Make McStasVirtualInstrument run without crashing

MDANSE/Src/MDANSE/Framework/Configurators/AxisSelectionConfigurator.py

@@ -58,10 +58,16 @@ def configure(self, value):
             self.update(value)
 
         e1 = find_atoms_in_molecule(
-            trajConfig["instance"].universe, self["molecule"], self["endpoint1"], True
+            trajConfig["instance"]._chemical_system,
+            self["molecule"],
+            self["endpoint1"],
+            True,
         )
         e2 = find_atoms_in_molecule(
-            trajConfig["instance"].universe, self["molecule"], self["endpoint2"], True
+            trajConfig["instance"]._chemical_system,
+            self["molecule"],
+            self["endpoint2"],
+            True,
         )
 
         self["value"] = value

MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py

@@ -42,6 +42,7 @@ def __init__(self, name, variables=None, **kwargs):
         InputFileConfigurator.__init__(self, name, **kwargs)
 
         self._variables = variables if variables is not None else []
+        self._units = {}
 
     def configure(self, value):
         """
@@ -67,6 +68,10 @@ def configure(self, value):
         for v in self._variables:
             if v in self["instance"]:
                 self[v] = self["instance"][v][:]
+                try:
+                    self._units[v] = self["instance"][v].attrs["units"]
+                except:
+                    self._units[v] = "unitless"
             else:
                 self.error_status = (
                     f"the variable {v} was not  found in {value} HDF file"
@@ -87,7 +92,7 @@ def variables(self):
 
     def get_information(self):
         """
-        Returns some basic informations about the contents of theHDF file.
+        Returns some basic informations about the contents of the HDF file.
 
         :return: the informations about the contents of the HDF file.
         :rtype: str

MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py

@@ -16,6 +16,7 @@
 import os
 import tempfile
 import time
+from typing import Dict, Any
 
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import (
@@ -24,6 +25,26 @@
 )
 
 
+def parse_dictionary(input: str) -> Dict[str, Any]:
+    big_line = input.strip("\{\}[] \n")
+    tokens = big_line.split(",")
+    result = {}
+    for entry in tokens:
+        temp = entry.split(":")
+        key, value = temp[0], ":".join(temp[1:])
+        key = key.strip("' ")
+        value = value.strip(" '")
+        try:
+            value = int(value)
+        except:
+            try:
+                value = float(value)
+            except:
+                pass
+        result[key] = value
+    return result
+
+
 class McStasOptionsConfigurator(IConfigurator):
     """
     This configurator allows to input the McStas options that will be used to run a McStas executable file.
@@ -50,7 +71,9 @@ def configure(self, value):
 
         options = self._default.copy()
 
-        for k, v in list(value.items()):
+        parsed = parse_dictionary(value)
+
+        for k, v in list(parsed.items()):
             if k not in options:
                 continue
             options[k] = v

MDANSE/Src/MDANSE/Framework/Configurators/McStasParametersConfigurator.py

@@ -19,14 +19,15 @@
 
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
+from MDANSE.Framework.Configurators.McStasOptionsConfigurator import parse_dictionary
 
 
 class McStasParametersConfigurator(IConfigurator):
     """
     This configurator allows to input the McStas instrument parameters that will be used to run a McStas executable file.
     """
 
-    _mcStasTypes = {"double": float, "int": int, "StringConfigurator": str}
+    _mcStasTypes = {"double": float, "int": int, "string": str}
 
     _default = {
         "beam_wavelength_Angs": 2.0,
@@ -77,20 +78,27 @@ def configure(self, value):
             [exePath, "-h"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT
         )
 
+        parameters_bytes = s.communicate()[0]
+        parameters_string = parameters_bytes.decode(encoding="utf-8")
+
         instrParameters = dict(
             [
                 (v[0], [v[1], v[2]])
                 for v in re.findall(
-                    "\s*(\w+)\s*\((\w+)\)\s*\[default='(\S+)'\]", s.communicate()[0]
+                    "\s*(\w+)\s*\((\w+)\)\s*\[default='(\S+)'\]", parameters_string
                 )
                 if v[0] not in self._exclude
             ]
         )
 
         val = {}
-        for k, v in list(value.items()):
+        parsed = parse_dictionary(value)
+        print(f"Parsed input: {parsed}")
+        print(f"Received from McStas: {instrParameters}")
+        for k, v in list(parsed.items()):
             if k not in instrParameters:
-                instrParameters.pop(k)
+                # instrParameters.pop(k)  # how was that supposed to work?
+                continue
             val[k] = self._mcStasTypes[instrParameters[k][0]](v)
 
         self["value"] = ["%s=%s" % (k, v) for k, v in list(val.items())]

MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py

@@ -1,5 +1,5 @@
 from MDANSE.Framework.Formats.IFormat import IFormat
-from MDANSE.Framework.OutputVariables import IOutputVariable
+from MDANSE.Framework.OutputVariables.IOutputVariable import IOutputVariable
 from .HDFFormat import HDFFormat
 
 

MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py

@@ -133,7 +133,7 @@ def run_step(self, index):
         variables = copy.deepcopy(current_configuration.variables)
         coords = variables.pop("coordinates")
         current_configuration = RealConfiguration(
-            trajectory.chemical_system, coords, None, **variables
+            trajectory.chemical_system, coords, **variables
         )
 
         trajectory.chemical_system.configuration = current_configuration

MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py

@@ -30,9 +30,10 @@
 from MDANSE.Framework.OutputVariables.IOutputVariable import IOutputVariable
 from MDANSE.Framework.Units import measure
 from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
+from MDANSE.MolecularDynamics.UnitCell import UnitCell
 
 MCSTAS_UNITS_LUT = {
-    "THz": measure(1, "THz", equivalent=True).toval("meV"),
+    "rad/ps": measure(1, "rad/ps", equivalent=True).toval("meV"),
     "nm2": measure(1, "nm2").toval("b"),
     "1/nm": measure(1, "1/nm").toval("1/ang"),
 }
@@ -74,7 +75,7 @@ class McStasVirtualInstrument(IJob):
         {
             "widget": "InputFileConfigurator",
             "label": "MDANSE Coherent Structure Factor",
-            "variables": ["q", "frequency", "s(q,f)_total"],
+            "variables": ["q", "omega", "s(q,f)_total"],
             "default": "dcsf_prot.h5",
         },
     )
@@ -83,11 +84,17 @@ class McStasVirtualInstrument(IJob):
         {
             "widget": "InputFileConfigurator",
             "label": "MDANSE Incoherent Structure Factor",
-            "variables": ["q", "frequency", "s(q,f)_total"],
+            "variables": ["q", "omega", "s(q,f)_total"],
             "default": "disf_prot.h5",
         },
     )
-    settings["temperature"] = ("FloatConfigurator", {"default": 298.0})
+    settings["temperature"] = (
+        "FloatConfigurator",
+        {
+            "default": 298.0,
+            "label": "The sample temperature to be used in the simulation.",
+        },
+    )
     settings["display"] = (
         "BooleanConfigurator",
         {"label": "trace the 3D view of the simulation"},
@@ -119,7 +126,8 @@ def initialize(self):
         self.numberOfSteps = 1
 
         symbols = sorted_atoms(
-            self.configuration["trajectory"]["instance"].universe, "symbol"
+            self.configuration["trajectory"]["instance"]._chemical_system.atom_list,
+            "symbol",
         )
 
         # Compute some parameters used for a proper McStas run
@@ -140,12 +148,10 @@ def initialize(self):
             * MCSTAS_UNITS_LUT["nm2"]
         )
         for frameIndex in self.configuration["frames"]["value"]:
-            self.configuration["trajectory"]["instance"].universe.setFromTrajectory(
-                self.configuration["trajectory"]["instance"], frameIndex
+            configuration = self.configuration["trajectory"]["instance"].configuration(
+                frameIndex
             )
-            cellVolume = self.configuration["trajectory"][
-                "instance"
-            ].universe.cellVolume()
+            cellVolume = configuration._unit_cell.volume
             self._mcStasPhysicalParameters["density"] += (
                 self._mcStasPhysicalParameters["weight"] / cellVolume
             )
@@ -186,8 +192,9 @@ def run_step(self, index):
                 fout.write("# %s\n" % var)
 
                 data = self.configuration[typ][var][:]
+                data_unit = self.configuration[typ]._units[var]
                 try:
-                    data *= MCSTAS_UNITS_LUT[self.configuration[typ][var].units]
+                    data *= MCSTAS_UNITS_LUT[data_unit]
                 except KeyError:
                     pass
 
@@ -220,7 +227,7 @@ def run_step(self, index):
         out, _ = s.communicate()
 
         for line in out.splitlines():
-            if "ERROR" in line:
+            if "ERROR" in line.decode(encoding="utf-8"):
                 raise McStasError("An error occured during McStas run: %s" % out)
 
         with open(
@@ -230,7 +237,7 @@ def run_step(self, index):
             ),
             "w",
         ) as f:
-            f.write(out)
+            f.write(out.decode(encoding="utf-8"))
 
         return index, None
 
@@ -439,7 +446,7 @@ def read_monitor(self, simFile):
             Line = Line.split(":")
             Field = Line[0]
             Value = ""
-            Value = string.join(string.join(Line[1 : len(Line)], ":").split("'"), "")
+            Value = "".join(":".join(Line[1 : len(Line)]).split("'"))
             strStruct = strStruct + "'" + Field + "':'" + Value + "'"
             if j < len(Header) - 1:
                 strStruct += ","

MDANSE/Tests/UnitTests/test_documentation.py

@@ -0,0 +1,14 @@
+
+import pytest
+
+from MDANSE.Framework.Jobs.IJob import IJob
+
+
+job_list = IJob.indirect_subclasses()
+
+
+@pytest.mark.parametrize("job_name", job_list)
+def test_documentation_building(job_name):
+    instance = IJob.create(job_name)
+    docs = instance.build_doc()
+    assert len(docs) > 0

MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobTree.py

@@ -65,6 +65,12 @@ def createNode(self, name: str, thing, filter: str = ""):
         self._nodes[new_number] = new_node
         self._values[new_number] = thing
         self._docstrings[new_number] = thing.__doc__
+        try:
+            self._docstrings[new_number] += "\n" + thing.build_doc()
+        except AttributeError:
+            pass
+        except TypeError:
+            pass
         if hasattr(thing, "category"):
             if filter:
                 if filter in thing.category: