Update CI

.github/workflows/deploy.yaml

@@ -19,7 +19,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash
+    shell: bash -l {0}
 
 
 jobs:
@@ -32,18 +32,17 @@ jobs:
       fail-fast: false
       matrix:
         buildplat:
-          - [ubuntu-20.04, manylinux_x86_64, x86_64]
-          - [macos-11, macosx_*, x86_64]
-          - [windows-2019, win_amd64, AMD64]
-          - [macos-14, macosx_*, arm64]
-        python: ["cp39", "cp310", "cp311", "cp312"]
+          - [ubuntu-22.04, manylinux_x86_64, x86_64]
+          - [windows-2022, win_amd64, AMD64]
+          - [macos-15-intel, macosx_*, arm64]
+        python: ["cp311", "cp312", "cp313", "cp314"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v3.4.0
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
@@ -53,8 +52,9 @@ jobs:
         if: |
           (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) ||
           (github.event_name == 'release' && github.event.action == 'published')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v7
         with:
+          name: wheel-${{ matrix.buildplat[0] }}-${{ matrix.python }}
           path: wheelhouse/*.whl
           retention-days: 7
 
@@ -63,20 +63,32 @@ jobs:
     name: build package source distribution
     runs-on: ubuntu-latest
     timeout-minutes: 10
+    outputs:
+      version: ${{ steps.extract-version.outputs.version }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Build sdist
         run: pipx run build --sdist
 
+      - name: Extract package version
+        id: extract-version
+        run: |
+          SDIST_FILE=$(ls dist/*.tar.gz)
+          # Extract version from sdist archive (format: mdaencore-1.0.1rc1.tar.gz)
+          VERSION=$(tar xf ${SDIST_FILE} -O --wildcards '*/*.egg-info/PKG-INFO' | awk '/^Version:/ {print $2}')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "Extracted version: $VERSION"
+
       - name: upload artifacts
         if: |
           (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) ||
           (github.event_name == 'release' && github.event.action == 'published')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v7
         with:
+          name: dist-files
           path: dist/*.tar.gz
           retention-days: 7
 
@@ -93,16 +105,16 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist]
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v8
         with:
-          name: artifact
           path: dist
+          merge-multiple: true
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.8.10
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         with:
-          skip_existing: true
-          repository_url: https://test.pypi.org/legacy/
+          skip-existing: true
+          repository-url: https://test.pypi.org/legacy/
 
   upload_pypi:
     if: |
@@ -117,13 +129,13 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist]
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v8
         with:
-          name: artifact
           path: dist
+          merge-multiple: true
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.8.10
+        uses: pypa/gh-action-pypi-publish@v1.14.0
 
   check_testpypi:
     if: |
@@ -132,22 +144,25 @@ jobs:
     name: testpypi check
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
-    needs: upload_testpypi
+    needs: [upload_testpypi, build_sdist]
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: pip install
+      - name: Wait for version to be available on TestPyPI (30 seconds)
+        run: sleep 30
+
+      - name: pip install mdaencore from testpypi (${{ needs.build_sdist.outputs.version }})
         run: |
-          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple mdaencore
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "mdaencore==${{ needs.build_sdist.outputs.version }}"
 
       - name: install test deps
         run: |

.github/workflows/docs.yaml

@@ -21,19 +21,19 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0         
 
     - name: setup_miniconda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v4
       with:
-        python-version: 3.11
+        python-version: 3.14
         environment-file: docs/requirements.yaml
         auto-update-conda: true
         channel-priority: flexible
         channels: conda-forge
-        miniforge-variant: Mambaforge
+        miniforge-version: latest
         use-mamba: true
 
     - name: Build and install package
@@ -55,7 +55,7 @@ jobs:
         user_name: 'github-actions'
         user_email: 'github-action@users.noreply.github.com'
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v7
       if: github.event_name == 'pull_request'
       with:
         name: pr_docs

