-isort==5.12.0
-nbval>=0.9.5
-pytest>=7.2.0
-pytest-cov>=2.10.1
-pytest_mock==3.11.1
+black==24.3.0
+codecov>=2.1.13
+coverage>=7.4.4
+flake8==7.0.0
+isort==5.13.2
+nbval>=0.11.0
+pytest>=8.1.1
+pytest-cov>=4.1.0
+pytest_mock==3.14.0

tests/test_MultiOutput.py

@@ -4,6 +4,7 @@
 python -m pytest tests/test_MultiOutput.py
 
 """
+
 import os
 import sys
 

tests/test_SOMClassifier.py

@@ -4,6 +4,7 @@
 python -m pytest tests/test_SOMClassifier.py
 
 """
+
 import itertools
 import os
 import sys

tests/test_SOMClustering.py

@@ -4,6 +4,7 @@
 python -m pytest tests/test_SOMClustering.py
 
 """
+
 import os
 import sys
 

tests/test_SOMEstimator.py

@@ -4,6 +4,7 @@
 python -m pytest tests/test_SOMEstimator.py
 
 """
+
 import os
 import sys
 

tests/test_SOMRegressor.py

@@ -4,6 +4,7 @@
 python -m pytest tests/test_SOMRegressor.py
 
 """
+
 import itertools
 import os
 import sys