pathview-plus 2.0.0__tar.gz → 2.0.2__tar.gz

pathview_plus-2.0.2/LICENSE

@@ -0,0 +1,28 @@
+Creative Commons Attribution-NonCommercial (CC BY-NC 4.0)
+
+Academic and Non-Commercial Use License
+
+Copyright (c) 2026 Richard Allen White III
+
+Permission is hereby granted, free of charge, to any person or organization obtaining a copy
+of this software and associated documentation files (the "Software"), to use, copy, modify,
+and distribute the Software for academic, research, and non-commercial purposes, subject to
+the following conditions:
+
+1. The above copyright notice and this permission notice shall be included in all copies
+   or substantial portions of the Software.
+
+2. The Software may not be used, in whole or in part, for commercial purposes without
+   prior written permission from the copyright holder.
+
+3. Commercial purposes include, but are not limited to, use in a product or service that
+   is sold, licensed, or generates revenue.
+
+4. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+   INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+   PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
+   FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+   OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+   DEALINGS IN THE SOFTWARE.
+
+For commercial licensing inquiries, please contact: Richard Allen White III, rwhit101@charlotte.edu

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: pathview-plus
-Version: 2.0.0
+Version: 2.0.2
 Summary: Complete pathway visualization: KEGG + SBGN + highlighting + splines
 Home-page: https://github.com/raw-lab/pathview-plus
 Author: Richard Allen White III
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -15,6 +14,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: polars>=0.19.0
 Requires-Dist: numpy>=1.24.0
 Requires-Dist: matplotlib>=3.7.0
@@ -33,6 +33,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
@@ -43,7 +44,6 @@ Dynamic: summary
 **Full-featured Python implementation of R pathview + SBGNview with support for KEGG, Reactome, MetaCyc, and more.**
 
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 ---
 
@@ -642,20 +642,29 @@ Contributions welcome! Areas for improvement:
 
 ## 📄 License
 
-GPL v3.0 — See LICENSE file
+Creative Commons Attribution-NonCommercial (CC BY-NC 4.0) — See LICENSE file
 
 **Citations:**
-- Original R pathview: Luo & Brouwer (2013). Bioinformatics
-- SBGNview: Shashikant et al. (2022). Bioinformatics
-- KEGG: Kanehisa et al. (2023). Nucleic Acids Research
-- Reactome: Gillespie et al. (2022). Nucleic Acids Research
+
+If you are publishing results obtained using Pathview-Plus, please cite: <br />
+- Pre-Print Pathview-Plus: Figueroa III JL, Brouwer CR, White III RA. 2026. Pathview-plus: unlocking the metabolic pathways from cells to ecosystems. bioRxiv.
+
+If you using the R version please cite: <br />
+- Original Pathview R: Luo, W., & Brouwer, C. 2013. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29(14), 1830–1831. [Pathview](https://doi.org/10.1093/bioinformatics/btt285)
+- Original SBGNview R: Shashikant, T., et al. 2022. SBGNview: Data analysis, integration and visualization on all pathways using SBGN. Bioinformatics, 38(11), 3006–3008. [SBGNview](https://doi.org/10.1093/bioinformatics/btab793) 
+
+---
+
+## Contributing to Pathview-plus
+
+We welcome contributions of other experts expanding features in Pathview-plus including the R and python versions. Please contact us via support. 
 
 ---
 
 ## 📞 Support
 
-- **Issues:** https://github.com/raw-lab/pathview-plus/issues
-- **Email:** rwhit101@charlotte.edu 
+- **Issues:** [open an issue](https://github.com/raw-lab/pathview-plus/issues).  
+- **Email:** [Dr. Richard Allen White III](mailto:rwhit101@uncc.edu)
 ---
 
 **Made with ❤️ for the pathway visualization community**

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/README.md

@@ -3,7 +3,6 @@
 **Full-featured Python implementation of R pathview + SBGNview with support for KEGG, Reactome, MetaCyc, and more.**
 
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 ---
 
@@ -602,20 +601,29 @@ Contributions welcome! Areas for improvement:
 
 ## 📄 License
 
-GPL v3.0 — See LICENSE file
+Creative Commons Attribution-NonCommercial (CC BY-NC 4.0) — See LICENSE file
 
 **Citations:**
-- Original R pathview: Luo & Brouwer (2013). Bioinformatics
-- SBGNview: Shashikant et al. (2022). Bioinformatics
-- KEGG: Kanehisa et al. (2023). Nucleic Acids Research
-- Reactome: Gillespie et al. (2022). Nucleic Acids Research
+
+If you are publishing results obtained using Pathview-Plus, please cite: <br />
+- Pre-Print Pathview-Plus: Figueroa III JL, Brouwer CR, White III RA. 2026. Pathview-plus: unlocking the metabolic pathways from cells to ecosystems. bioRxiv.
+
+If you using the R version please cite: <br />
+- Original Pathview R: Luo, W., & Brouwer, C. 2013. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29(14), 1830–1831. [Pathview](https://doi.org/10.1093/bioinformatics/btt285)
+- Original SBGNview R: Shashikant, T., et al. 2022. SBGNview: Data analysis, integration and visualization on all pathways using SBGN. Bioinformatics, 38(11), 3006–3008. [SBGNview](https://doi.org/10.1093/bioinformatics/btab793) 
+
+---
+
+## Contributing to Pathview-plus
+
+We welcome contributions of other experts expanding features in Pathview-plus including the R and python versions. Please contact us via support. 
 
