👌 Update package (#38)

* 👌 Update package

Updated according to aiidateam/aiida-plugin-cutter#88

* Update pyproject.toml

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.8"]
         backend: ['django']
 
     services:
@@ -50,7 +50,7 @@ jobs:
         AIIDA_TEST_BACKEND: ${{ matrix.backend }}
         # show timings of tests
         PYTEST_ADDOPTS: "--durations=0"
-      run: py.test --cov aiida_diff --cov-append .
+      run: pytest --cov aiida_diff --cov-append .
 
   docs:
     runs-on: ubuntu-latest
@@ -60,7 +60,7 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: "3.8"
     - name: Install python dependencies
       run: |
         pip install --upgrade pip
@@ -77,7 +77,7 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: "3.8"
     - name: Install python dependencies
       run: |
         pip install --upgrade pip

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

@@ -18,23 +18,16 @@ jobs:
     - name: Set up Python 3.8
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: '3.8'
 
-    - name: Upgrade setuptools and install package
+    - name: Install flit
       run: |
-        python -m pip install --upgrade pip setuptools
-        python -m pip install -e .
+        python -m pip install --upgrade pip
+        python -m 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

@@ -2,22 +2,28 @@
 # pre-commit install
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.1.0
   hooks:
-    - id: double-quote-string-fixer
     - id: end-of-file-fixer
-    - id: fix-encoding-pragma
     - id: mixed-line-ending
     - id: trailing-whitespace
     - id: check-json
 
-# yapf = yet another python formatter
-- repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.30.0
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.31.0
   hooks:
-  - id: yapf
-    name: yapf
-    args: ["-i"]
+  - id: pyupgrade
+    args: ["--py37-plus"]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+    - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 21.12b0
+  hooks:
+    - id: black
 
 - repo: local
   hooks:
@@ -31,9 +37,3 @@ repos:
           docs/.*|
       )$
     entry: pylint
-
-  - id: version-number
-    name: Check version numbers
-    entry: python ./.github/check_version.py
-    language: system
-    files: '^(setup.json)|(aiida_diff/__init__.py)'

.readthedocs.yml

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

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 The AiiDA Team.
+Copyright (c) 2022 The AiiDA Team.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,7 +1,7 @@
-[![Build Status](https://github.com/aiidateam/aiida-diff/workflows/ci/badge.svg?branch=master)](https://github.com/aiidateam/aiida-diff/actions)
-[![Coverage Status](https://coveralls.io/repos/github/aiidateam/aiida-diff/badge.svg?branch=master)](https://coveralls.io/github/aiidateam/aiida-diff?branch=master)
-[![Docs status](https://readthedocs.org/projects/aiida-diff/badge)](http://aiida-diff.readthedocs.io/)
-[![PyPI version](https://badge.fury.io/py/aiida-diff.svg)](https://badge.fury.io/py/aiida-diff)
+[![Build Status][ci-badge]][ci-link]
+[![Coverage Status][cov-badge]][cov-link]
+[![Docs status][docs-badge]][docs-link]
+[![PyPI version][pypi-badge]][pypi-link]
 
 # aiida-diff
 
@@ -25,22 +25,16 @@ intended to help developers get started with their AiiDA plugins.
 * [`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`.
-* [`.coveragerc`](.coveragerc): Configuration of [coverage.py](https://coverage.readthedocs.io/en/latest) tool reporting which lines of your plugin are covered by tests
 * [`.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
-* [`MANIFEST.in`](MANIFEST.in): Configure non-Python files to be included for publication on [PyPI](https://pypi.org/)
 * [`README.md`](README.md): This file
 * [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
-* [`pytest.ini`](pytest.ini): Configuration of [pytest](https://docs.pytest.org/en/latest/) test discovery
-* [`setup.json`](setup.json): Plugin metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
-* [`setup.py`](setup.py): Installation script for pip / [PyPI](https://pypi.org/)
-
+* [`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:
 
