Cleanup actions

.github/pull_request_template.md

@@ -21,8 +21,7 @@
 ## Checklist
 <!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
-- [ ] I have incremented the version number in the `pyproject.toml` file if a new version needs to be pushed to pypi (note that not incrementing the number won't push to pypi and throw an error, but it will update the documentation).
-- [ ] My code follows the code style of this project.
-- [ ] My change requires a change to the documentation.
-- [ ] I have updated the documentation as necessary and compiled locally to ensure it is clean.
-- [ ] I have added tests to cover my changes, and all new and existing tests passed.
+- [ ] I have incremented the version number in the `pyproject.toml` file if a new version needs to be pushed to pypi. *Note that if the number isn't incremented, the package will not be pushed to pypi, which is useful if this PR is only for updating documentation.*
+- [ ] My code follows the code style of this project and I have run `make format` to clean up the code with `black`.
+- [ ] My change requires a change to the documentation. I have updated the documentation as necessary and compiled locally to ensure it is clean.
+- [ ] I have added tests to cover my changes, and all new and existing tests passed (run `make tests`).

.github/workflows/publish_to_pypi.yml

@@ -23,24 +23,34 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: "3.9"
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
+      - name: Install dependencies for version check
+        run: pip install requests packaging build
+      - name: Get local version
+        id: get_local_version
+        run: |
+          local_version=$(grep -m1 version pyproject.toml | sed 's/.*= "\(.*\)"/\1/')
+          echo "local_version=$local_version" >> $GITHUB_OUTPUT
+      - name: Get PyPI version
+        id: get_pypi_version
+        run: |
+          pypi_version=$(python -c "import requests; print(requests.get('https://pypi.org/pypi/cereeberus/json').json()['info']['version'])")
+          echo "pypi_version=$pypi_version" >> $GITHUB_OUTPUT
+      - name: Check if version is incremented
+        id: check_version
+        run: |
+          if python -c "from packaging.version import parse; print(parse('${{ steps.get_local_version.outputs.local_version }}') > parse('${{ steps.get_pypi_version.outputs.pypi_version }}'))" | grep -q True; then
+            echo "publish=true" >> $GITHUB_OUTPUT
+          else
+            echo "publish=false" >> $GITHUB_OUTPUT
       - name: Install package for testing
         run: pip install .
       - name: Run tests
         run: make tests
       - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
+        run: |
+          python -m build --sdist --wheel --outdir dist/
       - name: Publish distribution 📦 to PyPI
+        if: steps.check_version.outputs.publish == 'true'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI }}

.github/workflows/run_tests.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Create venv and install dependencies
+      run: |
+        uv venv
+        source .venv/bin/activate
+        uv pip install -e .
+
+    - name: Run tests
+      run: |
+        source .venv/bin/activate
+        make tests
+

Makefile

@@ -1,16 +1,42 @@
-.PHONY: tests
+lint:
+	@flake8 cereeberus/
+
+format:
+	@black cereeberus/
 
-html:
+.PHONY: docs
+docs:
 	# Running sphinx-build to build html files in build folder.
 	rm -rf docs
 	mkdir -p docs
 	sphinx-build -M html doc_source docs
 	rsync -a docs/html/ docs/
 	rm -rf docs/html
 
+install-editable:
+	@pip install -e .
+
 release:
 	python -m build
 
+.PHONY: tests
 tests:
 	# Running unittests
-	@python -m unittest
+	@python -m unittest
+
+install-requirements:
+	@pip install -r requirements.txt
+
+all: install-requirements install-editable format tests docs 
+
+help: 
+	@echo "Makefile commands:"
+	@echo "  make lint                - Run flake8 linter on the code"
+	@echo "  make format              - Format code using black"
+	@echo "  make install-editable     - Install the package in editable mode for development"
+	@echo "  make docs                - Build the documentation in the docs/ folder"
+	@echo "  make release             - Build the package for release"
+	@echo "  make tests               - Run the unit tests"
+	@echo "  make install-requirements- Install all dependencies from requirements.txt"
+	@echo "  make all       - Run format, tests, docs, and release"
+	@echo "  make help      - Show this help message"

cereeberus/cereeberus/__init__.py

@@ -1,7 +1,16 @@
 __all__ = [
-	'ReebGraph', 'LowerStar', 'computeReeb',
-	'MergeTree', 'MapperGraph', 'EmbeddedGraph', 'Interleave', 'Assignment',
-	'data', 'dist', 'reeb', 'compute'
+    "ReebGraph",
+    "LowerStar",
+    "computeReeb",
+    "MergeTree",
+    "MapperGraph",
+    "EmbeddedGraph",
+    "Interleave",
+    "Assignment",
+    "data",
+    "dist",
+    "reeb",
+    "compute",
 ]
 
 from .reeb.reebgraph import ReebGraph
@@ -12,5 +21,11 @@
 from .reeb.lowerstar import LowerStar
 from .compute.computereeb import computeReeb
 
-# Examples 
-from .data import ex_reebgraphs, ex_mergetrees, ex_mappergraphs, ex_embedgraphs, ex_torus
+# Examples
+from .data import (
+    ex_reebgraphs,
+    ex_mergetrees,
+    ex_mappergraphs,
+    ex_embedgraphs,
+    ex_torus,
+)