From 0e51245e7ea7c9e65b0f4246513b95aafb11af7d Mon Sep 17 00:00:00 2001
From: ladinesa <67910858+ladinesa@users.noreply.github.com>
Date: Wed, 6 Dec 2023 18:08:45 +0100
Subject: [PATCH] Remove workflow schema from nomad (#78)

* Remove references to old workflow schema in nomad

* Add schema dependency

* Fix defs
---
 atomisticparsers/amber/metainfo/amber.py     | 3 ++-
 atomisticparsers/asap/metainfo/asap.py       | 6 +++---
 atomisticparsers/asap/parser.py              | 4 ++--
 atomisticparsers/bopfox/parser.py            | 2 +-
 atomisticparsers/dlpoly/metainfo/dl_poly.py  | 3 ++-
 atomisticparsers/gromacs/metainfo/gromacs.py | 3 ++-
 atomisticparsers/gromacs/parser.py           | 2 +-
 atomisticparsers/gromos/metainfo/gromos.py   | 3 ++-
 atomisticparsers/gulp/metainfo/gulp.py       | 5 +++--
 atomisticparsers/gulp/parser.py              | 2 +-
 atomisticparsers/lammps/metainfo/lammps.py   | 3 ++-
 atomisticparsers/lammps/parser.py            | 2 +-
 atomisticparsers/namd/metainfo/namd.py       | 3 ++-
 atomisticparsers/namd/parser.py              | 2 +-
 atomisticparsers/tinker/metainfo/tinker.py   | 5 +++--
 atomisticparsers/tinker/parser.py            | 2 +-
 atomisticparsers/utils/parsers.py            | 2 +-
 atomisticparsers/xtb/metainfo/xtb.py         | 5 +++--
 atomisticparsers/xtb/parser.py               | 2 +-
 pyproject.toml                               | 1 +
 20 files changed, 35 insertions(+), 25 deletions(-)

diff --git a/atomisticparsers/amber/metainfo/amber.py b/atomisticparsers/amber/metainfo/amber.py
index 8559e666..1bcc3aa9 100644
--- a/atomisticparsers/amber/metainfo/amber.py
+++ b/atomisticparsers/amber/metainfo/amber.py
@@ -23,6 +23,7 @@
     Reference
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -169,7 +170,7 @@ class System(simulation.system.System):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/asap/metainfo/asap.py b/atomisticparsers/asap/metainfo/asap.py
index ca0f9470..dbe3369f 100644
--- a/atomisticparsers/asap/metainfo/asap.py
+++ b/atomisticparsers/asap/metainfo/asap.py
@@ -22,13 +22,13 @@
     MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
     Reference
 )
-from nomad.datamodel.metainfo.simulation import workflow
+import simulationworkflowschema
 
 
 m_package = Package()
 
 
-class MolecularDynamics(workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -54,7 +54,7 @@ class MolecularDynamics(workflow.MolecularDynamics):
         ''')
 
 
-class GeometryOptimization(workflow.GeometryOptimization):
+class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/asap/parser.py b/atomisticparsers/asap/parser.py
index 7e0de91c..71c72923 100644
--- a/atomisticparsers/asap/parser.py
+++ b/atomisticparsers/asap/parser.py
@@ -27,8 +27,8 @@
 from nomad.datamodel.metainfo.simulation.run import Run, Program
 from nomad.datamodel.metainfo.simulation.method import (
     Method, ForceField, Model)
-from nomad.datamodel.metainfo.simulation.workflow import (
-    GeometryOptimization, GeometryOptimizationMethod,
+from simulationworkflowschema import (
+    GeometryOptimization, GeometryOptimizationMethod
 )
 from atomisticparsers.utils import MDParser
 from .metainfo.asap import MolecularDynamics  # pylint: disable=unused-import
diff --git a/atomisticparsers/bopfox/parser.py b/atomisticparsers/bopfox/parser.py
index d6a97459..6bd62a46 100644
--- a/atomisticparsers/bopfox/parser.py
+++ b/atomisticparsers/bopfox/parser.py
@@ -31,7 +31,7 @@
     Calculation, Energy, EnergyEntry, Forces, ForcesEntry, Stress, StressEntry, Charges,
     ChargesValue
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     GeometryOptimization, GeometryOptimizationMethod, SinglePoint
 )
 from atomisticparsers.utils import MDParser
diff --git a/atomisticparsers/dlpoly/metainfo/dl_poly.py b/atomisticparsers/dlpoly/metainfo/dl_poly.py
index d452e2ee..683380d2 100644
--- a/atomisticparsers/dlpoly/metainfo/dl_poly.py
+++ b/atomisticparsers/dlpoly/metainfo/dl_poly.py
@@ -23,6 +23,7 @@
     Reference, JSON
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -69,7 +70,7 @@ class x_dl_poly_section_md_topology(MSection):
         repeats=True)
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/gromacs/metainfo/gromacs.py b/atomisticparsers/gromacs/metainfo/gromacs.py
index 780632a6..113a41f4 100644
--- a/atomisticparsers/gromacs/metainfo/gromacs.py
+++ b/atomisticparsers/gromacs/metainfo/gromacs.py
@@ -22,6 +22,7 @@
     MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -1572,7 +1573,7 @@ class System(simulation.system.System):
         ''',)
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True,)
 
