Bump depedencies (#263)

* Move dependency specs to `nomad-lab[infrastructure]`

---------

Co-authored-by: ndaelman <[email protected]>

electronicparsers/magres/parser.py

@@ -41,8 +41,6 @@
     SpinSpinCoupling,
 )
 from .metainfo.magres import m_package
-
-from nomad.app.v1.models import MetadataRequired
 from ..utils import BeyondDFTWorkflowsParser
 
 
@@ -441,7 +439,7 @@ def parse(self, filepath, archive, logger):
 
         # Create Run with Program information
         sec_run = Run()
-        calculation_params = self.magres_file_parser.get('calculation')
+        calculation_params = self.magres_file_parser.get('calculation', {})
         program_name = calculation_params.get('code', '')
         if program_name != 'CASTEP':
             self.logger.error(

pyproject.toml

@@ -10,13 +10,13 @@ readme = "README.md"
 authors = [{ name = "The NOMAD Authors" }]
 license = { file = "LICENSE" }
 dependencies = [
+    "h5py>=3.6.0",
+    "lxml>=5.2",
     "nomad-lab>=1.3.6.dev1",
     "nomad-schema-plugin-simulation-workflow>=1.0.1",
     "nomad-schema-plugin-run>=1.0.1",
     "nomad-parser-plugins-simulation>=1.0.2",
-    "lxml>=5.2",
     "netCDF4==1.6.5",
-    "h5py>=3.6.0",
     "pyyaml>=6.0",
     "pydantic>=1.10.8,<2.0.0",
 ]
@@ -26,26 +26,18 @@ homepage = "https://github.com/nomad-coe/electronic-parsers"
 
 [project.optional-dependencies]
 dev = [
-    'mypy==1.0.1',
-    'pytest==3.10.0',
-    'pytest-timeout==1.4.2',
-    'pytest-cov==2.7.1',
     'astroid==2.11.7',
-    'typing-extensions==4.7.1',
-    'ruff==0.1.8'
+    'mypy==1.0.1',
+    'pytest>= 5.3.0, <8',
+    'pytest-timeout>=1.4.2',
+    'pytest-cov>=2.7.1',
+    'ruff>=0.6',
+    'typing-extensions>=4.12',
 ]
 # these are extra deps for nomad infra as a result of using nomad.search
 # TODO remove usage in magres and w2dynamics
 infrastructure = [
-    "mongoengine>=0.20",
-    "pyjwt[crypto]==2.6.0",
-    "structlog",
-    "python-logstash==0.4.6",
-    "pydantic>=1.10.8,<2.0.0",
-    "fastapi<0.100",
-    "elasticsearch==7.17.1",
-    "elasticsearch-dsl==7.4.0",
-    "zipstream-new==1.1.5",
+    "nomad-lab[infrastructure]>=1.3.10",
 ]
 
 [tool.ruff]