masster 0.3.0__tar.gz → 0.3.1__tar.gz

{masster-0.3.0 → masster-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.0
+Version: 0.3.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.0 → masster-0.3.1}/pyproject.toml

@@ -1,141 +1,141 @@
-
-[project]
-name = "masster"
-version = "0.3.0"
-description = "Mass spectrometry data analysis package"
-authors = [
-    { name = "Zamboni Lab" }
-]
-license = { file = "LICENSE" }
-readme = "README.md"
-requires-python = ">=3.11"
-keywords = ["mass spectrometry", "metabolomics", "lc-ms", "chromatography"]
-classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Chemistry"
-]
-urls.homepage = "https://github.com/zamboni-lab/masster"
-urls.repository = "https://github.com/zamboni-lab/masster"
-urls.documentation = "https://github.com/zamboni-lab/masster#readme"
-dependencies = [
-    "alphabase>=1.0.0",
-    "alpharaw>=0.4.8",
-    "altair>=5.5.0",
-    "bokeh>=3.7.3",
-    "datashader>=0.18.1",
-    "python-dotenv>=1.0.0",
-    "holoviews>=1.21.0",
-    "h5py>=3.14.0",
-    "hvplot>=0.11.3",
-    "loguru>=0.7.3",
-    "numpy>=2.0.0",
-    "marimo>=0.14.16",
-    "matchms>=0.30.2",
-    "matplotlib>=3.8.0",
-    "pandas>=2.2.0",
-    "panel>=1.7.0",
-    "plotly>=5.15.0",
-    "polars>=1.0.0",
-    "pyopenms>=3.3.0",
-    "pyteomics>=4.7.0",
-    "pythonnet>=3.0.0",
-    "scipy>=1.12.0",
-    "simple-parsing>=0.1.7",
-    "tqdm>=4.65.0",
-    "ipykernel>=6.30.0",
-    "openpyxl>=3.1.5",
-]
-
-[project.optional-dependencies]
-dev = [
-    "pytest>=7.0.0",
-    "pytest-cov>=4.0.0",
-    "pytest-mock>=3.10.0",
-    "black>=23.0.0",
-    "flake8>=5.0.0",
-    "mypy>=1.0.0",
-    "pre-commit>=3.0.0",
-    "twine>=4.0.0",
-    "build>=0.10.0",
-    "safety>=2.0.0",
-    "bandit>=1.7.0"
-]
-docs = [
-    "sphinx>=5.0.0",
-    "sphinx-rtd-theme>=1.2.0",
-    "sphinxcontrib-napoleon>=0.7"
-]
-test = [
-    "pytest>=7.0.0",
-    "pytest-cov>=4.0.0",
-    "pytest-mock>=3.10.0",
-    "coverage>=7.0.0"
-]
-
-[project.scripts]
-masster-version = "masster._version:main"
-
-[build-system]
-requires = ["hatchling>=1.18.0"]
-build-backend = "hatchling.build"
-
-# Testing configuration
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-python_files = ["test_*.py"]
-python_classes = ["Test*"]
-python_functions = ["test_*"]
-addopts = [
-    "--strict-markers",
-    "--strict-config",
-    "--verbose",
-    "--cov=masster",
-    "--cov-report=term-missing",
-    "--cov-report=html",
-    "--cov-report=xml",
-]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-    "integration: marks tests as integration tests",
-]
-filterwarnings = [
-    "error",
-    "ignore::UserWarning",
-    "ignore::DeprecationWarning",
-]
-
-# Coverage configuration
-[tool.coverage.run]
-source = ["masster"]
-omit = [
-    "*/tests/*",
-    "*/test_*.py",
-    "masster/_version.py",
-]
-
-[tool.coverage.report]
-exclude_lines = [
-    "pragma: no cover",
-    "def __repr__",
-    "raise AssertionError",
-    "raise NotImplementedError",
-    "if __name__ == .__main__.:",
-    "if TYPE_CHECKING:",
-]
-
-# Black configuration
-[tool.black]
-line-length = 88
-target-version = ['py311']
-include = '\.pyi?$'
+
+[project]
+name = "masster"
+version = "0.3.1"
+description = "Mass spectrometry data analysis package"
+authors = [
+    { name = "Zamboni Lab" }
+]
+license = { file = "LICENSE" }
+readme = "README.md"
+requires-python = ">=3.11"
+keywords = ["mass spectrometry", "metabolomics", "lc-ms", "chromatography"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry"
