Merge remote-tracking branch 'upstream/master' into dev

Author: exenGT

.gitattributes

@@ -1,5 +1,5 @@
 # declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
-**/test_files/**/* linguist-vendored
+tests/files/**/* linguist-vendored
 cmd_line/* linguist-vendored
 docs/**/* linguist-generated
 docs_rst/**/* linguist-documentation

.github/ISSUE_TEMPLATE/bug_report.md

@@ -5,7 +5,9 @@ about: Create a report to help us improve
 
 #### Description
 
-A clear and concise bug description.
+A clear and concise bug description. Please submit only issues regarding pymatgen only. If you encounter errors
+related to any of pymatgen's dependencies (e.g., [mp-api](https://github.com/materialsproject/api)), please post
+Issues on the respective Github Issues pages.
 
 #### Repro
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,27 +1,25 @@
 ## Summary
 
-Major updates:
+Major changes:
 
 - feature 1: ...
 - fix 1: ...
 
 ## Todos
 
-If this is a work in progress, about what else needs to be done?
+If this is work in progress, what else needs to be done?
 
 - feature 2: ...
 - fix 2:
 
 ## Checklist
 
-Ensure:
-
 - [ ] Google format doc strings added. Check with `ruff`.
 - [ ] Type annotations included. Check with `mypy`.
 - [ ] Tests added for new features/fixes.
-- [ ] All tests and linting pass.
+- [ ] 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))
 
