Merge pull request #166 from WMD-group/ruff

Overhaul pre-commit
WMD-group · Aug 19, 2024 · caa28af · caa28af
2 parents ab02a1f + ae3fa47
commit caa28af
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diff --git a/.flake8 b/.flake8
@@ -1,7 +1,7 @@
 [flake8]
 max-line-length = 88
-extend-ignore = 
+extend-ignore =
         # E203: whitespace before ':' (black compatibility)
         E203,
         #D105: Missing docstring in magic method
-        D105
+        D105
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -23,16 +23,15 @@ Please describe the tests that you ran to verify your changes. Provide instructi
 - [ ] Test B
 
 **Test Configuration**:
-* Python version:
-* Operating System:
 
+- Python version:
+- Operating System:
 
 ## Reviewers
 
 @mention individuals who you specifically want to involve in the discussion for this pull request and mention why they are needed in the discussion/why they are needed to review the pull request.
 
-
-## Checklist:
+## Checklist
 
 - [ ] My code follows the style guidelines of this project
 - [ ] I have performed a self-review of my own code

diff --git a/.github/release.yml b/.github/release.yml
@@ -1,29 +1,28 @@
-changelog:
-  exclude:
-    authors: [dependabot, github-actions, pre-commit-ci]
-  categories:
-    - title: 🎉 New Features
-      labels: [feature]
-    - title: 🐛 Bug Fixes
-      labels: [fix]
-    - title: 🛠 Enhancements
-      labels: [enhancement, DX, UX]
-    - title: 📖 Documentation
-      labels: [docs]
-    - title: 🧹 House-Keeping
-      labels: [housekeeping]
-    - title: 🚀 Performance
-      labels: [performance]
-    - title: 💡 Refactoring
-      labels: [refactor]
-    - title: 🧪 Tests
-      labels: [tests]
-    - title: 💥 Breaking Changes
-      labels: [breaking]
-    - title: 🔒 Security Fixes
-      labels: [security]
-    - title: 🏥 Package Health
-      labels: [pkg]
-    - title: 🤷‍♂️ Other Changes
-      labels: ["*"]
-
+changelog:
+  exclude:
+    authors: [dependabot, github-actions, pre-commit-ci]
+  categories:
+    - title: 🎉 New Features
+      labels: [feature]
+    - title: 🐛 Bug Fixes
+      labels: [fix]
+    - title: 🛠 Enhancements
+      labels: [enhancement, DX, UX]
+    - title: 📖 Documentation
+      labels: [docs]
+    - title: 🧹 House-Keeping
+      labels: [housekeeping]
+    - title: 🚀 Performance
+      labels: [performance]
+    - title: 💡 Refactoring
+      labels: [refactor]
+    - title: 🧪 Tests
+      labels: [tests]
+    - title: 💥 Breaking Changes
+      labels: [breaking]
+    - title: 🔒 Security Fixes
+      labels: [security]
+    - title: 🏥 Package Health
+      labels: [pkg]
+    - title: 🤷‍♂️ Other Changes
+      labels: ["*"]
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,7 +6,6 @@ on:
       - main
 
 jobs:
-
   qa:
     runs-on: ubuntu-latest
     steps:
@@ -18,33 +17,31 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9","3.10","3.11","3.12"]
-        os: [ubuntu-latest,macos-latest,windows-latest]
-    
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
     runs-on: ${{matrix.os}}
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install -e ".[dev]"
-    - name: Check package versions
-      run: |
-        pip show -V elementembeddings
-        pip show -V pytest
-        pip show -V matplotlib
-        
-
-    - name: Run tests
-      run: python -m pytest --mpl --mpl-baseline-path=src/elementembeddings/tests/baseline --cov=src/elementembeddings --cov-report=xml -v
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: false
-        verbose: true
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          python -m pip install -e ".[dev]"
+      - name: Check package versions
+        run: |
+          pip show -V elementembeddings
+          pip show -V pytest
+          pip show -V matplotlib
 
+      - name: Run tests
+        run: python -m pytest --mpl --mpl-baseline-path=src/elementembeddings/tests/baseline --cov=src/elementembeddings --cov-report=xml -v
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+          verbose: true
diff --git a/.github/workflows/combine-prs.yml b/.github/workflows/combine-prs.yml
@@ -1,25 +1,25 @@
-name: 'Combine PRs'
+name: "Combine PRs"
 
