Bump lobsterpy from 0.4.5 to 0.4.9 (#1001)

* Bump lobsterpy from 0.4.5 to 0.4.9

Bumps [lobsterpy](https://github.com/JaGeo/LobsterPy) from 0.4.5 to 0.4.9.
- [Release notes](https://github.com/JaGeo/LobsterPy/releases)
- [Changelog](https://github.com/JaGeo/LobsterPy/blob/main/CHANGELOG.md)
- [Commits](JaGeo/LobsterPy@v0.4.5...v0.4.9)

---
updated-dependencies:
- dependency-name: lobsterpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update pyproject.toml

* switch to one matches

* switch to molecule matcher

* make tests as strict as they need to be again

* remove unused import

* test pymatgen master

* Fix phonon workflow (#1005)

it failed because of using the old interface in atomate2

* new pymatgen version

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: J. George <[email protected]>
Co-authored-by: JaGeo <[email protected]>
Co-authored-by: Thomas Purcell <[email protected]>

Author: 3 people

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "numpy",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pymatgen>=2024.6.4",
+    "pymatgen>=2024.10.3",
 ]
 
 [project.optional-dependencies]
@@ -99,7 +99,7 @@ strict = [
     "emmet-core==0.84.2",
     "ijson==3.3.0",
     "jobflow==0.1.18",
-    "lobsterpy==0.4.5",
+    "lobsterpy==0.4.9",
     "mdanalysis==2.7.0",
     "monty==2024.7.30",
     "mp-api==0.42.2",
@@ -110,7 +110,7 @@ strict = [
     "pydantic-settings==2.5.2",
     "pydantic==2.9.2",
     "pymatgen-analysis-defects==2024.7.19",
-    "pymatgen==2024.6.10",
+    "pymatgen==2024.10.3",
     "python-ulid==2.7.0",
     "seekpath==2.1.0",
     "tblite==0.3.0; python_version < '3.12'",

tests/aims/test_flows/test_phonon_workflow.py

@@ -1,14 +1,11 @@
 """Test various makers"""
 
 import json
-import os
 
 import pytest
 
-cwd = os.getcwd()
 
-
-def test_phonon_flow(si, tmp_path, mock_aims, species_dir):
+def test_phonon_flow(si, clean_dir, mock_aims, species_dir):
     import numpy as np
     from jobflow import run_locally
     from pymatgen.io.aims.sets.core import StaticSetGenerator
@@ -57,9 +54,7 @@ def test_phonon_flow(si, tmp_path, mock_aims, species_dir):
     )
 
     # run the flow or job and ensure that it finished running successfully
-    os.chdir(tmp_path)
     responses = run_locally(flow, create_folders=True, ensure_success=True)
-    os.chdir(cwd)
 
     # validation the outputs of the job
     output = responses[flow.job_uuids[-1]][1].output
@@ -100,7 +95,7 @@ def test_phonon_flow(si, tmp_path, mock_aims, species_dir):
 
 
 @pytest.mark.skip(reason="Currently not mocked and needs FHI-aims binary")
-def test_phonon_socket_flow(si, tmp_path, mock_aims, species_dir):
+def test_phonon_socket_flow(si, clean_dir, mock_aims, species_dir):
     import numpy as np
     from jobflow import run_locally
     from pymatgen.io.aims.sets.core import StaticSetGenerator
@@ -153,9 +148,7 @@ def test_phonon_socket_flow(si, tmp_path, mock_aims, species_dir):
     )
 
     # run the flow or job and ensure that it finished running successfully
-    os.chdir(tmp_path)
     responses = run_locally(flow, create_folders=True, ensure_success=True)
-    os.chdir(cwd)
 
     # validation the outputs of the job
     output = responses[flow.job_uuids[-1]][1].output
@@ -194,9 +187,10 @@ def test_phonon_socket_flow(si, tmp_path, mock_aims, species_dir):
     assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 14.41
 
