Merge pull request #114 from issp-center-dev/develop

v3.2.0

.devcontainer/Dockerfile

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+FROM --platform=linux/x86_64 shinaoka/dcore_dev_triqs3
+
+ENV PYTHONUNBUFFERED=1
+
+
+# Install requirement
+RUN mkdir /tmp/setup
+WORKDIR /tmp/setup
+COPY ./ .
+
+RUN python3 setup.py egg_info
+RUN pip3 install `grep -v '^\[' src/*.egg-info/requires.txt`
+
+# Create non-root user
+ARG NB_USER=vscode
+ARG NB_UID=1000
+RUN useradd -u $NB_UID -m $NB_USER -s /bin/bash && \
+    echo 'vscode ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+USER $NB_USER
+ENV PATH "/home/${NB_USER}/.local/bin:/opt/pomerol2dcore/bin:${PATH}"
+#ENV PYTHONPATH "/home/${NB_USER}/work/src:${PYTONPATH}"
+
+# for vscode
+RUN mkdir /home/${NB_USER}/work
+
+# For DCore
+#ENV DCORE_TRIQS_COMPAT 0
+
+RUN echo "source /opt/triqs/share/triqsvars.sh" >> /home/${NB_USER}/.bashrc

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or the definition README at
+// https://github.com/microsoft/vscode-dev-containers/tree/master/containers/docker-existing-dockerfile
+{
+    "name": "Existing Dockerfile",
+    // Sets the run context to one level up instead of the .devcontainer folder.
+    "context": "..",
+    // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+    "dockerFile": "./Dockerfile",
+    // The optional 'runArgs' property can be used to specify additional runtime arguments.
+    "runArgs": [],
+    // Use 'settings' to set *default* container specific settings.json values on container create.
+    // You can edit these settings after create using File > Preferences > Settings > Remote.
+    // Uncomment the next line if you want to publish any ports.
+    // "appPort": [],
+    // Uncomment the next line to run commands after the container is created - for example installing git.
+    // "postCreateCommand": "apt-get update && apt-get install -y git",
+    // Add the IDs of extensions you want installed when the container is created in the array below.
+    "extensions": [
+      "ms-azuretools.vscode-docker",
+      "mutantdino.resourcemonitor",
+      "shardulm94.trailing-spaces",
+      "cliffordfajardo.hightlight-selections-vscode",
+      "wdawson.better-kill-ring",
+      "oderwat.indent-rainbow",
+      "github.vscode-pull-request-github",
+      "mhutchie.git-graph",
+      "donjayamanne.githistory",
+      "eamodio.gitlens",
+      "bungcip.better-toml",
+      "usernamehw.errorlens",
+      "ms-vscode.live-server",
+      "christian-kohler.path-intellisense",
+      "ms-python.python",
+      "ms-python.vscode-pylance",
+      "lextudio.restructuredtext"
+    ],
+    "remoteUser": "vscode",
+    "workspaceFolder": "/home/vscode/work",
+    "workspaceMount": "src=${localWorkspaceFolder},dst=/home/vscode/work,type=bind",
+  }

