Update repo config against aiida-core v2.5

.github/workflows/ci.yml

@@ -3,83 +3,36 @@ name: ci
 on: [push, pull_request]
 
 jobs:
-
-  tests:
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    strategy:
-      matrix:
-        python-version: ["3.8"]
-        aiida-version: ["stable"]
-
-    services:
-      postgres:
-        image: postgres:10
-        env:
-          POSTGRES_DB: test_aiida
-          POSTGRES_PASSWORD: ''
-          POSTGRES_HOST_AUTH_METHOD: trust
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-          - 5432:5432
-      rabbitmq:
-        image: rabbitmq:latest
-        ports:
-          - 5672:5672
-
-    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 .[testing]
-
-    - name: Run test suite
-      env:
-        # show timings of tests
-        PYTEST_ADDOPTS: "--durations=0"
-      run: pytest --cov aiida_quantum_transport --cov-append .
-
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: "3.8"
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[docs]
-    - name: Build docs
-      run: cd docs && make
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+      - name: Build docs
+        run: cd docs && make
 
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: "3.8"
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[pre-commit,docs,testing]
-    - name: Run pre-commit
-      run: |
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit,docs,testing]
+      - 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

@@ -12,22 +12,22 @@ jobs:
     if: github.repository == 'edan-bainglass/aiida-quantum-transport' && startsWith(github.ref, 'refs/tags/v')
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
+      - name: Checkout repository
+        uses: actions/checkout@v2
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.8'
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.10"
 
-    - name: Install flit
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flit~=3.4
+      - name: Install flit
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flit~=3.4
 
-    - name: Build and publish
-      run: |
-        flit publish
-      env:
-        FLIT_USERNAME: __token__
-        FLIT_PASSWORD:  ${{ secrets.pypi_token }}
+      - name: Build and publish
+        run: |
+          flit publish
+        env:
+          FLIT_USERNAME: __token__
+          FLIT_PASSWORD: ${{ secrets.pypi_token }}

.pre-commit-config.yaml

@@ -1,39 +1,67 @@
 # Install pre-commit hooks via:
 # pre-commit install
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-    - id: end-of-file-fixer
-    - id: mixed-line-ending
-    - id: trailing-whitespace
-    - id: check-json
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: check-json
+      - id: fix-encoding-pragma
+        args: [--remove]
+      - id: mixed-line-ending
+        args: [--fix=lf]
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-  - id: pyupgrade
-    args: ["--py37-plus"]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
 
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
+  - repo: https://github.com/ikamensh/flynt/
+    rev: 1.0.1
+    hooks:
+      - id: flynt
+        args: [--line-length=120, --fail-on-change]
 
-- repo: https://github.com/psf/black
-  rev: 22.12.0
-  hooks:
-    - id: black
+  - repo: https://github.com/executablebooks/mdformat
+    rev: "0.7.16"
+    hooks:
+      - id: mdformat
 
-- repo: local
-  hooks:
-  - id: pylint
-    language: system
-    types: [file, python]
-    name: pylint
-    description: "This hook runs the pylint static code analyzer"
-    exclude: &exclude_files >
-      (?x)^(
-          docs/.*|
-      )$
-    entry: pylint
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.13
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.12.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix]
+        exclude: >-
+          (?x)^(
+            pyproject.toml
+          )$
+      - id: pretty-format-yaml
+        args: [--autofix, --preserve-quotes, --offset, "2"]
+        exclude: >-
+          (?x)^(
+            tests/.*|
+            environment.yml
+          )$
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        args: [--config-file=pyproject.toml]
+        exclude: &exclude_files >
+          (?x)^(
+            docs/.*|
+            tests/.*(?<!\.py)$
+          )$

.readthedocs.yml

@@ -1,7 +1,6 @@
 version: 2
 
 python:
-  version: "3.8"
   install:
     - method: pip
       path: .

README.md

@@ -13,91 +13,50 @@ intended to help developers get started with their AiiDA plugins.
 
