Migrate CI from pip to uv

.github/workflows/deploy.yml

@@ -27,10 +27,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          pip install uv
+          uv pip install .[strict,docs] --system
           # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,docs]
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
 
       - name: Build
         run: sphinx-build docs docs_build

.github/workflows/docs.yml

@@ -32,10 +32,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          pip install uv
+          uv pip install .[strict,docs] --system
           # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,docs]
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
 
       - name: Build
         run: sphinx-build docs docs_build

.github/workflows/testing.yml

@@ -16,12 +16,12 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
-        with:
-          python-version: "3.9"
-          cache: pip
-          cache-dependency-path: pyproject.toml
 
-      - uses: pre-commit/[email protected]
+      - name: Install dependencies
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files --show-diff-on-failure
 
   test:
     services:
@@ -42,6 +42,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install LLVM and Clang
+        uses: KyleMayes/install-llvm-action@v2
+        with:
+          version: "10.0"
+
       - name: Install enumlib
         run: |
           cd ..
@@ -56,16 +61,20 @@ jobs:
           sudo cp aux_src/makeStr.py /usr/local/bin/
         continue-on-error: true # This is not critical to succeed.
 
+      # TODO figure out where the llvm-config bin is really located
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          pip install uv
+          LLVM_CONFIG=/home/runner/work/atomate2/atomate2/llvm/bin/llvm-config uv pip install .[strict,tests,abinit] --system --prerelease=allow
+          # latest ase needed to get FrechetCellFilter used by ML force fields
+          # TODO remove next line installing ase from main branch when FrechetCellFilter is released
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
+          uv pip install torch-runstats --system
+          uv pip install --no-deps nequip==0.5.6 --system
+
+          # Install pseudos for abinit tests
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,tests,abinit]
-          pip install torch-runstats
-          pip install --no-deps nequip==0.5.6
 
       - name: Install pymatgen from master if triggered by pymatgen repo dispatch
         if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
@@ -99,10 +108,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          pip install uv
+          uv pip install .[strict,docs] --system
           # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,docs]
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
 
       - name: Build
         run: sphinx-build docs docs_build

pyproject.toml

@@ -56,7 +56,8 @@ forcefields = [
     "mace-torch>=0.3.3",
     "matgl>=1.1.1",
     "quippy-ase>=0.9.14",
-    "torch<=2.2.1",       # incompatibility with dgl if newer versions are used
+    "torch-runstats>=0.2.0", # transitive dependency for NequIP
+    "torch<=2.2.1",          # incompatibility with dgl if newer versions are used
 ]
 docs = [
     "FireWorks==2.0.3",
@@ -106,7 +107,8 @@ strict = [
     "python-ulid==2.7.0",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
-    "torch==2.2.1",
+    "torch-runstats>=0.2.0",                # transitive dependency for NequIP
+    "torch==2.2.1",                         # incompatibility with dgl if newer versions are used
     "typing-extensions==4.12.2",
 ]
 

tests/vasp/jobs/test_eos.py

@@ -51,9 +51,7 @@ def test_mp_gga_eos_relax_maker(mock_vasp, clean_dir, vasp_test_dir):
 
 def test_mp_gga_eos_static_maker(mock_vasp, clean_dir, vasp_test_dir):
     # map from job name to directory containing reference output files
-    ref_paths = {
-        "EOS MP GGA static": "Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0",
-    }
+    ref_paths = {"EOS MP GGA static": "Si_EOS_MP_GGA/mp-149-PBE-EOS_Static_0"}
 
     # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings
     fake_run_vasp_kwargs = {

tests/vasp/test_base.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
+import numpy as np
 import pytest
 from custodian.vasp.handlers import ErrorHandler
-from pymatgen.core import Lattice, Structure
+from pymatgen.core import Structure
 
 from atomate2.vasp.run import DEFAULT_HANDLERS
 from atomate2.vasp.sets.base import get_magmoms
@@ -15,7 +16,7 @@ def test_get_magmoms(
 ) -> None:
     # structure with Co that will be assigned magmoms
     struct = Structure(
-        lattice=Lattice.cubic(3),
+        lattice=3 * np.eye(3),
         species=["Co", "Fe"],
         coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
     )
@@ -44,7 +45,7 @@ def test_get_magmoms_with_specie() -> None:
     # the code that checks for `Specie.spin`.
     # @jmmshn
     struct = Structure(
-        lattice=Lattice.cubic(3),
+        lattice=3 * np.eye(3),
         species=["Co2+", "Fe3+"],
         coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
     )

tests/vasp/test_sets.py

@@ -1,5 +1,6 @@
+import numpy as np
 import pytest
-from pymatgen.core import Lattice, Species, Structure
+from pymatgen.core import Species, Structure
 
 from atomate2.vasp.sets.core import StaticSetGenerator
 from atomate2.vasp.sets.mp import MPMetaGGARelaxSetGenerator
@@ -10,7 +11,7 @@ def struct_no_magmoms() -> Structure:
     """Dummy FeO structure with expected +U corrections but no magnetic moments
     defined."""
     return Structure(
-        lattice=Lattice.cubic(3),
+        lattice=3 * np.eye(3),
         species=("Fe", "O"),
         coords=((0, 0, 0), (0.5, 0.5, 0.5)),
     )
@@ -23,7 +24,7 @@ def struct_with_spin() -> Structure:
     oxi = Species("O2-", spin=0.63)
 
     return Structure(
-        lattice=Lattice.cubic(3),
+        lattice=3 * np.eye(3),
         species=(iron, oxi),
         coords=((0, 0, 0), (0.5, 0.5, 0.5)),
     )
@@ -41,7 +42,7 @@ def struct_with_magmoms(struct_no_magmoms) -> Structure:
 def struct_no_u_params() -> Structure:
     """Dummy SiO structure with no anticipated +U corrections"""
     return Structure(
-        lattice=Lattice.cubic(3),
+        lattice=3 * np.eye(3),
         species=("Si", "O"),
         coords=((0, 0, 0), (0.5, 0.5, 0.5)),
     )