.github/workflows/gh-ci.yaml

@@ -20,7 +20,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash  -l {0} 
+    shell: bash -el {0} 
 
 jobs:
   main-tests:
@@ -29,19 +29,17 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          # macos-13 is x86_64 and macos-14 is arm64
-          os: [ubuntu-latest, windows-latest, macos-14, macos-13]
-          python-version: ["3.10", "3.11", "3.12"]
+          # macos-latest = arm64, macos-15-intel = x86_64
+          os: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
+          python-version: ["3.11", "3.12", "3.13", "3.14"]
           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 #68)
-            - python-version: "3.12"
-              mdanalysis-version: "latest"
+          #exclude:
+          #  - python-version: "3.12"
+          #    mdanalysis-version: "latest"
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
@@ -53,15 +51,15 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Install conda dependencies
-      uses: conda-incubator/setup-miniconda@v3
+      uses: conda-incubator/setup-miniconda@v4
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
         add-pip-as-python-dependency: true
 
-        miniforge-variant: Mambaforge
+        miniforge-version: latest
         use-mamba: true
-        channels: conda-forge, defaults
+        channels: conda-forge
 
         activate-environment: mdaencore-test
         auto-update-conda: true
@@ -74,8 +72,8 @@ jobs:
       with:
         version: ${{ matrix.mdanalysis-version }}
         install-tests: true
-        installer:  mamba 
-        shell: bash  -l {0} 
+        installer:  conda 
+        shell: bash  -el {0} 
 
     - name: Install package
       run: |
@@ -101,9 +99,9 @@ jobs:
 
     - name: codecov
       if: github.repository == 'MDAnalysis/mdaencore' && github.event_name != 'schedule'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v6
       with:
-        file: coverage.xml
+        files: coverage.xml
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         token: ${{ secrets.CODECOV_TOKEN }}
         verbose: True
@@ -115,12 +113,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
-        python-version: "3.11"
+        python-version: "3.14"
 
     - name: Install Pylint
       run: |
@@ -140,12 +138,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
-        python-version: "3.11"
+        python-version: "3.14"
 
     - name: Install dependencies
       run: |

CHANGELOG.md

@@ -22,6 +22,7 @@ The rules for this file:
 - ianmkenney
 - tylerjereddy
 - IAlibay
+- orbeckst
 
 ### Added
 <!-- Added functionality -->
@@ -32,7 +33,7 @@ The rules for this file:
 
 ### Changed
 - Update CI and wheel deployment to include macos-arm64 and py3.12 (PR #63)
-- Minimum Python version has been raised to 3.10 (PR #66)
+- Minimum Python version has been raised to 3.11 (PR #66, PR #76)
 - Minimum MDAnalysis version has been raised to 2.1.0 (PR #66)
 
 ### Deprecated

devtools/conda-envs/test_env.yaml

@@ -1,7 +1,6 @@
 name: mdaencore-test
 channels:
   - conda-forge
-  - defaults
 dependencies:
   # Base depends
   - python

docs/requirements.yaml

@@ -1,6 +1,5 @@
 name: mdaencore-docs
 channels:
-    - default
     - conda-forge
 dependencies:
     # Base depends

pyproject.toml

@@ -13,7 +13,8 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "mdaencore"
 description = "Ensemble overlap comparison software for molecular data."
-license = {file = "LICENSE" }
+license = "GPL-2.0-or-later"
+license-files = ["LICENSE", "AUTHORS"]
 authors = [
     {name = "Matteo Tiberti", email = "tiberti@cancer.dk"},
     {name = "Wouter Boomsma", email = "wb@di.ku.dk"},    
@@ -29,20 +30,20 @@ classifiers = [
     "Development Status :: 6 - Mature",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX",
     "Programming Language :: C",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",    
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "MDAnalysis>=2.1.0",
     "joblib",
@@ -82,7 +83,6 @@ testpaths = [
 
 [tool.black]
 line-length = 80
-extend-exclude = "versioneer.py"
 
 [tool.versioningit]
 default-version = "1+unknown"

readthedocs.yaml

@@ -6,9 +6,9 @@ sphinx:
   configuration: docs/source/conf.py
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-4.10"
+    python: "miniforge3-latest"
 
 python:
   install:

setup.cfg

@@ -5,8 +5,6 @@
 omit =
     # Omit the tests
     */tests/*
-    # Omit generated versioneer
-    mdaencore/_version.py
 
 [coverage:report]
 exclude_also =
@@ -28,7 +26,6 @@ USE_TABS = False
 [flake8]
 # Flake8, PyFlakes, etc
 max-line-length = 80
-exclude = versioneer.py
 
 [aliases]
 test = pytest