-Tip: Install `pre-commit` hooks to auto-check before every commit:
+Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
 
 ```sh
 pip install -U pre-commit

.github/dependabot.yml

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

.github/workflows/lint.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: setup.py
 

.github/workflows/test.yml

@@ -5,8 +5,10 @@ name: Tests
 on:
   push:
     branches: [master]
+    paths-ignore: ["**/*.md", docs/**]
   pull_request:
     branches: [master]
+    paths-ignore: ["**/*.md", docs/**]
   release:
     types: [published]
   workflow_dispatch:
@@ -21,14 +23,15 @@ permissions:
   contents: read
 
 jobs:
-  pytest:
+  test:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
     strategy:
+      fail-fast: false
       matrix:
         # pytest-split automatically distributes work load so parallel jobs finish in similar time
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.11']
+        python-version: ["3.8", "3.11"]
         split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
         # include/exclude is meant to maximize CI coverage of different platforms and python
         # versions while minimizing the total number of jobs. We run all pytest splits with the
@@ -37,30 +40,31 @@ jobs:
         # coverage on unix). Also sample some splits on macos for all python versions
         exclude:
           - os: windows-latest
-            python-version: '3.11'
+            python-version: "3.11"
           - os: ubuntu-latest
-            python-version: '3.8'
+            python-version: "3.8"
         include:
           - os: macos-latest
-            python-version: '3.8'
+            python-version: "3.8"
             split: 1
           - os: macos-latest
-            python-version: '3.9'
+            python-version: "3.9"
             split: 2
           - os: macos-latest
-            python-version: '3.10'
+            python-version: "3.10"
             split: 3
           - os: macos-latest
-            python-version: '3.11'
+            python-version: "3.11"
             split: 4
 
     runs-on: ${{ matrix.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
       MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434
-      PMG_TEST_FILES_DIR: ${{ github.workspace }}/test_files
+      PMG_TEST_FILES_DIR: ${{ github.workspace }}/tests/files
       GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries
+      PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files
 
     steps:
       - uses: actions/checkout@v3
@@ -70,90 +74,117 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: setup.py
-      - name: Add CLIs to GITHUB_PATH
-        if: runner.os != 'Windows'
+      - name: Copy CLIs to bin
+        if: runner.os == 'Linux'
         # This is the way to update env variables in a way that persist for the entire job.
         run: |
-          for pkg in cmd_line/*;
-            do echo "$(pwd)/cmd_line/$pkg/Linux_64bit" >> "$GITHUB_PATH";
-          done
-      - name: Install m3gnet
-        # conditional install necessary because TF lacks py3.11 support
-        # https://github.com/tensorflow/tensorflow/issues/58032
-        if: matrix.python-version != '3.11'
-        run: python -m pip install m3gnet
+          sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
+      - name: Install Bader
+        if: runner.os == 'Linux'
+        run: |
+          wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
+          tar xvzf bader_lnx_64.tar.gz
+          sudo mv bader /usr/local/bin/
+        continue-on-error: true
+      - name: Install Enumlib
+        if: runner.os == 'Linux'
+        run: |
+          git clone --recursive https://github.com/msg-byu/enumlib.git
+          cd enumlib/symlib/src
+          export F90=gfortran
+          make
+          cd ../../src
+          make enum.x
+          sudo mv enum.x /usr/local/bin/
+          cd ..
+          sudo cp aux_src/makeStr.py /usr/local/bin/
+        continue-on-error: true
+      - name: Install Packmol
+        if: runner.os == 'Linux'
+        run: |
+          wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz
+          tar xvzf packmol.tar.gz
+          export F90=gfortran
+          cd packmol-20.14.2
+          ./configure
+          make
+          sudo mv packmol /usr/local/bin/
+          cd ..
+          rm -rf .coverage*
+        continue-on-error: true
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
           python -m pip install numpy cython packaging
           python -m pip install -e '.[dev,optional]'
       - name: pytest split ${{ matrix.split }}
-        # to update the test durations, run
-        # pytest --store-durations --durations-path test_files/.pytest-split-durations
+        # to update the test durations, do pip install pytest-split and run
+        # pytest --store-durations --durations-path tests/files/.pytest-split-durations
         # and commit the results (requires pip install pytest-split)
         run: |
-          pytest --cov=pymatgen --splits 10 --group ${{ matrix.split }} --durations-path test_files/.pytest-split-durations
+          pytest --cov=pymatgen --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
       - name: Upload coverage
+        # Only upload coverage for ubuntu py3.11 runs.
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
         uses: actions/upload-artifact@v3
         with:
           name: coverage-${{ matrix.split }}
           path: .coverage
 
   coverage:
-    needs: pytest
+    needs: test
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-      - name: Install Coverage
-        run: python -m pip install coverage
       - name: Download coverage artifacts
-        continue-on-error: true
         uses: actions/download-artifact@v3
-      - name: Run coverage
-        continue-on-error: true
+      - name: Combine coverage
         run: |
-          coverage combine coverage*/.coverage*
-          coverage report
-          coverage xml
-      - name: Coveralls Python
-        continue-on-error: true
-        uses: AndreMiras/coveralls-python-action@v20201129
+          pip install coverage[toml]
+          find . -name "*.pyc" -delete
+          for i in {1..10}; do mv coverage-$i/.coverage .coverage.$i; rm -rf coverage-$i; done
+          coverage combine
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
 
   build_sdist:
-    needs: pytest
-    name: Build source distribution
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
+    needs: test
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.10'
-      - run: python -m pip install build
+          python-version: "3.10"
+      - run: |
+          python -m pip install build
+          pip install -e .
       - name: Build sdist
         run: python -m build --sdist
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
 
   build_wheels:
-    needs: pytest
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
+    needs: test
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['38', '39', '310', '311']
+        python-version: ["38", "39", "310", "311"]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v3
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.14.1
         env:
           CIBW_BUILD: cp${{ matrix.python-version }}-*
-      - uses: actions/upload-artifact@v3
+      - name: Save artifact
+        uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
 
@@ -169,7 +200,8 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
-      - uses: actions/download-artifact@v3
+      - name: Get build artifacts
+        uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist

.gitignore

@@ -14,6 +14,7 @@ dependencies/spglib*/build
 pymatgen/pymatgen.cfg
 dist
 _build
+_site
 build
 .project
 .pydevproject

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|.*test_files|cmd_line|tasks.py)
+exclude: ^(docs|tests/files|cmd_line|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
@@ -7,8 +7,8 @@ ci:
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.272
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.284
     hooks:
       - id: ruff
         args: [--fix]
@@ -17,22 +17,21 @@ repos:
     rev: v4.4.0
     hooks:
       - id: check-yaml
-        exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.4.1
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -45,3 +44,13 @@ repos:
       - id: cython-lint
         args: [--no-pycodestyle]
       - id: double-quote-cython-strings
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.35.0
+    hooks:
+      - id: markdownlint
+        # MD013: line too long
+        # MD033: no inline HTML
+        # MD041: first line in a file should be a top-level heading
+        # MD025: single title
+        args: [--disable, MD013, MD025, MD033, MD041, "--"]