Update version to 0.10.9 in pyproject.toml and __init__.py; enhance ShimadzuReader with detailed logging for file processing and value mapping. (#48)

Author: haeussma

chromhandler/__init__.py

@@ -55,4 +55,4 @@ def __getattr__(name: str) -> Handler:
 
 __all__ = ["Handler", "ChromAnalyzer", "Molecule", "Protein", "to_enzymeml"]
 
-__version__ = "0.10.8"
+__version__ = "0.10.9"

chromhandler/readers/shimadzu.py

@@ -28,8 +28,29 @@ def read(self) -> list[Measurement]:
         if len(self.file_paths) == 0:
             raise ValueError("No files found. Is the directory empty?")
 
+        # #region agent log
+        import json
+
+        with open("/Users/max/code/aldol_addition/.cursor/debug.log", "a") as f:
+            f.write(
+                json.dumps(
+                    {
+                        "sessionId": "debug-session",
+                        "runId": "post-fix",
+                        "hypothesisId": "A",
+                        "location": "shimadzu.py:32",
+                        "message": "Using file_paths directly (no string sort)",
+                        "data": {"file_paths": self.file_paths, "values": self.values},
+                        "timestamp": __import__("time").time() * 1000,
+                    }
+                )
+                + "\n"
+            )
+        # #endregion
+
         measurements = []
-        for i, file in enumerate(sorted(self.file_paths)):
+        # Use self.file_paths directly - they are already sorted numerically by abstractreader.py
+        for i, file in enumerate(self.file_paths):
             content = self.open_file(file)
             sections = self.create_sections(content)
             self._get_available_detectors(sections)
@@ -51,6 +72,31 @@ def read(self) -> list[Measurement]:
             dilution_factor = sample_dict.get("Dilution Factor", 1)
             injection_volume = sample_dict.get("Injection Volume")
 
+            # #region agent log
+            import json
+
+            with open("/Users/max/code/aldol_addition/.cursor/debug.log", "a") as f:
+                f.write(
+                    json.dumps(
+                        {
+                            "sessionId": "debug-session",
+                            "runId": "post-fix",
+                            "hypothesisId": "C",
+                            "location": "shimadzu.py:55",
+                            "message": "Mapping file to value",
+                            "data": {
+                                "i": i,
+                                "file": file,
+                                "value": self.values[i],
+                                "all_values": self.values,
+                            },
+                            "timestamp": __import__("time").time() * 1000,
+                        }
+                    )
+                    + "\n"
+                )
+            # #endregion
+
             data = Data(
                 value=self.values[i],
                 unit=self.unit.name,
@@ -271,6 +317,29 @@ def _get_file_paths(self) -> None:
 
             files.append(str(file_path.absolute()))
 
+        # #region agent log
+        import json
+
+        with open("/Users/max/code/aldol_addition/.cursor/debug.log", "a") as f:
+            f.write(
+                json.dumps(
+                    {
+                        "sessionId": "debug-session",
+                        "runId": "run1",
+                        "hypothesisId": "D",
+                        "location": "shimadzu.py:264",
+                        "message": "File collection in _get_file_paths",
+                        "data": {
+                            "files": files,
+                            "values": self.values if hasattr(self, "values") else None,
+                        },
+                        "timestamp": __import__("time").time() * 1000,
+                    }
+                )
+                + "\n"
+            )
+        # #endregion
+
         assert (
             len(files) == len(self.values)
         ), f"Number of files ({len(files)}) does not match the number of reaction times ({len(self.values)})."

pyproject.toml

@@ -15,7 +15,7 @@ license = { text = "MIT" }
 name = "chromhandler"
 readme = "README.md"
 requires-python = ">=3.11,<3.14"
-version = "0.10.8"
+version = "0.10.9"
 
 [build-system]
 build-backend = "hatchling.build"