+]
+urls.homepage = "https://github.com/zamboni-lab/masster"
+urls.repository = "https://github.com/zamboni-lab/masster"
+urls.documentation = "https://github.com/zamboni-lab/masster#readme"
+dependencies = [
+    "alphabase>=1.0.0",
+    "alpharaw>=0.4.8",
+    "altair>=5.5.0",
+    "bokeh>=3.7.3",
+    "datashader>=0.18.1",
+    "python-dotenv>=1.0.0",
+    "holoviews>=1.21.0",
+    "h5py>=3.14.0",
+    "hvplot>=0.11.3",
+    "loguru>=0.7.3",
+    "numpy>=2.0.0",
+    "marimo>=0.14.16",
+    "matchms>=0.30.2",
+    "matplotlib>=3.8.0",
+    "pandas>=2.2.0",
+    "panel>=1.7.0",
+    "plotly>=5.15.0",
+    "polars>=1.0.0",
+    "pyopenms>=3.3.0",
+    "pyteomics>=4.7.0",
+    "pythonnet>=3.0.0",
+    "scipy>=1.12.0",
+    "simple-parsing>=0.1.7",
+    "tqdm>=4.65.0",
+    "ipykernel>=6.30.0",
+    "openpyxl>=3.1.5",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.10.0",
+    "black>=23.0.0",
+    "flake8>=5.0.0",
+    "mypy>=1.0.0",
+    "pre-commit>=3.0.0",
+    "twine>=4.0.0",
+    "build>=0.10.0",
+    "safety>=2.0.0",
+    "bandit>=1.7.0"
+]
+docs = [
+    "sphinx>=5.0.0",
+    "sphinx-rtd-theme>=1.2.0",
+    "sphinxcontrib-napoleon>=0.7"
+]
+test = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.10.0",
+    "coverage>=7.0.0"
+]
+
+[project.scripts]
+masster-version = "masster._version:main"
+
+[build-system]
+requires = ["hatchling>=1.18.0"]
+build-backend = "hatchling.build"
+
+# Testing configuration
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+    "--verbose",
+    "--cov=masster",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+    "--cov-report=xml",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+]
+filterwarnings = [
+    "error",
+    "ignore::UserWarning",
+    "ignore::DeprecationWarning",
+]
+
+# Coverage configuration
+[tool.coverage.run]
+source = ["masster"]
+omit = [
+    "*/tests/*",
+    "*/test_*.py",
+    "masster/_version.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]
+
+# Black configuration
+[tool.black]
+line-length = 88
+target-version = ['py311']
+include = '\.pyi?$'
 extend-exclude = '''
 /(
   # directories
@@ -148,42 +148,42 @@ extend-exclude = '''
   | build
   | dist
 )/
-'''
-
-# MyPy configuration
-[tool.mypy]
-python_version = "3.11"
-warn_return_any = true
-warn_unused_configs = true
-disallow_untyped_defs = false
-disallow_incomplete_defs = false
-check_untyped_defs = true
-disallow_untyped_decorators = false
-no_implicit_optional = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-warn_no_return = true
-warn_unreachable = true
-strict_equality = true
-ignore_missing_imports = true
-
-# Flake8 configuration
-[tool.flake8]
-max-line-length = 88
-extend-ignore = ["E203", "W503"]
-exclude = [
-    ".git",
-    "__pycache__",
-    "docs",
-    "build",
-    "dist",
-    ".eggs",
-    "*.egg-info",
-    ".venv",
-    "venv",
-]
-
-# Bandit configuration
-[tool.bandit]
-exclude_dirs = ["tests"]
-skips = ["B101", "B601"]
+'''
+
+# MyPy configuration
+[tool.mypy]
+python_version = "3.11"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+disallow_untyped_decorators = false
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+ignore_missing_imports = true
+
+# Flake8 configuration
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503"]
+exclude = [
+    ".git",
+    "__pycache__",
+    "docs",
+    "build",
+    "dist",
+    ".eggs",
+    "*.egg-info",
+    ".venv",
+    "venv",
+]
+
+# Bandit configuration
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B101", "B601"]

