masster 0.5.9__py3-none-any.whl → 0.5.10__py3-none-any.whl

masster/study/plot.py

@@ -9,6 +9,8 @@ import panel
 import polars as pl
 from tqdm import tqdm
 
+# Import cmap for colormap handling
+from cmap import Colormap
 hv.extension("bokeh")
 
 
@@ -17,6 +19,93 @@ hv.extension("bokeh")
 from bokeh.layouts import row as bokeh_row
 
 
+def _export_with_webdriver_manager(plot_obj, filename, format_type, logger=None):
+    """
+    Export plot to PNG or SVG using webdriver-manager for automatic driver management.
+    
+    Parameters:
+        plot_obj: Bokeh plot object or holoviews object to export
+        filename: Output filename 
+        format_type: Either "png" or "svg"
+        logger: Logger for error reporting (optional)
+        
+    Returns:
+        bool: True if export successful, False otherwise
+    """
+    try:
+        # Convert holoviews to bokeh if needed
+        if hasattr(plot_obj, 'opts'):  # Likely a holoviews object
+            import holoviews as hv
+            bokeh_plot = hv.render(plot_obj)
+        else:
+            bokeh_plot = plot_obj
+            
+        # Try webdriver-manager export first
+        try:
+            from webdriver_manager.chrome import ChromeDriverManager
+            from selenium import webdriver
+            from selenium.webdriver.chrome.service import Service
+            from selenium.webdriver.chrome.options import Options
+            
+            # Set up Chrome options for headless operation
+            chrome_options = Options()
+            chrome_options.add_argument("--headless")
+            chrome_options.add_argument("--no-sandbox")
+            chrome_options.add_argument("--disable-dev-shm-usage")
+            chrome_options.add_argument("--disable-gpu")
+            
+            # Use webdriver-manager to automatically get the correct ChromeDriver
+            service = Service(ChromeDriverManager().install())
+            driver = webdriver.Chrome(service=service, options=chrome_options)
+            
+            # Export with managed webdriver
+            if format_type == "png":
+                from bokeh.io import export_png
+                export_png(bokeh_plot, filename=filename, webdriver=driver)
+            elif format_type == "svg":
+                from bokeh.io import export_svg
+                export_svg(bokeh_plot, filename=filename, webdriver=driver)
+            else:
+                raise ValueError(f"Unsupported format: {format_type}")
+                
+            driver.quit()
+            return True
+            
+        except ImportError:
+            if logger:
+                logger.debug(f"webdriver-manager not available, using default {format_type.upper()} export")
+            # Fall back to default export
+            if format_type == "png":
+                from bokeh.io import export_png
+                export_png(bokeh_plot, filename=filename)
+            elif format_type == "svg":
+                from bokeh.io import export_svg
+                export_svg(bokeh_plot, filename=filename)
+            return True
+            
+        except Exception as e:
+            if logger:
+                logger.debug(f"{format_type.upper()} export with webdriver-manager failed: {e}, using default {format_type.upper()} export")
+            try:
+                # Final fallback to default export
+                if format_type == "png":
+                    from bokeh.io import export_png
+                    export_png(bokeh_plot, filename=filename)
+                elif format_type == "svg":
+                    from bokeh.io import export_svg
+                    export_svg(bokeh_plot, filename=filename)
+                return True
+            except Exception as e2:
+                if logger:
+                    logger.error(f"{format_type.upper()} export failed: {e2}")
+                return False
+                
+    except Exception as e:
+        if logger:
+            logger.error(f"Export preparation failed: {e}")
+        return False
+
+
 def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title="Plot"):
     """
     Save a plot using isolated file saving that doesn't affect global Bokeh state.
@@ -38,11 +127,10 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
         logger.info(f"Plot saved to: {abs_filename}")
 
     elif filename.endswith(".png"):
-        try:
-            from bokeh.io.export import export_png
-            export_png(plot_object, filename=filename)
+        success = _export_with_webdriver_manager(plot_object, filename, "png", logger)
+        if success:
             logger.info(f"Plot saved to: {abs_filename}")
-        except Exception as e:
+        else:
             # Fall back to HTML if PNG export not available
             html_filename = filename.replace('.png', '.html')
             abs_html_filename = html_filename if abs_filename == filename else abs_filename.replace('.png', '.html')
@@ -55,16 +143,15 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
             with open(html_filename, 'w', encoding='utf-8') as f:
                 f.write(html)
 
