Adds black and pre-commit hooks

.editorconfig

@@ -25,3 +25,6 @@ indent_size = 2
 
 [*.{md,Rmd}]
 trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

.github/workflows/ci.yml

@@ -1,13 +1,10 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Python package
 
 on:
   push:
     branches: [main]
   pull_request:
-      types: [opened, synchronize, reopened]
+    types: [opened, synchronize, reopened]
 
 jobs:
   build:
@@ -19,18 +16,18 @@ jobs:
       fail-fast: false
     name: Run tests in conda environment ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ewatercycle
-        environment-file: environment.yml
-        python-version: ${{ matrix.python-version }}
-        miniconda-version: "latest"
-        channels: conda-forge
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        pip3 install -e .[dev]
-    - name: Test with pytest
-      run: pytest
-      shell: bash -l {0}
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: ewatercycle
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          pip3 install -e .[dev]
+      - name: Test with pytest
+        run: pytest
+        shell: bash -l {0}

.github/workflows/sonar.yml

@@ -4,34 +4,38 @@ on:
   push:
     branches: [main]
   pull_request:
-      types: [opened, synchronize, reopened]
+    types: [opened, synchronize, reopened]
 
 jobs:
   sonarcloud:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-    - name: Set up Python
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: ewatercycle
-        environment-file: environment.yml
-        python-version: 3.8
-        miniconda-version: "latest"
-        channels: conda-forge
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        pip3 install -e .[dev]
-    - name: Tests with coverage
-      run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
-      shell: bash -l {0}
-    - name: Correct coverage paths
-      run: sed -i "s+$PWD/++g" coverage.xml
-    - name: SonarCloud Scan
-      uses: sonarsource/sonarcloud-github-action@master
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: ewatercycle
+          environment-file: environment.yml
+          python-version: 3.8
+          miniconda-version: "latest"
+          channels: conda-forge
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          pip3 install -e .[dev]
+      - name: Run pre commit hooks like linters and black formatter
+        uses: pre-commit/action@v2.0.3
+      - name: Tests with coverage
+        run: |
+          pytest --cov --cov-report term --cov-report xml \
+            --junitxml=xunit-result.xml
+        shell: bash -l {0}
+      - name: Correct coverage paths
+        run: sed -i "s+$PWD/++g" coverage.xml
+      - name: SonarCloud Scan
+        uses: sonarsource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,98 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+  - repo: https://github.com/adrienverge/yamllint
+    rev: "v1.26.0"
+    hooks:
+      - id: yamllint
+  - repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v1.17.0
+    hooks:
+      - id: setup-cfg-fmt
+  - repo: https://github.com/psf/black
+    rev: 21.7b0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.9.3"
+    hooks:
+      - id: isort
+  # TODO renable when errors are fixed/ignored
+  # - repo: https://github.com/pycqa/pylint
+  #   rev: "v2.9.6"
+  #   hooks:
+  #     - id: pylint
+  # TODO renable when errors are fixed/ignored
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: "3.9.2"
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          &fd [
+            flake8-annotations-complexity,
+            flake8-bandit,
+            flake8-blind-except,
+            flake8-bugbear,
+            flake8-builtins,
+            flake8-cognitive-complexity,
+            flake8-comprehensions,
+            flake8-docstrings,
+            flake8-eradicate,
+            flake8-executable,
+            flake8-expression-complexity,
+            flake8-if-expr,
+            flake8-implicit-str-concat,
+            flake8-logging-format,
+            flake8-pathlib,
+            flake8-print,
+            flake8-pytest,
+            flake8-pytest-style,
+            # flake8-quotes,  # conflicts with blacks double quote preference
+            flake8-raise,
+            flake8-return,
+            flake8-typing-imports,
+            flake8-variables-names,
+            flake8==3.9.2,
+            pandas-vet,
+            pep8-naming,
+            # wemake-python-styleguide,  # conflicts with black
+            yesqa,
+          ]
+        verbose: true
+        args: &fa [--statistics, --exit-zero]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-python-dateutil]
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.1.0
+    hooks:
+      - id: nbqa-black
+        # Match version of black used for .py and .ipynb
+        additional_dependencies: [black==21.7b0]
+      - id: nbqa-isort
+        additional_dependencies: [isort==5.9.3]
+      - id: nbqa-mypy
+        additional_dependencies: [mypy==0.910]
+      # TODO renable when errors are fixed/ignored
+      - id: nbqa-flake8
+        additional_dependencies: *fd
+        args: *fa
+        verbose: true
+      # TODO renable when errors are fixed/ignored
+      # - id: nbqa-pylint
+      #   additional_dependencies: [pylint==2.9.6]
+  - repo: https://github.com/regebro/pyroma
+    rev: "3.2"
+    hooks:
+      - id: pyroma

CONTRIBUTING.md

@@ -55,6 +55,7 @@ The sections below outline the steps in each case.
     and [here](https://help.github.com/articles/syncing-a-fork/));
 4. install the package in editable mode and its dependencies with
     `pip3 install -e .[dev]`;
+4. make sure pre commit hook is installed by running `pre-commit install`, causes linting and formatting to be applied during commit;
 5. make sure the existing tests still work by running `pytest`;
 6. make sure the existing documentation can still by generated without
     warnings by running `cd docs && make html`. [Pandoc](https://pandoc.org/) is required to generate docs, it can be installed with ``conda install -c conda-forge pandoc`` ;
@@ -81,24 +82,25 @@ This section is for maintainers of the package.
 2. Determine what new version (major, minor or patch) to use. Package uses `semantic versioning <https://semver.org>`_.
 3. Run ``bump2version <major|minor|patch>`` to update version in package files.
 4. Update CHANGELOG.md with changes between current and new version.
-5. Commit & push changes to GitHub.
-6. Wait for [GitHub
+5. Make sure pre-commit hooks are green for all files by running ``pre-commit run --all-files``.
+6. Commit & push changes to GitHub.
+7. Wait for [GitHub
     actions](https://github.com/eWaterCycle/ewatercycle/actions?query=branch%3Amain+)
     to be completed and green.
 
-7. Create a [GitHub release](https://github.com/eWaterCycle/ewatercycle/releases/new)
+8. Create a [GitHub release](https://github.com/eWaterCycle/ewatercycle/releases/new)
 
     - Use version as title and tag version.
     - As description use intro text from README.md (to give context to
         Zenodo record) and changes from CHANGELOG.md
 
-8. Create a PyPI release.
+9. Create a PyPI release.
 
     1. Create distribution archives with `python3 -m build`.
     2. Upload archives to PyPI with `twine upload dist/*` (use your
         personal PyPI account).
 
-9. Verify
+10. Verify
 
     1. Has [new Zenodo
         record](https://zenodo.org/search?page=1&size=20&q=ewatercycle)
@@ -109,4 +111,4 @@ This section is for maintainers of the package.
     3. Can new version be installed with pip using
         `pip3 install ewatercycle==<new version>`?
 
-10. Celebrate
+11. Celebrate

LICENSE

@@ -14,4 +14,3 @@ distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
-