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
index d04a879f..092630e5 100644
--- a/atomisticparsers/gromacs/parser.py
+++ b/atomisticparsers/gromacs/parser.py
@@ -39,7 +39,7 @@
 from nomad.datamodel.metainfo.simulation.system import (
     AtomsGroup
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     GeometryOptimization, GeometryOptimizationMethod, GeometryOptimizationResults
 )
 from .metainfo.gromacs import x_gromacs_section_control_parameters, x_gromacs_section_input_output_files
diff --git a/atomisticparsers/gromos/metainfo/gromos.py b/atomisticparsers/gromos/metainfo/gromos.py
index c5722564..1ccc8d54 100644
--- a/atomisticparsers/gromos/metainfo/gromos.py
+++ b/atomisticparsers/gromos/metainfo/gromos.py
@@ -23,6 +23,7 @@
     Reference
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -1388,7 +1389,7 @@ class System(simulation.system.System):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/gulp/metainfo/gulp.py b/atomisticparsers/gulp/metainfo/gulp.py
index 1407634f..94319514 100644
--- a/atomisticparsers/gulp/metainfo/gulp.py
+++ b/atomisticparsers/gulp/metainfo/gulp.py
@@ -24,6 +24,7 @@
     Reference
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -827,7 +828,7 @@ class Calculation(simulation.calculation.Calculation):
     x_gulp_bulk_optimisation = SubSection(sub_section=x_gulp_bulk_optimisation.m_def)
 
 
-class ElasticResults(simulation.workflow.ElasticResults):
+class ElasticResults(simulationworkflowschema.ElasticResults):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -909,7 +910,7 @@ class ElasticResults(simulation.workflow.ElasticResults):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/gulp/parser.py b/atomisticparsers/gulp/parser.py
index 810a4a9b..f1e55c91 100644
--- a/atomisticparsers/gulp/parser.py
+++ b/atomisticparsers/gulp/parser.py
@@ -35,7 +35,7 @@
 from nomad.datamodel.metainfo.simulation.calculation import (
     Calculation, Energy, EnergyEntry
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     Elastic, ElasticMethod, ElasticResults, MolecularDynamics, MolecularDynamicsMethod
 )
 from atomisticparsers.gulp.metainfo.gulp import x_gulp_bulk_optimisation, x_gulp_bulk_optimisation_cycle
diff --git a/atomisticparsers/lammps/metainfo/lammps.py b/atomisticparsers/lammps/metainfo/lammps.py
index 6e280bc8..1ed63a95 100644
--- a/atomisticparsers/lammps/metainfo/lammps.py
+++ b/atomisticparsers/lammps/metainfo/lammps.py
@@ -23,6 +23,7 @@
     Reference
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -99,7 +100,7 @@ class System(simulation.system.System):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py
index 44cb7446..ad47346f 100644
--- a/atomisticparsers/lammps/parser.py
+++ b/atomisticparsers/lammps/parser.py
@@ -31,7 +31,7 @@
 from nomad.datamodel.metainfo.simulation.system import (
     AtomsGroup
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     GeometryOptimization, GeometryOptimizationMethod, GeometryOptimizationResults
 )
 from .metainfo.lammps import x_lammps_section_input_output_files, x_lammps_section_control_parameters
diff --git a/atomisticparsers/namd/metainfo/namd.py b/atomisticparsers/namd/metainfo/namd.py
index 66fa6f07..a782a958 100644
--- a/atomisticparsers/namd/metainfo/namd.py
+++ b/atomisticparsers/namd/metainfo/namd.py
@@ -23,6 +23,7 @@
     Reference, JSON
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -1006,7 +1007,7 @@ class System(simulation.system.System):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/namd/parser.py b/atomisticparsers/namd/parser.py
index 4c565798..a9147ad3 100644
--- a/atomisticparsers/namd/parser.py
+++ b/atomisticparsers/namd/parser.py
@@ -27,7 +27,7 @@
 from nomad.parsing.file_parser import TextParser, Quantity
 from nomad.datamodel.metainfo.simulation.run import Run, Program
 from nomad.datamodel.metainfo.simulation.method import Method
-from nomad.datamodel.metainfo.simulation.workflow import MolecularDynamics
+from simulationworkflowschema import MolecularDynamics
 from atomisticparsers.utils import MDAnalysisParser, MDParser
 from .metainfo import m_env  # pylint: disable=unused-import
 
