cleanup

pyproject.toml

@@ -27,11 +27,11 @@ maintainers = [
 license = { file = "LICENSE" }
 dependencies = [
     "nomad-lab>=1.3.0",
-    "python-magic-bin; sys_platform == 'win32'",
+    "nomad-simulations>=0.0.6",
 ]
 
 [project.urls]
-Repository = "https://github.com/EBB2675/nomad-parser-qutip"
+Repository = "https://github.com/FAIRmat-NFDI/nomad-parser-qutip"
 
 [project.optional-dependencies]
 dev = ["ruff", "pytest", "structlog"]
@@ -77,7 +77,7 @@ select = [
     "UP",
     # isort
     "I",
-    # pylint 
+    # pylint
     "PL",
 ]
 

src/nomad_parser_qutip/parsers/__init__.py

@@ -12,7 +12,9 @@ def load(self):
 
 parser_entry_point = QutipEntryPoint(
     name='QuTiP Parser',
-    description='Parser for QuTiP outputs in text format.',
+    description='Parser for QuTiP outputs.',
+    # The following is a regular expression for the name of a potential mainfile.
+    # If this expression is given:
+    # the parser is only considered for a file, if the expression matches.
     mainfile_name_re='.*\.out.*',
-    mainfile_contents_re=r'EBB2675 Version [\d\.]*',  # to be fixed
 )

src/nomad_parser_qutip/parsers/parser.py

@@ -12,6 +12,7 @@
 
 from nomad.config import config
 from nomad.parsing.parser import MatchingParser
+from nomad.datamodel.metainfo.workflow import Workflow
 from nomad_simulations.schema_packages.general import Program, Simulation
 
 configuration = config.get_plugin_entry_point(
@@ -28,5 +29,7 @@ def parse(
         child_archives: dict[str, 'EntryArchive'] = None,
     ) -> None:
         simulation = Simulation()
+        # here we are populating the archive with the program name
         simulation.program = Program(name='QuTiP')
+        # put the simulation section into archive data
         archive.data = simulation

src/nomad_parser_qutip/schema_packages/schema_package.py

@@ -22,30 +22,30 @@ class Qobj(ArchiveSection):
     A section to semantically represent a QuTiP Qobj.
 
     The main quantities are:
-        dims   : Hilbert space dimensions as a nested list (e.g. [[2], [1]] for a ket).
-        shape  : SWape of the underlying data matrix (e.g. [2, 1] for a column vector).
+        dims   : Hilbert space dimensions.
+        shape  : Shape of the underlying data.
         type   : MEnum to label the Qobj (e.g. 'ket', 'bra', 'oper', 'super').
         dtype  :  The data type indicator (for example, 'Dense' or 'csr') showing the
         numerical storage format.
         isherm : Boolean flag indicating whether an operator is Hermitian.
-        data   : Numerical data stored as a 2D array.
+        data   : Matrix representing state or operator.
     """
 
     dims = Quantity(
-        type=list,
+        type=np.int32,
         shape=['*', '*'],
         description=(
-            """Hilbert space dimensions of the quantum object. For example, a ket
-            state in a 2-dimensional space may have dims=[[2], [1]]."""
+            """List of dimensions keeping track of the tensor structure.
+            Example for a ket: [[2], [1]]."""
         ),
     )
 
     shape = Quantity(
-        type=list,
+        type=np.int32,
         shape=['*'],
         description=(
-            """Shape of the underlying data matrix. For example, a state vector (ket)
-            might have shape=[2, 1]."""
+            """Shape of the underlying data array.
+            Example for a ket : [2, 1]."""
         ),
     )
 
@@ -74,11 +74,10 @@ class Qobj(ArchiveSection):
     )
 
     data = Quantity(
-        type=np.ndarray,
+        type=np.float64,
         shape=['*', '*'],
         description=(
-            """The numerical matrix data of the quantum object.
-            It is stored as a 2D array."""
+            """Sparse matrix characterizing the quantum object."""
         ),
     )
 
@@ -88,7 +87,7 @@ def normalize(self, archive, logger) -> None:
 
         """
         super().normalize(archive, logger)
-        # this is just a placeholder, will take care of it later.
+        # a simple example for the normalization function
         if self.data is not None:
             data_shape = list(self.data.shape)
             if self.shape != data_shape:

tests/parsers/test_parser.py

@@ -2,11 +2,11 @@
 
 from nomad.datamodel import EntryArchive
 
-from nomad_parser_qutip.parsers.parser import NewParser
+from nomad_parser_qutip.parsers.parser import QutipParser
 
 
 def test_parse_file():
-    parser = NewParser()
+    parser = QutipParser()
     archive = EntryArchive()
     parser.parse('tests/data/example.out', archive, logging.getLogger())