Rename annotation keys (#141)

* Rename annotation keys

* Fix h5md schema

* Update src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Close abinit parsers

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

 1. Annotation Key Namespacing (30 files)
  - Generic keys like 'out', 'xml', 'dos' are now prefixed with parser names
  - Examples:
    - 'out' → 'quantumespresso_out' (Quantum ESPRESSO)
    - 'xml' → 'vasp_xml' (VASP)
    - 'gpw' → 'gpaw_gpw' (GPAW)
    - 'out' → 'abinit_out' (ABINIT)

  2. Schema Reload Removal
  - Removes all reload(schema_module) calls from parsers
  - Previously, parsers were reloading schema packages to refresh annotations at runtime
  - This suggests annotations are now properly registered at import time

  3. Annotation Cleanup Removal
  - Removes calls to remove_mapping_annotations()
  - No longer needs to clean up annotations after parsing

  4. Resource Management Improvements
  - Adds missing close() calls for parsers (GPAW, Octopus, FHI-aims)
  - Ensures proper cleanup of file contexts

  5. Quantum ESPRESSO Refactoring (src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py)
  - Introduces shared OUT_KEY = 'quantumespresso_out' constant
  - Refactors from manual m_annotations manipulation to using add_mapping_annotation() helper

Author: ladinesa

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/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/parser.py

@@ -1,5 +1,4 @@
 import os
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -467,8 +466,6 @@ def write_to_archive(self):
         self._maindir = os.path.dirname(self.mainfile)
         self._gromacs_files = os.listdir(self._maindir)
         self._basename = os.path.basename(self.mainfile).rsplit('.', 1)[0]
-        # reload the schema annotations
-        reload(gromacs)
 
         # set up source parsers
         self._log_parser.filepath = self.mainfile

src/nomad_simulation_parsers/parsers/h5md/parser.py

@@ -1,5 +1,4 @@
 from collections.abc import Sequence
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -16,7 +15,6 @@
 from nomad_simulation_parsers.parsers.utils.mdparserutils import MDParser
 from nomad_simulation_parsers.schema_packages import h5md
 from nomad_simulation_parsers.schema_packages.h5md import MolecularDynamics, Simulation
-from nomad_simulation_parsers.schema_packages.utils import remove_mapping_annotations
 
 LOGGER = get_logger(__name__)
 
@@ -492,9 +490,6 @@ def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
     def write_to_archive(self) -> None:
-        # reload schema annotations
-        reload(h5md)
-
         # create h5 parser
         self.h5_parser.filepath = self.mainfile
 
@@ -528,9 +523,6 @@ def write_to_archive(self) -> None:
         self.simulation_parser.close()
         self.workflow_parser.close()
 
-        # remove mapping annotations
-        remove_mapping_annotations(self.archive.data.m_def)
-
 
 class H5MDParser(MatchingParser):
     def __init__(self, **kwargs) -> None:

src/nomad_simulation_parsers/parsers/octopus/parser.py

@@ -1,5 +1,4 @@
 import os
-from importlib import reload
 from typing import Any
 
 import numpy as np
@@ -417,9 +416,6 @@ class OctopusArchiveWriter(ArchiveWriter):
     eigenvalues_parser = OctopusEigenvalueParser(text_parser=EigenvalueParser())
 
     def write_to_archive(self) -> None:
-        # Reload the octopus package to update the mapping annotations
-        reload(octopus)
-
         self.mainfile_parser.filepath = self.mainfile
         # initialize auxiliary file parsers
         self.mainfile_parser.init_parser()
@@ -449,6 +445,11 @@ def write_to_archive(self) -> None:
         self.archive_parser.annotation_key = octopus.EIGENVALUES_KEY
         self.eigenvalues_parser.convert(self.archive_parser, update_mode='merge@-1')
 
+        self.eigenvalues_parser.close()
+        self.archive_parser.close()
+        self.mainfile_parser.close()
+        self.info_parser.close()
+
 
 class OctopusParser(MatchingParser):
     archive_writer = OctopusArchiveWriter()

src/nomad_simulation_parsers/parsers/quantumespresso/epw/parser.py

@@ -4,7 +4,7 @@
 from nomad_simulation_parsers.parsers.quantumespresso.parser import (
     QuantumEspressoArchiveWriter,
 )
-from nomad_simulation_parsers.schema_packages.quantumespresso import epw
+from nomad_simulation_parsers.schema_packages.quantumespresso import common, epw
 
 from ..parser import MainfileParser
 from .file_parser import EPWFileParser
@@ -23,5 +23,5 @@ class EPWArchiveWriter(QuantumEspressoArchiveWriter):
     mainfile_parser = EPWMainfileParser(text_parser=EPWFileParser())
 
     def parse_program(self, archive: EntryArchive, index: int) -> None:
-        self.simulation_parser.annotation_key = 'out'
+        self.simulation_parser.annotation_key = common.OUT_KEY
         super().parse_program(archive, index)