{masster-0.3.0 → masster-0.3.1}/src/masster/sample/plot.py

@@ -22,13 +22,13 @@ Dependencies:
 - `numpy`: For numerical computations.
 
 Functions:
-- `plot_eic()`: Generate extracted ion chromatograms with feature overlays.
+- `plot_chrom()`: Generate chromatograms with feature overlays.
 - `plot_2d()`: Create 2D mass spectrometry data visualizations.
 - `plot_features()`: Visualize detected features in retention time vs m/z space.
 - Various utility functions for plot styling and configuration.
 
 Supported Plot Types:
-- Extracted Ion Chromatograms (EIC)
+- Chromatograms
 - Total Ion Chromatograms (TIC)
 - Base Peak Chromatograms (BPC)
 - 2D intensity maps (RT vs m/z)
@@ -63,7 +63,74 @@ from matplotlib.colors import rgb2hex
 hv.extension("bokeh")
 
 
-def plot_eic(
+def _is_notebook_environment():
+    """
+    Detect if code is running in a notebook environment (Jupyter, JupyterLab, or Marimo).
+    
+    Returns:
+        bool: True if running in a notebook, False otherwise
+    """
+    try:
+        # Check for Jupyter/JupyterLab
+        from IPython import get_ipython
+        if get_ipython() is not None:
+            # Check if we're in a notebook context
+            shell = get_ipython().__class__.__name__
+            if shell in ['ZMQInteractiveShell', 'Shell']:  # Jupyter notebook/lab
+                return True
+        
+        # Check for Marimo
+        import sys
+        if 'marimo' in sys.modules:
+            return True
+        
+        # Additional check for notebook environments
+        if hasattr(__builtins__, '__IPYTHON__') or hasattr(__builtins__, '_ih'):
+            return True
+            
+    except ImportError:
+        pass
+    
+    return False
+
+
+def _display_plot(plot_object, layout=None):
+    """
+    Display a plot object in the appropriate way based on the environment.
+    
+    Args:
+        plot_object: The plot object to display (holoviews overlay, etc.)
+        layout: Optional panel layout object
+        
+    Returns:
+        The layout object if in notebook environment, None otherwise
+    """
+    if _is_notebook_environment():
+        # Display inline in notebook
+        try:
+            # For Jupyter notebooks, just return the plot object - 
+            # holoviews will handle the display automatically
+            return plot_object
+        except Exception:
+            # Fallback to panel display for other notebook environments
+            if layout is not None:
+                return layout
+            else:
+                # Create a simple layout if none provided
+                simple_layout = panel.Column(plot_object)
+                return simple_layout
+    else:
+        # Display in browser (original behavior)
+        if layout is not None:
+            layout.show()
+        else:
+            # Create a simple layout for browser display
+            simple_layout = panel.Column(plot_object)
+            simple_layout.show()
+        return None
+
+
+def plot_chrom(
     self,
     feature_uid=None,
     filename=None,
@@ -74,16 +141,16 @@ def plot_eic(
     link_x=False,
 ):
     """
-    Plot Extracted Ion Chromatograms (EICs) for one or more features using MS1 data and feature metadata.
+    Plot chromatograms for one or more features using MS1 data and feature metadata.
 
