Merge pull request #19 from nomad-coe/entry-point

Entry point

pyproject.toml

@@ -11,7 +11,7 @@ authors = [{ name = "The NOMAD Authors" }]
 license = { text = "Apache-2.0" }
 dependencies = [
     "nomad-lab>=1.2.0",
-    "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop",
+    "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@f5d348fec5cef89e76021b42e48ff49b1832034b",
 ]
 
 [project.urls]
@@ -70,5 +70,5 @@ line-ending = "auto"
 [tool.setuptools.packages.find]
 include = ["simulationworkflowschema*"]
 
-[tool.setuptools.package-data]
-simulationworkflowschema = ["*/nomad_plugin.yaml"]
+[project.entry-points.'nomad.plugin']
+simulationworkflowschema = "simulationworkflowschema:simulationworkflow_schema_entry_point"

simulationworkflowschema/__init__.py

@@ -16,52 +16,103 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from .general import (
-    SimulationWorkflow,
-    SimulationWorkflowMethod,
-    SimulationWorkflowResults,
-    ParallelSimulation,
-    SerialSimulation,
-    BeyondDFT,
-    DFTMethod,
-    ElectronicStructureOutputs,
-    MagneticOutputs,
+import importlib
+
+from nomad.config.models.plugins import SchemaPackageEntryPoint
+
+
+__all__ = [
+    'SimulationWorkflow',
+    'SimulationWorkflowMethod',
+    'SimulationWorkflowResults',
+    'ParallelSimulation',
+    'SerialSimulation',
+    'BeyondDFT',
+    'DFTMethod',
+    'ElectronicStructureOutputs',
+    'MagneticOutputs',
+    'SinglePoint',
+    'SinglePointMethod',
+    'SinglePointResults',
+    'GeometryOptimization',
+    'GeometryOptimizationMethod',
+    'GeometryOptimizationResults',
+    'MolecularDynamics',
+    'MolecularDynamicsMethod',
+    'MolecularDynamicsResults',
+    'Phonon',
+    'PhononMethod',
+    'PhononResults',
+    'EquationOfState',
+    'EquationOfStateMethod',
+    'EquationOfStateResults',
+    'ChemicalReaction',
+    'ChemicalReactionMethod',
+    'ChemicalReactionResults',
+    'Elastic',
+    'ElasticMethod',
+    'ElasticResults',
+    'FirstPrinciplesPlusTB',
+    'FirstPrinciplesPlusTBMethod',
+    'FirstPrinciplesPlusTBResults',
+    'DFTPlusGW',
+    'DFTPlusGWMethod',
+    'DFTPlusGWResults',
+    'XS',
+    'XSMethod',
+    'XSResults',
+    'DFTPlusTBPlusDMFT',
+    'DFTPlusTBPlusDMFTMethod',
+    'DFTPlusTBPlusDMFTResults',
+    'DMFTPlusMaxEnt',
+    'DMFTPlusMaxEntMethod',
+    'DMFTPlusMaxEntResults',
+    'PhotonPolarization',
+    'PhotonPolarizationMethod',
+    'PhotonPolarizationResults',
+    'Thermodynamics',
+    'ThermodynamicsMethod',
+    'ThermodynamicsResults',
+]
+
+
+def load_modules():
+    sub_modules = [
+        'general',
+        'single_point',
+        'geometry_optimization',
+        'molecular_dynamics',
+        'phonon',
+        'equation_of_state',
+        'chemical_reaction',
+        'elastic',
+        'tb',
+        'gw',
+        'xs',
+        'dmft',
+        'max_ent',
+        'photon_polarization',
+        'thermodynamics',
+    ]
+    import simulationworkflowschema
+
+    for name in sub_modules:
+        sub_module = importlib.import_module(f'simulationworkflowschema.{name}')
+        for method in sub_module.__dict__:
+            if method in __all__:
+                setattr(simulationworkflowschema, method, sub_module.__dict__[method])
+
+
+class SimulationWorkflowSchemaEntryPoint(SchemaPackageEntryPoint):
+    def load(self):
+        load_modules()
+
+        from .general import m_package
+
+        return m_package
+
+
+simulationworkflow_schema_entry_point = SimulationWorkflowSchemaEntryPoint(
+    name='SimulationWorkflowSchema',
+    description='Schema for the nomad simulation workflows.',
 )
-from .single_point import SinglePoint, SinglePointMethod, SinglePointResults
-from .geometry_optimization import (
-    GeometryOptimization,
-    GeometryOptimizationMethod,
-    GeometryOptimizationResults,
-)
-from .molecular_dynamics import (
-    MolecularDynamics,
-    MolecularDynamicsMethod,
-    MolecularDynamicsResults,
-)
-from .phonon import Phonon, PhononMethod, PhononResults
-from .equation_of_state import (
-    EquationOfState,
-    EquationOfStateMethod,
-    EquationOfStateResults,
-)
-from .chemical_reaction import (
-    ChemicalReaction,
-    ChemicalReactionMethod,
-    ChemicalReactionResults,
-)
-from .elastic import Elastic, ElasticMethod, ElasticResults
-from .tb import (
-    FirstPrinciplesPlusTB,
-    FirstPrinciplesPlusTBMethod,
-    FirstPrinciplesPlusTBResults,
-)
-from .gw import DFTPlusGW, DFTPlusGWMethod, DFTPlusGWResults
-from .xs import XS, XSMethod, XSResults
-from .dmft import DFTPlusTBPlusDMFT, DFTPlusTBPlusDMFTMethod, DFTPlusTBPlusDMFTResults
-from .max_ent import DMFTPlusMaxEnt, DMFTPlusMaxEntMethod, DMFTPlusMaxEntResults
-from .photon_polarization import (
-    PhotonPolarization,
-    PhotonPolarizationMethod,
-    PhotonPolarizationResults,
-)
-from .thermodynamics import Thermodynamics, ThermodynamicsMethod, ThermodynamicsResults