 
-def test_phonon_default_flow(si, tmp_path, mock_aims, species_dir):
+def test_phonon_default_flow(si, clean_dir, mock_aims, species_dir):
     import numpy as np
     from jobflow import run_locally
+    from pymatgen.core import SETTINGS
 
     from atomate2.aims.flows.phonons import PhononMaker
 
@@ -213,8 +207,8 @@ def test_phonon_default_flow(si, tmp_path, mock_aims, species_dir):
     # automatically use fake FHI-aims
     mock_aims(ref_paths, fake_run_aims_kwargs)
 
-    aims_sd = os.environ.get("AIMS_SPECIES_DIR")
-    os.environ["AIMS_SPECIES_DIR"] = str(species_dir / "light")
+    aims_sd = SETTINGS.get("AIMS_SPECIES_DIR")
+    SETTINGS["AIMS_SPECIES_DIR"] = str(species_dir / "light")
 
     maker = PhononMaker()
     maker.name = "phonons"
@@ -224,9 +218,7 @@ def test_phonon_default_flow(si, tmp_path, mock_aims, species_dir):
     )
 
     # run the flow or job and ensure that it finished running successfully
-    os.chdir(tmp_path)
     responses = run_locally(flow, create_folders=True, ensure_success=True)
-    os.chdir(cwd)
 
     # validation the outputs of the job
     output = responses[flow.job_uuids[-1]][1].output
@@ -265,18 +257,19 @@ def test_phonon_default_flow(si, tmp_path, mock_aims, species_dir):
     assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 15.02
 
     if aims_sd is not None:
-        os.environ["AIMS_SPECIES_DIR"] = aims_sd
+        SETTINGS["AIMS_SPECIES_DIR"] = aims_sd
 
 
 @pytest.mark.skip(reason="Currently not mocked and needs FHI-aims binary")
-def test_phonon_default_socket_flow(si, tmp_path, mock_aims, species_dir):
+def test_phonon_default_socket_flow(si, clean_dir, mock_aims, species_dir):
     import numpy as np
     from jobflow import run_locally
+    from pymatgen.core import SETTINGS
 
     from atomate2.aims.flows.phonons import PhononMaker
 
-    aims_sd = os.environ.get("AIMS_SPECIES_DIR")
-    os.environ["AIMS_SPECIES_DIR"] = str(species_dir / "light")
+    aims_sd = SETTINGS.get("AIMS_SPECIES_DIR")
+    SETTINGS["AIMS_SPECIES_DIR"] = str(species_dir / "light")
 
     # mapping from job name to directory containing test files
     ref_paths = {
@@ -301,9 +294,7 @@ def test_phonon_default_socket_flow(si, tmp_path, mock_aims, species_dir):
     )
 
     # run the flow or job and ensure that it finished running successfully
-    os.chdir(tmp_path)
     responses = run_locally(flow, create_folders=True, ensure_success=True)
-    os.chdir(cwd)
 
     # validation the outputs of the job
     output = responses[flow.job_uuids[-1]][1].output
@@ -343,4 +334,4 @@ def test_phonon_default_socket_flow(si, tmp_path, mock_aims, species_dir):
     assert np.round(output.phonon_bandstructure.bands[-1, 0], 2) == 15.02
 
     if aims_sd is not None:
-        os.environ["AIMS_SPECIES_DIR"] = aims_sd
+        SETTINGS["AIMS_SPECIES_DIR"] = aims_sd

tests/ase/test_jobs.py

@@ -45,6 +45,7 @@ def test_lennard_jones_static_maker(lj_fcc_ne_pars, fcc_ne_structure):
     assert output.output.energy == pytest.approx(-0.0179726955438795)
     assert output.structure.volume == pytest.approx(24.334)
     assert isinstance(output, AseStructureTaskDoc)
+    output.structure.properties = fcc_ne_structure.properties
     assert output.structure == fcc_ne_structure
 
 
@@ -102,4 +103,6 @@ def test_gfn_xtb_static_maker(h2o_3uud_trimer):
 
     assert output.output.energy_per_atom == pytest.approx(-46.05920227158222)
     assert isinstance(output, AseMoleculeTaskDoc)
+
+    output.molecule.properties = h2o_3uud_trimer.properties
     assert output.molecule == h2o_3uud_trimer