New spec

.github/workflows/gh-ci.yaml

@@ -1,5 +1,5 @@
 name: GH Actions CI
-on:
+'on':
   push:
     branches:
       - main
@@ -10,7 +10,7 @@ on:
     # Weekly tests at midnight on Sundays run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * 0"
+    - cron: 0 0 * * 0
 
 concurrency:
   # Specific group naming so CI is only cancelled
@@ -20,7 +20,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash -l {0} 
+    shell: bash -l {0}
 
 jobs:
   environment-config:
@@ -31,139 +31,145 @@ jobs:
     steps:
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: '3.11'
 
       - id: get-compatible-python
         uses: MDAnalysis/mdanalysis-compatible-python@main
         with:
-          release: "latest"
+          release: latest
 
   main-tests:
-    if: "github.repository == 'Becksteinlab/zarrtraj'"
+    if: github.repository == 'Becksteinlab/zarrtraj'
     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) }}
-          mdanalysis-version: ["latest", "develop"]
+      fail-fast: false
+      matrix:
+        os:
+          - macOS-latest
+          - ubuntu-latest
+          - windows-latest
+        python-version: ["3.10", "3.11", "3.12"]
+        mdanalysis-version:
+          - latest
+          - develop
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Build information
-      run: |
-        uname -a
-        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
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        add-pip-as-python-dependency: true
-        architecture: x64
-
-        channels: defaults
-
-        activate-environment: zarrtraj-test
-        auto-update-conda: true
-        auto-activate-base: false
-        show-channel-urls: true
-
-
-    - name: Install MDAnalysis version
-      uses: MDAnalysis/install-mdanalysis@main
-      with:
-        version: ${{ matrix.mdanalysis-version }}
-        install-tests: true
-        installer:  conda
-        shell: bash -l {0} 
-
-    - name: Install package
-      run: |
-        python --version
-        python -m pip install .  --no-deps 
-
-    - name: Python information
-      run: |
-        which python
-        which pip
-        pip list
-
-        conda info
-        conda list
-
-
-    - name: Run tests
-      run: |
-        pytest -n 2 -v --cov=zarrtraj --cov-report=xml --color=yes zarrtraj/tests/
-
-    - name: codecov
-      if: github.repository == 'Becksteinlab/zarrtraj' && github.event_name != 'schedule'
-      uses: codecov/[email protected]
-      with:
-        file: coverage.xml
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-        verbose: True
-        token: ${{ secrets.CODECOV_TOKEN }}
-        slug: Becksteinlab/zarrtraj
+      - uses: actions/checkout@v4
 
+      - name: Build information
+        run: |
+          uname -a
+          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
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: devtools/conda-envs/test_env.yaml
+          add-pip-as-python-dependency: true
+          architecture: x64
+
+          channels: defaults
+
+          activate-environment: zarrtraj-test
+          auto-update-conda: true
+          auto-activate-base: false
+          show-channel-urls: true
+          # Need this to ensure miniconda installed
+          # if not already on MacOS
+          miniconda-version: latest
+
+      - name: Install MDAnalysis version
+        uses: MDAnalysis/install-mdanalysis@main
+        with:
+          version: ${{ matrix.mdanalysis-version }}
+          install-tests: true
+          installer: conda
+          shell: bash -l {0}
+
+      - name: Install package
+        run: |
+          python --version
+          python -m pip install .  --no-deps
+
+      - name: Python information
+        run: |
+          which python
+          which pip
+          pip list
+          conda info
+          conda list
+
+      - name: Run tests
+        # Tests must be sequential to avoid 
+        # moto buckets and groups interfering with
+        # one another
+        run: |
+          pytest -v --cov=zarrtraj --cov-report=xml --color=yes zarrtraj/tests/
+
+      - name: codecov
+        if: github.repository == 'Becksteinlab/zarrtraj' && github.event_name !=
+          'schedule'
+        uses: codecov/[email protected]
+        with:
+          file: coverage.xml
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: Becksteinlab/zarrtraj
 
   pylint_check:
-    if: "github.repository == 'Becksteinlab/zarrtraj'"
+    if: github.repository == 'Becksteinlab/zarrtraj'
     needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
-
-    - name: Install Pylint
-      run: |
-        which pip
-        which python
-        pip install pylint mdanalysis
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ needs.environment-config.outputs.stable-python-version }}
 
-    - name: Run Pylint
-      env:
-        PYLINTRC: .pylintrc
-      run: |
-        pylint zarrtraj
+      - name: Install Pylint
+        run: |
+          which pip
+          which python
+          pip install pylint mdanalysis
 
+      - name: Run Pylint
+        env:
+          PYLINTRC: .pylintrc
+        run: |
+          pylint zarrtraj
 
   pypi_check:
-    if: "github.repository == 'Becksteinlab/zarrtraj'"
+    if: github.repository == 'Becksteinlab/zarrtraj'
     needs: environment-config
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ needs.environment-config.outputs.stable-python-version }}
-
-    - name: Install dependencies
-      run: |
-        pip install pipx twine
-
-    - name: Build package
-      run: |
-        python -m pipx run build --sdist
-
-    - name: Check package build
-      run: |
-        DISTRIBUTION=$(ls -t1 dist/zarrtraj-*.tar.gz | head -n 1)
-        test -n "${DISTRIBUTION}" || { echo "no distribution dist/zarrtraj-*.tar.gz found"; exit 1; }
-        echo "twine check $DISTRIBUTION"
-        twine check $DISTRIBUTION
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ needs.environment-config.outputs.stable-python-version }}
+
+      - name: Install dependencies
+        run: |
+          pip install pipx twine
+
+      - name: Build package
+        run: |
+          python -m pipx run build --sdist
+
+      - name: Check package build
+        run: |
+          DISTRIBUTION=$(ls -t1 dist/zarrtraj-*.tar.gz | head -n 1)
+          test -n "${DISTRIBUTION}" || { echo "no distribution dist/zarrtraj-*.tar.gz found"; exit 1; }
+          echo "twine check $DISTRIBUTION"
+          twine check $DISTRIBUTION

benchmarks/__init__.py

@@ -0,0 +1 @@
+