 ## Repository contents
 
-* [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
-  * [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit
-  * [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
-* [`aiida_quantum_transport/`](aiida_quantum_transport/): The main source code of the plugin package
-  * [`data/`](aiida_quantum_transport/data/): A new `DiffParameters` data class, used as input to the `DiffCalculation` `CalcJob` class
-  * [`calculations.py`](aiida_quantum_transport/calculations.py): A new `DiffCalculation` `CalcJob` class
-  * [`cli.py`](aiida_quantum_transport/cli.py): Extensions of the `verdi data` command line interface for the `DiffParameters` class
-  * [`helpers.py`](aiida_quantum_transport/helpers.py): Helpers for setting up an AiiDA code for `diff` automatically
-  * [`parsers.py`](aiida_quantum_transport/parsers.py): A new `Parser` for the `DiffCalculation`
-* [`docs/`](docs/): A documentation template ready for publication on [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)
-* [`examples/`](examples/): An example of how to submit a calculation using this plugin
-* [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
-* [`.gitignore`](.gitignore): Telling git which files to ignore
-* [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
-* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
-* [`LICENSE`](LICENSE): License for your plugin
-* [`README.md`](README.md): This file
-* [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
-* [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
-
-See also the following video sequences from the 2019-05 AiiDA tutorial:
-
- * [run aiida-diff example calculation](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=403s)
- * [aiida-diff CalcJob plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=685s)
- * [aiida-diff Parser plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=936s)
- * [aiida-diff computer/code helpers](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1238s)
- * [aiida-diff input data (with validation)](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1353s)
- * [aiida-diff cli](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1621s)
- * [aiida-diff tests](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1931s)
- * [Adding your plugin to the registry](https://www.youtube.com/watch?v=760O2lDB-TM&t=112s)
- * [pre-commit hooks](https://www.youtube.com/watch?v=760O2lDB-TM&t=333s)
-
-For more information, see the [developer guide](https://aiida-diff.readthedocs.io/en/latest/developer_guide) of your plugin.
-
+- [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
+  - [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit
+  - [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
+- [`src/aiida_quantum_transport/`](src/aiida_quantum_transport/): The main source code of the plugin package
+  - [`data/`](src/aiida_quantum_transport/data/): Custom data classes
+  - [`calculations.py`](src/aiida_quantum_transport/calculations.py): Quantum Transport AiiDA calculation classes
+  - [`cli.py`](src/aiida_quantum_transport/cli.py): Custom `verdi` CLI commands
+  - [`helpers.py`](src/aiida_quantum_transport/helpers.py): Helpers for setting up an AiiDA code
+  - [`parsers.py`](src/aiida_quantum_transport/parsers.py): Custom parser classes
+- [`docs/`](docs/): The documentation of the plugin
+- [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
+  - [`conftest.py`](tests/conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
+- [`.gitignore`](.gitignore): Telling git which files to ignore
+- [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
+- [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
+- [`LICENSE`](LICENSE): License for your plugin
+- [`README.md`](README.md): This file
+- [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
 
 ## Features
 
- * Add input files using `SinglefileData`:
-   ```python
-   SinglefileData = DataFactory('singlefile')
-   inputs['file1'] = SinglefileData(file='/path/to/file1')
-   inputs['file2'] = SinglefileData(file='/path/to/file2')
-   ```
-
- * Specify command line options via a python dictionary and `DiffParameters`:
-   ```python
-   d = { 'ignore-case': True }
-   DiffParameters = DataFactory('quantum_transport')
-   inputs['parameters'] = DiffParameters(dict=d)
-   ```
-
- * `DiffParameters` dictionaries are validated using [voluptuous](https://github.com/alecthomas/voluptuous).
-   Find out about supported options:
-   ```python
-   DiffParameters = DataFactory('quantum_transport')
-   print(DiffParameters.schema.schema)
-   ```
+Under development
 
 ## Installation
 
 ```shell
 pip install aiida-quantum-transport
-verdi quicksetup  # better to set up a new profile
-verdi plugin list aiida.calculations  # should now show your calclulation plugins
+verdi quicksetup
+verdi plugin list aiida.calculations
 ```
 
-
 ## Usage
 
 Here goes a complete example of how to submit a test calculation using this plugin.
 
 A quick demo of how to submit a calculation:
+
 ```shell
 verdi daemon start     # make sure the daemon is running
 cd examples
 ./example_01.py        # run test calculation
 verdi process list -a  # check record of calculation
 ```
 
-The plugin also includes verdi commands to inspect its data types:
-```shell
-verdi data quantum_transport list
-verdi data quantum_transport export <PK>
-```
-
 ## Development
 
 ```shell
@@ -114,11 +73,11 @@ See the [developer guide](http://aiida-quantum-transport.readthedocs.io/en/lates
 ## License
 
 MIT
+
 ## Contact
 
 [email protected]
 
-
 [ci-badge]: https://github.com/edan-bainglass/aiida-quantum-transport/workflows/ci/badge.svg?branch=master
 [ci-link]: https://github.com/edan-bainglass/aiida-quantum-transport/actions
 [cov-badge]: https://coveralls.io/repos/github/edan-bainglass/aiida-quantum-transport/badge.svg?branch=master