Update Python versions and dependencies

.github/workflows/docs.yml

@@ -13,66 +13,26 @@ permissions:
   contents: write
 
 jobs:
-  build:
+  docs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955  # v4
 
-      - name: Install python
-        uses: actions/setup-python@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@3259c6206f993105e3a61b142c2d97bf4b9ef83d # v7
         with:
-          python-version: 3.x
-
-      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-
-      - uses: actions/cache@v3
-        with:
-          key: mkdocs-material-${{ env.cache_id }}
-          path: .cache
-          restore-keys: |
-            mkdocs-material-
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install ".[doc]"
-
-      - name: Build docs
-        run: mkdocs build
-      - name: Upload static docs
-        uses: actions/upload-artifact@v3
-        with:
-          name: docs
-          path: site
-
-  deploy:
-    name: Pulish docs if a release was made
-    runs-on: ubuntu-latest
-    if: "startsWith(github.ref, 'refs/tags/')"
-    needs: [build]
-    steps:
-      - name: Checkout source
-        uses: actions/checkout@v3
-
-      - name: Install python
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.x
-
-      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-
-      - uses: actions/cache@v3
-        with:
-          key: mkdocs-material-${{ env.cache_id }}
-          path: .cache
-          restore-keys: |
-            mkdocs-material-
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install ".[doc]"
-
-      - name: Deploy to github pages
-        run: mkdocs gh-deploy --force
+          python-version: "3.11"
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            **/uv.lock
+            **/.tox/**/*
+            **/mkdocs.yml
+
+      - name: Build HTML documentation with tox
+        run: uv run mkdocs build
+
+      - name: Publish docs if a release was made
+        if: startsWith(github.ref, 'refs/tags/')
+        run:  uv run mkdocs gh-deploy --force

.github/workflows/linting.yml

@@ -11,25 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955  # v4
 
-      - name: Cache pre-commit
-        uses: actions/cache@v3
+      - name: Setup uv
+        uses: astral-sh/setup-uv@3259c6206f993105e3a61b142c2d97bf4b9ef83d # v7
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+          python-version: "3.11"
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            **/uv.lock
+            **/.tox/**/*
+            **/.pre-commit-config.yaml
 
-      - name: Set up python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-          cache: "pip"
-          cache-dependency-path: "pyproject.toml"
-
-      - name: Install dependencies
-        run: |-
-          python -m pip install pre-commit
-          pre-commit install
-
-      - name: Run pre-commit
-        run: pre-commit run --all-files --color always
+      - name: Test with tox
+        run: uv run -- pre-commit run --all-files --color always --verbose

.github/workflows/test_and_build.yaml

@@ -25,98 +25,99 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
+      - name: Checkout source
+        uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4
 
-    # first step checks out the code into
-    - uses: actions/checkout@v3
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: "pip"
-        cache-dependency-path: "pyproject.toml"
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox tox-gh-actions
-
-    - name: Test with tox
-      run: tox
-
-    # Using Codecov's action, upload the coverage report for the triggering commit/PR
-    - name: Upload coverage
-      uses: codecov/codecov-action@v3
-      with:
-        files: coverage.xml
-        fail_ci_if_error: true
-        verbose: true
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Setup uv
+        uses: astral-sh/setup-uv@3259c6206f993105e3a61b142c2d97bf4b9ef83d # v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            **/uv.lock
+            **/pytest.ini
+            **/tox.ini
+
+      - name: Run tests
+        run: uv run pytest --cov --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
+        with:
+          files: coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   twine_check:
-    if: "github.repository == 'p-j-smith/mda-tui'"
+    if: github.repository == 'p-j-smith/mda-tui'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
-
-    - name: Install dependencies
-      run: |
-        pip install setuptools twine wheel build
-
-    - name: Build package
-      run: |
-        python -m build .
-
-    - name: Check package build
-      run: |
-        DISTRIBUTION=$(ls -t1 dist/mda-tui-*.tar.gz | head -n 1)
-        test -n "${DISTRIBUTION}" || { echo "no dist/distribution mda-tui-*.tar.gz found"; exit 1; }
-        echo "twine check $DISTRIBUTION"
-        twine check $DISTRIBUTION
-
-    - name: Upload sdist
-      uses: actions/upload-artifact@v3
-      with:
-        name: wheels
-        path: dist
+      - name: Checkout source
+        uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@3259c6206f993105e3a61b142c2d97bf4b9ef83d # v7
+        with:
+          python-version: "3.11"
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            **/uv.lock
+
+      - name: Build package
+        run: uv build
+
+      - name: Check package with Twine
+        run: uv run --with twine twine check dist/*
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: wheels
+          path: dist
 
