Merge develop up to 6a568d0 (linting fixes)

Resolved conflict in vasp.py by adopting prefixed annotation key naming
(vasp_xml, vasp_outcar, etc.) and adding new keys with same pattern.

Author: ndaelman-hu

pyproject.toml

@@ -40,6 +40,8 @@ dependencies = [
     "mdanalysis>=2.8.0,<3.0.0 ; python_full_version >= '3.10'",
     "mdanalysis<2.8 ; python_full_version < '3.10'",
     "panedr>=0.2",
+    # issue with reading nc file in 1.7.3: https://github.com/Unidata/netcdf4-python/issues/1438
+    "netcdf4<=1.7.2",
 ]
 
 [project.urls]
@@ -162,6 +164,8 @@ vasp_parser = "nomad_simulation_parsers.parsers:vasp_parser"
 vasp_schema_package = "nomad_simulation_parsers.schema_packages:vasp_schema_package"
 wannier90_parser = "nomad_simulation_parsers.parsers:wannier90_parser"
 wannier90_schema_package = "nomad_simulation_parsers.schema_packages:wannier90_schema_package"
+yambo_parser = "nomad_simulation_parsers.parsers:yambo_parser"
+yambo_schema_package = "nomad_simulation_parsers.schema_packages:yambo_schema_package"
 
 
 [tool.cruft]

src/nomad_simulation_parsers/parsers/__init__.py

@@ -222,3 +222,15 @@ class Wannier90ParserEntryPoint(EntryPoint):
     code_homepage='http://www.wannier.org/',
     code_category='Atomistic code',
 )
+
+yambo_parser = EntryPoint(
+    name='parsers/yambo',
+    aliases=['parsers/yambo'],
+    description='NOMAD parser for YAMBO.',
+    parser_class_name='nomad_simulation_parsers.parsers.yambo.parser.YamboParser',
+    python_package='nomad_simulation_parsers',
+    mainfile_contents_re=r'Build[\s\S]+?http://www\.yambo-code\.org',
+    code_name='YAMBO',
+    code_homepage='http://www.yambo-code.org/',
+    code_category='Atomistic code',
+)

src/nomad_simulation_parsers/parsers/abinit/parser.py

@@ -1,7 +1,6 @@
 import os
 from collections.abc import Iterable
 from datetime import datetime
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -623,8 +622,6 @@ def parse_workflow(self):
         self.mainfile_parser.convert(self.metainfo_parser)
 
     def write_to_archive(self):
-        reload(abinit)
-
         self.archive.data = Simulation(program=Program(name=self.code_name))
         self.metainfo_parser.annotation_key = self.annotation_key
         self.metainfo_parser.data_object = self.archive.data
@@ -662,6 +659,10 @@ def write_to_archive(self):
                 tasks=[self.archive.workflow2, gw_archive.workflow2]
             )
 
+        self.metainfo_parser.close()
+        self.mainfile_parser.close()
+        self.dos_parser.close()
+
 
 class AbinitParser(MatchingParser):
     """

src/nomad_simulation_parsers/parsers/ams/parser.py

@@ -1,5 +1,4 @@
 import os
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -78,9 +77,6 @@ class AMSArchiveWriter(ArchiveWriter):
     rkf_parser = RKFParser(text_parser=RKFTextParser())
 
     def write_to_archive(self):
-        # reload schema package to use correct annotations
-        reload(ams)
-
         self.metainfo_parser.annotation_key = ams.OUT_KEY
         self.archive.data = Simulation(program=Program(name='AMS'))
         self.metainfo_parser.data_object = self.archive.data

src/nomad_simulation_parsers/parsers/crystal/parser.py

@@ -1,7 +1,6 @@
 import datetime
 import os
 import re
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -207,9 +206,6 @@ class CrystalArchiveWriter(ArchiveWriter):
     archive_parser = CrystalMetainfoParser()
 
     def write_to_archive(self):
-        # reload schema to update annotations
-        reload(crystal)
-
         # main output file
         self.archive_parser.annotation_key = crystal.OUT_KEY
         self.archive_parser.data_object = Simulation(program=Program(name='Crystal'))

src/nomad_simulation_parsers/parsers/exciting/parser.py

@@ -1,5 +1,4 @@
 import os
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -24,7 +23,6 @@
     search_files,
 )
 from nomad_simulation_parsers.schema_packages import exciting
-from nomad_simulation_parsers.schema_packages.utils import remove_mapping_annotations
 
 from .eigval_parser import EigvalFileParser
 from .info_parser import InfoFileParser
@@ -185,8 +183,6 @@ def get_eigenvalues(self, source: dict[str, Any]):
 
 class ExcitingArchiveWriter(ArchiveWriter):
     def write_to_archive(self) -> None:
-        reload(exciting)
-
         maindir = os.path.dirname(self.mainfile)
         mainbase = os.path.basename(self.mainfile)
 
@@ -248,9 +244,6 @@ def write_to_archive(self) -> None:
         info_parser.close()
         data_parser.close()
 
