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

Author: shyuep

.github/workflows/_install_opt_unit_deps.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+set -euo pipefail
+set -x
+
+# Use a custom bin directory for easier GitHub Actions caching
+BIN_DIR="${1:-$PWD/opt/bin}" && mkdir -p "$BIN_DIR"
+
+# Install BoltzTraP
+wget --no-verbose -O BoltzTraP.tar.bz2 https://owncloud.tuwien.ac.at/index.php/s/s2d55LYlZnioa3s/download
+tar -jxf BoltzTraP.tar.bz2
+cp boltztrap-1.2.5/src/{BoltzTraP,x_trans} "$BIN_DIR"
+
+# Install Vampire 5.0
+# TODO: Accepts self-signed cert (https://github.com/richard-evans/vampire/issues/122)
+wget --no-verbose --no-check-certificate 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
+cp vampire-5.0/vampire-serial "$BIN_DIR"
+
+# Install Voro++ and ZEO++
+wget --no-verbose http://www.zeoplusplus.org/zeo++-0.3.tar.gz
+tar -xzf zeo++-0.3.tar.gz
+make -C zeo++-0.3/voro++/src -s CFLAGS="-w"
+make -C zeo++-0.3 -s CFLAGS="-w"
+cp zeo++-0.3/voro++/src/voro++ "$BIN_DIR"
+cp zeo++-0.3/network "$BIN_DIR"
+
+# Install mcsqs (from ATAT)
+# TODO: cannot build on MacOS
+if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+  wget --no-verbose https://axelvandewalle.github.io/www-avdw/atat/atat3_50.tar.gz
+  tar -zxf atat3_50.tar.gz
+
+  # Replace `BINDIR` in makefile
+  sed -i "s|^BINDIR=.*|BINDIR=$BIN_DIR|" atat/makefile
+
+  sudo apt install csh -y -q
+  make -C atat && make -C atat install
+fi
+
+# Add to path
+echo "$BIN_DIR" >> "$GITHUB_PATH"

.github/workflows/test.yml

@@ -56,6 +56,7 @@ jobs:
       MPLBACKEND: Agg  # non-interactive backend for matplotlib
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
       PYTHONWARNDEFAULTENCODING: "true"  # PEP 597: Enable optional EncodingWarning
+      OPT_BIN_DIR: ${{ github.workspace }}/opt/bin  # for optional Unix dependencies
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
@@ -94,23 +95,17 @@ jobs:
           pip install --upgrade matgl>=1.2.6
           pip install torch==2.2.0 torchdata==0.7.1
 
-      - name: Install optional Ubuntu and macOS dependencies
+      - name: Restore cache for optional Ubuntu/MacOS dependencies
         if: matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-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 && 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
-          realpath vampire-5.0/ >> $GITHUB_PATH
-
-          # Install Voro++ and ZEO++
-          wget -q http://www.zeoplusplus.org/zeo++-0.3.tar.gz && tar -xzf zeo++-0.3.tar.gz
+        id: optbin-cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.OPT_BIN_DIR }}
+          key: opt-bin-${{ runner.os }}-${{ hashFiles('.github/workflows/_install_opt_unit_deps.sh') }}
 
-          cd zeo++-0.3/voro++/src && make -s CFLAGS="-w" && realpath . >> $GITHUB_PATH && cd ../..
-          make -s CFLAGS="-w" && realpath . >> $GITHUB_PATH
+      - name: Build optional Ubuntu/MacOS dependencies (when cache misses)
+        if: (matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest') && steps.optbin-cache.outputs.cache-hit != 'true'
+        run: bash .github/workflows/_install_opt_unit_deps.sh "$OPT_BIN_DIR"
 
       - name: pytest split ${{ matrix.split }}
         env:

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.2.5]
@@ -37,7 +37,7 @@ repos:
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.6
+    rev: v0.16.7
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -66,6 +66,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.401
+    rev: v1.1.402
     hooks:
       - id: pyright

dev_scripts/periodic_table_resources/_periodic_table.yaml

@@ -35,6 +35,7 @@ Atomic no:
     No: 102, Lr: 103, Rf: 104, Db: 105, Sg: 106, Bh: 107, Hs: 108, Mt: 109, Ds: 110,
     Rg: 111, Cn: 112, Nh: 113, Fl: 114, Mc: 115, Lv: 116, Ts: 117, Og: 118}
 Atomic orbitals:
+  unit: hartree
   data:
     H:
       1s: -0.233471
@@ -1086,7 +1087,7 @@ Boiling point:
     Pb: 2022, Bi: 1837, Po: 1235, Rn: 211.3, Ra: 2010, Ac: 3573, Th: 5093, U: 4200,
     Np: 4273, Pu: 3503, Am: 2880, Cm: 3383}
 Brinell hardness:
-  unit: MN m^-2
+  unit: MPa
   data: {Be: 600, Na: 0.69, Mg: 260, Al: 245, K: 0.363, Ca: 167, Sc: 750, Ti: 716,
     V: 628, Cr: 1120, Mn: 196, Fe: 490, Co: 700, Ni: 700, Cu: 874, Zn: 412, Ga: 60,
     As: 1440, Se: 736, Rb: 0.216, Y: 589, Zr: 650, Nb: 736, Mo: 1500, Ru: 2160, Rh: 1100,
@@ -2579,7 +2580,7 @@ Mineral hardness:
     Re: 7.0, Os: 7.0, Ir: 6.5, Pt: 3.5, Au: 2.5, Hg: 1.5, Tl: 1.2, Pb: 1.5, Bi: 2.25,
     Th: 3.0, U: 6.0}
 Molar volume:
-  unit: cm^3
+  unit: cm^3 mol^-1
   data: {H: 11.42, He: 21.0, Li: 13.02, Be: 4.85, B: 4.39, C: 5.29, N: 13.54, O: 17.36,
     F: 11.20, Ne: 13.23, Na: 23.78, Mg: 14.00, Al: 10.00, Si: 12.06, P: 17.02, S: 15.53,
     Cl: 17.39, Ar: 22.56, K: 45.94, Ca: 26.20, Sc: 15.00, Ti: 10.64, V: 8.32, Cr: 7.23,
@@ -4156,7 +4157,7 @@ Velocity of sound:
     Hf: 3010, Ta: 3400, W: 5174, Re: 4700, Os: 4940, Ir: 4825, Pt: 2680, Au: 1740,
     Hg: 1407, Tl: 818, Pb: 1260, Bi: 1790, Th: 2490, U: 3155, Pu: 2260}
 Vickers hardness:
-  unit: MN m^-2
+  unit: MPa
   data: {Be: 1670, B: 49000, Al: 167, Ti: 970, V: 628, Cr: 1060, Fe: 608, Co: 1043,
     Ni: 638, Cu: 369, Zr: 903, Nb: 1320, Mo: 1530, Rh: 1246, Pd: 461, Ag: 251, La: 491,
     Ce: 270, Pr: 400, Nd: 343, Sm: 412, Eu: 167, Gd: 570, Tb: 863, Dy: 540, Ho: 481,

