Update project configuration and version to 0.10.2 (#42)

* Update project configuration and version to 0.10.2

- Updated version in `__init__.py` and `pyproject.toml` to 0.10.2.
- Added `uv.lock` to `.gitignore`.
- Refactored `pyproject.toml` to use the new build system and dependency groups.
- Simplified GitHub Actions workflows for testing and release processes by consolidating OS and Python version specifications.

* Update Python version constraint in pyproject.toml

- Changed the Python version requirement from ">=3.10" to ">=3.10,<3.15" to restrict compatibility to specific versions.

* Update peak assignment summary and molecule names in usage notebook

- Enhanced the HTML and plain text representations of the peak assignment summary for better readability.
- Updated the molecule name for SAH from "Adenosylhomocysteine" to "S-adenosyl-L-homocysteine" for accuracy.
- Adjusted the Ado molecule name to "Adenosine" for consistency.
- Updated Python version in the notebook metadata from 3.12.11 to 3.13.7.

* Add pre-commit configuration for code quality checks

* run ruff

* fixed configuration

Author: haeussma

.github/workflows/release.yaml

@@ -99,12 +99,6 @@ jobs:
       with:
         name: python-package-distributions
         path: dist/
-    - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v3.0.1
-      with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
     - name: Create GitHub Release
       env:
         GITHUB_TOKEN: ${{ github.token }}
@@ -113,7 +107,7 @@ jobs:
         '${{ github.ref_name }}'
         --repo '${{ github.repository }}'
         --notes ""
-    - name: Upload artifact signatures to GitHub Release
+    - name: Upload distributions to GitHub Release
       env:
         GITHUB_TOKEN: ${{ github.token }}
       run: >-

.github/workflows/run_tests.yaml

@@ -4,33 +4,12 @@ on: push
 
 jobs:
   build:
-
-    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        include:
-          - os: ubuntu-latest
-            python-version: "3.10"
-          - os: ubuntu-latest
-            python-version: "3.11"
-          - os: ubuntu-latest
-            python-version: "3.12"
-          - os: ubuntu-latest
-            python-version: "3.13"
-          - os: macos-latest
-            python-version: "3.10"
-          - os: macos-latest
-            python-version: "3.11"
-          - os: macos-latest
-            python-version: "3.12"
-          - os: macos-latest
-            python-version: "3.13"
-          - os: windows-latest
-            python-version: "3.10"
-          - os: windows-latest
-            python-version: "3.11"
-          - os: windows-latest
-            python-version: "3.12"
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4

.gitignore

@@ -167,4 +167,5 @@ cython_debug/
 
 test.py
 
-.DS_Store
+.DS_Store
+uv.lock

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+  - repo: local
+    hooks:
+      - id: pyright
+        name: pyright (uv venv)
+        entry: uv run pyright
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+      - id: ruff
+        types_or: [python, pyi, jupyter, toml]
+        args: [--fix]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ["--maxkb=5000"]

chromhandler/__init__.py

@@ -55,4 +55,4 @@ def __getattr__(name: str) -> Handler:
 
 __all__ = ["Handler", "ChromAnalyzer", "Molecule", "Protein", "to_enzymeml"]
 
-__version__ = "0.10.1"
+__version__ = "0.10.2"

chromhandler/enzymeml.py

@@ -493,9 +493,9 @@ def add_data(
 
     if calibrator_type == CalibratorType.EXTERNAL:
         calibrator = calibrators[measurement_data.species_id]
-        assert isinstance(calibrator, Calibrator), (
-            "Calibrator must be of type Calibrator."
-        )
+        assert isinstance(
+            calibrator, Calibrator
+        ), "Calibrator must be of type Calibrator."
 
         if peak is not None:
             conc = calibrator.calculate_concentrations(
@@ -515,9 +515,9 @@ def add_data(
 
     elif calibrator_type == CalibratorType.INTERNAL:
         calibrator = calibrators[measurement_data.species_id]
-        assert isinstance(calibrator, InternalStandard), (
-            "Calibrator must be of type InternalStandard."
-        )
+        assert isinstance(
+            calibrator, InternalStandard
+        ), "Calibrator must be of type InternalStandard."
 
         if peak is not None:
             internal_std_peak = next(
@@ -578,9 +578,9 @@ def setup_external_calibrators(
         if molecule.standard:
             calibrators[molecule.id] = Calibrator.from_standard(molecule.standard)
 
