Add support for aiida-core==2.X

.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

.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

.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

.gitignore

@@ -271,4 +271,6 @@ tags
 [._]*.un~
 
 # End of https://www.gitignore.io/api/vim,linux,macos,python,pycharm
-submit_test
+submit_test
+
+.vscode

.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

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

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:
 ```

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.                                       #