-        # remove annotations
-        remove_mapping_annotations(exciting.general.Simulation.m_def)
-
 
 class ExcitingParser(MatchingParser):
     """

src/nomad_simulation_parsers/parsers/fhiaims/parser.py

@@ -1,7 +1,6 @@
 import os
 import re
 from collections.abc import Iterable
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -41,7 +40,6 @@
     search_files,
 )
 from nomad_simulation_parsers.schema_packages import fhiaims
-from nomad_simulation_parsers.schema_packages.utils import remove_mapping_annotations
 
 from .common import ControlParser, GeometryParser
 
@@ -446,9 +444,6 @@ def get_forces(
     def write_to_archive(
         self,
     ) -> None:
-        # reload module to refresh annotations
-        reload(fhiaims)
-
         out_parser = FHIAimsOutMappingParser()
         out_parser.text_parser = FHIAimsOutFileParser()
         out_parser.filepath = self.mainfile
@@ -545,13 +540,8 @@ def write_to_archive(
                 )
 
         # close file contexts
-        self.out_parser = out_parser
-        self.archive_handler = archive_handler
-        # out_parser.close()
-        # archive_handler.close()
-
-        # remove annotations
-        remove_mapping_annotations(fhiaims.general.Simulation.m_def)
+        out_parser.close()
+        archive_handler.close()
 
 
 class FHIAimsParser(MatchingParser):

src/nomad_simulation_parsers/parsers/gpaw/gpw_parser.py

@@ -234,24 +234,24 @@ def get_array(self, key: str) -> np.ndarray:
         if self.ulm is None:
             return
         values = {
-            'unitcell': lambda: self.ulm.atoms.cell,
-            'atomicnumbers': lambda: self.ulm.atoms.numbers,
-            'atom_positions': lambda: self.ulm.atoms.positions,
-            'boundaryconditions': lambda: self.ulm.atoms.pbc,
-            'momenta': lambda: self.ulm.atoms.momenta,
-            'atom_forces_free_raw': lambda: self.ulm.results.forces,
-            'magneticmoments': lambda: self.ulm.results.magmoms,
-            'eigenvalues': lambda: self.ulm.wave_functions.eigenvalues,
-            'occupation': lambda: self.ulm.wave_functions.occupations,
+            'unitcell': self.ulm.atoms.cell,
+            'atomicnumbers': self.ulm.atoms.numbers,
+            'atom_positions': self.ulm.atoms.positions,
+            'boundaryconditions': self.ulm.atoms.pbc,
+            'momenta': self.ulm.atoms.momenta,
+            'atom_forces_free_raw': self.ulm.results.forces,
+            'magneticmoments': self.ulm.results.magmoms,
+            'eigenvalues': self.ulm.wave_functions.eigenvalues,
+            'occupation': self.ulm.wave_functions.occupations,
             # TODO no koints data in ulm?
-            'kpoints': lambda: self.ulm.IBZKPoints,
-            'density': lambda: self.ulm.density.density,
-            'potential_effective': lambda: self.ulm.hamiltonian.potential,
-            'band_paths': lambda: self.ulm.wave_functions.band_paths.asdict(),
+            'kpoints': self.ulm.IBZKPoints,
+            'density': self.ulm.density.density,
+            'potential_effective': self.ulm.hamiltonian.potential,
+            'band_paths': self.ulm.wave_functions.band_paths.asdict(),
         }
         try:
             if key in values:
-                val = values.get(key)()
+                val = values.get(key)
             else:
                 val = self.ulm.asdict().get(key, None)
         except Exception:

src/nomad_simulation_parsers/parsers/gpaw/parser.py

@@ -1,4 +1,3 @@
-from importlib import reload
 from typing import Any
 
 from nomad.datamodel import EntryArchive
@@ -90,16 +89,16 @@ class GPAWArchiveWriter(ArchiveWriter):
     archive_parser = GPAWMetainfoParser()
 
     def write_to_archive(self):
-        # reload schema annotations
-        reload(gpaw)
-
         self.mainfile_parser.filepath = self.mainfile
         self.archive_parser.annotation_key = gpaw.GPW_KEY
         self.archive_parser.data_object = Simulation()
 
         self.mainfile_parser.convert(self.archive_parser)
         self.archive.data = self.archive_parser.data_object
 
+        self.mainfile_parser.close()
+        self.archive_parser.close()
+
 
 class GPAWParser(MatchingParser):
     """

src/nomad_simulation_parsers/parsers/gromacs/mdanalysis_parser.py

@@ -157,7 +157,7 @@ def get_force_field_parameters(
                 'Interactions will not be stored'
             )
             return []
-        gromacs_version = gromacs_version.split('.')[0] if gromacs_version else None
+        gromacs_version = gromacs_version.split('.', 1)[0] if gromacs_version else None
         if gromacs_version == '2024':
             self.logger.warning(
                 'Reading force field from tpr not yet supported for Gromacs 2024.'