switch to aiida-testing

run yapf for all and remove py2 compatibility

fix tests but qeq still failing

fix examples

put back output parsing

.github/check_version.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+"""Check that version numbers match.
+
+Check version number in setup.json and aiida_qeq/__init__.py and make sure
+they match.
+"""
+import os
+import json
+import sys
+
+THIS_PATH = os.path.split(os.path.realpath(__file__))[0]
+
+# Get content of setup.json
+SETUP_FNAME = 'setup.json'
+SETUP_PATH = os.path.join(THIS_PATH, os.pardir, SETUP_FNAME)
+with open(SETUP_PATH) as f:
+    SETUP_CONTENT = json.load(f)
+
+# Get version from python package
+sys.path.insert(0, os.path.join(THIS_PATH, os.pardir))
+import aiida_qeq  # pylint: disable=wrong-import-position
+VERSION = aiida_qeq.__version__
+
+if VERSION != SETUP_CONTENT['version']:
+    print('version number mismatch detected:')
+    print("version number in '{}': {}".format(SETUP_FNAME, SETUP_CONTENT['version']))
+    print("version number in '{}/__init__.py': {}".format('aiida_qeq', VERSION))
+    sys.exit(1)
+
+# Overwrite version in setup.json
+#SETUP_CONTENT['version'] = VERSION
+#with open(SETUP_PATH, 'w') as f:
+#	json.dump(SETUP_CONTENT, f, indent=4, sort_keys=True)

.github/workflows/ci.yml

@@ -0,0 +1,85 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: [3.7]
+        backend: ['django']
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        wget -O - "https://github.com/rabbitmq/signing-keys/releases/download/2.0/rabbitmq-release-signing-key.asc" | sudo apt-key add -
+        echo 'deb https://dl.bintray.com/rabbitmq-erlang/debian bionic erlang' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
+        sudo apt update
+        sudo apt install postgresql-10 rabbitmq-server graphviz
+        sudo systemctl status rabbitmq-server.service
+
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[testing,cp2k]
+        reentry scan -r aiida
+
+    - name: Run test suite
+      env:
+        AIIDA_TEST_BACKEND: ${{ matrix.backend }}
+        PYTEST_ADDOPTS: "--cov-report xml --cov-append"
+      run: py.test
+
+    - name: Upload coverage report
+      if: github.repository == 'lsmo-epfl/aiida-qeq'
+      uses: codecov/codecov-action@v1
+      with:
+        name: aiida-ddec
+        file: ./coverage.xml
+        fail_ci_if_error: true
+
+#  docs:
+#    runs-on: ubuntu-latest
+#    timeout-minutes: 15
+#    steps:
+#    - uses: actions/checkout@v1
+#    - name: Set up Python 3.7
+#      uses: actions/setup-python@v1
+#      with:
+#        python-version: 3.7
+#    - name: Install python dependencies
+#      run: |
+#        pip install --upgrade pip
+#        pip install -e .[docs]
+#        reentry scan -r aiida
+#    - name: Build docs
+#      run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[pre-commit,testing]
+        reentry scan -r aiida
+    - name: Run pre-commit
+      run: |
+        pre-commit install
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

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

@@ -0,0 +1,40 @@
+name: Publish on PyPI
+
+on:
+  push:
+    tags:
+      # After vMajor.Minor.Patch _anything_ is allowed (without "/") !
+    - v[0-9]+.[0-9]+.[0-9]+*
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    if: github.repository == 'lsmo-epfl/aiida-qeq' && startsWith(github.ref, 'refs/tags/v')
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Upgrade setuptools and install package
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -e .
+
+    - name: Assert package version
+      env:
+        TAG_VERSION: ${{ github.ref }}
+      run: python ./.github/check_version.py
+
+    - name: Build source distribution
+      run: python ./setup.py sdist
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_token }}

.gitignore

@@ -11,3 +11,4 @@ dist/
 build/
 .vscode
 .pytest_cache/
+pip-wheel-metadata/

.pre-commit-config.yaml

@@ -51,3 +51,9 @@
     entry: pylint
     types: [python]
     language: system
+
+  - id: version-number
+    name: Check version numbers
+    entry: python ./.github/check_version.py
+    language: system
+    files: '^(setup.json)|(aiida_qeq/__init__.py)'

README.md

@@ -95,11 +95,20 @@ verdi process list -a  # check status of calculation
 ## Development
 
 ```shell
-git clone https://github.com/ltalirz/aiida-qeq .
+git clone https://github.com/lsmo-epfl/aiida-qeq
 cd aiida-qeq
-pip install -e .[pre-commit,testing]
-pre-commit install  # enable pre-commit hooks
-pytest              # run unit tests
+pip install -e .['pre-commit','testing']
+pytest
+```
+
+If you are changing the inputs of existing tests or need to regenerate test data, place an `.aiida-testing-config.yml`
+file in your repository that points to the required simulation codes:
+```yaml
+---
+mock_code:
+  # code-label: absolute path
+  egulp-fc4d7b7: /path/to/cp2k.sopt
+  eqeq-6490320: /path/to/Chargemol_09_02_2017_linux_serial
 ```
 
 ## License

aiida_qeq/__init__.py

@@ -1,7 +1,8 @@
+# -*- coding: utf-8 -*-
 """
 aiida_qeq
 
 AiiDA plugin for computing electronic charges on atoms using equilibration-type models (QEq, EQEq, ...).
 """
 
-__version__ = "1.0.0a1"
+__version__ = '1.0.0a1'

aiida_qeq/calculations/__init__.py

@@ -1,6 +1,6 @@
+# -*- coding: utf-8 -*-
 """
 Calculations provided by aiida_qeq.
 
 Register calculations via the "aiida.calculations" entry point in setup.json.
 """
-from __future__ import absolute_import