simulationworkflowschema/general.py

@@ -19,7 +19,7 @@
 import numpy as np
 
 from nomad.datamodel.data import ArchiveSection
-from nomad.metainfo import SubSection, Section, Quantity, Reference
+from nomad.metainfo import SubSection, Section, Quantity, Reference, Package
 from nomad.datamodel.metainfo.common import FastAccess
 from nomad.datamodel.metainfo.workflow import Workflow, Link, Task, TaskReference
 from runschema.method import (
@@ -41,6 +41,9 @@
 )
 
 
+m_package = Package()
+
+
 def resolve_difference(values):
     delta_values = None
 
@@ -497,3 +500,6 @@ class MagneticOutputs(SimulationWorkflowResults):
         Reference to the magnetic susceptibility tensors.
         """,
     )
+
+
+m_package.__init_metainfo__()

simulationworkflowschema/molecular_dynamics.py

@@ -986,7 +986,11 @@ def normalize(self, archive, logger):
         if self._rg_results:
             self.type = self._rg_results.get('type')
             self.label = self._rg_results.get('label')
-            self.atomsgroup_ref = self._rg_results.get('atomsgroup_ref')
+            # TODO Fix this assignment fails with TypeError
+            try:
+                self.atomsgroup_ref = self._rg_results.get('atomsgroup_ref')
+            except Exception:
+                pass
             self.n_frames = self._rg_results.get('n_frames')
             self.times = self._rg_results.get('times')
             self.value = self._rg_results.get('value')
@@ -1245,11 +1249,11 @@ def normalize(self, archive, logger):
                 else []
             )
             sec_diffusion.error_type = 'Pearson correlation coefficient'
-            sec_diffusion.errors = (
-                self._msd_results['error_diffusion_constant'][i_type]
-                if self._msd_results.get('error_diffusion_constant') is not None
-                else []
-            )
+            if self._msd_results.get('error_diffusion_constant') is not None:
+                errors = self._msd_results['error_diffusion_constant'][i_type]
+                sec_diffusion.errors = (
+                    list(errors) if isinstance(errors, (list, np.ndarray)) else [errors]
+                )
 
 
 class MolecularDynamicsResults(ThermodynamicsResults):
@@ -1394,7 +1398,11 @@ def normalize(self, archive, logger):
                     sec_rg_values = sec_rgs_calc.m_create(
                         RadiusOfGyrationValuesCalculation
                     )
-                    sec_rg_values.atomsgroup_ref = rg.get('atomsgroup_ref')
+                    # TODO Fix this assignment fails with TypeError
+                    try:
+                        sec_rg_values.atomsgroup_ref = rg.get('atomsgroup_ref')
+                    except Exception:
+                        pass
                     sec_rg_values.label = rg.get('label')
                     sec_rg_values.value = rg.get('value')[sys_ind]
 

tests/conftest.py

@@ -83,25 +83,33 @@
     RadialDistributionFunctionValues,
 )
 from simulationworkflowschema.equation_of_state import EOSFit
-from simulationworkflowschema import (
+from simulationworkflowschema.molecular_dynamics import (
+    MolecularDynamics,
     MolecularDynamicsMethod,
     MolecularDynamicsResults,
-    SinglePoint,
+)
+from simulationworkflowschema.single_point import SinglePoint
+from simulationworkflowschema.geometry_optimization import (
     GeometryOptimization,
     GeometryOptimizationMethod,
-    Elastic,
-    ElasticResults,
-    MolecularDynamics,
+)
+from simulationworkflowschema.elastic import Elastic, ElasticResults
+from simulationworkflowschema.equation_of_state import (
     EquationOfState,
     EquationOfStateResults,
-    DFTPlusGWMethod,
-    DFTPlusGW as GWworkflow,
+)
+from simulationworkflowschema.gw import DFTPlusGWMethod, DFTPlusGW as GWworkflow
+from simulationworkflowschema.dmft import (
     DFTPlusTBPlusDMFTMethod,
     DFTPlusTBPlusDMFT as DMFTworkflow,
+)
+from simulationworkflowschema.photon_polarization import (
     PhotonPolarization,
     PhotonPolarizationMethod,
     PhotonPolarizationResults,
-    XS as XSworkflow,
+)
+from simulationworkflowschema.xs import XS as XSworkflow
+from simulationworkflowschema.max_ent import (
     DMFTPlusMaxEntMethod,
     DMFTPlusMaxEnt as MaxEntworkflow,
 )