Mat cleanup

release-notes/next-release.md

@@ -4,6 +4,12 @@
 
 ## Fixes
 
+* Reformatted example files (e_coli_core.xml, mini_cobra.xml, mini.json, mini.yml, textbook.xml.gz) to be more compliant with identifiers.org. ncbigi is not a valid identifiers.org, so it was replaced with ncbiprotein.
+* make sbml.py subsystem reading add partonomy, which matches the definition
+of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
+* Correct reading and writing of subysstem in mat.
+* General cleanup of code in mat.py
+
 ## Other
 
 * Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (#1212).

src/cobra/io/mat.py

@@ -525,27 +525,30 @@ def annotations_to_mat(
     empty_lists = [[""] * len(annotation_list) for _ in annotation_matlab]
     annotation_cells_to_be = dict(zip(annotation_matlab.values(), empty_lists))
     for i in range(len(annotation_list)):
-        for provider_key, v in annotation_list[i].items():
-            if isinstance(v, str):
-                v = [v]
+        for provider_key, obj_annotation in annotation_list[i].items():
+            if isinstance(obj_annotation, str):
+                obj_annotation = [obj_annotation]
             if provider_key == "pubmed":
-                v = ", ".join(
-                    ["PMID:" + annot if "PMID:" not in annot else annot for annot in v]
+                obj_annotation = ", ".join(
+                    [
+                        "PMID:" + annot if "PMID:" not in annot else annot
+                        for annot in obj_annotation
+                    ]
                 )
             elif provider_key == "CHEBI":
-                v = ", ".join(
+                obj_annotation = ", ".join(
                     [
                         "CHEBI:" + annot if "CHBEI:" not in annot else annot
-                        for annot in v
+                        for annot in obj_annotation
                     ]
                 )
             elif provider_key == "ec-code":
-                v = " or ".join(v)
+                obj_annotation = " or ".join(obj_annotation)
             else:
-                v = ", ".join(v)
+                obj_annotation = ", ".join(obj_annotation)
             if provider_key not in providers_used:
                 continue
-            annotation_cells_to_be[annotation_matlab[provider_key]][i] = v
+            annotation_cells_to_be[annotation_matlab[provider_key]][i] = obj_annotation
     for annotation_key, item_list in annotation_cells_to_be.items():
         mat_dict[annotation_key] = _cell(item_list)
 
@@ -582,18 +585,18 @@ def notes_to_mat(
     empty_lists = [[""] * len(note_list) for _ in annotation_matlab]
     annotation_cells_to_be = dict(zip(annotation_matlab.values(), empty_lists))
     for i in range(len(note_list)):
-        for provider_key, v in note_list[i].items():
+        for provider_key, object_note in note_list[i].items():
             if provider_key not in providers_used:
                 continue
             if provider_key == CONFIDENCE_STR:
-                v = float(v)
+                object_note = float(object_note)
             if not len(annotation_cells_to_be[annotation_matlab[provider_key]][i]):
-                annotation_cells_to_be[annotation_matlab[provider_key]][i] = v
+                annotation_cells_to_be[annotation_matlab[provider_key]][i] = object_note
             else:
                 # References that aren't MIRIAM compliant will go to rxnNotes
                 annotation_cells_to_be[annotation_matlab[provider_key]][i] = (
                     annotation_cells_to_be[annotation_matlab[provider_key]][i]
-                    + f"; {v}"
+                    + f"; {object_note}"
                 )
     for annotation_key, item_list in annotation_cells_to_be.items():
         mat_dict[annotation_key] = _cell(item_list)
@@ -753,9 +756,7 @@ def from_mat_struct(
             new_names[new_names.index(old_field)] = new_field
             m.dtype.names = new_names
 
-    model = (
-        Model()
-    )  # TODO - Model() creates models with name=None, while SBML creates them with name=''
+    model = Model()
     if model_id is not None:
         model.id = model_id
     elif "description" in m.dtype.names:
@@ -903,9 +904,7 @@ def from_mat_struct(
         rxn_group_names = set(rxn_subsystems).difference({None})
         new_groups = []
         for g_name in sorted(rxn_group_names):
-            group_members = model.reactions.query(
-                lambda x, g_n=g_name: x.subsystem == g_n
-            )
+            group_members = model.reactions.query(lambda x: x.subsystem == g_name)
             new_group = Group(
                 id=g_name, name=g_name, members=group_members, kind="partonomy"
             )