Merge pull request #44 from RangamaniLabUCSD/development

Major updates to infrastructure

.github/CONTRIBUTING.md

@@ -0,0 +1,42 @@
+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into `Mem3dg`.
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/#/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of `Mem3dg` on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the Mem3dg devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+## Description
+Provide a brief description of the PR's purpose here.
+
+## Todos
+Notable points that this PR has either accomplished or will accomplish.
+  - [ ] TODO 1
+
+## Questions
+- [ ] Question1
+
+## Status
+- [ ] Ready to go

.github/workflows/ci.yaml

@@ -0,0 +1,228 @@
+name: Testing and release
+
+on:
+  push:
+    branches:
+      - master
+      - development
+    tags:
+      # The regex: /^v?((\d+)(\.\d+)*)(-?(a|b|c|rc|alpha|beta)([0-9]+)?)?$
+      - 'v[0-9].[0-9]+.[0-9]+*'
+  pull_request:
+    branches: 
+      - master
+      - development
+
+jobs:
+  build_linux:
+    name: Build-Test Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04, ubuntu-20.04]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Setup python libs
+        id: pyexe
+        run: |
+          python3 --version
+          python3 -m pip install pytest
+          py_exe_path=$(which python3)
+          echo ::set-output name=path::$py_exe_path
+
+      - name: Resolve dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libnetcdf-c++4-dev libnetcdf-dev xorg-dev libeigen3-dev pybind11-dev
+
+      - name: Build and test
+        run: |
+          mkdir -p build && cd build;
+          cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.path }} ..
+          cmake --build . --config Release -j 4
+          ctest -C Release -V -j 4
+
+  build_macos:
+    name: Build-Test macOS
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-10.15]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Setup python libs
+        id: pyexe
+        run: |
+          python3 --version
+          python3 -m pip install pytest
+          py_exe_path=$(which python3)
+          echo ::set-output name=path::$py_exe_path
+      
+      - name: Resolve dependencies
+        run: brew install netcdf eigen pybind11
+
+      - name: Build and test
+        run: |
+          mkdir -p build && cd build;
+          cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.path }} ..
+          cmake --build . --config Release -j 4
+          ctest -C Release -V -j 4
+
+
+  build_windows:
+    name: Build-Test Windows
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Setup python libs
+        id: pyexe
+        run: |
+          python --version
+          python -m pip install pytest
+          py_exe_path=$(which python)
+          echo ::set-output name=path::$py_exe_path
+
+      - name: Restore from cache and install vcpkg
+        # Download and build vcpkg, without installing any port. If content is cached already, it is a no-op.
+        uses: lukka/run-vcpkg@v6
+        with:
+          vcpkgGitCommitId: 5568f110b509a9fd90711978a7cb76bae75bb092
+          setupOnly: true
+
+      - name: Download libraries
+        run: $VCPKG_ROOT/vcpkg install netcdf-c:x64-windows netcdf-cxx4:x64-windows eigen3:x64-windows
+
+      - name: Build and test
+        run: |
+          mkdir -p build && cd build;
+          cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.path }} -DCMAKE_TOOLCHAIN_FILE="$VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake" ..
+          cmake --build . --config Release -j 4
+          ctest -C Release -V -j 4
+
+
+  deploy_documentation:
+    name: Deploy documentation to Github pages
+    runs-on: ubuntu-latest
+    # needs: [build_windows, build_linux, build_macos]
+    # if: github.ref == 'refs/heads/master'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        submodules: recursive
+
+    - name: Get Project Version
+      id: version
+      run: |
+        mem3dg_version=$(git describe --tags --always --dirty)
+        echo $mem3dg_version
+        echo ::set-output name=version::$mem3dg_version
+
+    - name: Configure python version
+      uses: actions/setup-python@v2
+      with: 
+        python-version: 3.8
+
+    - name: Setup python libs
+      id: pyexe
+      run: |
+        python3 --version
+        python3 -m pip install -r ./docs/rtd-requirements.txt
+        py_exe_path=$(which python3)
+        echo ::set-output name=path::$py_exe_path
+
+    - name: Resolve dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install libnetcdf-c++4-dev libnetcdf-dev xorg-dev libeigen3-dev pybind11-dev ninja-build doxygen
+
+    - name: Build pymem3dg and install
+      run: |
+        ${{ steps.pyexe.outputs.path }} setup.py install -- -DWITH_NETCDF=ON     
+
+    - name: Build docs
+      run: |
+        mkdir -p build && cd build;
+        cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_MEM3DG_DOCS=ON -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.path }} ..
+        cmake --build . --target mem3dg_doxy_docs --config Release -j 4
+        cmake --build . --target mem3dg_sphinx_docs --config Release -j 4
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        destination_dir: ${{ steps.version.outputs.version }}/cpp
+        publish_dir: ./build/docs/cpp/html
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        destination_dir: ${{ steps.version.outputs.version }}/py
+        publish_dir: ./build/docs/py/html
+
+
+  deploy_to_pypi:
+    name: Deploy to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    needs: [build_windows, build_linux, build_macos]
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        submodules: recursive
+
+    - name: Update python libs
+      run: python -m pip install scikit-build pytest
+
+    - name: Configures source dist
+      run: python setup.py sdist
+
+    - name: Display structure of files
+      run: ls -R
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+
+    # - name: Publish package to TestPyPI
+    #   uses: pypa/gh-action-pypi-publish@release/v1
+    #   with:
+    #     user: __token__
+    #     password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+    #     repository_url: https://test.pypi.org/legacy/

.github/workflows/doc_versioning.yaml

@@ -0,0 +1,31 @@
+name: Tracking Documentation Versions 
+
+on:
+  push:
+    tags:
+      - 'v[0-9].[0-9]+.[0-9]+*'
+
+jobs:
+  check_for_doc_versions:
+    name: Update documented versions
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+        ref: gh-pages
+
+    - name: Get the version
+      id: get_version
+      run: echo ::set-output name=VERSION::$(echo $GITHUB_REF | cut -d / -f 3)
+
+    - run: |
+        echo "- tag: ${{ steps.get_version.outputs.VERSION }}" >> _data/tags.yml
+        cat _data/tags.yml
+
+        git config user.name github-actions
+        git config user.email github-actions@github.com
+        git add _data/tags.yml
+        git commit -m "Auto adding tag ${{ steps.get_version.outputs.VERSION }}"
+        git push

.gitignore

@@ -144,3 +144,12 @@ CMakeSettings.json
 docs/html/
 .polyscope.ini
 _skbuild/
+
+
+pymem3dg/__init__.py
+
+docs/src/_pythonapi/
+docs/src/conf.py
+
+python_src/pymem3dg/include
+python_src/pymem3dg/lib

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "libraries/polyscope"]
 	path = libraries/polyscope
 	url = https://github.com/nmwsharp/polyscope.git
+[submodule "libraries/libigl"]
+	path = libraries/libigl
+	url = https://github.com/libigl/libigl.git

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  image: latest
+
+submodules:
+  include: all
+  recursive: true
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/src/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3
+  install:
+    - requirements: docs/rtd-requirements.txt
+    - method: setuptools
+      path: .