Remove environment config from CI

.github/workflows/gh-ci.yaml

@@ -23,31 +23,21 @@ defaults:
     shell: bash  -l {0} 
 
 jobs:
-  environment-config:
-    runs-on: ubuntu-latest
-    outputs:
-      stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
-      python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
-    steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-
-      - id: get-compatible-python
-        uses: MDAnalysis/mdanalysis-compatible-python@main
-        with:
-          release: "latest"
-
   main-tests:
     if: "github.repository == 'MDAnalysis/transport-analysis'"
-    needs: environment-config
     runs-on: ${{ matrix.os }}
     strategy:
         fail-fast: false
         matrix:
           os: [macOS-latest, ubuntu-latest, windows-latest]
-          python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }}
+          python-version: ["3.10", "3.11", "3.12"]
           mdanalysis-version: ["latest", "develop"]
+          # Manually exclude any combinations of the test matrix that can't be run 
+          exclude:
+            # The latest release of MDAnalysis only supports up to Python 3.11
+            # so we exclude 3.12 from the test matrix (issue #37)
+            - python-version: "3.12"
+              mdanalysis-version: "latest"
 
     steps:
     - uses: actions/checkout@v4
@@ -58,10 +48,9 @@ jobs:
         df -h
         ulimit -a
 
-
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
@@ -77,7 +66,6 @@ jobs:
         auto-activate-base: false
         show-channel-urls: true
 
-
     - name: Install MDAnalysis version
       uses: MDAnalysis/install-mdanalysis@main
       with:
@@ -100,23 +88,22 @@ jobs:
         conda info
         conda list
 
-
     - name: Run tests
       run: |
-        pytest -n 2 -v --cov=transport_analysis --cov-report=xml --color=yes transport_analysis/tests/
+        pytest -n auto -v --cov=transport_analysis --cov-report=xml --color=yes transport_analysis/tests/
 
     - name: codecov
       if: github.repository == 'MDAnalysis/transport-analysis' && github.event_name != 'schedule'
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: coverage.xml
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         verbose: True
+        token: ${{ secrets.CODECOV_TOKEN }}
 
 
   pylint_check:
     if: "github.repository == 'MDAnalysis/transport-analysis'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
@@ -125,7 +112,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install Pylint
       run: |
@@ -142,7 +129,6 @@ jobs:
 
   black_check:
     if: "github.repository == 'MDAnalysis/transport-analysis'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
@@ -156,16 +142,15 @@ jobs:
 
   pypi_check:
     if: "github.repository == 'MDAnalysis/transport-analysis'"
-    needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |

CHANGELOG.md

@@ -33,6 +33,8 @@ xhgchen, hmacdope, orionarcher, IAlibay
 
 ### Changed
 <!-- Changes in existing functionality -->
+  * Minimum Python version has been increased to 3.10 (PR #50)
+  * Minimum MDAnalysis version has been increased to 2.1.0 (PR #50)
 
 ### Deprecated
 <!-- Soon-to-be removed features -->

pyproject.toml

@@ -16,9 +16,9 @@ maintainers = [
     {name = "Xu Hong Chen", email = "[email protected]"},
 ]
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
-    "MDAnalysis>=2.0.0",
+    "MDAnalysis>=2.1.0",
     "tidynamics>=1.0.0",
 ]
 keywords = [

setup.py

@@ -44,13 +44,13 @@
     # Customize MANIFEST.in if the general case does not suit your needs
     # Comment out this line to prevent the files from being packaged with your software
     include_package_data=True,
-    python_requires=">=3.9",          # Python version restrictions
+    python_requires=">=3.10",          # Python version restrictions
     # Allows `setup.py test` to work correctly with pytest
     setup_requires=[] + pytest_runner,
     # Required packages, pulls from pip if needed
     # do not use for Conda deployment
     install_requires=[
-        "mdanalysis>=2.0.0",
+        "mdanalysis>=2.1.0",
         "tidynamics>=1.0.0",
     ],
     # Additional entries you may want simply uncomment the lines you want and fill in the data