Merge branch 'master' into enable_using_check_functions_on_gzipped_fi…

…les_for_VASP

.coderabbit.yaml

@@ -0,0 +1,17 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+language: "en-US"
+early_access: false
+reviews:
+  request_changes_workflow: false
+  high_level_summary: false
+  poem: false
+  review_status: false
+  collapse_walkthrough: false
+  auto_review:
+    enabled: true
+    ignore_title_keywords:
+      - "WIP"
+      - "DO NOT MERGE"
+    drafts: false
+chat:
+  auto_reply: true

.gitattributes

@@ -0,0 +1,3 @@
+# declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
+**/tests/files/**/* linguist-vendored
+docs/**/* linguist-documentation

.github/release.yml

@@ -0,0 +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: ["*"]

.github/workflows/lint.yml

@@ -0,0 +1,26 @@
+name: Linting
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: pip
+
+      - name: Run pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit run --all-files

.github/workflows/release.yml

@@ -6,46 +6,21 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
-    strategy:
-      max-parallel: 1
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ['3.9']
-
-    runs-on: ${{ matrix.os }}
+  test:
+    # run test.yml first to ensure that the test suite is passing
+    uses: ./.github/workflows/test.yml
 
+  build:
+    needs: test
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install OpenBabel
-        shell: bash -l {0}
-        run: conda install -c conda-forge openbabel
-
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-ci.txt
-          pip install -e .
-      - name: pytest
-        shell: bash -l {0}
-        env:
-          PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-          MPLBACKEND: "Agg"
-        run: |
-          pytest custodian --color=yes
       - name: release
-        shell: bash -l {0}
+        run: |
+          pip install build twine
+          python -m build
+          twine upload --skip-existing dist/*.tar.gz
         env:
           TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
-        run: |
-          pip install setuptools wheel twine
-          python setup.py sdist bdist_wheel
-          twine upload --skip-existing dist/*.tar.gz

.github/workflows/test.yml

@@ -0,0 +1,60 @@
+name: Testing
+
+on:
+  push:
+    branches: [master]
+    paths-ignore: [docs/**]
+  pull_request:
+    branches: [master]
+    paths-ignore: [docs/**]
+  workflow_dispatch:
+  # make this workflow reusable by release.yml
+  workflow_call:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-14]
+        # not testing on 3.9 because tests use glob("*", root_dir=TEST_FILES)
+        # and root_dir only added in 3.10
+        python-version: ["3.10", "3.12"]
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install uv
+        run: pip install uv
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: qchem
+
+      - name: Install OpenBabel
+        run: conda install -c conda-forge openbabel
+
+      - name: Install dependencies
+        run: uv pip install numpy==1.26.4 ; uv pip install -e '.[dev]' --system
+
+      - name: pytest
+        env:
+          PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+          MPLBACKEND: Agg
+        run: pytest --cov=custodian --color=yes tests
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -41,7 +41,9 @@ nosetests.xml
 .mr.developer.cfg
 .project
 .pydevproject
-
+_build
+_site
+Gemfile.lock
 .DS_Store
 docs/_build
 

.pre-commit-config.yaml

@@ -1,55 +1,36 @@
-exclude: ^(docs|.*test_files|cmd_line|dev_scripts)
-
-default_language_version:
-  python: python3.8
+exclude: ^(docs|tests/files)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy]
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
-
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.1.1
-    hooks:
-      - id: autoflake
-        args:
-          - --in-place
-          - --remove-unused-variables
-          - --remove-all-unused-imports
-          - --expand-star-imports
-          - --ignore-init-module-imports
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.2
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.7
     hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+      - id: ruff
+        args: [--fix, --ignore, D, --unsafe-fixes]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
         exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.2.0
+    rev: v1.10.0
     hooks:
       - id: mypy
+        additional_dependencies: [types-requests]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11