-    assert calibrators, (
-        "No calibrators were created. Please define standards for the molecules."
-    )
+    assert (
+        calibrators
+    ), "No calibrators were created. Please define standards for the molecules."
 
     return calibrators
 
@@ -669,24 +669,24 @@ def extract_measurement_conditions(
     ]
 
     assert len(set(phs)) == 1, "All measurements need to have the same pH."
-    assert len(set(temperatures)) == 1, (
-        "All measurements need to have the same temperature."
-    )
-    assert len(set(time_units)) == 1, (
-        "All measurements need to have the same time unit."
-    )
-    assert len(set(temperature_units)) == 1, (
-        "All measurements need to have the same temperature unit."
-    )
+    assert (
+        len(set(temperatures)) == 1
+    ), "All measurements need to have the same temperature."
+    assert (
+        len(set(time_units)) == 1
+    ), "All measurements need to have the same time unit."
+    assert (
+        len(set(temperature_units)) == 1
+    ), "All measurements need to have the same temperature unit."
 
     assert measurements[0].ph is not None, "The pH needs to be defined."
-    assert measurements[0].temperature is not None, (
-        "The temperature needs to be defined."
-    )
+    assert (
+        measurements[0].temperature is not None
+    ), "The temperature needs to be defined."
     assert measurements[0].data.unit is not None, "The time unit needs to be defined."
-    assert measurements[0].temperature_unit is not None, (
-        "The temperature unit needs to be defined."
-    )
+    assert (
+        measurements[0].temperature_unit is not None
+    ), "The temperature unit needs to be defined."
 
     ph = measurements[0].ph
     temperature = measurements[0].temperature

chromhandler/handler.py

@@ -6,7 +6,6 @@
 from pathlib import Path
 from typing import Any, Literal, Optional
 
-import plotly.graph_objects as go
 from calipytion.model import Calibration
 from calipytion.tools.utility import pubchem_request_molecule_name
 from loguru import logger
@@ -165,13 +164,13 @@ def define_molecule(
         """
 
         if conc_unit:
-            assert init_conc is not None, (
-                "Initial concentration must be provided if concentration unit is given."
-            )
+            assert (
+                init_conc is not None
+            ), "Initial concentration must be provided if concentration unit is given."
         if init_conc:
-            assert conc_unit, (
-                "Concentration unit must be provided if initial concentration is given."
-            )
+            assert (
+                conc_unit
+            ), "Concentration unit must be provided if initial concentration is given."
 
         if name is None:
             name = pubchem_request_molecule_name(pubchem_cid)
@@ -904,21 +903,6 @@ def get_molecule(self, molecule_id: str) -> Molecule:
 
         raise ValueError(f"Molecule with ID {molecule_id} not found.")
 
-    def visualize_all(
-        self, assigned_only: bool = False, dark_mode: bool = False, show: bool = False
-    ) -> go.Figure:
-        """Plots the fitted peaks of the chromatograms in an interactive figure.
-
-        Args:
-            assigned_only (bool, optional): If True, only the peaks that are assigned to a molecule are plotted. Defaults to False.
-            dark_mode (bool, optional): If True, the figure is displayed in dark mode. Defaults to False.
-            show (bool, optional): If True, shows the figure. Defaults to False.
-
-        Returns:
-            go.Figure: The plotly figure object.
-        """
-        return visualize.visualize_all(self, assigned_only, dark_mode, show)
-
     def add_standard(
         self,
         molecule: Molecule,
@@ -932,25 +916,25 @@ def add_standard(
             wavelength (float | None, optional): The wavelength of the detector. Defaults to None.
             visualize (bool, optional): If True, the standard curve is visualized. Defaults to True.
         """
-        assert any([molecule in [mol for mol in self.molecules]]), (
-            "Molecule not found in molecules of handler."
-        )
+        assert any(
+            [molecule in [mol for mol in self.molecules]]
+        ), "Molecule not found in molecules of handler."
 
