add docs, have tests ci compatible, clean up build tools

.github/workflows/ci.yaml

@@ -0,0 +1,68 @@
+name: Run CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    name: Run tests
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v5.0.0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Crossflow and its testing dependencies
+        run: pip install -e .[testing]
+
+      - name: Run test suite
+        run: pytest --cov crossflow --cov-report term-missing --cov-append .
+
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v2.3.6
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v5.0.0
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+      - name: Build docs
+        run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v5.0.0
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit,docs,testing]
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/release.yaml

@@ -0,0 +1,140 @@
+
+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        required: true
+        default: 'x.y.z'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  checks:
+    name: Version check
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout repository
+      id: repo
+      uses: actions/checkout@v5.0.0
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.0.0
+      with:
+        python-version: 3.13
+
+    - name: Get latest release from pip
+      id: latestreleased
+      run: |
+        PREVIOUS_VERSION=$(python -m pip index versions crossflow | grep "crossflow" | cut -d "(" -f2 | cut -d ")" -f1)
+        echo "pip_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+        echo $PREVIOUS_VERSION
+
+    - name: version comparison
+      id: compare
+      run: |
+        pip3 install semver
+        output=$(pysemver compare ${{ steps.latestreleased.outputs.pip_tag }} ${{ github.event.inputs.version }})
+        if [ $output -ge 0 ]; then exit 1; fi
+
+  version:
+    name: prepare ${{ github.event.inputs.version }}
+    needs: checks
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@v5.0.0
+
+      - name: Change version in repo
+        run: sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" crossflow/__init__.py
+
+      - name: send PR
+        id: pr_id
+        uses: peter-evans/create-pull-request@v7.0.8
+        with:
+          commit-message: Update version to ${{ github.event.inputs.version }}
+          branch: version-update
+          title: "Update to version ${{ github.event.inputs.version }}"
+          body: |
+            Update version
+            - Update the __init__.py with new release
+            - Auto-generated by [CI]
+          committer: version-updater <vu.bot@users.noreply.github.com>
+          author: version-updater <vu.bot@users.noreply.github.com>
+          base: main
+          signoff: false
+          draft: false
+
+      - name: auto approve review
+        uses: hmarr/auto-approve-action@v4.0.0
+        with:
+          pull-request-number: ${{ steps.pr_id.outputs.pull-request-number }}
+          review-message: "Auto approved version bump PR"
+          github-token: ${{ secrets.AUTO_PR_MERGE }}
+
+      - name: merge PR
+        run: gh pr merge --merge --delete-branch --auto "${{ steps.pr_id.outputs.pull-request-number }}"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  tag:
+    name: tag release
+    needs: version
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5.0.0
+        with:
+          ref: main
+
+      - name: tag v${{ github.event.inputs.version }}
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git tag ${{ github.event.inputs.version }}
+          git push origin tag ${{ github.event.inputs.version }}
+
+  release:
+    name: make github release
+    needs: tag
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: create release
+        uses: softprops/action-gh-release@v2.3.3
+        with:
+          name: v${{ github.event.inputs.version }}
+          generate_release_notes: true
+          tag_name: ${{ github.event.inputs.version }}
+
+  pypi:
+    name: make pypi release
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+    steps:
+
+    - name: checkout
+      uses: actions/checkout@v5.0.0
+      with:
+        ref: main
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.0.0
+      with:
+        python-version: 3.13
+
+    - name: Install flit
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flit~=3.9
+
+    - name: Build and publish
+      run: |
+        flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,8 +1,133 @@
+# Byte-compiled / optimized / DLL files
 __pycache__/
-.vscode
-.idea
-*.egg_info/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
 build/
+develop-eggs/
 dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/autosummary/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# result and temp file
+*.out
+*.obj
+*.npz
+*.pkl
+*.csv
+Example_output/
+Example/data/*.csv
+
+# profraw files from LLVM? Unclear exactly what triggers this
+# There are reports this comes from LLVM profiling, but also Xcode 9.
+*profraw
+# trajectory file too big
+Example/data/1AKI_prod.trr
+Example/data/1AKI_prod.tpr
+
+# output directories, log file and outputs
+job*
+*.json
+*.err
+*.com
+*.txt
+.idea
+
+# dask
 dask-worker-space
-.ipynb_checkpoints/
+
+# visual studio
+.vscode