Merge branch 'master' of https://github.com/materialsproject/pymatgen

.gitattributes

@@ -1,4 +1,6 @@
-test_files/* linguist-vendored
+# declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
+tests/files/**/* linguist-vendored
 cmd_line/* linguist-vendored
-docs/* linguist-documentation
-docs_rst/* linguist-documentation
+docs/**/* linguist-generated
+docs_rst/**/* linguist-documentation
+dev_scripts/**/* linguist-vendored

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,31 +1,34 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+#### Description
+
+A clear and concise bug description.
+
+#### Repro
 
-**To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+1. Click on '....'
+1. Scroll down to '....'
+1. See error
+
+Provide any example files that are needed to reproduce the error, especially if the bug pertains to parsing a file. If the file format is not supported by GitHub, zip it into an archive and upload that.
+
+#### Expected behavior
+
+What do you expect to happen?
 
-Provide any example files that are needed to reproduce the error,
-especially if the bug pertains to parsing of a file.
+#### Environment
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+Relevant versions and platform info:
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+- OS: (e.g. Mac, Windows, Linux)
+- Version (e.g. v2023.05.10)
 
-**Desktop (please complete the following information):**
- - OS: [e.g. Mac,Windows,Linux]
- - Version [e.g. 2019.9.16]
+#### Additional context
 
-**Additional context**
-Add any other context about the problem here.
+More context like related issues/PRs.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,20 @@
 ---
-name: Feature request
-about: Suggest an idea for this project
-
+name: Feature Request
+about: Propose a new idea for this project
 ---
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+#### Problem
+
+Briefly describe the problem you're experiencing.
+
+#### Proposed Solution
+
+Detail the feature or solution you'd like to see implemented.
+
+#### Alternatives
 
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
+List any alternative solutions or features you've considered.
 
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
+#### Additional Info
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+Provide any further context or relevant screenshots.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,47 +1,27 @@
 ## Summary
 
-Include a summary of major changes in bullet points:
+Major changes:
 
-* Feature 1
-* Feature 2
-* Fix 1
-* Fix 2
+- feature 1: ...
+- fix 1: ...
 
-## Additional dependencies introduced (if any)
+## Todos
 
-* List all new dependencies needed and justify why. While adding dependencies that bring
-significantly useful functionality is perfectly fine, adding ones that
-add trivial functionality, e.g., to use one single easily implementable
-function, is frowned upon. Provide a justification why that dependency is needed.
-Especially frowned upon are circular dependencies, e.g., depending on derivative
-modules of pymatgen such as custodian or Fireworks.
+If this is work in progress, what else needs to be done?
 
-## TODO (if any)
+- feature 2: ...
+- fix 2:
 
-If this is a work-in-progress, write something about what else needs
-to be done
+## Checklist
 
-* Feature 1 supports A, but not B.
+- [ ] Google format doc strings added. Check with `ruff`.
+- [ ] Type annotations included. Check with `mypy`.
+- [ ] Tests added for new features/fixes.
+- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
 
-## Checklist
+Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
 
-Work-in-progress pull requests are encouraged, but please put [WIP]
-in the pull request title.
-
-Before a pull request can be merged, the following items must be checked:
-
-- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
-      is to run the following in the **correct sequence** on your local machine. Start with running
-      [black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
-      your code to PEP8 conventions and removes most issues. Then run
-      [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
-      [flake8](http://flake8.pycqa.org/en/latest/).
-- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
-      Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
-- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
-- [ ] Tests have been added for any new functionality or bug fixes.
-- [ ] All linting and tests pass.
-
-Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
-errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
-repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
+```sh
+pip install -U pre-commit
+pre-commit install
+```

.github/dependabot.yml

@@ -1,6 +1,11 @@
-version: 2
-updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    schedule:
-      interval: "weekly"
+# version: 2
+# updates:
+#   - package-ecosystem: github-actions
+#     directory: /
+#     schedule:
+#       interval: monthly
+
+#   - package-ecosystem: pip
+#     directory: /
+#     schedule:
+#       interval: monthly

.github/workflows/lint.yml

@@ -1,49 +1,45 @@
 name: Linting
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
 
 permissions:
   contents: read
 
 jobs:
-  build:
+  lint:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 1
-      matrix:
-        python-version: [3.9]
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
+
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.11"
           cache: pip
-          cache-dependency-path: requirements-dev.txt
+          cache-dependency-path: setup.py
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements-dev.txt --quiet
-      - name: mypy
-        run: |
-          mypy --version
-          rm -rf .mypy_cache
-          mypy pymatgen
-      - name: pydocstyle
-        run: |
-          pydocstyle --count pymatgen
-      - name: pylint
+          pip install -e '.[dev]'
+
+      - name: ruff
         run: |
-          pylint pymatgen
+          ruff --version
+          ruff . --ignore D
+
       - name: black
         run: |
           black --version
           black --check --diff --color pymatgen
-      - name: flake8
+
+      - name: mypy
         run: |
-          flake8 --version
-          flake8 --count --show-source --statistics pymatgen
-          # exit-zero treats all errors as warnings.
-          flake8 --count --exit-zero --max-complexity=20 --statistics pymatgen
+          mypy --version
+          rm -rf .mypy_cache
+          mypy pymatgen