     This function filters MS1 data based on retention time (rt) and mass-to-charge ratio (mz) windows
-    derived from feature information in `features_df`. It then generates interactive EIC plots using
+    derived from feature information in `features_df`. It then generates interactive chromatogram plots using
     HoloViews, with feature retention time windows annotated. Plots can be displayed interactively or
     saved to a file.
 
     Parameters:
         feature_uid (int or list of int, optional):
-            Feature identifier(s) for EIC generation. If None, EICs for all features in `features_df` are plotted.
+            Feature identifier(s) for chromatogram generation. If None, chromatograms for all features in `features_df` are plotted.
         filename (str, optional):
             Output file path. If ending with `.html`, saves as interactive HTML; otherwise, saves as PNG.
             If not provided, displays the plot interactively.
@@ -96,7 +163,7 @@ def plot_eic(
         mz_tol_factor_plot (float, default=1):
             m/z time tolerance factor.
         link_x (bool, default=True):
-            If True, links the x-axes (retention time) across all EIC subplots.
+            If True, links the x-axes (retention time) across all chromatogram subplots.
 
     Returns:
         None
@@ -106,7 +173,7 @@ def plot_eic(
         - Aggregates MS1 intensities by retention time.
         - Utilizes HoloViews for visualization and Panel for layout/display.
     """
-    # plots the EIC for a given feature id
+    # plots the chromatogram for a given feature id
     # If rt or mz are not provided, they are extracted from features_df using the supplied feature id (feature_uid)
 
     feature_uids = feature_uid
@@ -121,7 +188,7 @@ def plot_eic(
 
     # make sure feature_uid is a list of integers
 
-    eic_plots = []
+    chrom_plots = []
     feature_uids = feats["feature_uid"].values.tolist()
     mz_tol_plot = mz_tol * mz_tol_factor_plot
     rt_tol_plot = rt_tol * rt_tol_factor_plot
@@ -137,29 +204,29 @@ def plot_eic(
         mz_end = feature_row["mz_end"].values[0]
 
         # filter self.ms1_df with rt_start, rt_end, mz_start, mz_end
-        eic_df = self.ms1_df.filter(
+        chrom_df = self.ms1_df.filter(
             pl.col("rt") >= rt_start - rt_tol_plot,
             pl.col("rt") <= rt_end + rt_tol_plot,
         )
-        eic_df = eic_df.filter(
+        chrom_df = chrom_df.filter(
             pl.col("mz") >= mz_start - mz_tol_plot,
             pl.col("mz") <= mz_end + mz_tol_plot,
         )
 
-        if eic_df.is_empty():
+        if chrom_df.is_empty():
             print("No MS1 data found in the specified window.")
             continue
 
         # convert to pandas DataFrame
-        eic_df = eic_df.to_pandas()
+        chrom_df = chrom_df.to_pandas()
         # aggregate all points with the same rt using the sum of inty
-        eic_df = eic_df.groupby("rt").agg({"inty": "sum"}).reset_index()
+        chrom_df = chrom_df.groupby("rt").agg({"inty": "sum"}).reset_index()
         yname = f"inty_{feature_uid}"
-        eic_df.rename(columns={"inty": yname}, inplace=True)
+        chrom_df.rename(columns={"inty": yname}, inplace=True)
 
-        # Plot the EIC using bokeh and ensure axes are independent by setting axiswise=True
-        eic = hv.Curve(eic_df, kdims=["rt"], vdims=[yname]).opts(
-            title=f"EIC for feature {feature_uid}, mz = {mz:.4f}",
+        # Plot the chromatogram using bokeh and ensure axes are independent by setting axiswise=True
+        chrom = hv.Curve(chrom_df, kdims=["rt"], vdims=[yname]).opts(
+            title=f"Chromatogram for feature {feature_uid}, mz = {mz:.4f}",
             xlabel="Retention time (s)",
             ylabel="Intensity",
             width=1000,
@@ -170,13 +237,13 @@ def plot_eic(
         )
 
