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.

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/[email protected]
-      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

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/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
@@ -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,
@@ -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,