Added repository skeleton

.codecov.yml

@@ -0,0 +1,12 @@
+coverage:
+  ignore:
+    - tests/.*
+  status:
+    project:
+      default:
+        target: 90%
+    patch:
+      default:
+        target: 90%
+
+comment: off

.github/workflows/build.yml

@@ -0,0 +1,24 @@
+# This workflow builds and checks the package for release
+name: Build
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Test build integrity
+      run: tox -e build
+      env:
+        # Use the CPU only version of torch when building/running the code
+        PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu

.github/workflows/docs.yml

@@ -0,0 +1,51 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request:
+    # Check all PR
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: install dependencies
+        run: |
+          python -m pip install tox
+
+      - name: build documentation
+        run: tox -e docs
+        env:
+          # Use the CPU only version of torch when building/running the code
+          PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+
+      # - name: put documentation in the website
+      #   run: |
+      #     git clone https://github.com/$GITHUB_REPOSITORY --branch gh-pages gh-pages
+      #     rm -rf gh-pages/.git
+      #     cd gh-pages
+
+      #     REF_KIND=$(echo $GITHUB_REF | cut -d / -f2)
+      #     if [[ "$REF_KIND" == "tags" ]]; then
+      #         TAG=${GITHUB_REF#refs/tags/}
+      #         mv ../docs/build/html $TAG
+      #     else
+      #         rm -rf latest
+      #         mv ../docs/build/html latest
+      #     fi
+
+      # - name: deploy to gh-pages
+      #   if: github.event_name == 'push'
+      #   uses: peaceiris/actions-gh-pages@v3
+      #   with:
+      #     github_token: ${{ secrets.GITHUB_TOKEN }}
+      #     publish_dir: ./gh-pages/
+      #     force_orphan: true

.github/workflows/documentation-links.yml

@@ -0,0 +1,17 @@
+name: readthedocs/actions
+
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: meshlode

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Lint the code
+      run: tox -e lint

.github/workflows/tests.yml

@@ -0,0 +1,46 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    # Check all PR
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-22.04
+            python-version: "3.8"
+          - os: ubuntu-22.04
+            python-version: "3.11"
+          - os: macos-11
+            python-version: "3.8"
+          - os: macos-11
+            python-version: "3.11"
+          #- os: windows-2019
+          #  python-version: "3.8"
+          #- os: windows-2019
+          #  python-version: "3.11"
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - run: pip install tox
+
+    - name: run Python tests
+      run: tox -e tests
+      env:
+        # Use the CPU only version of torch when building/running the code
+        PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+
+    - name: Upload codecoverage
+      uses: codecov/codecov-action@v3
+      with:
+        files: ./tests/coverage.xml

.gitignore

@@ -1,160 +1,13 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
+*.pyc
+*.ipynb_checkpoints*
+__pycache__
+*.egg-info
+*.swp
+*.swo
+*DS_Store
+*coverage*
 
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
+.tox/
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.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/
-cover/
-
-# 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
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .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
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+docs/src/examples

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools we need
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - cmake
+  tools:
+    python: "3.10"
+    rust: "1.64"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/src/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        # The documentation runs "examples" to produce outputs via sphinx-gallery.
+        - examples