masster 0.5.24__tar.gz → 0.5.26__tar.gz

{masster-0.5.24 → masster-0.5.26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.24
+Version: 0.5.26
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -684,7 +684,6 @@ Requires-Dist: alpharaw>=0.4.8
 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
@@ -852,5 +851,10 @@ python -c "from masster import Wizard; wiz = Wizard(source='D:/Data/studies/my_s
 ## License
 GNU Affero General Public License v3
 
+See the [LICENSE](LICENSE) file for details.
+
+### Third-Party Licenses
+This project uses several third-party libraries, including pyOpenMS which is licensed under the BSD 3-Clause License. For complete information about third-party dependencies and their licenses, see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
+
 ## Citation
 If you use Masster in your research, please cite this repository.

{masster-0.5.24 → masster-0.5.26}/README.md

@@ -124,5 +124,10 @@ python -c "from masster import Wizard; wiz = Wizard(source='D:/Data/studies/my_s
 ## License
 GNU Affero General Public License v3
 
+See the [LICENSE](LICENSE) file for details.
+
+### Third-Party Licenses
+This project uses several third-party libraries, including pyOpenMS which is licensed under the BSD 3-Clause License. For complete information about third-party dependencies and their licenses, see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
+
 ## Citation
 If you use Masster in your research, please cite this repository.

masster-0.5.26/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,64 @@
+# Third-Party Licenses and Notices
+
+This project uses third-party libraries and components that are distributed under their own licenses. Below is a list of these dependencies and their respective license information.
+
+---
+
+## pyOpenMS
+
+**License:** BSD 3-Clause License  
+**Copyright:** OpenMS Team  
+**Source:** https://github.com/OpenMS/OpenMS
+
+pyOpenMS is a Python wrapper for OpenMS, a library for mass spectrometry data analysis.
+
+### BSD 3-Clause License
+
+```
+Copyright (c) 2002-2025, The OpenMS Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+```
+
+---
+
+## Other Dependencies
+
+This project also depends on the following open-source libraries. Please refer to their respective repositories for detailed license information:
+
+- **NumPy** - BSD License
+- **Pandas** - BSD License
+- **SciPy** - BSD License
+- **Matplotlib** - PSF-based License
+- **h5py** - BSD License
+- **Bokeh** - BSD License
+- **Panel** - BSD License
+- **Polars** - MIT License
+- **scikit-learn** - BSD License
+- **and others** - See pyproject.toml for complete dependency list
+
+For the most up-to-date license information for these dependencies, please refer to their official repositories and documentation.

{masster-0.5.24 → masster-0.5.26}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.24"
+version = "0.5.26"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
@@ -47,7 +47,6 @@ dependencies = [
     "scikit-learn>=1.7.1",
     "umap-learn>=0.5.9.post2",
     "hdbscan>=0.8.40",
-    "get-gecko-driver>=1.4",
     "webdriver-manager>=4.0.2",
 ]
 

{masster-0.5.24 → masster-0.5.26}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.24"
+__version__ = "0.5.25"
 
 
 def get_version():

{masster-0.5.24 → masster-0.5.26}/src/masster/study/export.py

@@ -1305,10 +1305,34 @@ def export_parquet(self, filename: str | None = None) -> None:
     if self.consensus_df is not None and not self.consensus_df.is_empty():
         consensus_file = f"{filename}_consensus.parquet"
         try:
-            self.consensus_df.write_parquet(consensus_file)
+            # Create a copy of consensus_df for parquet export
+            consensus_export_df = self.consensus_df.clone()
+            
+            # Handle Object dtype columns that can't be serialized to parquet
+            for col in consensus_export_df.columns:
+                if consensus_export_df[col].dtype == pl.Object:
+                    if col == "iso":
+                        # Convert numpy arrays to string representation for parquet compatibility
+                        # This preserves the data while making it parquet-serializable
+                        consensus_export_df = consensus_export_df.with_columns([
+                            pl.col("iso").map_elements(
+                                lambda x: str(x.tolist()) if x is not None else None,
+                                return_dtype=pl.String
+                            ).alias("iso")
+                        ])
+                    else:
+                        # For other Object columns, convert to string representation
+                        consensus_export_df = consensus_export_df.with_columns([
+                            pl.col(col).map_elements(
+                                lambda x: str(x) if x is not None else None,
+                                return_dtype=pl.String
+                            ).alias(col)
+                        ])
+            
+            consensus_export_df.write_parquet(consensus_file)
             exported_files.append(consensus_file)
             self.logger.debug(
-                f"Exported consensus to {consensus_file} ({self.consensus_df.height} rows)",
+                f"Exported consensus to {consensus_file} ({consensus_export_df.height} rows)",
             )
         except Exception as e:
             self.logger.error(f"Error writing consensus parquet file: {e}")

{masster-0.5.24 → masster-0.5.26}/uv.lock

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 [[package]]
@@ -1473,14 +1449,13 @@ wheels = [
 
 [[package]]
 name = "masster"
-version = "0.5.24"
+version = "0.5.26"
 source = { editable = "." }
 dependencies = [
     { name = "alpharaw" },
     { name = "bokeh" },
     { name = "cmap" },
     { name = "datashader" },
-    { name = "get-gecko-driver" },
     { name = "h5py" },
     { name = "hdbscan" },
     { name = "holoviews" },
@@ -1538,7 +1513,6 @@ requires-dist = [
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     { name = "datashader", specifier = ">=0.18.1" },
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