WIP: Adding support for reading vaspwave.h5 in Wavecar and Chgcar class

.github/release.yml

@@ -22,6 +22,8 @@ changelog:
       labels: [refactor]
     - title: 🧪 Tests
       labels: [tests]
+    - title: 🧹 Linting
+      labels: [linting]
     - title: 🔒 Security Fixes
       labels: [security]
     - title: 🏥 Package Health

.github/workflows/issue-metrics.yml

@@ -2,7 +2,7 @@ name: Monthly issue metrics
 on:
   workflow_dispatch:
   schedule:
-    - cron: '3 2 1 * *'
+    - cron: "3 2 1 * *" # Run at 2:03am on the first of every month
 
 permissions:
   contents: read
@@ -17,28 +17,28 @@ jobs:
       issues: write
       pull-requests: read
     steps:
-    - name: Get dates for last month
-      shell: bash
-      run: |
-        # Calculate the first day of the previous month
-        first_day=$(date -d "last month" +%Y-%m-01)
+      - name: Get dates for last month
+        shell: bash
+        run: |
+          # Calculate the first day of the previous month
+          first_day=$(date -d "last month" +%Y-%m-01)
 
-        # Calculate the last day of the previous month
-        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+          # Calculate the last day of the previous month
+          last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
 
-        #Set an environment variable with the date range
-        echo "$first_day..$last_day"
-        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+          #Set an environment variable with the date range
+          echo "$first_day..$last_day"
+          echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
 
-    - name: Run issue-metrics tool
-      uses: github/issue-metrics@v3
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
+      - name: Run issue-metrics tool
+        uses: github/issue-metrics@v3
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
 
-    - name: Create issue
-      uses: peter-evans/create-issue-from-file@v5
-      with:
-        title: Monthly issue metrics report
-        token: ${{ secrets.GITHUB_TOKEN }}
-        content-filepath: ./issue_metrics.md
+      - name: Create issue
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: Monthly issue metrics report
+          token: ${{ secrets.GITHUB_TOKEN }}
+          content-filepath: ./issue_metrics.md

.github/workflows/release.yml

@@ -36,7 +36,7 @@ jobs:
           pip install build
           python -m build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -45,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["39", "310", "311", "312"]
+        python-version: ["310", "311", "312"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
@@ -57,8 +57,9 @@ jobs:
           CIBW_BUILD: cp${{ matrix.python-version }}-*
 
       - name: Save artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
+          name: dist-${{ matrix.os }}-${{ matrix.python-version }}
           path: ./wheelhouse/*.whl
 
   release:
@@ -74,9 +75,10 @@ jobs:
           python-version: "3.12"
 
       - name: Get build artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: dist-*
+          merge-multiple: true
           path: dist
 
       - name: Publish to PyPi or TestPyPI

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-# Runs the complete test suite incl. many external command line dependencies (like Openbabel)
+# Run the complete test suite incl. many external command line dependencies (like Openbabel)
 # as well as the pymatgen.ext package. Coverage used to be computed based on this workflow.
 name: Tests
 
@@ -17,29 +17,33 @@ permissions:
 
 jobs:
   test:
-    # prevent this action from running on forks
+    # Prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
     defaults:
       run:
-        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+        shell: bash -l {0} # Enable conda/mamba env activation by reading bash profile
     strategy:
       fail-fast: false
       matrix:
-        # maximize CI coverage of different platforms and python versions while minimizing the
+        # 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 3.9) on windows (seems most likely to surface errors) and with
+        # version (currently 3.10) on windows (seems most likely to surface errors) and with
         # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
         config:
           - os: windows-latest
-            python: "3.9"
+            python: "3.10"
             resolution: highest
             extras: ci,optional
+          - os: windows-latest
+            python: "3.10"
+            resolution: highest
+            extras: ci,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
           - os: ubuntu-latest
-            python: '>3.9'
+            python: ">3.10"
             resolution: lowest-direct
             extras: ci,optional
           - os: macos-latest
-            python: '3.10'
+            python: "3.11"
             resolution: lowest-direct
             extras: ci # test with only required dependencies installed
 
