Add support for aiida-core==2.X

Update the codebase to support `aiida-core` v2.X, mostly via: 1. Adding `core.` prefix to entry points. 2. Removing `dict=`/`list=` keyword arguments in the corresponding constructors. 3. Use new `base` name spacing. Since the CI was failing in many ways, this has been tweaked and fixed as well: 1. Updates to the `pre-commit`, switching to the `black` formatter, using `isort` and updating `pylint`. 2. Adapting the Docker build for running the examples to: * use the `2.3.1` version of the `aiida-core` image. * Update RASPA to v2.0.47 * Include the `run_examples.sh` file, where we select the examples to run for the CI. 3. The CI tests are now split in the actual `pytest` tests, and examples. Running the examples via `pytest` seemed quite broken, and this way we can split the two so we can e.g. only run the examples for release PRs. The repository was also cleaned up of several files that no longer served any purpose.
lsmo-epfl · Aug 26, 2023 · fb1860c · fb1860c
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diff --git a/.ci/check_travis_tag.py b/.ci/check_travis_tag.py
diff --git a/.coveragerc b/.coveragerc
diff --git a/.docker/raspa-code.yml b/.docker/raspa-code.yml
@@ -5,4 +5,7 @@ input_plugin: raspa
 on_computer: True
 remote_abs_path: /opt/RASPA2_installed/bin/simulate
 append_text:
-prepend_text: export RASPA2_DIR=/opt/RASPA2_installed/
+prepend_text: |
+  export RASPA_DIR=/opt/RASPA2_installed/
+  export DYLD_LIBRARY_PATH=/opt/RASPA2_installed/lib
+  export LD_LIBRARY_PATH=/opt/RASPA2_installed/lib
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,98 +1,103 @@
-name: Continuous Integration
+name: CI
 
 on: [push, pull_request]
 
 jobs:
 
-  test-plugin:
+  tests:
+    name: Test Suite
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+
+      - name: Check out repository
+        uses: actions/checkout@v3
 
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Run test suite
+        run: pytest
+
+  examples:
+    name: Run examples
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
     steps:
 
-    - uses: actions/checkout@v2
-
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
-
-    # see https://github.com/docker/build-push-action/blob/master/docs/advanced/cache.md#github-cache
-    - name: Cache Docker layers
-      uses: actions/cache@v2
-      with:
-        path: /tmp/.buildx-cache
-        key: ${{ runner.os }}-buildx-${{ github.sha }}
-        restore-keys: |
-          ${{ runner.os }}-buildx-
-
-    - name: Build #and push
-      uses: docker/build-push-action@v2
-      with:
-        context: .
-        push: false
-        load: true
-        tags: aiida_raspa_test
-        cache-from: type=local,src=/tmp/.buildx-cache
-        cache-to: type=local,dest=/tmp/.buildx-cache-new
-
-    # Temp fix
-    # https://github.com/docker/build-push-action/issues/252
-    # https://github.com/moby/buildkit/issues/1896
-    - name: Move cache
-      run: |
-        rm -rf /tmp/.buildx-cache
-        mv /tmp/.buildx-cache-new /tmp/.buildx-cache
-
-    - name: Run tests
-      run: |
-        export DOCKERID=`docker run -d aiida_raspa_test`
-        docker exec --tty $DOCKERID wait-for-services
-        docker logs $DOCKERID
-        docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-raspa/ && py.test --cov aiida_raspa --cov-append .'
-        # see https://docs.github.com/en/actions/reference/environment-variables#default-environment-variables
-        docker exec --tty --user aiida --env-file <(env | grep GITHUB_) -e GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }} $DOCKERID /bin/bash -l -c 'cd /opt/aiida-raspa/ && coveralls --service=github'
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Build #and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: false
+          load: true
+          tags: aiida_raspa_test
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
 
+      - name: Run examples
+        run: |  # Examples stored and copied from .github/workflows/run_examples.sh
+          export DOCKERID=`docker run -d aiida_raspa_test`
+          docker exec --tty $DOCKERID wait-for-services
+          docker logs $DOCKERID
+          docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd $HOME; bash run_examples.sh'
 
