initial commit with docs, tests, and speedups

.github/workflows/actions.yml

@@ -1,43 +1,44 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# Run the aframe test suite on pushes and pull requests to main.
 
 name: Tests
 
-# Whenever there is a pull request (PR) or push to the "main" branch, the jobs specified below will run.
-on: 
+on:
   push:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
 
-# Here, we specify the automatic cloud based testing that will be ran on pushes/PRs to "main"
 jobs:
-  build:
-
-    # The tests will run on ubuntu with python versions 3.8, 3.9, and 3.10.
-    # Add other OSes like windows and macOS if needed as well as other Python versions  
+  test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        # the Python versions CSDL_alpha is tested on
+        python-version: ["3.9", "3.10"]
 
     steps:
-      # The steps here are essentially command-line arguments that will be ran on the cloud with the above configurations  
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: pyproject.toml
+
+    # virtual display for the off-screen PyVista plotting test
+    - name: Set up headless display
+      uses: pyvista/setup-headless-display-action@v3
 
-      # Here we install the package of this repositories as well as other required packages 
     - name: Install dependencies
-      run: | 
+      run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install -e .
+        # CSDL_alpha is not on PyPI
+        pip install git+https://github.com/LSDOlab/CSDL_alpha.git
+        # optional: runs the JAX backend test (tests/test_jax.py)
+        pip install jax
+        pip install -e ".[dev,plot]"
 
-      # Finally, we run the package unit-tests on the specified OS and python versions.
     - name: Test with pytest
-      run: |
-        pytest
+      run: pytest

.github/workflows/docs.yml

@@ -0,0 +1,62 @@
+# Build the pdoc API documentation on every push and pull request, and publish
+# it to GitHub Pages on pushes to main (https://lsdolab.github.io/aframe/).
+
+name: Docs
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+# one Pages deployment at a time; don't cancel a deployment in progress
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: pyproject.toml
+
+    # PyVista is imported to document the plotting helpers
+    - name: Set up headless display
+      uses: pyvista/setup-headless-display-action@v3
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # CSDL_alpha is not on PyPI
+        pip install git+https://github.com/LSDOlab/CSDL_alpha.git
+        pip install -e ".[plot,docs]"
+
+    - name: Build documentation
+      run: python docs/make_docs.py -o site
+
+    - uses: actions/upload-pages-artifact@v3
+      with:
+        path: site
+
+  deploy:
+    # only the main branch is published
+    if: github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+    - id: deployment
+      uses: actions/deploy-pages@v4

.gitignore

@@ -1,144 +1,52 @@
-# Byte-compiled / optimized / DLL files
+# Python bytecode
 __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
+# Packaging / build artifacts
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
 wheels/
-pip-wheel-metadata/
-share/python-wheels/
 *.egg-info/
-.installed.cfg
+.eggs/
 *.egg
-MANIFEST
-
-# 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/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
+pip-wheel-metadata/
 
-# Environments
+# Virtual environments
 .env
-.venv
+.venv/
 env/
 venv/
 ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
 
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
+# Test, coverage and type-checker caches
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+.tox/
+.nox/
+.hypothesis/
 .mypy_cache/
 .dmypy.json
 dmypy.json
-
-# Pyre type checker
 .pyre/
+.ruff_cache/
 
-.DS_Store
-
-# Directory with files generated before building documentation
-_temp
-
-# Sphinx
-top_level_req.in
-top_level_req.txt
-_autosummary
-_conf_master.py
+# Jupyter
+.ipynb_checkpoints/
 
+# Documentation builds
+docs/_build/
+/site
 
+# Solver / optimizer output (e.g. csdl JaxSimulator saves, modopt records)
+*.hdf5
+*.h5
 
-.vscode/
+# Editors and OS files
+.vscode/
+.idea/
+*.swp
+.DS_Store
+Thumbs.db