nomad-schema-plugin-simulation-workflow 1.0.10__tar.gz → 1.0.12__tar.gz

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/.github/workflows/actions.yaml

@@ -6,7 +6,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.9", "3.10", "3.11"]
+        python_version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
 

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/.github/workflows/publish.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - name: Install pypa/build
         run: >-
           python3 -m

{nomad_schema_plugin_simulation_workflow-1.0.10/nomad_schema_plugin_simulation_workflow.egg-info → nomad_schema_plugin_simulation_workflow-1.0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-schema-plugin-simulation-workflow
-Version: 1.0.10
+Version: 1.0.12
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12/nomad_schema_plugin_simulation_workflow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-schema-plugin-simulation-workflow
-Version: 1.0.10
+Version: 1.0.12
 Summary: Simulation workflow schema plugin for NOMAD.
 Author: The NOMAD Authors
 License: Apache-2.0

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/nomad_schema_plugin_simulation_workflow.egg-info/SOURCES.txt

@@ -26,6 +26,8 @@ nomad_schema_plugin_simulation_workflow.egg-info/SOURCES.txt
 nomad_schema_plugin_simulation_workflow.egg-info/dependency_links.txt
 nomad_schema_plugin_simulation_workflow.egg-info/entry_points.txt
 nomad_schema_plugin_simulation_workflow.egg-info/requires.txt
+nomad_schema_plugin_simulation_workflow.egg-info/scm_file_list.json
+nomad_schema_plugin_simulation_workflow.egg-info/scm_version.json
 nomad_schema_plugin_simulation_workflow.egg-info/top_level.txt
 simulationworkflowschema/__init__.py
 simulationworkflowschema/chemical_reaction.py

nomad_schema_plugin_simulation_workflow-1.0.12/nomad_schema_plugin_simulation_workflow.egg-info/scm_file_list.json

