Move basic parser out of nomad

nomad-coe · Dec 8, 2023 · 475e0e3 · 475e0e3
1 parent af1e078
commit 475e0e3
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Showing 7 changed files with 28 additions and 27 deletions.
diff --git a/atomisticparsers/amber/metainfo/amber.py b/atomisticparsers/amber/metainfo/amber.py
@@ -22,7 +22,7 @@
     MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
     Reference
 )
-from nomad.datamodel.metainfo import simulation
+import runschema
 import simulationworkflowschema
 
 
@@ -85,7 +85,7 @@ class x_amber_section_single_configuration_calculation(MSection):
     m_def = Section(validate=False)
 
 
-class System(simulation.system.System):
+class System(runschema.system.System):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -265,7 +265,7 @@ class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
         ''')
 
 
-class AtomParameters(simulation.method.AtomParameters):
+class AtomParameters(runschema.method.AtomParameters):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -284,12 +284,12 @@ class AtomParameters(simulation.method.AtomParameters):
         ''')
 
 
-class Interaction(simulation.method.Interaction):
+class Interaction(runschema.method.Interaction):
 
     m_def = Section(validate=False, extends_base_section=True)
 
     x_amber_interaction_atom_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type of each interaction atoms.
@@ -303,7 +303,7 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_amber_pair_interaction_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['x_amber_number_of_defined_pair_interactions', 'number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type for pair interactions.
@@ -317,7 +317,7 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_amber_molecule_interaction_atom_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type of each molecule interaction atoms.
@@ -338,14 +338,14 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_amber_pair_molecule_interaction_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['x_amber_number_of_defined_pair_interactions', 'number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type for pair interactions within a molecule.
         ''')
 
 
-class Run(simulation.run.Run):
+class Run(runschema.run.Run):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -431,7 +431,7 @@ class Run(simulation.run.Run):
         repeats=False)
 
 
-class Calculation(simulation.calculation.Calculation):
+class Calculation(runschema.calculation.Calculation):
 
     m_def = Section(validate=False, extends_base_section=True)
 

diff --git a/atomisticparsers/amber/parser.py b/atomisticparsers/amber/parser.py
@@ -18,7 +18,7 @@
 #
 
 from nomad.units import ureg
-from nomad.parsing.file_parser import BasicParser
+from simulationparsers.utils import BasicParser
 
 
 class AmberParser:

diff --git a/atomisticparsers/gromos/metainfo/gromos.py b/atomisticparsers/gromos/metainfo/gromos.py
@@ -22,7 +22,7 @@
     MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
     Reference
 )
-from nomad.datamodel.metainfo import simulation
+import runschema
 import simulationworkflowschema
 
 
@@ -1290,7 +1290,7 @@ class x_gromos_section_single_configuration_calculation(MSection):
     m_def = Section(validate=False)
 
 
-class System(simulation.system.System):
+class System(runschema.system.System):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -1484,7 +1484,7 @@ class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
         ''')
 
 
-class AtomParameters(simulation.method.AtomParameters):
+class AtomParameters(runschema.method.AtomParameters):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -1531,12 +1531,12 @@ class AtomParameters(simulation.method.AtomParameters):
         ''')
 
 
-class Interaction(simulation.method.Interaction):
+class Interaction(runschema.method.Interaction):
 
     m_def = Section(validate=False, extends_base_section=True)
 
     x_gromos_interaction_atom_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type of each interaction atoms.
@@ -1550,7 +1550,7 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_gromos_pair_interaction_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['x_gromos_number_of_defined_pair_interactions', 'number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type for pair interactions.
@@ -1564,7 +1564,7 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_gromos_molecule_interaction_atom_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type of each molecule interaction atoms.
@@ -1585,14 +1585,14 @@ class Interaction(simulation.method.Interaction):
         ''')
 
     x_gromos_pair_molecule_interaction_to_atom_type_ref = Quantity(
-        type=simulation.method.AtomParameters,
+        type=runschema.method.AtomParameters,
         shape=['x_gromos_number_of_defined_pair_interactions', 'number_of_atoms_per_interaction'],
         description='''
         Reference to the atom type for pair interactions within a molecule.
         ''')
 
 
-class Run(simulation.run.Run):
+class Run(runschema.run.Run):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -1748,7 +1748,7 @@ class Run(simulation.run.Run):
         repeats=True)
 
 
-class Calculation(simulation.calculation.Calculation):
+class Calculation(runschema.calculation.Calculation):
 
     m_def = Section(validate=False, extends_base_section=True)
 

diff --git a/atomisticparsers/gromos/parser.py b/atomisticparsers/gromos/parser.py
@@ -20,7 +20,7 @@
 import re
 
 from nomad.units import ureg
-from nomad.parsing.file_parser import BasicParser
+from simulationparsers.utils import BasicParser
 
 
 class GromosParser:

diff --git a/atomisticparsers/libatoms/metainfo/lib_atoms.py b/atomisticparsers/libatoms/metainfo/lib_atoms.py
@@ -22,7 +22,7 @@
     MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
     Reference
 )
-from nomad.datamodel.metainfo import simulation
+import runschema
 
 
 m_package = Package()
@@ -36,7 +36,7 @@ class x_lib_atoms_section_gap(MSection):
     m_def = Section(validate=False)
 
     x_lib_atoms_training_config_refs = Quantity(
-        type=simulation.calculation.Calculation,
+        type=runschema.calculation.Calculation,
         shape=['n_sparseX'],
         description='''
         References to frames in training configuration.
@@ -190,7 +190,7 @@ class x_lib_atoms_section_gap(MSection):
         ''')
 
 
-class Run(simulation.run.Run):
+class Run(runschema.run.Run):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -199,7 +199,7 @@ class Run(simulation.run.Run):
         repeats=False)
 
 
-class Calculation(simulation.calculation.Calculation):
+class Calculation(runschema.calculation.Calculation):
 
     m_def = Section(validate=False, extends_base_section=True)
 

diff --git a/atomisticparsers/libatoms/parser.py b/atomisticparsers/libatoms/parser.py
@@ -17,7 +17,7 @@
 # limitations under the License.
 #
 
-from nomad.parsing.file_parser import BasicParser
+from simulationparsers.utils import BasicParser
 from nomad.units import ureg
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -13,6 +13,7 @@ dependencies = [
     'nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop',
     "nomad-schema-plugin-simulation-workflow@git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop",
     "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop",
+i   "simulationparsers@git+https://github.com/nomad-coe/simulation-parsers.git@develop",
     'lxml==4.7.1',
     'MDAnalysis',
     'panedr==0.2',