         # Add vertical lines at the start and end of the retention time
-        eic = eic * hv.VLine(rt_start).opts(
+        chrom = chrom * hv.VLine(rt_start).opts(
             color="blue",
             line_width=1,
             line_dash="dashed",
             axiswise=True,
         )
-        eic = eic * hv.VLine(rt_end).opts(
+        chrom = chrom * hv.VLine(rt_end).opts(
             color="blue",
             line_width=1,
             line_dash="dashed",
@@ -184,12 +251,12 @@ def plot_eic(
         )
 
         # Append the subplot without linking axes
-        eic_plots.append(eic)
+        chrom_plots.append(chrom)
     if link_x:
-        # Create a layout with shared x-axis for all EIC plots
-        layout = hv.Layout(eic_plots).opts(shared_axes=True)
+        # Create a layout with shared x-axis for all chromatogram plots
+        layout = hv.Layout(chrom_plots).opts(shared_axes=True)
     else:
-        layout = hv.Layout(eic_plots).opts(shared_axes=False)
+        layout = hv.Layout(chrom_plots).opts(shared_axes=False)
 
     layout = layout.cols(1)
     layout = panel.Column(layout)
@@ -201,8 +268,8 @@ def plot_eic(
             # save the panel layout as a png
             hv.save(layout, filename, fmt="png")
     else:
-        # Display the panel layout
-        layout.show()
+        # Check if we're in a notebook environment and display appropriately
+        return _display_plot(layout.object, layout)
 
 
 def plot_2d(
@@ -513,8 +580,8 @@ def plot_2d(
             # save the panel layout as a png
             hv.save(overlay, filename, fmt="png")
     else:
-        # Display the panel layout
-        layout.show()
+        # Check if we're in a notebook environment and display appropriately
+        return _display_plot(overlay, layout)
 
 
 def plot_2d_oracle(
@@ -922,8 +989,8 @@ def plot_2d_oracle(
             # save the panel layout as a png
             hv.save(overlay, filename, fmt="png")
     else:
-        # Display the panel layout
-        layout.show()
+        # Check if we're in a notebook environment and display appropriately
+        return _display_plot(overlay, layout)
 
 
 def plot_ms2_eic(
@@ -1070,7 +1137,9 @@ def plot_ms2_eic(
         else:
             hv.save(layout, filename, fmt="png")
     else:
-        panel.panel(layout).show()
+        # Check if we're in a notebook environment and display appropriately
+        layout_obj = panel.panel(layout)
+        return _display_plot(layout, layout_obj)
 
 
 def plot_ms2_cycle(
@@ -1290,8 +1359,8 @@ def plot_ms2_cycle(
             # save the panel layout as a png
             hv.save(overlay, filename, fmt="png")
     else:
-        # Display the panel layout
-        layout.show()
+        # Check if we're in a notebook environment and display appropriately
+        return _display_plot(overlay, layout)
 
 
 def plot_ms2_q1(
@@ -1393,7 +1462,9 @@ def plot_ms2_q1(
         else:
             hv.save(layout, filename, fmt="png")
     else:
-        panel.panel(layout).show()
+        # Check if we're in a notebook environment and display appropriately
+        layout_obj = panel.panel(layout)
+        return _display_plot(layout, layout_obj)
 
 
 def plot_dda_stats(
@@ -1468,7 +1539,9 @@ def plot_dda_stats(
         else:
             hv.save(layout, filename, fmt="png")
     else:
-        panel.panel(layout).show()
+        # Check if we're in a notebook environment and display appropriately
+        layout_obj = panel.panel(layout)
+        return _display_plot(layout, layout_obj)
 
 
 def plot_feature_stats(
@@ -1584,7 +1657,9 @@ def plot_feature_stats(
         else:
             hv.save(layout, filename, fmt="png")
     else:
-        panel.panel(layout).show()
+        # Check if we're in a notebook environment and display appropriately
+        layout_obj = panel.panel(layout)
+        return _display_plot(layout, layout_obj)
 
 
 def plot_tic(