@@ -0,0 +1,149 @@
+{
+  "files": [
+    ".github/workflows/actions.yaml",
+    ".github/workflows/mkdocs-deploy.yml",
+    ".github/workflows/publish.yml",
+    ".gitignore",
+    "CITATION.cff",
+    "LICENSE",
+    "README.md",
+    "docs/assets/.gitignore",
+    "docs/assets/favicon.png",
+    "docs/assets/nomad-plugin-logo.png",
+    "docs/explanation/explanation.md",
+    "docs/how_to/contribute_to_the_documentation.md",
+    "docs/how_to/contribute_to_this_plugin.md",
+    "docs/how_to/install_this_plugin.md",
+    "docs/how_to/use_this_plugin.md",
+    "docs/index.md",
+    "docs/reference/references.md",
+    "docs/stylesheets/extra.css",
+    "docs/theme/partials/header.html",
+    "docs/tutorial/tutorial.md",
+    "mkdocs.yml",
+    "pyproject.toml",
+    "simulationworkflowschema/__init__.py",
+    "simulationworkflowschema/chemical_reaction.py",
+    "simulationworkflowschema/dmft.py",
+    "simulationworkflowschema/elastic.py",
+    "simulationworkflowschema/equation_of_state.py",
+    "simulationworkflowschema/general.py",
+    "simulationworkflowschema/geometry_optimization.py",
+    "simulationworkflowschema/gw.py",
+    "simulationworkflowschema/max_ent.py",
+    "simulationworkflowschema/molecular_dynamics.py",
+    "simulationworkflowschema/nomad_plugin.yaml",
+    "simulationworkflowschema/phonon.py",
+    "simulationworkflowschema/photon_polarization.py",
+    "simulationworkflowschema/single_point.py",
+    "simulationworkflowschema/tb.py",
+    "simulationworkflowschema/thermodynamics.py",
+    "simulationworkflowschema/xs.py",
+    "tests/conftest.py",
+    "tests/data/ase/Cu.traj",
+    "tests/data/chemical_reaction/.NPdAg_vasprun.xml.swp",
+    "tests/data/chemical_reaction/N/run.archive.json",
+    "tests/data/chemical_reaction/N/vasprun.xml",
+    "tests/data/chemical_reaction/NPdAg/run.archive.json",
+    "tests/data/chemical_reaction/NPdAg/vasprun.xml",
+    "tests/data/chemical_reaction/PdAg/run.archive.json",
+    "tests/data/chemical_reaction/PdAg/vasprun.xml",
+    "tests/data/chemical_reaction/RhCu/INCAR",
+    "tests/data/chemical_reaction/RhCu/OUTCAR",
+    "tests/data/chemical_reaction/RhCu/run.archive.json",
+    "tests/data/chemical_reaction/RhCu_CH3/INCAR",
+    "tests/data/chemical_reaction/RhCu_CH3/OUTCAR",
+    "tests/data/chemical_reaction/RhCu_CH3/run.archive.json",
+    "tests/data/chemical_reaction/RhCu_CH3_H/INCAR",
+    "tests/data/chemical_reaction/RhCu_CH3_H/OUTCAR",
+    "tests/data/chemical_reaction/RhCu_CH3_H/run.archive.json",
+    "tests/data/chemical_reaction/RhCu_CH4/INCAR",
+    "tests/data/chemical_reaction/RhCu_CH4/OUTCAR",
+    "tests/data/chemical_reaction/RhCu_CH4/run.archive.json",
+    "tests/data/chemical_reaction/RhCu_xHfcc/INCAR",
+    "tests/data/chemical_reaction/RhCu_xHfcc/OUTCAR",
+    "tests/data/chemical_reaction/RhCu_xHfcc/run.archive.json",
+    "tests/data/elastic.archive.json",
+    "tests/data/elastic/Distorted_Parameters",
+    "tests/data/elastic/Dst01/Dst01-Energy.dat",
+    "tests/data/elastic/Dst02/Dst02-Energy.dat",
+    "tests/data/elastic/Dst03/Dst03-Energy.dat",
+    "tests/data/elastic/ElaStic_2nd.in",
+    "tests/data/elastic/ElaStic_2nd.out",
+    "tests/data/elastic/Energy-vs-Strain/Dst01-Energy.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst01_CVe.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst01_d2E.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst02-Energy.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst02_CVe.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst02_d2E.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst03-Energy.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst03_CVe.dat",
+    "tests/data/elastic/Energy-vs-Strain/Dst03_d2E.dat",
+    "tests/data/elastic/Energy-vs-Strain/ElaStic_2nd.out",
+    "tests/data/elastic/INFO_ElaStic",
+    "tests/data/elastic/sgroup.out",
+    "tests/data/geometry_optimization.archive.json",
+    "tests/data/gromacs/fe_test/conf.gro",
+    "tests/data/gromacs/fe_test/confout.gro",
+    "tests/data/gromacs/fe_test/dhdl.xvg",
+    "tests/data/gromacs/fe_test/ener.edr",
+    "tests/data/gromacs/fe_test/grompp.err",
+    "tests/data/gromacs/fe_test/grompp.mdp",
+    "tests/data/gromacs/fe_test/grompp.out",
+    "tests/data/gromacs/fe_test/mdout.mdp",
+    "tests/data/gromacs/fe_test/mdrun.out",
+    "tests/data/gromacs/fe_test/reference_d.edr",
+    "tests/data/gromacs/fe_test/reference_d.tpr",
+    "tests/data/gromacs/fe_test/reference_d.trr",
+    "tests/data/gromacs/fe_test/reference_d.warn",
+    "tests/data/gromacs/fe_test/reference_s.edr",
+    "tests/data/gromacs/fe_test/reference_s.tpr",
+    "tests/data/gromacs/fe_test/reference_s.trr",
+    "tests/data/gromacs/fe_test/reference_s.warn",
+    "tests/data/gromacs/fe_test/state.cpt",
+    "tests/data/gromacs/fe_test/state_prev.cpt",
+    "tests/data/gromacs/fe_test/topol.top",
+    "tests/data/gromacs/fe_test/topol.tpr",
+    "tests/data/gromacs/fe_test/traj.trr",
+    "tests/data/gromacs/protein_small_nowater/confout.gro",
+    "tests/data/gromacs/protein_small_nowater/ener.edr",
+    "tests/data/gromacs/protein_small_nowater/md.log",
+    "tests/data/gromacs/protein_small_nowater/mdout.mdp",
+    "tests/data/gromacs/protein_small_nowater/protein_small_nowater.gro",
+    "tests/data/gromacs/protein_small_nowater/protein_small_nowater.mdp",
+    "tests/data/gromacs/protein_small_nowater/protein_small_nowater.top",
+    "tests/data/gromacs/protein_small_nowater/protein_small_nowater.tpr",
+    "tests/data/gromacs/protein_small_nowater/protein_small_nowater.trr",
+    "tests/data/gromacs/protein_small_nowater/state.cpt",
+    "tests/data/gromacs/protein_small_nowater/state_prev.cpt",
+    "tests/data/lammps/64xmethane/64xmethane-nvt.lammpstrj",
+    "tests/data/lammps/64xmethane/log.lammps",
+    "tests/data/lammps/hexane_cyclohexane/data.hexane_cyclohexane",
+    "tests/data/lammps/hexane_cyclohexane/hexane_cyclohexane_nvt_20ps.lammpstrj",
+    "tests/data/lammps/hexane_cyclohexane/in.hexane_cyclohexane_nvt",
+    "tests/data/lammps/hexane_cyclohexane/log.hexane_cyclohexane_nvt",
+    "tests/data/lammps/hexane_cyclohexane/log.hexane_cyclohexane_nvt-thermo_style_multi",
+    "tests/data/molecular_dynamics.archive.json",
+    "tests/data/no_workflow.archive.json",
+    "tests/data/phonon.archive.json",
+    "tests/data/phonopy/control.in",
+    "tests/data/phonopy/geometry.in",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/aims.sub",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/aims.sub.o449118",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/aims.sub.po449118",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/control.in",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/geometry.in",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/phonopy-FHI-aims-displacement-01.out",
+    "tests/data/phonopy/phonopy-FHI-aims-displacement-01/tmp.out",
+    "tests/data/radius_of_gyration.archive.json",
+    "tests/data/rdf_2.archive.json",
+    "tests/data/rdf_and_msd.archive.json",
+    "tests/data/single_point.archive.json",
+    "tests/data/temp.json",
+    "tests/data/vasp/vasprun.xml",
+    "tests/data/vasp/vasprun.xml.static",
+    "tests/data/vasp_outcar/OUTCAR_broken",
+    "tests/test_simulationworkflowschema.py",
+    "uv.lock"
+  ]
+}

