Fix internal std (#43)

* Refactor assertions in enzymeml.py for improved readability

- Simplified assertion statements in the add_data, setup_external_calibrators, and extract_measurement_conditions functions for better clarity.
- Updated the handling of concentration unit representation in setup_internal_calibrators to directly use the unit name.
- Ensured consistent formatting of assertion messages across the file.

* Update version to 0.10.3 and reorganize pyproject.toml

- Bumped the version in `__init__.py` and `pyproject.toml` to 0.10.3.
- Reorganized the `pyproject.toml` file to move the build-system and dependency-groups sections to the correct position for clarity.

* Refactor assertion statements in utility.py for improved readability

- Simplified assertion formatting in the _resolve_chromatogram function to enhance clarity and maintain consistency in error messages when handling multiple chromatograms.

* Sort file paths in AgilentCSVReader for consistent processing order

Author: haeussma

chromhandler/__init__.py

@@ -55,4 +55,4 @@ def __getattr__(name: str) -> Handler:
 
 __all__ = ["Handler", "ChromAnalyzer", "Molecule", "Protein", "to_enzymeml"]
 
-__version__ = "0.10.2"
+__version__ = "0.10.3"

chromhandler/enzymeml.py

@@ -639,7 +639,7 @@ def setup_internal_calibrators(
                 standard_molecule_id=internal_standard.id,
                 molecule_init_conc=molecule.init_conc,
                 standard_init_conc=internal_standard.init_conc,
-                molecule_conc_unit=molecule.conc_unit.name,
+                molecule_conc_unit=molecule.conc_unit,
                 molecule_t0_signal=peak_analyte.area,
                 standard_t0_signal=peak_internal_standard.area,
             )

chromhandler/readers/agilent_csv.py

@@ -20,7 +20,7 @@ def read(self) -> list[Measurement]:
         """
 
         measurements = []
-        for path_idx, csv_path in enumerate(self.file_paths):
+        for path_idx, csv_path in enumerate(sorted(self.file_paths)):
             peaks = self._read_peaks_from_csv(csv_path)
             chromatogram = Chromatogram(peaks=peaks)
 

chromhandler/utility.py

@@ -19,14 +19,14 @@ def _resolve_chromatogram(
         return chromatograms[0]
 
     if len(chromatograms) > 1:
-        assert wavelength is not None, (
-            "Multiple chromatograms found, but no wavelength is specified."
-        )
+        assert (
+            wavelength is not None
+        ), "Multiple chromatograms found, but no wavelength is specified."
 
         # check that any of the chromatograms has the specified wavelength
-        assert any([chrom.wavelength == wavelength for chrom in chromatograms]), (
-            f"No chromatogram found with wavelength {wavelength} nm."
-        )
+        assert any(
+            [chrom.wavelength == wavelength for chrom in chromatograms]
+        ), f"No chromatogram found with wavelength {wavelength} nm."
 
         return next(chrom for chrom in chromatograms if chrom.wavelength == wavelength)
 

pyproject.toml

@@ -1,20 +1,3 @@
-[build-system]
-build-backend = "hatchling.build"
-requires = ["hatchling>=1.27"]
-
-[dependency-groups]
-dev = [
-  "pre-commit>=3.7,<4",
-  "ruff>=0.6,<1",
-  "pytest>=8.0.2",
-  "devtools>=0.12.2",
-  "mkdocs-material>=9.6.16",
-  "mkdocstrings[python]>=0.30.0",
-  "nbval>=0.11.0",
-  "mkdocs-jupyter>=0.25.1",
-  "pyright>=1.1.405"
-]
-
 [project]
 authors = [{email = "83341109+haeussma@users.noreply.github.com", name = "haeussma"}]
 dependencies = [
@@ -30,7 +13,24 @@ license = {text = "MIT"}
 name = "chromhandler"
 readme = "README.md"
 requires-python = ">=3.10,<3.15"
-version = "0.10.2"
+version = "0.10.3"
+
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling>=1.27"]
+
+[dependency-groups]
+dev = [
+  "pre-commit>=3.7,<4",
+  "ruff>=0.6,<1",
+  "pytest>=8.0.2",
+  "devtools>=0.12.2",
+  "mkdocs-material>=9.6.16",
+  "mkdocstrings[python]>=0.30.0",
+  "nbval>=0.11.0",
+  "mkdocs-jupyter>=0.25.1",
+  "pyright>=1.1.405",
+]
 
 [project.urls]
 Homepage = "https://github.com/haeussma/chromhandler"