moreniius 0.2.3__tar.gz → 0.2.5__tar.gz

{moreniius-0.2.3 → moreniius-0.2.5}/.github/workflows/pip.yml

@@ -20,7 +20,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

{moreniius-0.2.3 → moreniius-0.2.5}/.github/workflows/wheels.yml

@@ -26,7 +26,7 @@ jobs:
     - name: Check metadata
       run: pipx run twine check dist/*
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         path: dist/*
 
@@ -42,9 +42,9 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
 
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: artifact
         path: dist

{moreniius-0.2.3/src/moreniius.egg-info → moreniius-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: moreniius
-Version: 0.2.3
+Version: 0.2.5
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -8,7 +8,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
 Requires-Dist: importlib_metadata; python_version < "3.8"
-Requires-Dist: mccode-antlr[hdf5]>=0.7.1
+Requires-Dist: mccode-antlr[hdf5]>=0.9.2
 Requires-Dist: nexusformat>=1.0.6
 
 # moreniius

{moreniius-0.2.3 → moreniius-0.2.5}/pyproject.toml

@@ -8,7 +8,7 @@ dependencies = [
     'zenlog>=1.1',
     'platformdirs>=3.11',
     "importlib_metadata; python_version<'3.8'",
-    'mccode-antlr[hdf5]>=0.7.1',
+    'mccode-antlr[hdf5]>=0.9.2',
     'nexusformat>=1.0.6'
 ]
 readme = "README.md"

{moreniius-0.2.3 → moreniius-0.2.5}/src/moreniius/mccode/instr.py

@@ -2,7 +2,7 @@ from zenlog import log
 from dataclasses import dataclass, field
 from mccode_antlr.instr import Instr
 from mccode_antlr.common import Expr
-from nexusformat.nexus import NXfield, NXcollection
+from nexusformat.nexus import NXfield, NXgroup, NXcollection
 
 
 @dataclass
@@ -15,7 +15,8 @@ class NXInstr:
         """Start the C translation to ensure McCode-oddities are handled before any C-code parsing."""
         from mccode_antlr.common import ShapeType, DataType, Value
         from mccode_antlr.translators.target import MCSTAS_GENERATOR
-        from mccode_antlr.translators.c import CTargetVisitor, CDeclaration
+        from mccode_antlr.translators.c import CTargetVisitor
+        from mccode_antlr.translators.c_listener import CDeclarator
         from mccode_antlr.translators.c_listener import evaluate_c_defined_expressions
         config = dict(default_main=True, enable_trace=False, portable=False, include_runtime=True,
                       embed_instrument_file=False, verbose=False, output=None)
@@ -25,9 +26,9 @@ class NXInstr:
         # translator.component_uservars is a dictionary of lists for each component type of `CDeclaration` objects.
 
         # only worry about instrument level variables for the moment, and convert the CDeclarations into Expr objects
-        def c_declaration_to_expr(dec: CDeclaration) -> Expr:
+        def c_declaration_to_expr(dec: CDeclarator) -> Expr:
             expr = Expr(Value(None)) if dec.init is None else Expr.parse(dec.init)
-            expr.data_type = DataType.from_name(dec.type)
+            expr.data_type = DataType.from_name(dec.dtype)
             if dec.is_pointer or dec.is_array:
                 expr.shape_type = ShapeType.vector
             return expr
@@ -83,8 +84,29 @@ class NXInstr:
                 'expression' in nx_args[0]:
             not_expr = [x for x in nx_args[0] if x != 'expression']
             if len(not_expr) == 1:
+                not_expr_arg = nx_args[0][not_expr[0]]
+                # if isinstance(not_expr_arg, NXfield):
+                #     # We have and want an NXfield, but it might be missing attributes specified in the nx_kwargs
+                #     # Passing the keywords to the NXfield constructor versus this method is not identical,
+                #     # since some keyword arguments are reserved (and only some of which are noted)
+                #     #   Explicit keywords, used in the constructor:
+                #     #       value, name, shape, dtype, group, attrs
+                #     #   Keywords extracted from the kwargs dict, if present (and all controlling HDF5 file attributes?):
+                #     #       chunks, compression, compression_opts, fillvalue, fletcher32, maxshape, scaleoffset, shuffle
+                #     # For now, just assume all keywords provided here are _actually_ attributes for the NXfield
+                #     # which is an extension of a dict, but can *not* use the update method, since the __setitem__
+                #     # method is overridden to wrap inputs in NXattr objects :/
+                #     for k, v in nx_kwargs.items():
+                #         not_expr_arg.attrs[k] = v
+                #     return not_expr_arg
+
                 # TODO make this return an nx_class once we're sure that nx_kwargs is parseable (no mccode_antlr.Expr)
-                return nx_class(nx_args[0][not_expr[0]], **nx_kwargs)
+                if all(x in not_expr_arg for x in ('module', 'config')):
+                    # This is a file-writer stream directive? So make a group
+                    return NXgroup(entries={not_expr[0]: not_expr_arg}, **nx_kwargs)
+                print('!!')
+                print(not_expr_arg)
+                return nx_class(not_expr_arg, **nx_kwargs)
             else:
                 raise RuntimeError('Not sure what I should do here')
         return nx_class(*nx_args, **nx_kwargs)