nomad_schema_plugin_simulation_workflow-1.0.12/nomad_schema_plugin_simulation_workflow.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.0.12",
+  "distance": 0,
+  "node": "gb808d6d5688bdd6ee64f462af4f5653dd92a143c",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-11-06"
+}

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/pyproject.toml

@@ -27,10 +27,10 @@ dev-dependencies = [
     "nomad-normalizer-plugin-bandstructure>=1.0.3",
     "nomad-normalizer-plugin-system>=1.0.3",
     'mypy>=1.15',
-    'pytest>= 5.3.0, <8',
-    'pytest-timeout>=1.4.2',
-    'pytest-cov>=2.7.1',
-    'ruff>=0.6',
+    'pytest',
+    'pytest-timeout',
+    'pytest-cov',
+    'ruff',
     'typing-extensions>=4.12',
 
 ]
@@ -59,6 +59,7 @@ ignore = [
     "PLW2901", # redefined-loop-name
     "PLR1714", # consider-using-in
     "PLR5501", # else-if-used
+    "PLR0917", # Too many positional arguments
 ]
 fixable = ["ALL"]
 

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/simulationworkflowschema/__init__.py

@@ -94,7 +94,7 @@ def load_modules():
         'photon_polarization',
         'thermodynamics',
     ]
-    import simulationworkflowschema
+    import simulationworkflowschema  # noqa
 
     for name in sub_modules:
         sub_module = importlib.import_module(f'simulationworkflowschema.{name}')
@@ -107,7 +107,7 @@ class SimulationWorkflowSchemaEntryPoint(SchemaPackageEntryPoint):
     def load(self):
         load_modules()
 
-        from .general import m_package
+        from .general import m_package  # noqa
 
         return m_package
 

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/simulationworkflowschema/molecular_dynamics.py

@@ -568,7 +568,7 @@ def _get_molecular_bead_groups(
 
     if not moltypes:
         atoms_moltypes = getattr(universe.atoms, 'moltypes', [])
-        moltypes = np.unique(atoms_moltypes)
+        moltypes = np.unique(atoms_moltypes).tolist()
     bead_groups = {}
     for moltype in moltypes:
         ags_by_moltype = universe.select_atoms('moltype ' + moltype)