-            logger.warning(f"PNG export not available ({str(e)}). Use export_png. Saved as HTML instead: {abs_html_filename}")
-    elif filename.endswith(".pdf"):
-        # Try to save as PDF, fall back to HTML if not available
-        try:
-            from bokeh.io.export import export_pdf
-            export_pdf(plot_object, filename=filename)
+            logger.warning(f"PNG export not available. Saved as HTML instead: {abs_html_filename}")
+    elif filename.endswith(".svg"):
+        success = _export_with_webdriver_manager(plot_object, filename, "svg", logger)
+        if success:
             logger.info(f"Plot saved to: {abs_filename}")
-        except ImportError:
-            # Fall back to HTML if PDF export not available
-            html_filename = filename.replace('.pdf', '.html')
+        else:
+            # Fall back to HTML if SVG export not available
+            html_filename = filename.replace('.svg', '.html')
+            abs_html_filename = html_filename if abs_filename == filename else abs_filename.replace('.svg', '.html')
             from bokeh.resources import Resources
             from bokeh.embed import file_html
 
@@ -74,27 +161,13 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
             with open(html_filename, 'w', encoding='utf-8') as f:
                 f.write(html)
 
-            logger.warning(f"PDF export not available, saved as HTML instead: {html_filename}")
-    elif filename.endswith(".svg"):
-        # Try to save as SVG, fall back to HTML if not available
-        try:
-            from bokeh.io.export import export_svg
-            export_svg(plot_object, filename=filename)
-            logger.info(f"Plot saved to: {abs_filename}")
-        except Exception as e:
-            # Fall back to HTML if SVG export not available
-            html_filename = filename.replace('.svg', '.html')
-            abs_html_filename = html_filename if abs_filename == filename else abs_filename.replace('.svg', '.html')
-            from bokeh.resources import Resources
-            from bokeh.embed import file_html
-
-            resources = Resources(mode='cdn')
+            logger.warning(f"SVG export not available. Saved as HTML instead: {abs_html_filename}")
             html = file_html(plot_object, resources, title=plot_title)
 
             with open(html_filename, 'w', encoding='utf-8') as f:
                 f.write(html)
 
-            logger.warning(f"SVG export not available ({str(e)}). Saved as HTML instead: {abs_html_filename}")
+            logger.warning(f"SVG export not available. Saved as HTML instead: {abs_html_filename}")
     else:
         # Default to HTML for unknown extensions using isolated approach
         from bokeh.resources import Resources
@@ -548,11 +621,11 @@ def plot_consensus_2d(
     self,
     filename=None,
     colorby="number_samples",
-    cmap=None,
+    cmap="viridis",
+    alpha=0.7,
     markersize=8,
     sizeby="inty_mean",
     scaling="static",
-    alpha=0.7,
     width=600,
     height=450,
     mz_range=None,
@@ -639,7 +712,7 @@ def plot_consensus_2d(
     if cmap is None:
         cmap = "viridis"
     elif cmap == "grey":
-        cmap = "Greys256"
+        cmap = "greys"
 
     # plot with bokeh
     import bokeh.plotting as bp
@@ -657,9 +730,6 @@ def plot_consensus_2d(
         from bokeh.models.annotations import ColorBar
     from bokeh.palettes import viridis, Category20
 
-    # Import cmap for colormap handling
-    from cmap import Colormap
-
     # Convert Polars DataFrame to pandas for Bokeh compatibility
     data_pd = data.to_pandas()
     source = ColumnDataSource(data_pd)

masster/study/processing.py

@@ -86,7 +86,7 @@ def align(self, **kwargs):
         self.logger.error(f"Unknown alignment algorithm '{algorithm}'")
         return
 
-    self.logger.debug("Alignment completed successfully.")
+    self.logger.success("Alignment completed.")
 
