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

Author: jonathanjdenney

.github/workflows/release.yml

@@ -0,0 +1,141 @@
+# Runs the complete test suite incl. many external command line dependencies (like Openbabel)
+# as well as the pymatgen.ext package. Coverage is computed based on this workflow.
+name: Tests
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      task:
+        type: choice
+        options: [tests, release]
+        default: tests
+        description: Only run tests or release a new version of pymatgen to PyPI after tests pass.
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+
+    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 }}/tests/files
+      GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries
+      PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: setup.py
+      - name: Copy GULP to bin
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
+      - name: Install Bader
+        if: matrix.os == 'ubuntu-latest'
+        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  # This is not critical to succeed.
+      - name: Install Enumlib
+        if: matrix.os == 'ubuntu-latest'
+        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  # This is not critical to succeed.
+      - 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
+        run: |
+          pytest --cov=pymatgen tests
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+
+  build_sdist:
+    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
+          pip install -e .
+      - name: Build sdist
+        run: python -m build --sdist
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  build_wheels:
+    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: ["39", "310", "311"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp${{ matrix.python-version }}-*
+      - name: Save artifact
+        uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  release:
+    needs: [build_wheels, build_sdist]
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
+    runs-on: ubuntu-latest
+    permissions:
+      # For pypi trusted publishing
+      id-token: write
+    steps:
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Get build artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - name: Publish to PyPi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          verbose: true

.github/workflows/test.yml

@@ -9,8 +9,6 @@ on:
   pull_request:
     branches: [master]
     paths-ignore: ["**/*.md", docs/**]
-  release:
-    types: [published]
   workflow_dispatch:
     inputs:
       task:
@@ -22,10 +20,6 @@ on:
 permissions:
   contents: read
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
 jobs:
   test:
     # prevent this action from running on forks
@@ -35,31 +29,18 @@ jobs:
       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: ["3.9", "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
-        # oldest supported python version (currently 3.8) on windows (seems most likely to surface
+        # oldest supported python version (currently 3.9) on windows (seems most likely to surface
         # errors) and with newest version (currently 3.11) on ubuntu (to get complete and speedy
-        # coverage on unix). Also sample some splits on macos for all python versions
+        # coverage on unix). We ignore mac-os, which is assumed to be similar to ubuntu.
         exclude:
           - os: windows-latest
             python-version: "3.11"
           - os: ubuntu-latest
-            python-version: "3.8"
-        include:
-          - os: macos-latest
-            python-version: "3.8"
-            split: 1
-          - os: macos-latest
             python-version: "3.9"
-            split: 2
-          - os: macos-latest
-            python-version: "3.10"
-            split: 3
-          - os: macos-latest
-            python-version: "3.11"
-            split: 4
 
     runs-on: ${{ matrix.os }}
 
@@ -78,20 +59,19 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: setup.py
-      - 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.
+      - name: Copy GULP to bin
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
       - name: Install Bader
-        if: runner.os == 'Linux'
+        if: matrix.os == 'ubuntu-latest'
         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
+        continue-on-error: true  # This is not critical to succeed.
       - name: Install Enumlib
-        if: runner.os == 'Linux'
+        if: matrix.os == 'ubuntu-latest'
         run: |
           git clone --recursive https://github.com/msg-byu/enumlib.git
           cd enumlib/symlib/src
@@ -102,9 +82,9 @@ jobs:
           sudo mv enum.x /usr/local/bin/
           cd ..
           sudo cp aux_src/makeStr.py /usr/local/bin/
-        continue-on-error: true
+        continue-on-error: true  # This is not critical to succeed.
       - name: Install Packmol
-        if: runner.os == 'Linux'
+        if: matrix.os == 'ubuntu-latest'
         run: |
           wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz
           tar xvzf packmol.tar.gz
@@ -114,102 +94,12 @@ jobs:
           make
           sudo mv packmol /usr/local/bin/
           cd ..
-          rm -rf .coverage*
-        continue-on-error: true
+        continue-on-error: true  # This is not critical to succeed.
       - 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 }}
         run: |
-          pytest --cov=pymatgen --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
-      - name: Upload coverage
-        # Only upload coverage for ubuntu py3.11 runs. Continue on error as coverage is not critical.
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
-        uses: actions/upload-artifact@v3
-        with:
-          name: coverage-${{ matrix.split }}
-          path: .coverage
-
-  coverage:
-    # Only upload coverage for ubuntu py3.11 runs. Continue on error as coverage is not critical.
-    if: github.event_name != 'pull_request'
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Download coverage artifacts
-        uses: actions/download-artifact@v3
-      - name: Combine coverage
-        run: |
-          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:
-    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
-          pip install -e .
-      - name: Build sdist
-        run: python -m build --sdist
-      - uses: actions/upload-artifact@v3
-        with:
-          path: dist/*.tar.gz
-
-  build_wheels:
-    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"]
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v3
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_BUILD: cp${{ matrix.python-version }}-*
-      - name: Save artifact
-        uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
-
-  release:
-    needs: [build_wheels, build_sdist]
-    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
-    runs-on: ubuntu-latest
-    permissions:
-      # For pypi trusted publishing
-      id-token: write
-    steps:
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: Get build artifacts
-        uses: actions/download-artifact@v3
-        with:
-          name: artifact
-          path: dist
-      - name: Publish to PyPi
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          skip-existing: true
-          verbose: true
+          pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

CONTRIBUTING.md

@@ -68,7 +68,7 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec
 
 Given that `pymatgen` is intended to be a long-term code base, we adopt very strict quality control and coding guidelines for all contributions to `pymatgen`. The following must be satisfied for your contributions to be accepted into `pymatgen`.
 
-1. **Unit tests** are required for all new modules and methods. The only way to minimize code regression is to ensure that all code is well tested. Untested contributions will not be accepted.
+1. **Unit tests** are required for all new modules and methods. The only way to minimize code regression is to ensure that all code is well-tested. Untested contributions will not be accepted.
 1. **Python PEP 8** [code style](https://python.org/dev/peps/pep-0008). We allow a few exceptions when they are well-justified (e.g., Element's atomic number is given a variable name of capital Z, in line with accepted scientific convention), but generally, PEP 8 must be observed. Code style will be automatically checked for all PRs and must pass before any PR is merged. To aid you, you can install and run the same set of formatters and linters that will run in CI using
 
    ```sh
@@ -78,7 +78,7 @@ Given that `pymatgen` is intended to be a long-term code base, we adopt very str
     pre-commit run --all-files  # ensure your entire codebase passes linters
    ```
 
-1. **Python 3**. We only support Python 3.8+.
+1. **Python 3**. We only support Python 3.9+.
 1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of the algorithm should be provided and preferably with a link to a publication outlining the method in detail.
 
 For the above, if in doubt, please refer to the core classes in `pymatgen` for examples of what is expected.

README.md

@@ -64,7 +64,7 @@ If you'd like to use the latest unreleased changes on the main branch, you can i
 pip install -U git+https://github.com/materialsproject/pymatgen
 ```
 
-The minimum Python version is 3.8. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
+The minimum Python version is 3.9. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
 
 ## Change Log
 

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -4,7 +4,7 @@
 
 import copy
 import json
-from typing import Sequence
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -26,6 +26,9 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "2.0"