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 10
-    strategy:
-      matrix:
-        python-version: [3.8]
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[pre-commit,test,docs]
-        reentry scan
-    - name: Run pre-commit
-      run: |
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit,tests,docs]
+
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
-    strategy:
-      matrix:
-        python-version: [3.8]
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[docs,test]
-        reentry scan
-
-    - name: Build docs
-      run: |
-        cd docs && make
+
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+
+      - name: Build docs
+        run: |
+          make -C docs html
diff --git a/.github/workflows/run_examples.sh b/.github/workflows/run_examples.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+verdi run /opt/aiida-raspa/examples/simple_calculations/example_base.py --submit raspa
+verdi run /opt/aiida-raspa/examples/simple_calculations/example_base_restart.py --previous_calc 4 --submit raspa
+verdi run /opt/aiida-raspa/examples/simple_calculations/example_binary_mixture.py --submit raspa
+verdi run /opt/aiida-raspa/examples/simple_calculations/example_block_pockets_2frameworks_2molecules.py --submit raspa
+verdi run /opt/aiida-raspa/examples/simple_calculations/example_block_pockets_simple.py --submit raspa
diff --git a/.gitignore b/.gitignore
@@ -271,4 +271,6 @@ tags
 [._]*.un~
 
 # End of https://www.gitignore.io/api/vim,linux,macos,python,pycharm
-submit_test
+submit_test
+
+.vscode
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,26 +2,25 @@
 # pre-commit install
 
 repos:
-- repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.30.0
-  hooks:
-  # yapf = yet another python formatter
-  - id: yapf
-    name: yapf
-    types: [python]
-    exclude: >
-      (?x)^(
-          docs/.*|
-      )$
-    args: ['-i']
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
 
-- repo: local
-  hooks:
-  # yapf = yet another python formatter
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.10
 
-  # prospector: collection of linters
-  - id: pylint
-    language: system
-    types: [file, python]
-    name: pylint
-    entry: pylint
+  - repo: local
+    hooks:
+    - id: pylint
+      language: system
+      types: [file, python]
+      name: pylint
+      entry: pylint
diff --git a/.style.yapf b/.style.yapf
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM aiidateam/aiida-core:latest
+FROM aiidateam/aiida-core:2.3.1
 
 # Set HOME, PATH and RASPA_DIR variables:
 ENV PATH="/opt/RASPA2_installed/bin/:${PATH}"
@@ -12,7 +12,7 @@ RUN apt-get clean && rm -rf /var/lib/apt/lists/* && apt-get update && apt-get in
 
 # Download, compile and install RASPA into ~/code folder.
 WORKDIR /opt/
-RUN git clone --depth 1 --branch v2.0.41 https://github.com/iRASPA/RASPA2.git RASPA2
+RUN git clone --depth 1 --branch v2.0.47 https://github.com/iRASPA/RASPA2.git RASPA2
 WORKDIR /opt/RASPA2
 RUN rm -rf autom4te.cache
 RUN mkdir m4
@@ -26,13 +26,21 @@ RUN make install
 
 WORKDIR /opt/
 
+# Grab the raspa data files from the aiida-lsmo-codes repository
+RUN git clone https://github.com/lsmo-epfl/aiida-lsmo-codes.git
+RUN rsync -av /opt/aiida-lsmo-codes/data/raspa/ /opt/RASPA2_installed
+RUN rm -rf aiida-lsmo-codes 
+
 # Install coveralls.
 RUN pip install coveralls
 
 # Copy and install aiida-raspa plugin.
 COPY . aiida-raspa
-RUN pip install ./aiida-raspa[pre-commit,test,docs]
+RUN pip install -e aiida-raspa[pre-commit,tests,docs]
 
 # Install the RASPA code to AiiDA.
 COPY .docker/opt/add-codes.sh /opt/
 COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/50_add-codes.sh
+
+# COPY the examples test script
+COPY .github/workflows/run_examples.sh /home/aiida/run_examples.sh
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -1,5 +1,4 @@
-[![Build Status](https://travis-ci.org/yakutovicha/aiida-raspa.svg?branch=develop)](https://travis-ci.org/yakutovicha/aiida-raspa)
-[![Coverage Status](https://coveralls.io/repos/github/yakutovicha/aiida-raspa/badge.svg?branch=develop)](https://coveralls.io/github/yakutovicha/aiida-raspa?branch=develop)
+![Build Status](https://github.com/lsmo-epfl/aiida-raspa/actions/workflows/ci.yml/badge.svg)
 [![PyPI version](https://badge.fury.io/py/aiida-raspa.svg)](https://badge.fury.io/py/aiida-raspa)
 
 # AiiDA RASPA
@@ -10,7 +9,6 @@ Designed to work with with RASPA 2.0.37 or later.
 # Documentation
 The documentation for this package can be found on [Read the Docs](https://aiida-raspa.readthedocs.io/en/latest/).
 
-
 # Installation
 If you use ``pip``, you can install it as:
 ```

diff --git a/aiida_raspa/__init__.py b/aiida_raspa/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 ##############################################################################
 # Copyright (c), The AiiDA team. All rights reserved.                        #
 # This file is part of the AiiDA code.                                       #