     # Reset consensus data structures after alignment since RT changes invalidate consensus
     consensus_reset_count = 0
@@ -225,8 +225,8 @@ def find_ms2(self, **kwargs):
         unique_consensus_features = self.consensus_ms2["consensus_uid"].n_unique()
     else:
         unique_consensus_features = 0
-    self.logger.info(
-        f"Linking completed. {len(self.consensus_ms2)} MS2 spectra associated to {unique_consensus_features} consensus features.",
+    self.logger.success(
+        f"Linking completed. Found {len(self.consensus_ms2)} MS2 spectra associated to {unique_consensus_features} consensus features.",
     )
 
 
@@ -514,7 +514,7 @@ def _integrate_chrom_impl(self, **kwargs):
                 ],
             ).drop("__row_idx")  # Remove the temporary row index column
 
-            self.logger.debug(
+            self.logger.success(
                 f"Integration completed. Updated {len(update_rows)} features with chromatogram data.",
             )
         except Exception as e:
@@ -1091,7 +1091,7 @@ def _align_kd_algorithm(study_obj, params):
         ).alias("rt")
     )
 
-    study_obj.logger.info(
+    study_obj.logger.success(
         f"Alignment completed. Reference sample UID {ref_sample_uid} (index {ref_index}).",
     )
 
@@ -1365,7 +1365,7 @@ def find_iso(self, rt_tol=0.1, mz_tol=0.01, uids=None):
     # Count how many consensus features have isotope data
     iso_count = sum(1 for data in consensus_iso_data.values() if data is not None and len(data) > 0)
     
-    self.logger.success(f"Optimized isotope detection completed. Found isotope patterns for {iso_count}/{len(self.consensus_df)} consensus features.")
+    self.logger.success(f"Isotope detection completed. Found isotope patterns for {iso_count}/{len(self.consensus_df)} consensus features.")
 
 
 def reset_iso(self):

masster/study/study5_schema.json

@@ -255,6 +255,9 @@
       },
       "ms2_specs": {
         "dtype": "pl.Object"
+      },
+      "ms1_spec": {
+        "dtype": "pl.Object"
       }
     }
   },

{masster-0.5.9.dist-info → masster-0.5.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.9
+Version: 0.5.10
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -685,6 +685,7 @@ Requires-Dist: altair>=5.5.0
 Requires-Dist: bokeh>=3.7.3
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: datashader>=0.18.1
+Requires-Dist: get-gecko-driver>=1.4
 Requires-Dist: h5py>=3.14.0
 Requires-Dist: hdbscan>=0.8.40
 Requires-Dist: holoviews>=1.21.0
@@ -703,6 +704,7 @@ Requires-Dist: scikit-learn>=1.7.1
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: tqdm>=4.65.0
 Requires-Dist: umap-learn>=0.5.9.post2
+Requires-Dist: webdriver-manager>=4.0.2
 Provides-Extra: dev
 Requires-Dist: bandit>=1.7.0; extra == 'dev'
 Requires-Dist: black>=23.0.0; extra == 'dev'