         # check if all measurements only contain one chromatogram
         if all([len(meas.chromatograms) == 1 for meas in self.measurements]):
             chroms = [
                 chrom for meas in self.measurements for chrom in meas.chromatograms
             ]
         else:
-            assert wavelength is not None, (
-                "Multiple chromatograms found for each measurment, wavelength needs to be provided."
-            )
+            assert (
+                wavelength is not None
+            ), "Multiple chromatograms found for each measurment, wavelength needs to be provided."
 
             chroms = self._get_chromatograms_by_wavelegnth(wavelength)
 
-            assert len(chroms) > 0, (
-                "No chromatograms found at the specified wavelength."
-            )
+            assert (
+                len(chroms) > 0
+            ), "No chromatograms found at the specified wavelength."
 
         peak_areas = [
             peak.area for chrom in chroms for peak in chrom.peaks if peak.molecule_id
@@ -959,13 +943,13 @@ def add_standard(
         concs = [meas.data.value for meas in self.measurements]
         conc_unit = self.measurements[0].data.unit
 
-        assert len(peak_areas) == len(concs), (
-            f"Number of {molecule.name} peak areas {len(peak_areas)} and concentrations {len(concs)} do not match."
-        )
+        assert (
+            len(peak_areas) == len(concs)
+        ), f"Number of {molecule.name} peak areas {len(peak_areas)} and concentrations {len(concs)} do not match."
 
-        assert all(meas.ph == self.measurements[0].ph for meas in self.measurements), (
-            "All measurements need to have the same pH value."
-        )
+        assert all(
+            meas.ph == self.measurements[0].ph for meas in self.measurements
+        ), "All measurements need to have the same pH value."
         ph = self.measurements[0].ph
 
         assert all(
@@ -1030,18 +1014,6 @@ def _update_protein(self, protein: Protein) -> None:
 
         self.proteins.append(protein)
 
-    def visualize_spectra(self, dark_mode: bool = False) -> go.Figure:
-        """
-        Plots all chromatograms in the Handler in a single plot.
-
-        Args:
-            dark_mode (bool, optional): If True, the figure is displayed in dark mode. Defaults to False.
-
-        Returns:
-            go.Figure: The plotly figure object.
-        """
-        return visualize.visualize_spectra(self, dark_mode)
-
     def visualize(
         self,
         n_cols: int = 2,

chromhandler/model.py

@@ -179,9 +179,9 @@ def set_attr_term(
             AssertionError: If the attribute is not found in the model
         """
 
-        assert attr in self.model_fields, (
-            f"Attribute {attr} not found in {self.__class__.__name__}"
-        )
+        assert (
+            attr in self.model_fields
+        ), f"Attribute {attr} not found in {self.__class__.__name__}"
 
         if prefix:
             validate_prefix(term, prefix)
@@ -298,9 +298,9 @@ def set_attr_term(
             AssertionError: If the attribute is not found in the model
         """
 
-        assert attr in self.model_fields, (
-            f"Attribute {attr} not found in {self.__class__.__name__}"
-        )
+        assert (
+            attr in self.model_fields
+        ), f"Attribute {attr} not found in {self.__class__.__name__}"
 
         if prefix:
             validate_prefix(term, prefix)
@@ -406,9 +406,9 @@ def set_attr_term(
             AssertionError: If the attribute is not found in the model
         """
 
-        assert attr in self.model_fields, (
-            f"Attribute {attr} not found in {self.__class__.__name__}"
-        )
+        assert (
+            attr in self.model_fields
+        ), f"Attribute {attr} not found in {self.__class__.__name__}"
 
         if prefix:
             validate_prefix(term, prefix)
@@ -549,9 +549,9 @@ def set_attr_term(
             AssertionError: If the attribute is not found in the model
         """
 
-        assert attr in self.model_fields, (
-            f"Attribute {attr} not found in {self.__class__.__name__}"
-        )
+        assert (
+            attr in self.model_fields
+        ), f"Attribute {attr} not found in {self.__class__.__name__}"
 
         if prefix:
             validate_prefix(term, prefix)

chromhandler/readers/asm.py

@@ -43,19 +43,19 @@ def _get_file_paths(self) -> None:
         # check if directory exists
         assert directory.exists(), f"Directory '{self.dirpath}' does not exist."
         assert directory.is_dir(), f"'{self.dirpath}' is not a directory."
-        assert any(directory.rglob("*.json")), (
-            f"No .json files found in '{self.dirpath}'."
-        )
+        assert any(
+            directory.rglob("*.json")
+        ), f"No .json files found in '{self.dirpath}'."
 
         for file_path in directory.iterdir():
             if file_path.name.startswith(".") or not file_path.name.endswith(".json"):
                 continue
 
             files.append(str(file_path.absolute()))
 
-        assert len(files) == len(self.values), (
-            f"Number of files ({len(files)}) does not match the number of reaction times ({len(self.values)})."
-        )
+        assert (
+            len(files) == len(self.values)
+        ), f"Number of files ({len(files)}) does not match the number of reaction times ({len(self.values)})."
 
         self.file_paths = sorted(files)