Clean up package boilerplate

.github/workflows/publish_release.yml

@@ -0,0 +1,23 @@
+name: Publish release
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+jobs:
+  publish-release:
+    runs-on: ubuntu-22.04
+    env:
+      VERSION: ${{ github.ref_name }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - run: pip install -e '.[dev]'
+      - run: python -m build
+      - run:
+          twine upload
+          -u __token__
+          -p ${{ secrets.PYPI_API_TOKEN }}
+          dist/*

.github/workflows/tests.yml

@@ -0,0 +1,82 @@
+name: Tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+jobs:
+  ruff:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - run: pip install '.[dev]'
+      - run: ruff check src/ tests/ docs/
+  mypy:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - run: pip install '.[dev]'
+      - run: mypy src/ tests/ docs/
+  ruff-format:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - run: pip install '.[dev]'
+      - run: ruff format --check src/ tests/ docs/
+  pytest:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - uses: actions/cache@v3
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          channel-priority: strict
+          environment-file: environment.yml
+          use-only-tar-bz2: true
+      - run: pip install '.[dev]'
+      - shell: bash -el {0}
+        run: pytest
+      - run: python -m coverage xml
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+  doctest:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - run: pip install '.[dev]'
+      - run: make -C docs doctest

.gitignore

@@ -26,6 +26,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+src/omlt/_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -50,6 +51,8 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+docs/notebooks/data/MNIST
+docs/notebooks/neuralnet/*.keras
 
 # Translations
 *.mo
@@ -70,6 +73,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary
 
 # PyBuilder
 target/

.readthedocs.yml

@@ -16,7 +16,7 @@ build:
 
   tools:
 
-    python: "3.8"
+    python: "3.12"
 
     # You can also specify other tool versions:
 
@@ -58,7 +58,8 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 
 python:
-
   install:
-
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.rst

@@ -142,14 +142,14 @@ Example
 Development
 ===========
 
-OMLT uses `tox` to manage development tasks:
+OMLT uses `just <https://github.com/casey/just>`_ to manage development tasks:
 
-* `tox -av` to list available tasks
-* `tox` to run tests
-* `tox -e lint` to check formatting and code styles
-* `tox -e format` to automatically format files
-* `tox -e docs` to build the documentation
-* `tox -e publish` to publish the package to PyPi
+* ``just`` to list available tasks
+* ``just check`` to run all checks
+* ``just fix`` to apply any auto-fixes
+* ``just dev`` to install development dependencies in your current Python environment
+* ``just dev-gpu`` same as ``dev`` but with GPU support
+* ``just docs`` to build the documentation
 
 Contributors
 ============
@@ -224,4 +224,4 @@ Contributors
 
 .. _zshiqiang: https://github.com/zshiqiang
 .. |zshiqiang| image:: https://avatars.githubusercontent.com/u/91337036?v=4
-   :width: 80px 
+   :width: 80px

docs/Makefile

@@ -1,27 +1,18 @@
-# Makefile for Sphinx documentation
+# Minimal makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+SPHINXOPTS    ?= -W --keep-going
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
-#AUTODOCDIR    = api
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
-endif
-
-.PHONY: help clean Makefile
 
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-clean:
-	rm -rf $(BUILDDIR)/* #$(AUTODOCDIR)
+.PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).