Migrate to new MP API, fix failing examples

.github/workflows/test.yml

@@ -1,5 +1,4 @@
-# Runs 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.
+# Runs the complete test suite incl. many external dependencies (like Openbabel)
 name: Tests
 
 on:
@@ -15,19 +14,18 @@ jobs:
   test:
     defaults:
       run:
-        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+        shell: bash -l {0}  # enables conda/mamba env activation by reading bash profile
     strategy:
       fail-fast: false
       matrix:
-        # pytest-split automatically distributes work load so parallel jobs finish in similar time
         os: [ubuntu-latest]
         python-version: ["3.11"]
 
     runs-on: ${{ matrix.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      PMG_VASP_PSP_DIR: /home/runner/work/matgenb/matgenb/psp
+      PMG_VASP_PSP_DIR: "${{ github.workspace }}/psp"
 
     steps:
       - name: Check out repo
@@ -42,7 +40,9 @@ jobs:
           micromamba install -n venv -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
 
       - name: Install uv
-        run: micromamba run -n venv pip install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
 
       - name: Install dependencies
         run: |
@@ -54,5 +54,4 @@ jobs:
         run: |
           micromamba activate venv
           cd notebooks
-          pwd
           pytest --ignore-glob=*notest.ipynb --nbmake .

.pre-commit-config.yaml

@@ -5,48 +5,48 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.3
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         args: [--py39-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.3.1
     hooks:
       - id: autoflake
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.13.0
     hooks:
       - id: mypy
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.3
+    rev: 1.9.1
     hooks:
       - id: nbqa-pyupgrade
         args: [--py39-plus]
       - id: nbqa-isort
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

requirements-ci.txt

@@ -5,5 +5,5 @@ nbmake
 pymatgen
 pymatgen-analysis-diffusion
 mp-api
-# BoltzTraP2  # Does not work because numpy not detected.
+BoltzTraP2
 phonopy