 ---
 
 ## 📞 Support
 
-- **Issues:** https://github.com/raw-lab/pathview-plus/issues
-- **Email:** rwhit101@charlotte.edu 
+- **Issues:** [open an issue](https://github.com/raw-lab/pathview-plus/issues).  
+- **Email:** [Dr. Richard Allen White III](mailto:rwhit101@uncc.edu)
 ---
 
 **Made with ❤️ for the pathway visualization community**

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/bin/pathview-cli.py

@@ -42,7 +42,7 @@ import sys
 import polars as pl
 
 from pathview.rendering import kegg_legend
-from pathview.orchestrator import pathview
+from pathview import pathview
 from pathview.mol_data import sim_mol_data
 
 
@@ -211,6 +211,9 @@ def main(argv: list[str] | None = None) -> None:
             "Provide at least one of --gene-data, --cpd-data, or --simulate."
         )
 
+    # Cast ID column to string for merging
+    gene_data = gene_data.cast({gene_data.columns[0]: pl.String})
+
     # -- Run pathview --------------------------------------------------------
     result = pathview(
         pathway_id    = args.pathway_id,
@@ -245,8 +248,9 @@ def main(argv: list[str] | None = None) -> None:
             print(f"Info: Compound plot data — {cdf.height} nodes mapped.")
     else:
         print("Warning: Pathway was skipped or no data could be mapped.", file=sys.stderr)
-        sys.exit(1)
+        return 1
+    return 0
 
 
 if __name__ == "__main__":
-    main()
+    sys.exit(main())

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/pathview_plus.egg-info/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: pathview-plus
-Version: 2.0.0
+Version: 2.0.2
 Summary: Complete pathway visualization: KEGG + SBGN + highlighting + splines
 Home-page: https://github.com/raw-lab/pathview-plus
 Author: Richard Allen White III
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -15,6 +14,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: polars>=0.19.0
 Requires-Dist: numpy>=1.24.0
 Requires-Dist: matplotlib>=3.7.0
@@ -33,6 +33,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
@@ -43,7 +44,6 @@ Dynamic: summary
 **Full-featured Python implementation of R pathview + SBGNview with support for KEGG, Reactome, MetaCyc, and more.**
 
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 ---
 
@@ -642,20 +642,29 @@ Contributions welcome! Areas for improvement:
 
 ## 📄 License
 
-GPL v3.0 — See LICENSE file
+Creative Commons Attribution-NonCommercial (CC BY-NC 4.0) — See LICENSE file
 
 **Citations:**
-- Original R pathview: Luo & Brouwer (2013). Bioinformatics
-- SBGNview: Shashikant et al. (2022). Bioinformatics
-- KEGG: Kanehisa et al. (2023). Nucleic Acids Research
-- Reactome: Gillespie et al. (2022). Nucleic Acids Research
+
+If you are publishing results obtained using Pathview-Plus, please cite: <br />
+- Pre-Print Pathview-Plus: Figueroa III JL, Brouwer CR, White III RA. 2026. Pathview-plus: unlocking the metabolic pathways from cells to ecosystems. bioRxiv.
+
+If you using the R version please cite: <br />
+- Original Pathview R: Luo, W., & Brouwer, C. 2013. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29(14), 1830–1831. [Pathview](https://doi.org/10.1093/bioinformatics/btt285)
+- Original SBGNview R: Shashikant, T., et al. 2022. SBGNview: Data analysis, integration and visualization on all pathways using SBGN. Bioinformatics, 38(11), 3006–3008. [SBGNview](https://doi.org/10.1093/bioinformatics/btab793) 
+
+---
+
+## Contributing to Pathview-plus
+
+We welcome contributions of other experts expanding features in Pathview-plus including the R and python versions. Please contact us via support. 
 
 ---
 
 ## 📞 Support
 
-- **Issues:** https://github.com/raw-lab/pathview-plus/issues
-- **Email:** rwhit101@charlotte.edu 
+- **Issues:** [open an issue](https://github.com/raw-lab/pathview-plus/issues).  
+- **Email:** [Dr. Richard Allen White III](mailto:rwhit101@uncc.edu)
 ---
 
 **Made with ❤️ for the pathway visualization community**

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/pathview_plus.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+LICENSE
 README.md
 setup.py
 bin/pathview-cli.py

{pathview_plus-2.0.0 → pathview_plus-2.0.2}/setup.py

@@ -10,7 +10,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setup(
     name="pathview-plus",
-    version="2.0.0",
+    version="2.0.2",
     author="Richard Allen White III",
     description="Complete pathway visualization: KEGG + SBGN + highlighting + splines",
     long_description=long_description,
@@ -23,7 +23,6 @@ setup(
         "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",