{moreniius-0.2.3 → moreniius-0.2.5}/src/moreniius/mccode/orientation.py

@@ -18,6 +18,7 @@ class NXPart:
         return self.instr.make_nx(nx_class, *args, **kwargs)
 
     def make_translation(self, norm, vec, dep):
+        # if `norm` is a link or NXlog, we should make a group not an NXfield
         return self.make_nx(NXfield, norm, vector=vec, depends_on=dep, transformation_type='translation', units='m')
 
     def translations(self, dep: str, name: str) -> list[tuple[str, NXfield]]:
@@ -28,7 +29,6 @@ class NXPart:
         pos = self.o.position()
         if any(isinstance(c, (Expr, Value)) for c in (pos.x, pos.y, pos.z)):
             translations = []
-            print(f'{pos.x=} {pos.y=} {pos.z=}')
             for n, c, v in (('x', pos.x, [1, 0, 0]), ('y', pos.y, [0, 1, 0]), ('z', pos.z, [0, 0, 1])):
                 if c != Expr.parse('0'):
                     next_name = f'{name}_{n}'
@@ -51,7 +51,6 @@ class NXPart:
             print(repr(self.o))
             raise NotImplementedError()
 
-        # print(f'rotation {axis}, {angle}')
         # handle the case where angle is not a constant?
         return self.make_nx(NXfield, angle, vector=axis, depends_on=dep, transformation_type='rotation', units=angle_unit)
 

{moreniius-0.2.3 → moreniius-0.2.5}/src/moreniius/utils.py

@@ -1,5 +1,5 @@
 from mccode_antlr.instr import Instance
-from nexusformat.nexus import NXevent_data
+from nexusformat.nexus import NXevent_data, NXfield
 
 class NotNXdict:
     """Wrapper class to prevent NXfield-parsing of the held dictionary"""
@@ -12,6 +12,10 @@ class NotNXdict:
     def __repr__(self):
         return f"NotNXdict<{self.value}>"
 
+    def __str__(self):
+        from json import dumps
+        return dumps(self.value)
+
 
 def outer_transform_dependency(transformations):
     """For a NXtransformations group, find the most-dependent transformation name
@@ -36,7 +40,20 @@ def outer_transform_dependency(transformations):
         obj = getattr(transformations, name)
         if not hasattr(obj, 'depends_on'):
             raise ValueError(f'{name} in {names} dependency chain missing "depends_on" attribute')
-        return obj.depends_on
+        if isinstance(obj.depends_on, NXfield):
+            # obj.depends_on is an NXfield object; which has a number of properties
+            #   nxgroup - the parent group
+            #   dtype - string or numpy dtype
+            #   shape - list or tuple of ints
+            #   attrs - dict of attributes
+            #   nxdata - a scalar or numpy array or string
+            #   nxpath - string, where this object is in the tree
+            #   nxroot - the root NXgroup object containing this object
+            # I _think_ we *always* want the data stored in this object
+            return obj.depends_on.nxdata
+        elif isinstance(obj.depends_on, str):
+            return obj.depends_on
+        raise ValueError(f"depends_on attribute of {name} is not an NXfield or str")
 
