Add aiida-core==2.X and Python 3.8-3.11 support

Some small changes here and there to fully switch to `aiida-core==2.X`:

1. Added `core.` prefix where needed.
2. Removal of superfluous `dict` keyword argument.

The package metadata is now also all moved to `pyproject.toml`, and support is
extended to Python v3.8-3.11.

Other changes mainly involve switching to `black`, using `isort` and updating
`pylint` to a more recent version.

.github/workflows/build.yml

@@ -4,41 +4,14 @@ on: [push, pull_request]
 
 jobs:
 
-  #compile:
-  #  runs-on: ubuntu-latest
-  #  timeout-minutes: 30
-  #  steps:
-  #  - uses: actions/checkout@v1
-  #  - name: Get network binary from cache (or start caching)
-  #    id: zeopp-cache
-  #    uses: actions/cache@v1
-  #    with:
-  #      path: ./zeoplusplus/bin
-  #      key: zeopp
-  #  - name: Install Zeo++
-  #    if: steps.zeopp-cache.outputs.cache-hit != 'true'
-  #    run: |
-  #      git clone https://github.com/lsmo-epfl/zeopp-lsmo -b master zeoplusplus
-  #      cd zeoplusplus
-  #      wget https://gitlab.com/libeigen/eigen/-/archive/3.2.7/eigen-3.2.7.tar.bz2
-  #      tar xf eigen-3.2.7.tar.bz2
-  #      cd voro++/src
-  #      make
-  #      cd ../..
-  #      make
-  #      mkdir bin
-  #      cp network bin
-
   tests:
+    strategy:
+      matrix:
+        python: ['3.8', '3.9', '3.10', '3.11']
     runs-on: ubuntu-latest
     timeout-minutes: 15
     continue-on-error: true
 
-    strategy:
-      matrix:
-        python-version: [3.8]
-        aiida-version: ['stable', 'develop']
-
     services:
       postgres:
         image: postgres:12
@@ -68,53 +41,32 @@ jobs:
         ls /usr/share/miniconda/bin
         echo /usr/share/miniconda/bin >> $GITHUB_PATH
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v3
       with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install aiida develop version
-      run: |
-        pip install git+git://github.com/aiidateam/aiida-core
-      if: ${{ matrix.aiida-version == 'develop' }}
+        python-version: ${{ matrix.python }}
 
     - name: Install python dependencies
       run: |
-        pip install -e .[testing]
-
-    - name: Populate reentry cache
-      run: |
-        reentry scan -r aiida
-      if: ${{ matrix.aiida-version == 'stable' }}
+        pip install -e .[tests]
 
     - name: Run pytest
       run: |
-        pytest --cov-report=xml --cov=./aiida_zeopp
-    - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
-      with:
-        token: ${{secrets.CODECOV_TOKEN}}
-        file: ./coverage.xml
-      continue-on-error: ${{ matrix.aiida-version == 'develop' }}  # allow failures against develop
-
+        pytest 
 
   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
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.10'
     - name: Install python dependencies
       run: |
         pip install --upgrade pip
-        pip install -e .[pre-commit,testing]
-        reentry scan -r aiida
+        pip install -e .[pre-commit,tests]
     - name: Run pre-commit
       run: |
         pre-commit install

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

@@ -9,32 +9,22 @@ on:
 jobs:
   publish:
     runs-on: ubuntu-latest
-    if: github.repository == 'ltalirz/aiida-zeopp' && startsWith(github.ref, 'refs/tags/v')
+    if: github.repository == 'lsmo-epfl/aiida-zeopp' && 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
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
       with:
-        python-version: 3.7
+        python-version: '3.10'
 
-    - name: Upgrade setuptools and install package
-      run: |
-        python -m pip install --upgrade pip setuptools
-        python -m pip install -e .
+    - name: Install flit
+      run: pip install flit~=3.4
 
-    - name: Assert package version
+    - name: Build and publish
+      run: flit publish
       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 }}
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD: ${{ secrets.pypi_token }}

.pre-commit-config.yaml

@@ -1,44 +1,34 @@
 # # Install pre-commit hooks via
 # pre-commit install
 
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.2.3
-  hooks:
-  - id: trailing-whitespace
-    types: [python]
-  - id: double-quote-string-fixer
-    types: [python]
+repos:
 
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
 
-- 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/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
 
-- repo: local
-  hooks:
+  - repo: local
+    hooks:
 
-  # prospector: collection of linters
-  - id: pylint
-    name: pylint
-    entry: pylint
-    types: [python]
-    language: system
-    exclude: &exclude_files >
-      (?x)^(
-        .*/test_.*.py
-      )$
-
-  - id: version-number
-    name: Check version numbers
-    entry: python ./.github/check_version.py
-    language: system
-    files: '^(setup.json)|(aiida_zeopp/__init__.py)'
+    # prospector: collection of linters
+    - id: pylint
+      name: pylint
+      entry: pylint
+      types: [python]
+      language: system
+      exclude: &exclude_files >
+        (?x)^(
+          .*/test_.*.py
+        )$

aiida_zeopp/__init__.py

@@ -3,9 +3,10 @@
 
 """
 
-__version__ = '1.1.2'
+__version__ = "1.1.2"
 
 # disable psycopg2 warning
 import warnings
-warnings.filterwarnings('ignore', category=UserWarning, module='psycopg2')
-warnings.filterwarnings('ignore', category=UserWarning, module='pymatgen')
+
+warnings.filterwarnings("ignore", category=UserWarning, module="psycopg2")
+warnings.filterwarnings("ignore", category=UserWarning, module="pymatgen")