moreniius 0.5.1__tar.gz → 0.6.0__tar.gz

{moreniius-0.5.1 → moreniius-0.6.0}/.github/workflows/pip.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

{moreniius-0.5.1/src/moreniius.egg-info → moreniius-0.6.0}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.4
 Name: moreniius
-Version: 0.5.1
+Version: 0.6.0
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -14,8 +13,9 @@ Classifier: Programming Language :: Python :: 3.13
 Description-Content-Type: text/markdown
 Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
-Requires-Dist: mccode-antlr[hdf5]>=0.15.1
+Requires-Dist: mccode-antlr[hdf5]>=0.16.1
 Requires-Dist: nexusformat>=1.0.6
+Requires-Dist: networkx
 
 # moreniius
 A project to contain custom components required to use `eniius` to produce `NeXus Structure` `JSON` from `mccode-antlr` simulated instruments.

{moreniius-0.5.1 → moreniius-0.6.0}/pyproject.toml

@@ -7,8 +7,9 @@ name = "moreniius"
 dependencies = [
     'zenlog>=1.1',
     'platformdirs>=3.11',
-    'mccode-antlr[hdf5]>=0.15.1',
-    'nexusformat>=1.0.6'
+    'mccode-antlr[hdf5]>=0.16.1',
+    'nexusformat>=1.0.6',
+    'networkx'
 ]
 readme = "README.md"
 authors = [
@@ -19,7 +20,6 @@ classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -41,7 +41,6 @@ legacy_tox_ini = """
         py312
         py311
         py310
-        py39
         type
 
     [testenv]

{moreniius-0.5.1 → moreniius-0.6.0}/src/moreniius/mccode/mccode.py

@@ -1,5 +1,7 @@
 from zenlog import log
 from dataclasses import dataclass, field
+from networkx import DiGraph
+from typing import Union
 from mccode_antlr.instr import Orient
 from .instr import NXInstr
 
@@ -9,9 +11,11 @@ log.level('error')
 @dataclass
 class NXMcCode:
     nx_instr: NXInstr
-    origin_name: str = None
+    origin_name: Union[str, None] = None
     indexes: dict[str, int] = field(default_factory=dict)
     orientations: dict[str, Orient] = field(default_factory=dict)
+    graph: Union[DiGraph, None] = None
+    reversed_graph: Union[DiGraph, None] = None
 
     def __post_init__(self):
         from copy import deepcopy
@@ -37,30 +41,52 @@ class NXMcCode:
             for name in self.orientations:
                 self.orientations[name] = self.orientations[name] - origin
 
+        if self.graph is None:
+            self.graph = self.build_graph()
+        if self.reversed_graph is None:
+            self.reversed_graph = self.graph.reverse(copy=True)
+
     def transformations(self, name):
         from .orientation import NXOrient
         return NXOrient(self.nx_instr, self.orientations[name]).transformations(name)
 
+    def inputs(self, name):
+        """Return the other end of edges ending at the named node"""
+        return list(self.reversed_graph[name])
+
+    def outputs(self, name):
+        """Return the other end of edges starting at the named node"""
+        return list(self.graph[name])
+
     def component(self, name, only_nx=True):
         """Return a NeXus NXcomponent corresponding to the named McStas component instance"""
         from .instance import NXInstance
         instance = self.nx_instr.instr.components[self.indexes[name]]
         transformations = self.transformations(name)
-        nx = NXInstance(self.nx_instr, instance, self.indexes[name], transformations, only_nx=only_nx)
-        if transformations and nx.nx['transformations'] != transformations:
+        nxinst = NXInstance(self.nx_instr, instance, self.indexes[name], transformations, only_nx=only_nx)
+        if transformations and nxinst.nx['transformations'] != transformations:
             # if the component modifed the transformations group, make sure we don't use our version again
             del self.orientations[name]
-        return nx
+        if len(inputs := self.inputs(name)):
+            nxinst.nx.attrs['inputs'] = inputs
+        if len(outputs := self.outputs(name)):
+            nxinst.nx.attrs['outputs'] = outputs
+        return nxinst
 
     def instrument(self, only_nx=True):
-        from .instr import NXInstr
         from nexusformat.nexus import NXinstrument
         nx = NXinstrument()  # this is a NeXus class
         nx['mcstas'] = self.nx_instr.to_nx()
-        # hack the McCode component index into the name of the NeXus group
-        width = len(str(max(self.indexes.values())))
-        for name, index in self.indexes.items():
-            nx_name = f'{index:0{width}d}_{name}'
-            nx[nx_name] = self.component(name, only_nx=only_nx).nx
+        for name in self.indexes.keys():
+            nx[name] = self.component(name, only_nx=only_nx).nx
 
         return nx
+
+    def build_graph(self):
+        # FIXME expand this to a full-description if/when McCode includes graph information
+        graph = DiGraph()
+        names = [x.name for x in self.nx_instr.instr.components]
+        graph.add_nodes_from(names)
+        # By default, any McCode instrument is a linear object:
+        graph.add_edges_from([(names[i], names[i+1]) for i in range(len(names)-1)])
+        return graph

{moreniius-0.5.1 → moreniius-0.6.0}/src/moreniius/moreniius.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+from networkx import Graph
 from mccode_antlr.instr import Instr
 