.devcontainer_notriqs/Dockerfile

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+FROM python:3.9-slim
+
+ENV PYTHONUNBUFFERED=1
+
+RUN apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+    build-essential \
+    curl \
+    ca-certificates \
+    git \
+    zip \
+    vim \
+    gosu \
+    hdf5-tools \
+    libopenblas-base \
+    libopenblas-dev \
+    libhdf5-103 \
+    libhdf5-dev \
+    libeigen3-dev \
+    cmake \
+    pkg-config \
+    gfortran \
+    openmpi-bin \
+    libopenmpi-dev \
+    sudo \
+    libboost-dev \
+    libboost-mpi-dev \
+    && \
+    apt-get clean && rm -rf /var/cache/apt/archives/* /var/lib/apt/lists/* # clean up
+
+
+# pomerol
+WORKDIR /root
+RUN git clone https://github.com/aeantipov/pomerol.git && cd pomerol && git checkout 7a45b6a8b8254dcbf8 && cd .. && \
+    mkdir pomerol.build && cd pomerol.build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/opt/pomerol -DPOMEROL_COMPLEX_MATRIX_ELEMENTS=ON ../pomerol && \
+    make install && cd .. && rm -rf pomerol.build pomerol
+
+# pomerol2dcore
+WORKDIR /root
+RUN git clone https://github.com/j-otsuki/pomerol2dcore.git && \
+    mkdir pomerol2dcore.build && cd pomerol2dcore.build && \
+    cmake -Dpomerol_DIR=/opt/pomerol -DCMAKE_INSTALL_PREFIX=/opt/pomerol2dcore ../pomerol2dcore && \
+    make install
+
+# Create non-root user
+ARG NB_USER=vscode
+ARG NB_UID=1000
+RUN useradd -u $NB_UID -m $NB_USER -s /bin/bash && \
+    echo 'vscode ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+USER $NB_USER
+ENV PATH "/home/${NB_USER}/.local/bin:/opt/pomerol2dcore/bin:${PATH}"
+ENV PYTHONPATH "/home/${NB_USER}/work/src:${PYTONPATH}"
+
+# for vscode
+RUN mkdir /home/${NB_USER}/work
+
+# For DCore
+ENV DCORE_TRIQS_COMPAT 1
+
+RUN pip3 install scipy, h5py>2.10.0, toml, dcorelib, mpi4py, matplotlib

.devcontainer_notriqs/devcontainer.json

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+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or the definition README at
+// https://github.com/microsoft/vscode-dev-containers/tree/master/containers/docker-existing-dockerfile
+{
+    "name": "Existing Dockerfile",
+    // Sets the run context to one level up instead of the .devcontainer folder.
+    "context": "..",
+    // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+    "dockerFile": "./Dockerfile",
+    // The optional 'runArgs' property can be used to specify additional runtime arguments.
+    "runArgs": [],
+    // Use 'settings' to set *default* container specific settings.json values on container create.
+    // You can edit these settings after create using File > Preferences > Settings > Remote.
+    // Uncomment the next line if you want to publish any ports.
+    // "appPort": [],
+    // Uncomment the next line to run commands after the container is created - for example installing git.
+    // "postCreateCommand": "apt-get update && apt-get install -y git",
+    // Add the IDs of extensions you want installed when the container is created in the array below.
+    "extensions": [
+      "ms-azuretools.vscode-docker",
+      "mutantdino.resourcemonitor",
+      "shardulm94.trailing-spaces",
+      "cliffordfajardo.hightlight-selections-vscode",
+      "wdawson.better-kill-ring",
+      "oderwat.indent-rainbow",
+      "github.vscode-pull-request-github",
+      "mhutchie.git-graph",
+      "donjayamanne.githistory",
+      "eamodio.gitlens",
+      "bungcip.better-toml",
+      "usernamehw.errorlens",
+      "ms-vscode.live-server",
+      "christian-kohler.path-intellisense",
+    "ms-python.python",
+    ],
+   "remoteUser": "vscode",
+   "workspaceFolder": "/home/vscode/work",
+   "workspaceMount": "src=${localWorkspaceFolder},dst=/home/vscode/work,type=bind",
+  }

.github/workflows/ci.yml

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+name: Run all tests
+on: [push, pull_request]
+jobs:
+  all-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo "This job is now running on a ${{ runner.os }} server hosted by GitHub!"
+      - run: echo "The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - run: echo "The ${{ github.repository }} repository has been cloned to the runner."
+      - name: pytest
+        run: |
+          export LOCAL_UID=$(id -u $USER)
+          export LOCAL_GID=$(id -g $USER)
+          echo "LOCAL_UID=${LOCAL_UID}" > .env
+          echo "LOCAL_GID=${LOCAL_GID}" >> .env
+          docker-compose up -d
+      - run: echo "This job's status is ${{ job.status }}."

.github/workflows/deploy_docs.yml

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+name: deploy
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+      - gh_actions  # test branch
+      - '**-autodoc'
+      - '!gh-pages'
+    tags: '*'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+    steps:
+    - name: Inject slug/short variables
+      uses: rlespinasse/[email protected]
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        path: main
+
+    - name: Checkout gh-pages
+      uses: actions/checkout@v2
+      with:
+        ref: gh-pages
+        path: gh-pages
+
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install matplotlib sphinx wild_sphinx_theme
+
+    - name: Build
+      run: |
+        cd ${GITHUB_WORKSPACE}/main/
+        export PYTHONPATH=./src
+        python3 -m dcore.option_tables doc/reference
+        sphinx-build -b html ./doc ./built_doc
+
+    - name: Deploy Configuration
+      run: |
+          mkdir ~/.ssh
+          ssh-keyscan -t rsa github.com >> ~/.ssh/known_hosts
+          echo "${{ secrets.GH_ACTIONS_DEPLOY_KEY }}" > ~/.ssh/id_rsa
+          chmod 400 ~/.ssh/id_rsa
+
+    - name: Push
+      env:
+        GIT_USER: "DCore Developers"
+        GIT_EMAIL: "[email protected]"
+        REF_SLUG: ${{ env.GITHUB_REF_SLUG }}
+      run: |
+          cd ${GITHUB_WORKSPACE}
+          feature_branch=${REF_SLUG%-autodoc}
+          if [ "_${REF_SLUG}" != "_${feature_branch}" ]; then
+            TARGET_NAME=${feature_branch}
+          else
+            TARGET_NAME=${REF_SLUG}
+          fi
+          rm -rf "gh-pages/${TARGET_NAME}"
+          cp -r "main/built_doc" "gh-pages/${TARGET_NAME}"
+          cd gh-pages
+          git config --local user.name "${GIT_USER}"
+          git config --local user.email "${GIT_EMAIL}"
+          git remote set-url origin [email protected]:${GITHUB_REPOSITORY}.git
+          git add ${TARGET_NAME}
+          if git commit -m "Deploy docs to ${TARGET_NAME} by GitHub Actions triggered by ${GITHUB_SHA}"
+          then
+            git push origin gh-pages
+          else
+            echo "Nothing to deploy"
+          fi

.github/workflows/wheel.yml

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+name: Build and upload to PyPI
+
+# Triggered a new tag starting with "v" is pushed
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build dist
+        run: python setup.py sdist bdist_wheel
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: dist
+          path: |
+            dist/*.tar.gz
+            dist/*.whl
+          if-no-files-found: error
+
+  upload_pypi:
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: dist
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          skip_existing: true

.github_scripts/entrypoint.sh

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+#!/bin/bash
+
+USER_ID=${LOCAL_UID:-9001}
+GROUP_ID=${LOCAL_GID:-9001}
+
+echo "Starting with UID : $USER_ID, GID: $GROUP_ID"
+ls -al /home/
+useradd -u $USER_ID -o -m user -s /bin/bash
+groupmod -g $GROUP_ID user
+export HOME=/home/user
+
+cd /var/dcoretest
+#git clean -xdf
+
+pip3 install pytest matplotlib
+pip3 install git+https://github.com/shinaoka/dcorelib.git
+pip3 install .
+
+chown -R user /var/dcoretest
+chgrp -R user /var/dcoretest
+gosu user bash -c 'source /opt/triqs/share/triqsvars.sh;pytest tests/non-mpi/*/*.py'
+gosu user bash -c 'source /opt/triqs/share/triqsvars.sh;pytest tests/non-mpi/test*.py'
+gosu user bash -c 'source /opt/triqs/share/triqsvars.sh;mpirun -np 2 pytest tests/mpi/*/*.py'
+echo "TEST DONE"
+#echo "Use Ctrl+C to stop the container!"