@@ -64,24 +68,38 @@ jobs:
         run: |
           micromamba create -n pmg python=${{ matrix.config.python }} --yes
 
-      - name: Install uv
-        run: micromamba run -n pmg pip install uv
-
       - name: Install ubuntu-only conda dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |
-          micromamba install -n pmg -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
+          micromamba install -n pmg -c conda-forge bader enumlib openff-toolkit packmol pygraphviz tblite --yes
 
-      - name: Install pymatgen and dependencies
+      - name: Install pymatgen and dependencies via uv
         run: |
           micromamba activate pmg
-          # TODO remove temporary fix. added since uv install torch is flaky.
-          # track https://github.com/astral-sh/uv/issues/1921 for resolution
-          pip install torch --upgrade
 
-          uv pip install numpy cython
+          pip install uv
+
+          # TODO1 (use uv over pip) uv install torch is flaky, track #3826
+          # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
+          # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
+          pip install torch==2.2.1
+
           uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 
+      - name: Install optional Ubuntu dependencies
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+          # Install BoltzTraP
+          wget -q -O BoltzTraP.tar.bz2 https://owncloud.tuwien.ac.at/index.php/s/s2d55LYlZnioa3s/download
+          tar -jxf BoltzTraP.tar.bz2
+          echo "$(realpath boltztrap-1.2.5/src/)" >> $GITHUB_PATH
+
+          # Install Vampire 5.0
+          wget -q https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
+          tar -zxf vampire-5.0-linux.tar.gz
+          mv linux vampire-5.0
+          echo "$(realpath vampire-5.0/)" >> $GITHUB_PATH
+
       - name: pytest split ${{ matrix.split }}
         run: |
           micromamba activate pmg
@@ -90,7 +108,7 @@ jobs:
   trigger_atomate2_ci:
     needs: test
     runs-on: ubuntu-latest
-    # only run if changes were pushed to master
+    # Only run if changes are pushed to master
     if: github.ref == 'refs/heads/master'
     steps:
       - name: Trigger Atomate2 CI

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.4
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
 
@@ -65,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.374
+    rev: v1.1.379
     hooks:
       - id: pyright

ADMIN.md

@@ -16,7 +16,7 @@ The general procedure for releasing `pymatgen` comprises the following steps:
 
 ## Initial setup
 
-Pymatgen uses [invoke](http://pyinvoke.org) to automate releases.
+Pymatgen uses [invoke](https://pyinvoke.org) to automate releases.
 You will also need `sphinx` and `doc2dash`.
 
 ```sh

CITATION.cff

@@ -5,7 +5,7 @@ message: |
 
   In addition, some of pymatgen's functionality is based on scientific advances
   / principles developed by the computational materials scientists in our team.
-  Please refer to pymatgen's docs at http://pymatgen.org on how to cite them.
+  Please refer to pymatgen's docs at https://pymatgen.org on how to cite them.
 authors:
 - family-names: Ong
   given-names: Shyue Ping

CONTRIBUTING.md

@@ -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 3.9+.
+1. **Python 3**. We only support Python 3.10+.
 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

@@ -12,7 +12,7 @@ height="70">
 [![codecov](https://codecov.io/gh/materialsproject/pymatgen/branch/master/graph/badge.svg?token=XC47Un1LV2)](https://codecov.io/gh/materialsproject/pymatgen)
 [![PyPI Downloads](https://img.shields.io/pypi/dm/pymatgen?logo=pypi&logoColor=white&color=blue&label=PyPI)](https://pypi.org/project/pymatgen)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pymatgen?logo=condaforge&color=blue&label=Conda)](https://anaconda.org/conda-forge/pymatgen)
-[![Requires Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
+[![Requires Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 [![Paper](https://img.shields.io/badge/J.ComMatSci-2012.10.028-blue?logo=elsevier&logoColor=white)](https://doi.org/10.1016/j.commatsci.2012.10.028)
 
 </h4>
@@ -63,7 +63,7 @@ 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 3.9. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
+The minimum Python version is 3.10. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
 
 ## Change Log