     # depends = {name: getattr(transformations, name).depends_on for name in names}
     depends = {name: depends_on_per(name) for name in names}

{moreniius-0.2.3 → moreniius-0.2.5}/src/moreniius/writer.py

@@ -113,7 +113,6 @@ class Writer:
                 if absolute_depends_on and 'depends_on' == name and not obj.nxdata.startswith('/'):
                     obj.nxdata = _to_absolute(top_obj.nxpath, obj.nxdata)
                 if obj.nxclass == 'NXfield':
-                    # print(f'to_json_dict for NXfield {name=}')
                     typ, val = convert_types(obj.nxdata, only_nx)
                     # typ is None if obj.nxdata is a NotNXdict (such that val _is_ the contained dict)
                     entry = dict(module='dataset', config=dict(name=name, values=val, type=typ)) if typ else val
@@ -123,7 +122,6 @@ class Writer:
                     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():
-                    # print(f'to_json_dict for attribute of {name=}, named {n=}')
                     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)

{moreniius-0.2.3 → moreniius-0.2.5/src/moreniius.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: moreniius
-Version: 0.2.3
+Version: 0.2.5
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Development Status :: 2 - Pre-Alpha
@@ -8,7 +8,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
 Requires-Dist: importlib_metadata; python_version < "3.8"
-Requires-Dist: mccode-antlr[hdf5]>=0.7.1
+Requires-Dist: mccode-antlr[hdf5]>=0.9.2
 Requires-Dist: nexusformat>=1.0.6
 
 # moreniius

{moreniius-0.2.3 → moreniius-0.2.5}/src/moreniius.egg-info/requires.txt

@@ -1,6 +1,6 @@
 zenlog>=1.1
 platformdirs>=3.11
-mccode-antlr[hdf5]>=0.7.1
+mccode-antlr[hdf5]>=0.9.2
 nexusformat>=1.0.6
 
 [:python_version < "3.8"]

