Fix case-sensitive morphology path handling on Linux

bluecellulab/cell/core.py

@@ -97,12 +97,6 @@ def __init__(self,
             emodel_properties: Template specific emodel properties.
         """
         super().__init__()
-        self.template_params = TemplateParams(
-            template_filepath=template_path,
-            morph_filepath=morphology_path,
-            template_format=template_format,
-            emodel_properties=emodel_properties,
-        )
         if cell_id is None:
             cell_id = CellId("", Cell.last_id)
             Cell.last_id += 1
@@ -111,6 +105,12 @@ def __init__(self,
 
         # Load the template
         neuron_template = NeuronTemplate(template_path, morphology_path, template_format, emodel_properties)
+        self.template_params = TemplateParams(
+            template_filepath=template_path,
+            morph_filepath=neuron_template.morph_filepath,
+            template_format=template_format,
+            emodel_properties=emodel_properties,
+        )
         self.template_id = neuron_template.template_name  # useful to map NEURON and python objects
         self.cell = neuron_template.get_cell(self.cell_id.id)
         if template_format == 'v6':

bluecellulab/cell/morphio_wrapper.py

@@ -357,7 +357,6 @@ def __init__(self, input_file, options=0):
         if not is_h5_container_path(input_file):
             input_file = resolve_case_insensitive_path(input_file)
         self._collection_dir, self._morph_name, self._morph_ext = split_morphology_path(input_file)
-        self._morph_ext = self._morph_ext.lower()
         self._options = options
         self._build_morph()
         # This logic is similar to what's in BaseCell, but at this point we are still

bluecellulab/cell/template.py

@@ -25,7 +25,7 @@
 
 import neuron
 
-from bluecellulab.cell.morphio_wrapper import split_morphology_path
+from bluecellulab.cell.morphio_wrapper import is_h5_container_path, resolve_case_insensitive_path, split_morphology_path
 from bluecellulab.circuit import EmodelProperties
 from bluecellulab.exceptions import BluecellulabError
 from bluecellulab.type_aliases import HocObjectType
@@ -110,6 +110,9 @@ def __init__(
         if not os.path.exists(template_filepath):
             raise FileNotFoundError(f"Couldn't find template file: {template_filepath}")
 
+        if not is_h5_container_path(morph_filepath):
+            morph_filepath = resolve_case_insensitive_path(morph_filepath)
+
         # Check morphology path - handle H5 container paths
         if not self._is_valid_morphology_path(morph_filepath):
             raise FileNotFoundError(f"Couldn't find morphology file: {morph_filepath}")

tests/test_cell/test_morphology_wrapper.py

@@ -9,6 +9,7 @@
     SectionName,
     split_morphology_path,
 )
+from bluecellulab.cell.template import NeuronTemplate
 
 
 class TestMorphologyWrapper:
@@ -59,42 +60,52 @@ def test_split_morphology_path_container_with_cell_name(self, tmp_path):
         assert morph_name == "cell_name"
         assert morph_ext == ""
 
-    def test_case_insensitive_morphology_path(self, tmp_path):
+    def test_case_insensitive_morphology_path_linux_like(self, tmp_path):
         p = tmp_path / "cell.ASC"
         p.write_text("dummy")
 
-        with patch.object(MorphIOWrapper, "_build_morph"):
-            with patch.object(MorphIOWrapper, "_get_section_names", return_value=[]):
-                with patch.object(MorphIOWrapper, "_build_sec_typeid_distrib"):
-                    wrapper = MorphIOWrapper(str(tmp_path / "cell.asc"))
+        wrong_case = tmp_path / "cell.asc"
+        original_exists = Path.exists
+
+        def linux_like_exists(path):
+            if path == wrong_case:
+                return False
+            return original_exists(path)
+
+        with (
+            patch.object(Path, "exists", linux_like_exists),
+            patch.object(MorphIOWrapper, "_build_morph"),
+            patch.object(MorphIOWrapper, "_get_section_names", return_value=[]),
+            patch.object(MorphIOWrapper, "_build_sec_typeid_distrib"),
+        ):
+            wrapper = MorphIOWrapper(str(wrong_case))
 
         assert wrapper._morph_name == "cell"
-        assert wrapper._morph_ext == ".asc"
+        assert wrapper._morph_ext == ".ASC"
 
-    def test_case_insensitive_morphology_path_reverse(self, tmp_path):
-        """Should also work if file is lowercase and input is uppercase."""
-        p = tmp_path / "cell.asc"
-        p.write_text("dummy")
+    def test_neuron_template_resolves_case_insensitive_morphology_path(self, tmp_path):
+        """NeuronTemplate should validate wrong-case morphology filenames."""
+        morph_file = tmp_path / "cell.ASC"
+        morph_file.write_text("dummy")
 
-        with patch.object(MorphIOWrapper, "_build_morph"):
-            with patch.object(MorphIOWrapper, "_get_section_names", return_value=[]):
-                with patch.object(MorphIOWrapper, "_build_sec_typeid_distrib"):
-                    wrapper = MorphIOWrapper(str(tmp_path / "cell.ASC"))
+        template_file = tmp_path / "template.hoc"
+        template_file.write_text("begintemplate T\nendtemplate T\n")
 
-        assert wrapper._morph_name == "cell"
-        assert wrapper._morph_ext == ".asc"
+        wrong_case = tmp_path / "cell.asc"
+        original_exists = Path.exists
 
-    def test_extension_normalization(self, tmp_path):
-        """Extension should always be normalized to lowercase."""
-        p = tmp_path / "cell.SWC"
-        p.write_text("dummy")
+        def linux_like_exists(path):
+            if path == wrong_case:
+                return False
+            return original_exists(path)
 
-        with patch.object(MorphIOWrapper, "_build_morph"):
-            with patch.object(MorphIOWrapper, "_get_section_names", return_value=[]):
-                with patch.object(MorphIOWrapper, "_build_sec_typeid_distrib"):
-                    wrapper = MorphIOWrapper(str(p))
+        with (
+            patch.object(Path, "exists", linux_like_exists),
+            patch.object(NeuronTemplate, "load", return_value="T"),
+        ):
+            template = NeuronTemplate(str(template_file), str(wrong_case), "v5", None)
 
-        assert wrapper._morph_ext == ".swc"
+        assert template.morph_filepath == str(morph_file)
 
     def test_morphology_wrapper_init_success(self):
         """Test successful MorphologyWrapper initialization with real H5 file."""

tox.ini

@@ -41,7 +41,7 @@ deps =
     pandas-stubs>=2.0.0
     types-setuptools>=67.8.0.0
     ruff>=0.0.270
-    docformatter>=1.7.2
+    docformatter>=1.7.2,<1.7.8  # docformatter 1.7.8 has tokenisation regressions; pin until upstream fixes
 commands =
     ruff check . --select F541,F401 --per-file-ignores="__init__.py:F401"
     pycodestyle {[base]name} --ignore=E501,W504,W503