diff --git a/atomisticparsers/tinker/metainfo/tinker.py b/atomisticparsers/tinker/metainfo/tinker.py
index b4640ac3..ef1e377d 100644
--- a/atomisticparsers/tinker/metainfo/tinker.py
+++ b/atomisticparsers/tinker/metainfo/tinker.py
@@ -22,6 +22,7 @@
     Reference, JSON
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -778,7 +779,7 @@ class System(simulation.system.System):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -872,7 +873,7 @@ class MolecularDynamics(simulation.workflow.MolecularDynamics):
         ''')
 
 
-class GeometryOptimization(simulation.workflow.GeometryOptimization):
+class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/tinker/parser.py b/atomisticparsers/tinker/parser.py
index ea4876e2..1b46eead 100644
--- a/atomisticparsers/tinker/parser.py
+++ b/atomisticparsers/tinker/parser.py
@@ -34,7 +34,7 @@
 from nomad.datamodel.metainfo.simulation.calculation import (
     Calculation, Energy, EnergyEntry, VibrationalFrequencies
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     GeometryOptimization, GeometryOptimizationMethod
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
diff --git a/atomisticparsers/utils/parsers.py b/atomisticparsers/utils/parsers.py
index ec000e55..75c95808 100644
--- a/atomisticparsers/utils/parsers.py
+++ b/atomisticparsers/utils/parsers.py
@@ -28,7 +28,7 @@
 from nomad.datamodel.metainfo.simulation.run import Run
 from nomad.datamodel.metainfo.simulation.system import System
 from nomad.datamodel.metainfo.simulation.calculation import Calculation
-from nomad.datamodel.metainfo.simulation.workflow import MolecularDynamics
+from simulationworkflowschema import MolecularDynamics
 from nomad.datamodel.metainfo.simulation.method import Interaction
 
 
diff --git a/atomisticparsers/xtb/metainfo/xtb.py b/atomisticparsers/xtb/metainfo/xtb.py
index caa280e2..e4b370a0 100644
--- a/atomisticparsers/xtb/metainfo/xtb.py
+++ b/atomisticparsers/xtb/metainfo/xtb.py
@@ -22,6 +22,7 @@
     Package, Quantity, Section, SubSection, JSON
 )
 from nomad.datamodel.metainfo import simulation
+import simulationworkflowschema
 
 
 m_package = Package()
@@ -87,7 +88,7 @@ class MultipolesEntry(simulation.calculation.MultipolesEntry):
         ''')
 
 
-class GeometryOptimization(simulation.workflow.GeometryOptimization):
+class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -146,7 +147,7 @@ class GeometryOptimization(simulation.workflow.GeometryOptimization):
         ''')
 
 
-class MolecularDynamics(simulation.workflow.MolecularDynamics):
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
 
     m_def = Section(validate=False, extends_base_section=True)
 
diff --git a/atomisticparsers/xtb/parser.py b/atomisticparsers/xtb/parser.py
index c1d9968c..a10cf61c 100644
--- a/atomisticparsers/xtb/parser.py
+++ b/atomisticparsers/xtb/parser.py
@@ -31,7 +31,7 @@
 from nomad.datamodel.metainfo.simulation.calculation import (
     Calculation, ScfIteration, Energy, EnergyEntry, BandEnergies, Multipoles, MultipolesEntry
 )
-from nomad.datamodel.metainfo.simulation.workflow import (
+from simulationworkflowschema import (
     SinglePoint, GeometryOptimization, GeometryOptimizationMethod
 )
 from atomisticparsers.utils import MDParser
diff --git a/pyproject.toml b/pyproject.toml
index 8ed2db95..66ef7565 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,7 @@ authors = [{ name = "The NOMAD Authors" }]
 license = { file = "LICENSE" }
 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",
     'lxml==4.7.1',
     'MDAnalysis',
     'panedr==0.2',