Major dependency updates after numpy 2.0.0. pymatgen, monty, h5py, sc…

…ikit-learn, scipy versions updated accordingly. Pyscipopt now contains bundled solver library, no longer needs stand-alone binary installation.

.github/workflows/test.yml

@@ -1,8 +1,5 @@
 name: test
 
-env:
-  scip-version: 8.0.0
-
 on:
   push:
     branches:
@@ -16,15 +13,14 @@ on:
 
 jobs:
   test:
-    # Only 20.04 is known to work with scip 8.0.0
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       #max-parallel: 10
       matrix:
         config:
-          - python: "3.9"
           - python: "3.10"
           - python: "3.11"
+          - python: "3.12"
 
         split: [1, 2, 3, 4, 5, 6, 7, 8]
 
@@ -35,11 +31,6 @@ jobs:
         with:
           python-version:  ${{ matrix.config.python }}
 
-      - name: Install dependencies
-        run: |
-          wget --quiet --no-check-certificate https://scipopt.org/download/release/SCIPOptSuite-${{ env.scip-version }}-Linux-ubuntu.deb
-          sudo apt-get update && sudo apt install -y ./SCIPOptSuite-${{ env.scip-version }}-Linux-ubuntu.deb
-
       - name: Cache pip
         uses: actions/cache@v4
         with:

.pre-commit-config.yaml

@@ -38,7 +38,7 @@ repos:
     - --profile=black
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.19.0
+  rev: v3.19.1
   hooks:
     - id: pyupgrade
       args: [--py38-plus]

binder/requirements.txt

@@ -1,7 +1,7 @@
 nbgitpuller
-numpy>=1.20.1
-monty==2023.9.25
-pymatgen==2023.8.10
-scikit-learn==1.3.2
-h5py==3.11.0
+numpy==2.2.1
+monty==2024.12.10
+pymatgen==2024.11.13
+scikit-learn==1.6.0
+h5py==3.12.1
 crystal_toolkit

pyproject.toml

@@ -19,17 +19,19 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules"
 ]
 dependencies = [
-    "numpy >=1.24,<2.0",
-    "pymatgen >=2023.08.10",
-    "monty >=v2022.9.8",
-    "h5py >=3.10.0"
+    "numpy >=2.0.0,<3.0",
+    "pymatgen >=2024.11.13",
+    "monty >=2024.12.10",
+    "h5py >=3.12.0"
 ]
 authors = [
     {name = "Luis Barroso-Luque", email = "[email protected]"},
-    {name = "Fengyu Xie", email = "lbluque@berkeley.edu"}
+    {name = "Fengyu Xie", email = "fengyu_xie@berkeley.edu"}
 ]
 maintainers = [
-    {name = "Luis Barroso-Luque", email = "[email protected]"}
+    {name = "Luis Barroso-Luque", email = "[email protected]"},
+    {name = "Fengyu Xie", email = "[email protected]"},
+    {name = "Ronald Kam", email = "[email protected]"}
 ]
 
 [project.optional-dependencies]
@@ -55,7 +57,7 @@ test = [
     "pytest-cov >=4.0.0",
     "pytest-split>=0.9.0",
     "scikit-learn >=1.1.2",
-    "h5py >=3.10.0",
+    "h5py >=3.12.0",
     "coverage",
     "polytope",
     "cvxpy",
@@ -79,7 +81,7 @@ changelog = "https://cedergrouphub.github.io/smol/CHANGES.md"
 tracker = "https://github.com/CederGroupHub/smol/issues"
 
 [build-system]
-requires = ["setuptools", "setuptools-scm[toml]>=6.2", "cython>= 0.29.34", "numpy>=1.24"]
+requires = ["setuptools", "setuptools-scm[toml]>=6.2", "cython>= 0.29.34", "numpy>=2.0.0"]
 # Use legacy backend to import local packages in setup.py
 build-backend = "setuptools.build_meta:__legacy__"
 

requirements.txt

@@ -1,4 +1,4 @@
-numpy==1.25.2
-monty==2023.9.25
-pymatgen==2023.9.10
-h5py==3.11.0
+numpy==2.2.1
+monty==2024.12.10
+pymatgen==2024.11.13
+h5py==3.12.1