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/simulationworkflowschema/thermodynamics.py

@@ -193,7 +193,7 @@ class ThermodynamicsResults(SimulationWorkflowResults):
         """Returns the specific heat capacity by dividing the heat capacity per
         cell with the mass of the atoms in the cell.
         """
-        import nomad.atomutils
+        import nomad.atomutils  # noqa
 
         workflow = self.m_parent
         if not workflow._systems or not workflow._systems[0].atoms:
@@ -226,7 +226,7 @@ class ThermodynamicsResults(SimulationWorkflowResults):
     def vibrational_free_energy_at_constant_volume_specific(
         self,
     ) -> Optional[np.ndarray]:
-        import nomad.atomutils
+        import nomad.atomutils  # noqa
 
         workflow = self.m_parent
         if not workflow._systems or not workflow._systems[0].atoms:

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/tests/conftest.py

@@ -551,8 +551,8 @@ def get_template_gw_workflow() -> EntryArchive:
         GWworkflow.outputs,
         Link(name='Output GW calculation', section=archive_gw.run[-1].calculation[-1]),
     )
-    workflow.m_add_sub_section(GWworkflow.tasks, task_dft)
-    workflow.m_add_sub_section(GWworkflow.tasks, task_gw)
+    workflow.tasks.append(task_dft)
+    workflow.tasks.append(task_gw)
     template.workflow2 = workflow
     return template
 
@@ -607,8 +607,8 @@ def get_template_dmft_workflow() -> EntryArchive:
             name='Output DMFT calculation', section=archive_dmft.run[-1].calculation[-1]
         ),
     )
-    workflow.m_add_sub_section(DMFTworkflow.tasks, task_proj)
-    workflow.m_add_sub_section(DMFTworkflow.tasks, task_dmft)
+    workflow.tasks.append(task_proj)
+    workflow.tasks.append(task_dmft)
     template.workflow2 = workflow
     return template
 
@@ -675,8 +675,8 @@ def get_template_maxent_workflow() -> EntryArchive:
         ),
     ]
     workflow.outputs = outputs
-    workflow.m_add_sub_section(MaxEntworkflow.tasks, task_dmft)
-    workflow.m_add_sub_section(MaxEntworkflow.tasks, task_maxent)
+    workflow.tasks.append(task_dmft)
+    workflow.tasks.append(task_maxent)
     template.workflow2 = workflow
     return template
 
@@ -783,8 +783,8 @@ def get_template_bse_workflow() -> EntryArchive:
             section=archive_photon_2.run[-1].calculation[-1],
         ),
     )
-    workflow.m_add_sub_section(PhotonPolarization.tasks, task_photon_1)
-    workflow.m_add_sub_section(PhotonPolarization.tasks, task_photon_2)
+    workflow.tasks.append(task_photon_1)
+    workflow.tasks.append(task_photon_2)
     template.workflow2 = workflow
     return template
 
@@ -839,8 +839,8 @@ def get_template_xs_workflow() -> EntryArchive:
         XSworkflow.outputs,
         Link(name='Polarization 2', section=archive_bse.workflow2.outputs[1].section),
     )
-    workflow.m_add_sub_section(XSworkflow.tasks, task_dft)
-    workflow.m_add_sub_section(XSworkflow.tasks, task_bse)
+    workflow.tasks.append(task_dft)
+    workflow.tasks.append(task_bse)
     template.workflow2 = workflow
     return template
 

{nomad_schema_plugin_simulation_workflow-1.0.10 → nomad_schema_plugin_simulation_workflow-1.0.12}/tests/test_simulationworkflowschema.py

@@ -448,9 +448,12 @@ def test_rdf_and_msd():
         .units
         == 'meter'
     )
+    # Allow for variation across supported numerical library versions.
     assert section_md.radial_distribution_functions[
         0
-    ].radial_distribution_function_values[10].value[101] == approx(1.4750986777470825)
+    ].radial_distribution_function_values[10].value[101] == approx(
+        1.4750986777470825, rel=1e-5
+    )
     assert (
         section_md.radial_distribution_functions[0]
         .radial_distribution_function_values[10]