moreniius-0.2.5/tests/test_motorized_positions.py

@@ -0,0 +1,111 @@
+
+def make_motorized_instrument():
+    from mccode_antlr.assembler import Assembler
+    from mccode_antlr.reader import MCSTAS_REGISTRY, LocalRegistry
+    from mccode_to_kafka.writer import da00_dataarray_config, da00_variable_config
+
+    inst = Assembler('inst', registries=[MCSTAS_REGISTRY])
+    inst.parameter('double ex/"m"=0')
+    inst.parameter('double phi/"degree"=0')
+
+    inst.component('origin', 'Arm', at=(0, 0, 0))
+    inst.component('source', 'Source_simple', at=[(0, 0, 0), 'origin'])
+    inst.component('xpos', 'Arm', at=[('ex', 0, 0), 'source'])
+    inst.component('zrot', 'Arm', at=[(0, 0, 0), 'xpos'], rotate=[(0, 0, 'phi'), 'xpos'])
+    inst.component('aposrot', 'Arm', at=(1, 2, 3), rotate=(45, 55, 60))
+
+    return inst.instrument
+
+
+def test_motorized_instrument():
+    import moreniius
+    motorized = make_motorized_instrument()
+    nx = moreniius.MorEniius.from_mccode(motorized, origin='origin', only_nx=False, absolute_depends_on=True)
+    assert nx is not None
+    #TODO add actual tests for the contents of, e.g., the dumped NeXus Structure
+    ns = nx.to_nexus_structure()
+
+    expected = {
+        'entry': {
+            'type': 'group',
+            'children': 1,
+            'next': 0,
+            'attributes': [{'name': 'NX_class', 'dtype': 'string', 'values': 'NXentry'}]
+        },
+        'instrument': {
+            'type': 'group',
+            'children': 7,
+            'next': 0,
+            'attributes': [{'name': 'NX_class', 'dtype': 'string', 'values': 'NXinstrument'}]
+        },
+    }
+    for name, has in expected.items():
+        assert 'children' in ns
+        assert len(ns['children']) >= has['next']
+        ns = ns['children'][has['next']]
+        assert all(x in ns for x in ('type', 'name', 'children', 'attributes'))
+        assert ns['name'] == name
+        assert ns['attributes'] == has['attributes']
+        assert len(ns['children']) == has['children']
+
+    xpos = ns['children'][3]
+    zrot = ns['children'][4]
+    aposrot = ns['children'][5]
+
+
+    from json import dumps
+
+    for cns in (xpos, zrot, aposrot):
+        assert 'children' in cns
+        assert 'transformations' in [c['name'] for c in cns['children'] if 'name' in c]
+        t = [c for c in cns['children'] if 'name' in c and c['name'] == 'transformations'][0]
+        assert 'children' in t
+        t = t['children']
+        for c in t:
+            # Each child can _either_ be a dataset, with 'module' at its top level
+            # Or a group, with 'name', etc. at its top level
+
+            if 'module' in c:
+                # this transformation is static, and a dataset
+                assert 'dataset' == c['module']
+                assert all(x in c for x in ('config', 'attributes'))
+                assert all(x in c['config'] for x in ('name', 'values', 'type'))
+                attrs = c['attributes']
+                assert len(attrs) == 4
+                assert all(all(x in a for x in ('name', 'values', 'dtype')) for a in attrs)
+                assert all(a['name'] in ('vector', 'depends_on', 'transformation_type', 'units') for a in attrs)
+            else:
+                # this transformation is dynamic and a group
+                assert all(x in c for x in ('name', 'type', 'children', 'attributes'))
+                assert 'group' == c['type']
+                attrs = c['attributes']
+                assert len(attrs) == 1
+                attr = attrs[0]
+                assert all(x in attr for x in ('name', 'dtype', 'values'))
+                assert 'NX_class' == attr['name']
+                assert 'NXgroup' == attr['values']
+
+                # The children should contain a link to the log ... is the order important?
+                # Must the number of children always be the same?
+                assert all('module' in cc for cc in c['children'])
+                assert sum('link' == cc['module'] for cc in c['children']) <= 1
+                for cc in c['children']:
+                    if 'link' == cc['module']:
+                        assert all(x in cc['config'] for x in ('name', 'source'))
+                    else:
+                        assert all(x in cc['config'] for x in ('name', 'values', 'type'))
+                        assert cc['config']['name'] in ('vector', 'depends_on', 'transformation_type', 'units')
+
+    # for name, has in expected.items():
+    #     print({x : list(ns[x]) for x in ns})
+    #     assert all(x in ns for x in has)
+    #     assert len(ns['children']) == 1
+    #     assert ns['name'] == name
+    #     ns = ns['children'][0]
+
+    #
+    # instr = ns['entry']['instrument']
+    # #
+    # print(dumps(xpos, indent=2))
+    # print(dumps(zrot, indent=1))
+    # print(dumps(aposrot, indent=1))

moreniius-0.2.3/tests/test_motorized_positions.py

@@ -1,24 +0,0 @@
-
-def make_motorized_instrument():
-    from mccode_antlr.assembler import Assembler
-    from mccode_antlr.reader import MCSTAS_REGISTRY, LocalRegistry
-    from mccode_to_kafka.writer import da00_dataarray_config, da00_variable_config
-
-    inst = Assembler('inst', registries=[MCSTAS_REGISTRY])
-    inst.parameter('double ex/"m"=0')
-    inst.parameter('double phi/"degree"=0')
-
-    inst.component('origin', 'Arm', at=(0, 0, 0))
-    inst.component('source', 'Source_simple', at=[(0, 0, 0), 'origin'])
-    inst.component('xpos', 'Arm', at=[('ex', 0, 0), 'source'])
-    inst.component('zrot', 'Arm', at=[(0, 0, 0), 'xpos'], rotate=[(0, 0, 'phi'), 'xpos'])
-
-    return inst.instrument
-
-
-def test_motorized_instrument():
-    import moreniius
-    motorized = make_motorized_instrument()
-    nx = moreniius.MorEniius.from_mccode(motorized, origin='origin', only_nx=False, absolute_depends_on=True)
-    assert nx is not None
-    #TODO add actual tests for the contents of, e.g., the dumped NeXus Structure