MALA v1.2.0

.github/workflows/cpu-tests.yml

@@ -22,10 +22,10 @@ env:
 jobs:
   build-docker-image-cpu:
     # Build and push temporary Docker image to GitHub's container registry
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set environment variables
         run: |
@@ -37,7 +37,7 @@ jobs:
           echo "IMAGE_REPO=$IMAGE_REPO"
 
       - name: Restore cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         id: cache-docker
         with:
           path: ${{ env.DOCKER_CACHE_PATH }}
@@ -47,17 +47,17 @@ jobs:
         id: check_file
         run: |
           if [[ -f "$DOCKER_CACHE_PATH/docker-image.tar.gz" ]]; then
-            echo '::set-output name=file_exists::true'
+            echo "FILE_EXISTS=true" >> $GITHUB_OUTPUT
           else
-            echo '::set-output name=file_exists::false'
+            echo "FILE_EXISTS=false" >> $GITHUB_OUTPUT
           fi
 
       - name: Pull latest image from container registry
         run: docker pull $IMAGE_REPO/$IMAGE_NAME || true
 
       - name: Build temporary Docker image
         run: |
-          if [[ "${{ steps.check_file.outputs.file_exists }}" == 'true' ]]
+          if [[ "${{ steps.check_file.outputs.FILE_EXISTS }}" == 'true' ]]
           then
             docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz
             CACHE=$IMAGE_NAME:$GITHUB_RUN_ID
@@ -114,7 +114,7 @@ jobs:
     steps:
       - name: "Prepare environment: Restore cache"
         if: env.DOCKER_TAG != 'latest'
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         id: cache-docker
         with:
           path: ${{ env.DOCKER_CACHE_PATH }}
@@ -145,7 +145,7 @@ jobs:
           [[ $(docker inspect --format '{{json .State.Running}}' mala-cpu) == 'true' ]]
 
       - name: Check out repository (mala)
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install mala package
         # Exec all commands inside the mala-cpu container
@@ -168,20 +168,20 @@ jobs:
           diff env_1.yml env_2.yml
 
       - name: Check out repository (data)
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: mala-project/test-data
           path: mala_data
-          ref: v1.3.0
-          lfs: false
+          ref: v1.7.0
+          lfs: true
 
       - name: Test mala
         shell: 'bash -c "docker exec -i mala-cpu bash < {0}"'
         run: MALA_DATA_REPO=$(pwd)/mala_data pytest -m "not examples" --disable-warnings
 
   retag-docker-image-cpu:
     needs: [cpu-tests, build-docker-image-cpu]
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     permissions:
       packages: write
     env:
@@ -194,11 +194,11 @@ jobs:
       || startsWith(github.ref, 'refs/tags/')
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: "Prepare environment: Restore cache"
         if: env.DOCKER_TAG != 'latest'
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         id: cache-docker
         with:
           path: ${{ env.DOCKER_CACHE_PATH }}

.github/workflows/gh-pages.yml

@@ -11,13 +11,13 @@ on:
 
 jobs:
   test-docstrings:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.8'
 
@@ -29,19 +29,19 @@ jobs:
 
       - name: Check docstrings
          # Ignoring the cached_properties because pydocstyle (sometimes?) treats them as functions.
-        run: pydocstyle --convention=numpy --ignore-decorators=cached_property mala
+        run: pydocstyle --convention=numpy --ignore-decorators=[cached_property,property] mala
 
   build-and-deploy-pages:
     needs: test-docstrings
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0  # 0 fetches complete history and tags
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.8'
 

.github/workflows/mirror-to-casus.yml

@@ -4,13 +4,15 @@ on: [push, delete]
 
 jobs:
   mirror-to-CASUS:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - name: mirror-repository
-      uses: spyoungtech/mirror-action@v0.4.0
+      uses: spyoungtech/mirror-action@v0.6.0
       with:
-        REMOTE: [email protected]:casus/mala.git
+        REMOTE: 'ssh://[email protected]/casus/mala.git'
         GIT_SSH_PRIVATE_KEY: ${{ secrets.GIT_SSH_KEY }}
         GIT_SSH_NO_VERIFY_HOST: "true"
         DEBUG: "true"

.github/workflows/publish-to-pypi.yml

@@ -14,13 +14,13 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.8'
 