 # Controls when the action will run - in this case triggered manually
 on:
   workflow_dispatch:
     inputs:
       branchPrefix:
-        description: 'Branch prefix to find combinable PRs based on'
+        description: "Branch prefix to find combinable PRs based on"
         required: true
-        default: 'dependabot'
+        default: "dependabot"
       mustBeGreen:
-        description: 'Only combine PRs that are green (status is success)'
+        description: "Only combine PRs that are green (status is success)"
         required: true
         default: true
       combineBranchName:
-        description: 'Name of the branch to combine PRs into'
+        description: "Name of the branch to combine PRs into"
         required: true
-        default: 'combine-prs-branch'
+        default: "combine-prs-branch"
       ignoreLabel:
-        description: 'Exclude PRs with this label'
+        description: "Exclude PRs with this label"
         required: true
-        default: 'nocombine'
+        default: "nocombine"
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -115,7 +115,7 @@ jobs:
               core.setFailed('Failed to create combined branch - maybe a branch by that name already exists?');
               return;
             }
-            
+
             let combinedPRs = [];
             let mergeFailedPRs = [];
             for(const { branch, prString } of branchesAndPRStrings) {
@@ -133,7 +133,7 @@ jobs:
                 mergeFailedPRs.push(prString);
               }
             }
-            
+
             console.log('Creating combined PR');
             const combinedPRsString = combinedPRs.join('\n');
             let body = '✅ This PR was created by the Combine PRs action by combining the following PRs:\n' + combinedPRsString;
@@ -148,4 +148,4 @@ jobs:
               head: '${{ github.event.inputs.combineBranchName }}',
               base: baseBranch,
               body: body
-            });
+            });
diff --git a/.github/workflows/latest_docs.yml b/.github/workflows/latest_docs.yml
@@ -1,4 +1,4 @@
-name: Build/Publish Develop Docs 
+name: Build/Publish Develop Docs
 on:
   push:
     branches:
@@ -22,6 +22,6 @@ jobs:
           git fetch origin gh-pages --depth=1
           git config --global user.name "Docs Deploy"
           git config --global user.email "[email protected]"
-          
+
       - name: Build Docs Website
         run: mike deploy --push main latest
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -17,23 +17,22 @@ permissions:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,46 +1,55 @@
+ci:
+  autoupdate_schedule: quarterly
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
+  skip: [eslint, pyright]
+
 repos:
-  - repo: https://github.com/timothycrosley/isort
-    rev: "5.12.0"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.5
     hooks:
-      - id: isort
-        additional_dependencies: [toml]
-        args: ["--profile", "black", "--filter-files"]
-  - repo: https://github.com/psf/black
-    rev: "23.10.1"
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
     hooks:
-      - id: black-jupyter
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.41.0
     hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+      - id: markdownlint
+        # MD013: line too long
+        # MD024: Multiple headings with the same content
+        # MD033: no inline HTML
+        # MD041: first line in a file should be a top-level heading
+        # MD025: single title
+        args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
-  #- repo: https://github.com/pre-commit/mirrors-autopep8
-    #rev: v2.0.0
-    #hooks:
-    #  - id: autopep8
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: "1.7.0"
+      - id: nbstripout
+        args: [--drop-empty-cells, --keep-output]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
     hooks:
-      #- #id: nbqa-isort
-        #additional_dependencies: [isort==5.10.1]
-      #- id: nbqa-flake8
-      #  additional_dependencies: [flake8==6.0.0]
-      #  args: [--ignore=E501] # E501 line too long
-      - id: nbqa-pyupgrade
-        additional_dependencies: [pyupgrade==3.3.1]
-      - id: nbqa-autopep8
-        additional_dependencies: [autopep8==2.0.0]
-        args: ["--ignore=E501"]
-  - repo: https://github.com/roy-ht/pre-commit-jupyter
-    rev: v1.2.1
+      - id: prettier
+        args: [--write] # edit files in-place
+        additional_dependencies:
+          - prettier
+  - repo: https://github.com/RobertCraigie/pyright-python
+    rev: v1.1.376
     hooks:
-      - id: jupyter-notebook-cleanup
-        args:
-          # - --remove-kernel-metadata
-          - --pin-patterns
-          - "[pin];[donotremove]"
+      - id: pyright
+        args: [--level, error]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        args: [--toml, pyproject.toml]
+        additional_dependencies:
+          - tomli
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 <!-- insertion marker -->
+
 ## Unreleased
 
 <small>[Compare with latest](https://github.com/WMD-group/ElementEmbeddings/compare/v0.3.0...HEAD)</small>
@@ -19,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Removed warning ([271f61e](https://github.com/WMD-group/ElementEmbeddings/commit/271f61e8653b706a6dd716bf6c0ced9396965750) by Anthony Onwuli).
 
 <!-- insertion marker -->
+
 ## [v0.3.0](https://github.com/WMD-group/ElementEmbeddings/releases/tag/v0.3.0) - 2023-08-07
 
 <small>[Compare with v0.2.0](https://github.com/WMD-group/ElementEmbeddings/compare/v0.2.0...v0.3.0)</small>
@@ -53,7 +55,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Fix package name in contributing.md ([075e657](https://github.com/WMD-group/ElementEmbeddings/commit/075e657d260aa72fca91c7f8cc57466235788426) by Anthony Onwuli).
 - Fixed bug with is_standarised attribute ([ebaf773](https://github.com/WMD-group/ElementEmbeddings/commit/ebaf773134c8ab4988f071da9eca2193e4340f60) by Anthony Onwuli).
-- Fixed composistion featuriser test ([3b729c9](https://github.com/WMD-group/ElementEmbeddings/commit/3b729c9584bf7cc4de2fd5c70baff41c8753800b) by Anthony Onwuli).
+- Fixed composition featuriser test ([3b729c9](https://github.com/WMD-group/ElementEmbeddings/commit/3b729c9584bf7cc4de2fd5c70baff41c8753800b) by Anthony Onwuli).
 - Fixed dim for linear/scalar representations ([f6cc681](https://github.com/WMD-group/ElementEmbeddings/commit/f6cc681ee4f343240f5bb4d49cf9dfc5fa89f455) by Anthony Onwuli).
 
 ### Changed
@@ -174,4 +176,3 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - removed numba from requirements.txt ([1eb833e](https://github.com/WMD-group/ElementEmbeddings/commit/1eb833ec1769ead345de23e2c09c92cee72cc545) by Anthony).
 - removed the old AtomicEmbeddings.py file ([9b1b2e8](https://github.com/WMD-group/ElementEmbeddings/commit/9b1b2e82e0426136020f5112d12c18051d9b7c30) by Anthony).
 - removed itertools from reqssetup.py ([c9c21ca](https://github.com/WMD-group/ElementEmbeddings/commit/c9c21ca8a8e242fc99f19d1fee204da7a1bbdc62) by Anthony).
-