{masster-0.5.9.dist-info → masster-0.5.10.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=bhol39keZ-JZvzEVotG6tOww8JjVuPt66rihFwTiraE,256
+masster/_version.py,sha256=ykzsX9zBanG6fFefFoIDPED_UySJmLofW0r3TROBhFY,257
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=XT2gUcUIct8LWzTp9n484g5MaB89toT76CGA41oBvfA,18375
 masster/spectrum.py,sha256=TWIgDcl0lveG40cLVZTWGp8-FxMolu-P8EjZyRBtXL4,49850
@@ -19,16 +19,16 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
 masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
 masster/lib/lib.py,sha256=SSN06UtiM-hIdjS3eCiIHsJ_8S4YHRGOLGmdPIh-efo,27481
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/adducts.py,sha256=nl5KEuat0hvktgar6Ca4PbY8JXt9SD05EeTn0HOKt64,32592
+masster/sample/adducts.py,sha256=aBDoBKRjh6rMIF65yH6vx7KpQxeMUv796q3H46TySwY,32603
 masster/sample/h5.py,sha256=X5VBHBpgJ2FJc9mtCggJ1HSQ3ujRmb1Wnpr9sJ8bGVA,115445
-masster/sample/helpers.py,sha256=27eZFFidr02-DlSi4-eF4bpSk_y-qU3eoFCAOshRO20,42138
+masster/sample/helpers.py,sha256=Mt9LX-Dy1Xro1a_Sy6nxQzCkP_-q7nK4xVnNm44v7UA,43872
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
 masster/sample/load.py,sha256=swjRBCoFGni9iPztHIKPVB5ru_xDMVryB_inPXdujTw,51819
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=3_2SO88uTird4cSlrVAZofuIrxjQDIIAH2l0ESxddB8,86629
-masster/sample/processing.py,sha256=uqa5QeXJSo3b6bg3Xl62vkaDxz09NLAXJekBFrPDe_Q,55924
+masster/sample/plot.py,sha256=Cf_kuUiZnVHSlZfJQbV8Wtmdw1PPG5D3g1UbLobaXMs,96483
+masster/sample/processing.py,sha256=qk-6_v424nwfaoVmdbHj-_lJiW7OkWS7SuQzQWNAFGI,55919
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=VhQik_ev1liRqGUtbZvV1NOjfFzgfZI1orfQT87gai4,20643
+masster/sample/sample.py,sha256=pw4fIE5gecdupZOOWFUiRCs0x-3qa3Nv7V_UdJ-CAsc,22202
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
 masster/sample/save.py,sha256=pbiRoWEA2DnhDKmMJncjveNlBqizJLOVRm5cug4ZwyM,38658
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
@@ -41,17 +41,17 @@ masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
 masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
 masster/study/export.py,sha256=joFK9jip2UM4lVAvhkdKVeUdNdM4D8uP2WE49IaVJgw,60172
-masster/study/h5.py,sha256=hLp3sd95MRMBwMsLDbC1SXsYKeIlIdUG6-lChTJxuHw,95367
-masster/study/helpers.py,sha256=Y96XJsxo0IuuMh_u1asxJeSjjvR3PUp5RAXIACty8QM,190846
+masster/study/h5.py,sha256=KpvV6-0RGIAjYBNa7AodbLmlGtoDUvbeC_jB2IZdYvA,96118
+masster/study/helpers.py,sha256=QwPyGTuRKZoimK_y1kX4Ag_0rJNB1MYoP0Q2mXEVshs,191930
 masster/study/id.py,sha256=heKU309cUsNeFxbWYvqxVIAJLrR1H0YqMgLanLx9Do4,80091
-masster/study/load.py,sha256=7d11294YYEGrSKox3cwvetv2vqcstYT1SnyAhHH5V_Q,107706
-masster/study/merge.py,sha256=_-J29kYu65S9wE5bgxMdsmPcf_VupVxWmjGpqKWJDI0,169513
+masster/study/load.py,sha256=BMjoUDkXNI6iU2tRE2eBRzxMrvW0gRyLepqYOWaMPXU,101192
+masster/study/merge.py,sha256=aEZjNhrsQZxkRhyyuOUjlIN_tdA6y2VX2BAkvfPd_Sc,169300
 masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
-masster/study/plot.py,sha256=LEIzoYiUyq1aswh-sw8S-ESvN2DaQKN5l22yLW8gZe8,107647
-masster/study/processing.py,sha256=8TB6olWoda5ytz7-kSqGXmniYVnMnUj7-J6Szcoc8Fg,58544
+masster/study/plot.py,sha256=ftQAVgEYkZuKAVIlbTR5bUypF8DpMOxSXwOyYz_BsOQ,110610
+masster/study/processing.py,sha256=n-JbH1ZHtSE1xlyi69ZrcHMsxw7dAyodC5hnaNld2to,58537
 masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
 masster/study/study.py,sha256=gudugPJk3LOtZh-YsszSRCBDrBG78cexoG0CSM86EPs,38701
-masster/study/study5_schema.json,sha256=0IZxM9VVI0TUlx74BPzJDT44kySi6NZZ6iLR0j8bU_s,7736
+masster/study/study5_schema.json,sha256=lTFePwY8bQngyBnNCP60-UP9tnZLGhFo3YtJgwHTWdo,7797
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=Du0F592ej2einT8kOx8EUs610axSvur8_-6N19O-uJY,10209
 masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
@@ -67,8 +67,8 @@ masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,1414
 masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
 masster/wizard/wizard.py,sha256=UobIGFZtp1s_9WJlpl6DQ2-pp7flPQ6dlYZJqYE92OM,38131
-masster-0.5.9.dist-info/METADATA,sha256=atBSD9cWS2CByNIoDwdlY3c3oZa_7CRvQmObin496hU,45113
-masster-0.5.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.5.9.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.5.9.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.5.9.dist-info/RECORD,,
+masster-0.5.10.dist-info/METADATA,sha256=wPI5dLDPHYjlcafoYNdUWlnUDc-bS-HjBruaVnVDxpA,45191
+masster-0.5.10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.5.10.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.5.10.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.5.10.dist-info/RECORD,,