 
@@ -13,12 +14,13 @@ class MorEniius:
                     origin: str | None = None,
                     only_nx: bool = False,
                     nxlog_root: str | None = None,
-                    absolute_depends_on: bool = False
+                    absolute_depends_on: bool = False,
+                    graph: Graph | None = None,
                     ):
         from nexusformat.nexus import NXfield
         from .mccode import NXMcCode, NXInstr
         nxlog_root = nxlog_root or '/entry/parameters'
-        nx_mccode = NXMcCode(NXInstr(instr, nxlog_root=nxlog_root), origin_name=origin)
+        nx_mccode = NXMcCode(NXInstr(instr, nxlog_root=nxlog_root), origin_name=origin, graph=graph)
         nxs_obj = nx_mccode.instrument(only_nx=only_nx)
         nxs_obj['name'] = NXfield(value=instr.name)
         return cls(nxs_obj, only_nx=only_nx, absolute_depends_on=absolute_depends_on)

{moreniius-0.5.1 → moreniius-0.6.0}/src/moreniius/writer.py

@@ -2,7 +2,7 @@ from zenlog import log
 
 
 def convert_types(obj, only_nx=True):
-    from numpy import dtype, ndarray
+    from numpy import dtype, ndarray, array
     from nexusformat.nexus import NXattr
     py_data_type = type(obj)
     np_data_type = dtype(py_data_type)
@@ -24,11 +24,16 @@ def convert_types(obj, only_nx=True):
                 val = val.tolist()
             if obj.dtype == 'object':
                 (tp, vl) = (dtype(type(obj.nxdata)).name, val)
+                # If still 'object', this will throw an error below
+                if tp == 'object' and isinstance(val, list):
+                    tp = dtype(type(val[0])).name
             else:
                 (tp, vl) = (obj.dtype, val)
         elif not only_nx and hasattr(obj, 'to_json_dict'):
             # Shoe-horn in an object-defined dictionary:
             tp, vl = None, obj.to_json_dict()
+        elif isinstance(obj, list):
+            return convert_types(array(obj))
         else:
             raise RuntimeError(f'unrecognised type {py_data_type} / {np_data_type} for {repr(obj)}')
     else:
@@ -38,7 +43,7 @@ def convert_types(obj, only_nx=True):
     elif tp == 'float64':
         tp = 'double'
     elif tp == 'object':
-        raise RuntimeError(f'Internal logical error attempting to convert {obj}')
+        raise RuntimeError(f'Internal logical error attempting to convert {obj} of type {type(obj)}')
     elif tp == 'int':
         tp = 'int64'
     elif tp == 'float':
@@ -124,8 +129,12 @@ class Writer:
                     attrs = [dict(name='NX_class', dtype='string', values=obj.nxclass)]
                     if len(list(obj)):
                         entry['children'] = self._to_json_dict(obj, only_nx=only_nx, absolute_depends_on=absolute_depends_on)
-                for n, v in obj.attrs.items():
-                    typ, val = convert_types(v, only_nx)
+                for n in obj.attrs:
+                    typ, val = convert_types(obj.attrs[n], only_nx)
+                # FIXME accessing an attribute value via the dict values gives
+                #       a NXattr object *not* the underlying value!?
+                # for n, v in obj.attrs.items():
+                #     typ, val = convert_types(v, only_nx)
                     if absolute_depends_on and n == 'depends_on' and '/' != val[0]:
                         val = _to_absolute(top_obj.nxpath, val)
                     attrs.append(dict(name=n, dtype=typ, values=val) if typ else val)

{moreniius-0.5.1 → moreniius-0.6.0/src/moreniius.egg-info}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.4
 Name: moreniius
-Version: 0.5.1
+Version: 0.6.0
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -14,8 +13,9 @@ Classifier: Programming Language :: Python :: 3.13
 Description-Content-Type: text/markdown
 Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
-Requires-Dist: mccode-antlr[hdf5]>=0.15.1
+Requires-Dist: mccode-antlr[hdf5]>=0.16.1
 Requires-Dist: nexusformat>=1.0.6
+Requires-Dist: networkx
 
 # moreniius
 A project to contain custom components required to use `eniius` to produce `NeXus Structure` `JSON` from `mccode-antlr` simulated instruments.

{moreniius-0.5.1 → moreniius-0.6.0}/src/moreniius.egg-info/requires.txt

@@ -1,4 +1,5 @@
 zenlog>=1.1
 platformdirs>=3.11
-mccode-antlr[hdf5]>=0.15.1
+mccode-antlr[hdf5]>=0.16.1
 nexusformat>=1.0.6
+networkx

{moreniius-0.5.1 → moreniius-0.6.0}/tests/test_nexus_structure.py

@@ -28,7 +28,7 @@ class NexusStrctureTestCase(unittest.TestCase):
         END
         """
         self.instr = parse_mcstas_instr(instr)
-        self.structures = {'2_mon0': m0, '5_mon1': m1}
+        self.structures = {'mon0': m0, 'mon1': m1}
 
     def test_moreniius(self):
         from moreniius import MorEniius
@@ -72,7 +72,7 @@ class NexusStrctureTestCase(unittest.TestCase):
         nx = nx['children'][3]
         for x in group_keys:
             self.assertTrue(x in nx)
-        self.assertEqual(nx['name'], '2_mon0')
+        self.assertEqual(nx['name'], 'mon0')
         self.assertEqual(len(nx['children']), 4)  # removed mcstas child
         nx = nx['children'][1] # this is now a NXdata group
         self.assertTrue('attributes' in nx)
@@ -80,7 +80,7 @@ class NexusStrctureTestCase(unittest.TestCase):
         self.assertEqual(nx['attributes'][0]['name'], 'NX_class')
         self.assertEqual(nx['attributes'][0]['values'], 'NXdata')
         nx = nx['children'][0]
-        self.assertEqual(self.structures['2_mon0'], nx)
+        self.assertEqual(self.structures['mon0'], nx)
 
 
 if __name__ == '__main__':