Fix openkim (#13)

* Fix openkim * Fix openkim metainfo * Update gh actions
nomad-coe · Apr 26, 2024 · de625ab · de625ab
1 parent f1ee000
commit de625ab
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diff --git a/.github/workflows/python-actions.yaml b/.github/workflows/python-actions.yaml
@@ -12,16 +12,10 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
+        pip install '.[tests]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
         # we need the latest nomad version for testing
         pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
-        pip install '.[tests]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
         pip install coverage coveralls
-    - name: pycodestyle
-      run: |
-        python -m pycodestyle --ignore=E501,E701,E731 *parsers tests
-    - name: pylint
-      run: |
-        python -m pylint *parsers tests
     - name: mypy
       run: |
         python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional *parsers tests

diff --git a/databaseparsers/openkim/metainfo/openkim.py b/databaseparsers/openkim/metainfo/openkim.py
@@ -16,11 +16,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-import numpy as np            # pylint: disable=unused-import
-import typing                 # pylint: disable=unused-import
+import numpy as np  # pylint: disable=unused-import
+import typing  # pylint: disable=unused-import
 from nomad.metainfo import (  # pylint: disable=unused-import
-    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
-    Reference, JSON
+    MSection,
+    MCategory,
+    Category,
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+    SectionProxy,
+    Reference,
+    JSON,
 )
 import runschema.run  # pylint: disable=unused-import
 import runschema.calculation  # pylint: disable=unused-import
@@ -33,145 +41,156 @@
 
 
 class Run(runschema.run.Run):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_openkim_build_date = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         build date as string
-        ''')
+        """,
+    )
 
     x_openkim_src_date = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         date of last modification of the source as string
-        ''')
+        """,
+    )
 
     x_openkim_inserted_on = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         title for the property
-        ''')
+        """,
+    )
 
     x_openkim_property_id = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         unique ID of the property
-        ''')
+        """,
+    )
 
     x_openkim_property_title = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         title for the property
-        ''')
+        """,
+    )
 
     x_openkim_property_description = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         title for the property
-        ''')
+        """,
+    )
 
     x_openkim_instance_id = Quantity(
-        type=np.dtype(np.int32),
+        type=np.int32,
         shape=[],
-        description='''
+        description="""
         unique ID of the property
-        ''')
+        """,
+    )
 
     x_openkim_latest = Quantity(
         type=bool,
         shape=[],
-        description='''
-        ''')
+        description="""
+        """,
+    )
 
     x_openkim_meta = Quantity(
         type=JSON,
         shape=[],
-        description='''
-        openkim metadata'''
+        description="""
+        openkim metadata""",
     )
 
 
 class System(runschema.system.System):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_openkim_short_name = Quantity(
         type=str,
         shape=[1],
-        description='''
+        description="""
         short name defining the crystal
-        ''')
+        """,
+    )
 
     x_openkim_space_group = Quantity(
         type=str,
         shape=[1],
-        description='''
+        description="""
         short name defining the crystal
-        ''')
+        """,
+    )
 
 
 class Elastic(simulationworkflowschema.Elastic):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_openkim_excess = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        unit='pascal',
-        description='''
+        unit="pascal",
+        description="""
         total square numerical asymmetry of the calculated elastic constants
-        ''')
+        """,
+    )
 
 
 class Phonon(simulationworkflowschema.Phonon):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_openkim_wave_number = Quantity(
-        type=np.dtype(np.float64),
-        shape=['n_spin_channels', 'n_kpoints'],
-        unit='1 / m',
-        description='''
+        type=np.float64,
+        shape=["n_spin_channels", "n_kpoints"],
+        unit="1 / m",
+        description="""
         wave numbers for each k-point
-        ''')
-
+        """,
+    )
 
-class SimulationWorkflow(simulationworkflowschema.general.SimulationWorkflow):
 
+class SimulationWorkflow(simulationworkflowschema.SimulationWorkflow):
     m_def = Section(validate=False, extends_base_section=True)
 
     x_openkim_property = Quantity(
         type=str,
         shape=[],
-        description='''
+        description="""
         name of the property to be compared to nomad
-        ''')
+        """,
+    )
 
     x_openkim_nomad_rms_error = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         root mean square difference of the openkim data with respect to nomad
-        ''')
+        """,
+    )
 
     x_openkim_nomad_std = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         standard deviation of the nomad data
-        ''')
+        """,
+    )
 
     x_openkim_n_nomad_data = Quantity(
-        type=np.dtype(np.int32),
+        type=np.int32,
         shape=[],
-        description='''
+        description="""
         number of nomad entries with property corresponding to x_openkim_property
-        ''')
+        """,
+    )