Merge pull request #145 from mala-project/develop

Create release for Aluminium PRB article

.github/workflows/cpu-tests.yml

@@ -0,0 +1,97 @@
+name: CPU
+
+on:
+  pull_request:
+    branches:
+      - master
+      - develop
+
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+jobs:
+  # Build and push Docker image to GitHub Packages.
+  build-docker-image-cpu:
+    runs-on: ubuntu-18.04
+    env:
+      IMAGE_NAME: mala_conda_cpu
+    permissions:
+      packages: write
+      contents: read
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Log into registry
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+
+      - name: Set environment variables
+        run: |
+          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Create environment variable to which all subsequent actions in this job have access
+          echo "IMAGE_ID=$IMAGE_ID" >> $GITHUB_ENV
+
+      - name: Pull image from registry
+        run: docker pull $IMAGE_ID || true
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag $IMAGE_NAME --cache-from=$IMAGE_ID --build-arg DEVICE=cpu --label "runnumber=${GITHUB_RUN_ID}"
+
+      - name: Push image
+        run: |
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "develop" ] && VERSION=latest
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
+
+  cpu-tests:
+    needs: build-docker-image-cpu
+    runs-on: ubuntu-18.04
+    container:
+      image: ghcr.io/mala-project/mala_conda_cpu:latest
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Check out repository (mala)
+        uses: actions/checkout@v2
+
+      - name: Install mala package
+        run: pip --no-cache-dir install -e .
+
+      - name: Check out repository (data)
+        uses: actions/checkout@v2
+        with:
+          repository: mala-project/test-data
+          token: ${{ secrets.ACCESS_TOKEN }}
+          path: mala_data
+          ref: v0.1.0
+          lfs: false
+
+      - name: Data setup
+        shell: bash
+        run: |
+          cd mala_data
+          chmod +x ../install/data_repo_link/link_data_repo.sh
+          ../install/data_repo_link/link_data_repo.sh `pwd`
+
+      - name: Test basic functions
+        run: python test/mala_tests.py
+
+      - name: Test workflow
+        run: python examples/ex99_verify_all_examples.py

.github/workflows/gh-pages.yml

@@ -0,0 +1,64 @@
+name: docs
+
+on:
+  pull_request:
+    branches:
+      - master
+      - develop
+  push:
+    branches:
+      - develop
+
+jobs:
+  test-docstrings:
+    runs-on: ubuntu-18.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        run: python3 -m pip install --upgrade pip
+
+      - name: Install dependencies
+        run: pip install -qU pydocstyle
+
+      - name: Check docstrings
+        run: pydocstyle --convention=numpy mala
+
+  deploy-pages:
+    needs: test-docstrings
+    runs-on: ubuntu-18.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # 0 fetches complete history and tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        run: python3 -m pip install --upgrade pip
+
+      - name: Install dependencies
+        run: |
+          pip install -q -r docs/requirements.txt
+
+      - name: Build API and docs
+        run: |
+          sphinx-apidoc -o docs/source/api mala
+          sphinx-build -W --keep-going -b html -d docs/_build/doctrees docs/source docs/_build/html
+          mv -v docs/_build/html public
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public

.gitignore

@@ -156,3 +156,8 @@ cython_debug/
 *.pth
 /install/data_repo_link/data_repo_path.py
 /test/data_repo_path.py
+
+
+# JupyterNotebooks
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*

Copyright.txt

@@ -0,0 +1,18 @@
+ ************************************************************************
+
+                        MALA v. 0.1.0
+
+ Under the terms of Contract DE-NA0003525 with NTESS,
+ the U.S. Government retains certain rights in this software.
+
+ Questions? Contact Attila Cangi ([email protected])
+                    Siva Rajamanickam ([email protected])
+
+ ************************************************************************
+
+Copyright 2021 National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.
+
+Copyright 2021, (in alphabetical order) Attila Cangi, J. Austin Ellis, Lenz Fiedler, Daniel Kotik, Normand Modine, Sivasankaran Rajamanickam, Steve Schmerler, Aidan Thompson 
+
+All rights reserved.
+

Dockerfile

@@ -1,14 +1,16 @@
 FROM continuumio/miniconda3:4.9.2
 
+# Choose 'cpu' or 'gpu'
+ARG DEVICE=cpu
+
 # Update the image to the latest packages
 RUN apt-get update && apt-get upgrade -y
 
-RUN apt-get install --no-install-recommends -y build-essential \
-                                               libz-dev swig git-lfs && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN apt-get install --no-install-recommends -y build-essential libz-dev swig git-lfs
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
 
-COPY install/mala_cpu_environment.yml .
-RUN conda env create -q -f mala_cpu_environment.yml && rm -rf /opt/conda/pkgs/*
+COPY install/mala_${DEVICE}_environment.yml .
+RUN conda env create -f mala_${DEVICE}_environment.yml && rm -rf /opt/conda/pkgs/*
 
-RUN echo "source activate mala-cpu" > ~/.bashrc
-ENV PATH /opt/conda/envs/mala-cpu/bin:$PATH
+RUN echo "source activate mala-${DEVICE}" > ~/.bashrc
+ENV PATH /opt/conda/envs/mala-${DEVICE}/bin:$PATH

LICENSE

@@ -0,0 +1,26 @@
+BSD 3-Clause License
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.