.gitignore

@@ -173,3 +173,9 @@ cython_debug/
 
 # Git files
 .gitconfig
+
+# HDF5 files
+*.h5
+
+*.zip
+*~

CITATION.cff

@@ -2,6 +2,12 @@
 cff-version: 1.1.0
 message: "If you use this software, please cite it using these metadata."
 authors:
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Brzoza
+    given-names: Bartosz
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Callow
+    given-names: Timothy J.
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Cangi
     given-names: Attila
@@ -10,38 +16,71 @@ authors:
     family-names: Ellis
     given-names: J. Austin
     orcid: https://orcid.org/0000-0002-9901-102X
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Faruk
+    given-names: Omar
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Fiedler
     given-names: Lenz
     orcid: https://orcid.org/0000-0002-8311-0613
+  - affiliation: "Sandia National Laboratories (SNL)"
+    family-names: Fox
+    given-names: James S.
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Hoffmann
+    given-names: Nils
+  - affiliation: "Sandia National Laboratories (SNL)"
+    family-names: Miller
+    given-names: Kyle D.
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Kotik
     given-names: Daniel
     orcid: https://orcid.org/0000-0001-8735-3199
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Kulkarni
+    given-names: Somashekar
   - affiliation: "Sandia National Laboratories (SNL)"
     family-names: Modine
     given-names: Normand A.
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Mohammed
+    given-names: Parvez
   - affiliation: "Oak Ridge National Laboratory (ORNL)"
     family-names: Oles
     given-names: Vladyslav
   - affiliation: "Sandia National Laboratories (SNL)"
     family-names: Popoola
     given-names: Gabriel A.
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Pöschel
+    given-names: Franz
   - affiliation: "Sandia National Laboratories (SNL)"
     family-names: Rajamanickam
-    given-names: Siva
+    given-names: Sivasankaran
     orcid: https://orcid.org/0000-0002-5854-409X
+  - affiliation: "Nvidia Corporation"
+    family-names: Romero
+    given-names: Josh
   - affiliation: "Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Schmerler
     given-names: Steve
     orcid: https://orcid.org/0000-0003-1354-0578
   - affiliation: "Sandia National Laboratories (SNL)"
     family-names: Stephens
     given-names: J. Adam
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Tahmasbi
+    given-names: Hossein
   - affiliation: "Sandia National Laboratories (SNL)"
     family-names: Thompson
     given-names: Aidan P.
     orcid: https://orcid.org/0000-0002-0324-9114
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Verma
+    given-names: Sneha
+  - affiliation: "Sandia National Laboratories (SNL)"
+    family-names: Vogel
+    given-names: D. Jon
 
 
 date-released: 2022-10-18

Dockerfile

@@ -1,19 +1,28 @@
-FROM continuumio/miniconda3:4.9.2
-MAINTAINER Daniel Kotik <[email protected]>
+FROM continuumio/miniconda3:22.11.1
+LABEL maintainer="[email protected]"
 
-# Update the image to the latest packages
-RUN apt-get --allow-releaseinfo-change update && apt-get upgrade -y
-
-RUN apt-get install --no-install-recommends -y build-essential libz-dev swig git-lfs cmake
-RUN apt-get clean && rm -rf /var/lib/apt/lists/*
+# Update the image and install essential packages
+RUN apt-get --allow-releaseinfo-change update && apt-get upgrade -y && \
+    apt-get install --no-install-recommends -y \
+    build-essential \
+    libz-dev \
+    swig \
+    git-lfs \
+    cmake && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Choose 'cpu' or 'gpu'
 ARG DEVICE=cpu
 COPY install/mala_${DEVICE}_environment.yml .
 RUN conda env create -f mala_${DEVICE}_environment.yml && rm -rf /opt/conda/pkgs/*
 
 # Install optional MALA dependencies into Conda environment with pip
-RUN /opt/conda/envs/mala-${DEVICE}/bin/pip install --no-input --no-cache-dir pytest oapackage==2.6.8 pqkmeans
+RUN /opt/conda/envs/mala-${DEVICE}/bin/pip install --no-input --no-cache-dir \
+    pytest \
+    oapackage==2.6.8 \
+    openpmd-api==0.15.1 \
+    pqkmeans
 
 RUN echo "source activate mala-${DEVICE}" > ~/.bashrc
 ENV PATH /opt/conda/envs/mala-${DEVICE}/bin:$PATH
+

README.md

@@ -25,47 +25,24 @@ This repository is structured as follows:
 
 > **WARNING**: Even if you install MALA via PyPI, please consult the full installation instructions afterwards. External modules (like the QuantumESPRESSO bindings) are not distributed via PyPI!
 
-Please refer to [Installation of MALA](docs/source/install/README.md).
+Please refer to [Installation of MALA](docs/source/install/installing_mala.rst).
 
 ## Running
 
 You can familiarize yourself with the usage of this package by running
 the examples in the `example/` folder.
 
-## Institutions
-### Founding Institutions
+## Contributors
+
+MALA is jointly maintained by 
 
 - [Sandia National Laboratories](https://www.sandia.gov/) (SNL), USA.
+    - Scientific supervisor: Sivasankaran Rajamanickam, code maintenance: 
+Jon Vogel
 - [Center for Advanced Systems Understanding](https://www.casus.science/) (CASUS), Germany.
+    - Scientific supervisor: Attila Cangi, code maintenance: Lenz Fiedler
 
-### Contributing Institutions
-
-- [Oak Ridge National Laboratory](https://www.ornl.gov/) (ORNL), USA
-
-## Developers
-### Scientific Supervision
-- Attila Cangi (CASUS)
-- Siva Rajamanickam (SNL)
-
-### Core Developers
-
-- Austin Ellis (ORNL)
-- Lenz Fiedler (CASUS)
-- Daniel Kotik (CASUS)
-- Normand Modine (SNL)
-- Vladyslav Oles (ORNL)
-- Gabriel Popoola (SNL)
-- Aidan Thompson (SNL)
-- Steve Schmerler (HZDR)
-- Adam Stephens (SNL)
-
-### Contributors
-
-- Sneha Verma (CASUS)
-- Parvez Mohammed (CASUS)
-- Nils Hoffmann (CASUS)
-- Omar Faruk (CASUS)
-- Somashekhar Kulkarni (CASUS)
+A full list of contributors can be found [here](docs/source/CONTRIBUTE.md).
 
 ## Citing MALA
 

docs/requirements.txt

@@ -3,3 +3,4 @@ Sphinx==4.5.*
 sphinx-rtd-theme==1.0.0
 myst-parser==0.17.2
 sphinx-markdown-tables==0.0.17
+sphinx-copybutton==0.5.1