   release-test:
     name: Publish to Test PyPI
     runs-on: ubuntu-latest
     needs: [test, twine_check]
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4
         with:
           name: wheels
           path: dist
+
       - name: Publish to Test PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1
         with:
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository-url: https://test.pypi.org/legacy/
           skip-existing: true
+          attestations: false
 
   release:
     name: Publish to PyPI
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs: [release-test]
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4
         with:
           name: wheels
           path: dist
+
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: false  # fail if already exists
+          attestations: false

.pre-commit-config.yaml

@@ -4,16 +4,16 @@
 #   pre-commit install-hooks
 repos:
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.287
+      rev: v0.14.1
       hooks:
         - id: ruff
     - repo: https://github.com/Lucas-C/pre-commit-hooks
-      rev: v1.5.4
+      rev: v1.5.5
       hooks:
         - id: remove-tabs
           exclude: Makefile|docs/Makefile|docs/make.bat
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v6.0.0
       hooks:
           - id: check-case-conflict
           - id: check-docstring-first
@@ -28,7 +28,7 @@ repos:
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
     - repo: https://github.com/psf/black
-      rev: 23.7.0
+      rev: 25.9.0
       hooks:
           - id: black
             exclude: versioneer.py|src/mda_tui/_version.py

README.md

@@ -34,55 +34,40 @@ MDanalysis TUI is alpha software and may change without warning.
 ## Installation
 
 When installing MDAnalysis TUI, we highly recommend using virtual environments.
-If possible, we strongly recommend that you use
-[Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) as your package manager.
+We recommend that you use
+[uv](https://docs.astral.sh/uv/getting-started/installation/) or
+[pixi](https://pixi.sh/latest/installation/)
+as your package manager.
 
-First ensure that you have [mamba](https://mamba.readthedocs.io/en/latest/index.html) installed.
+Assuming you're using `uv`, create and activate a new virtual environment with:
 
-Create a virtual environment and activate it:
-
-```
-mamba create --name mda-tui -c conda-forge python=3.10 pip
-mamba activate mda-tui
+```sh
+uv venv --python=3.14
+source .venv/bin/activate
 ```
 
-Then install MDAnalysis TUI:
+Then install MDAnalysis TUI with:
 
-```
-python -m pip install mda-tui
-```
-
-And when you are finished, you can exit the virtual environment with:
-
-```
-mamba deactivate
+```sh
+uv pip install mda_tui
 ```
 
-To use conda instead, replace all `mamba` commands with `conda`.
-
-
 ### Installation from source
 
 To build MDAnalysis TUI from source, follow the above steps for creating a virtual environment, clone this repository:
 
-```
+```sh
 git clone https://github.com/p-j-smith/mda-tui.git
 ```
 
 Then inside your virtual environment type:
 
-```
-python -m pip install .
+```sh
+uv sync
 ```
 
-If you want to create a development environment, you can
-install MDAnalysis TUI in editible mode along with
-the dependencies required for running tests and and building docs with
-the following command:
-
-```
-python -m pip install -e ".[dev]"
-```
+By default, this will install MDAnalysis TUI in editable mode along with the dependencies
+required for development (testing, linting, and building the documentation).
 
 ## Code of conduct
 

mkdocs.yml

@@ -3,7 +3,7 @@ site_name: MDAnalysis TUI
 markdown_extensions:
   - attr_list
   - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
       emoji_generator: !!python/name:materialx.emoji.to_svg
   - md_in_html
   - admonition