- * [aiida-diff setup.json](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=240s)
  * [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)
@@ -109,6 +103,7 @@ verdi data diff export <PK>
 ```shell
 git clone https://github.com/aiidateam/aiida-diff .
 cd aiida-diff
+pip install --upgrade pip
 pip install -e .[pre-commit,testing]  # install extra dependencies
 pre-commit install  # install pre-commit hooks
 pytest -v  # discover and run all tests
@@ -119,3 +114,13 @@ See the [developer guide](http://aiida-diff.readthedocs.io/en/latest/developer_g
 ## License
 
 MIT
+
+
+[ci-badge]: https://github.com/aiidateam/aiida-diff/workflows/ci/badge.svg?branch=master
+[ci-link]: https://github.com/aiidateam/aiida-diff/actions
+[cov-badge]: https://coveralls.io/repos/github/aiidateam/aiida-diff/badge.svg?branch=master
+[cov-link]: https://coveralls.io/github/aiidateam/aiida-diff?branch=master
+[docs-badge]: https://readthedocs.org/projects/aiida-diff/badge
+[docs-link]: http://aiida-diff.readthedocs.io/
+[pypi-badge]: https://badge.fury.io/py/aiida-diff.svg
+[pypi-link]: https://badge.fury.io/py/aiida-diff

aiida_diff/__init__.py

@@ -1,8 +1,7 @@
-# -*- coding: utf-8 -*-
 """
 aiida_diff
 
 AiiDA demo plugin that wraps the `diff` executable for computing the difference between two files.
 """
 
-__version__ = '1.2.0'
+__version__ = "1.2.0"

aiida_diff/calculations.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Calculations provided by aiida_diff.
 
@@ -9,7 +8,7 @@
 from aiida.orm import SinglefileData
 from aiida.plugins import DataFactory
 
-DiffParameters = DataFactory('diff')
+DiffParameters = DataFactory("diff")
 
 
 class DiffCalculation(CalcJob):
@@ -18,28 +17,45 @@ class DiffCalculation(CalcJob):
 
     Simple AiiDA plugin wrapper for 'diffing' two files.
     """
+
     @classmethod
     def define(cls, spec):
         """Define inputs and outputs of the calculation."""
-        # yapf: disable
         super().define(spec)
 
         # set default values for AiiDA options
-        spec.inputs['metadata']['options']['resources'].default = {
-            'num_machines': 1,
-            'num_mpiprocs_per_machine': 1,
+        spec.inputs["metadata"]["options"]["resources"].default = {
+            "num_machines": 1,
+            "num_mpiprocs_per_machine": 1,
         }
-        spec.inputs['metadata']['options']['parser_name'].default = 'diff'
+        spec.inputs["metadata"]["options"]["parser_name"].default = "diff"
 
         # new ports
-        spec.input('metadata.options.output_filename', valid_type=str, default='patch.diff')
-        spec.input('parameters', valid_type=DiffParameters, help='Command line parameters for diff')
-        spec.input('file1', valid_type=SinglefileData, help='First file to be compared.')
-        spec.input('file2', valid_type=SinglefileData, help='Second file to be compared.')
-        spec.output('diff', valid_type=SinglefileData, help='diff between file1 and file2.')
-
-        spec.exit_code(300, 'ERROR_MISSING_OUTPUT_FILES', message='Calculation did not produce all expected output files.')
+        spec.input(
+            "metadata.options.output_filename", valid_type=str, default="patch.diff"
+        )
+        spec.input(
+            "parameters",
+            valid_type=DiffParameters,
+            help="Command line parameters for diff",
+        )
+        spec.input(
+            "file1", valid_type=SinglefileData, help="First file to be compared."
+        )
+        spec.input(
+            "file2", valid_type=SinglefileData, help="Second file to be compared."
+        )
+        spec.output(
+            "diff",
+            valid_type=SinglefileData,
+            help="diff between file1 and file2.",
+        )
 
+        spec.exit_code(
+            300,
+            "ERROR_MISSING_OUTPUT_FILES",
+            message="Calculation did not produce all expected output files.",
+        )
 
     def prepare_for_submission(self, folder):
         """
@@ -51,8 +67,8 @@ def prepare_for_submission(self, folder):
         """
         codeinfo = datastructures.CodeInfo()
         codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
-            file1_name=self.inputs.file1.filename,
-            file2_name=self.inputs.file2.filename)
+            file1_name=self.inputs.file1.filename, file2_name=self.inputs.file2.filename
+        )
         codeinfo.code_uuid = self.inputs.code.uuid
         codeinfo.stdout_name = self.metadata.options.output_filename
         codeinfo.withmpi = self.inputs.metadata.options.withmpi
@@ -61,8 +77,16 @@ def prepare_for_submission(self, folder):
         calcinfo = datastructures.CalcInfo()
         calcinfo.codes_info = [codeinfo]
         calcinfo.local_copy_list = [
-            (self.inputs.file1.uuid, self.inputs.file1.filename, self.inputs.file1.filename),
-            (self.inputs.file2.uuid, self.inputs.file2.filename, self.inputs.file2.filename),
+            (
+                self.inputs.file1.uuid,
+                self.inputs.file1.filename,
+                self.inputs.file1.filename,
+            ),
+            (
+                self.inputs.file2.uuid,
+                self.inputs.file2.filename,
+                self.inputs.file2.filename,
+            ),
         ]
         calcinfo.retrieve_list = [self.metadata.options.output_filename]