Testing pipeline

nomad.yaml

@@ -6,7 +6,8 @@ plugins:
   # We only include our schema here. Without the explicit include, all plugins will be
   # loaded. Many build in plugins require more dependencies. Install nomad-lab[parsing]
   # to make all default plugins work.
-  include: 'parsers/magres'
+  include:
+    - 'parsers/magres'
   options:
     parsers/magres:
       python_package: nomad_parser_magres

pyproject.toml

@@ -22,7 +22,9 @@ classifiers = [
     "License :: OSI Approved :: Apache Software License",
 ]
 dependencies = [
-    "nomad-lab>=1.2.2dev457",
+    "nomad-lab@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",
 ]
 
 [project.urls]
@@ -41,6 +43,7 @@ dev = [
     "unidecode==1.3.2",
     "fastapi==0.92.0",
     "zipstream-new==1.1.5",
+    "lxml_html_clean>=0.1.0",
 ]
 
 [tool.ruff]
@@ -93,4 +96,4 @@ line-ending = "auto"
 where = ["src"]
 
 [tool.setuptools.package-data]
-nomad_analysis = ['*/nomad_plugin.yaml']
+nomad_parser_magres = ['*/nomad_plugin.yaml']

src/nomad_parser_magres/__init__.py

@@ -1 +1 @@
-from .parser import *
+from .parser import MagresParser

src/nomad_parser_magres/parser.py

@@ -45,7 +45,7 @@
 # For the automatic workflow NMR
 from nomad.search import search
 from nomad.app.v1.models import MetadataRequired
-from ..utils import BeyondDFTWorkflowsParser
+from .utils import BeyondDFTWorkflowsParser
 
 
 re_float = r' *[-+]?\d+\.\d*(?:[Ee][-+]\d+)? *'

src/nomad_parser_magres/utils/__init__.py

@@ -0,0 +1,20 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .utils import get_files, numpy_type_to_json_serializable, BeyondDFTWorkflowsParser
+from .magres_workflow import NMRMagRes, NMRMagResMethod, NMRMagResResults

src/nomad_parser_magres/utils/magres_workflow.py

@@ -0,0 +1,61 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+from nomad.metainfo import SubSection, Quantity, Reference
+from nomad.datamodel.metainfo.simulation.method import Method
+from simulationworkflowschema import (
+    SimulationWorkflowResults,
+    SimulationWorkflowMethod,
+    SerialSimulation,
+)
+
+
+class NMRMagResResults(SimulationWorkflowResults):
+    """
+    Groups the NMR magres outputs.
+    """
+
+    pass
+
+
+class NMRMagResMethod(SimulationWorkflowMethod):
+    """
+    References the NMR (first principles) input methodology.
+    """
+
+    nmr_method_ref = Quantity(
+        type=Reference(Method),
+        description="""
+        Reference to the NMR (first principles) methodology.
+        """,
+    )
+
+
+class NMRMagRes(SerialSimulation):
+    """
+    The NMR MagRes workflow is generated in an extra EntryArchive IF both the NMR (first
+    principles) and the NMR magres SinglePoint EntryArchives are present in the
+    upload.
+    """
+
+    method = SubSection(sub_section=NMRMagResMethod)
+
+    results = SubSection(sub_section=NMRMagResResults)
+
+    def normalize(self, archive, logger):
+        super().normalize(archive, logger)