dev_scripts/periodic_table_resources/elemental_properties.yaml

@@ -244,6 +244,7 @@ Atomic no:
     D: 1
     T: 1
 Atomic orbitals:
+  unit: hartree
   data:
     Ac:
       1s: -3443.110367
@@ -1349,7 +1350,7 @@ Boiling point:
     Zn: 1180
     Zr: 4682
 Brinell hardness:
-  unit: MN m^-2
+  unit: MPa
   data:
     Ag: 24.5
     Al: 245
@@ -2584,7 +2585,7 @@ Mineral hardness:
     Zn: 2.5
     Zr: 5.0
 Molar volume:
-  unit: cm^3
+  unit: cm^3 mol^-1
   data:
     Ac: 22.55
     Ag: 10.27
@@ -3183,7 +3184,7 @@ Velocity of sound:
     Zn: 3700
     Zr: 3800
 Vickers hardness:
-  unit: MN m^-2
+  unit: MPa
   data:
     Ag: 251
     Al: 167

docs/Gemfile.lock

@@ -105,7 +105,7 @@ mlp = ["matgl>=1.2.7 ; python_version<'3.13'"]
 numba = ["numba>=0.55"]
 numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [
-    "pymatgen[abinit,ase,mlp,tblite,matcalc]",
+    "pymatgen[abinit,ase,matcalc,mlp,tblite,zeopp]",
     "beautifulsoup4",
     # PR4347: BoltzTraP2 needs to bump cmake version for spglib build
     # "BoltzTraP2>=24.9.4",
@@ -125,7 +125,7 @@ symmetry = ["moyopy[interface]>=0.3", "spglib>=2.5"]
 # https://github.com/tblite/tblite/issues/175
 tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
 vis = ["vtk>=6.0.0"]
-zeopp = ["pyzeo"]  # Note: requires Voro++ and Zeo++ to be installed
+zeopp = ["pyzeo; platform_system != 'Windows'"]  # Note: requires Voro++ and Zeo++ to be installed
 
 [project.scripts]
 pmg = "pymatgen.cli.pmg:main"

pyproject.toml

@@ -347,11 +347,11 @@ def combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=Fa
         )
 
         if arranged_neb_analyses:
-            neb1_energies = (
-                neb1_energies[0 : len(neb1_energies) - 1]
-                + [(neb1_energies[-1] + neb2_energies[0]) / 2]
-                + neb2_energies[1:]
-            )
+            neb1_energies = [
+                *neb1_energies[0 : len(neb1_energies) - 1],
+                (neb1_energies[-1] + neb2_energies[0]) / 2,
+                *neb2_energies[1:],
+            ]
             neb1_structures += neb2.structures[1:]
             neb1_forces = list(neb1_forces) + list(neb2.forces)[1:]
             neb1_r = list(neb1_r) + [i + neb1_r[-1] for i in list(neb2.r)[1:]]

src/pymatgen/analysis/transition_state.py

@@ -146,7 +146,7 @@ def run_mcsqs(
 
         raise RuntimeError("mcsqs exited before timeout reached")
 
-    except TimeoutExpired:
+    except TimeoutExpired as exc:
         for process in mcsqs_find_sqs_processes:
             process.kill()
             process.communicate()
@@ -157,7 +157,7 @@ def run_mcsqs(
                 raise RuntimeError(
                     "mcsqs did not generate output files, "
                     "is search_time sufficient or are number of instances too high?"
-                )
+                ) from exc
 
             process = Popen(["mcsqs", "-best"])
             process.communicate()
@@ -166,7 +166,7 @@ def run_mcsqs(
             return _parse_sqs_path(".")
 
         os.chdir(original_directory)
-        raise TimeoutError("Cluster expansion took too long.")
+        raise TimeoutError("Cluster expansion took too long.") from exc
 
 
 def _parse_sqs_path(path) -> Sqs:

src/pymatgen/command_line/mcsqs_caller.py

@@ -2816,7 +2816,7 @@ def from_slabs(
         min_height = np.abs(film_max_c - film_min_c) + np.abs(sub_max_c - sub_min_c)
 
         # Construct new lattice
-        abc = substrate_slab.lattice.abc[:2] + (min_height + gap + vacuum_over_film,)
+        abc = (*substrate_slab.lattice.abc[:2], min_height + gap + vacuum_over_film)
         angles = substrate_slab.lattice.angles
         lattice = Lattice.from_parameters(*abc, *angles)