ScreenPro2 0.5.1__tar.gz → 0.7.0__tar.gz

{screenpro2-0.5.1 → screenpro2-0.7.0}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2024 ScreenPro2 Development Team.
+Copyright (c) 2022-2026 ScreenPro2 Development Team.
 All rights reserved.
 Gilbart Lab, UCSF / Arc Institute.
 Multi-Omics Tech Center, Arc Insititue.

{screenpro2-0.5.1 → screenpro2-0.7.0}/PKG-INFO

@@ -1,11 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: ScreenPro2
-Version: 0.5.1
+Version: 0.7.0
 Summary: Flexible analysis of high-content CRISPR screening
 License: MIT
+License-File: LICENSE
 Keywords: CRISPR,screening,bioinformatics
-Author: Abe Arab
-Author-email: abea@arcinstitute.org
+Author: Abolfazl Arab
+Author-email: abolfazl.arab@ucsf.edu
 Requires-Python: >=3.9
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
@@ -14,16 +15,19 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Project-URL: Homepage, https://github.com/ArcInstitute/ScreenPro2
 Project-URL: Repository, https://github.com/ArcInstitute/ScreenPro2
 Description-Content-Type: text/markdown
 
 [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2)
+[![zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
+[![NCB](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z)
 [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2)
 [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest)
 [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2)
 [![Downloads](https://static.pepy.tech/badge/screenpro2/month)](https://pepy.tech/project/screenpro2)
-[![CodeQL](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql/badge.svg)](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql)
+
 # ScreenPro2
 
 ## Introduction
@@ -356,11 +360,13 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE
 by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute.  
 
 ## Citation
-If you use ScreenPro2 in your research, please cite the following paper.
+If you use ScreenPro2 in your research, please cite both the software release and the published paper.
 
-  Coming soon...
+**Final publication note**: The final ScreenPro2 publication is now available in _Nature Chemical Biology_ (2026): https://doi.org/10.1038/s41589-026-02312-z
+
+- **Software (Zenodo)**: 
+> Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467
 
-## Development
-### Testing
-Tests can be easily run using the `pytest` framework.
+- **Paper (Nature Chemical Biology)**:
+> O’Loughlin, T.A., Arab, A., et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z
 

{screenpro2-0.5.1 → screenpro2-0.7.0}/README.md

@@ -1,9 +1,11 @@
 [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2)
+[![zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
+[![NCB](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z)
 [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2)
 [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest)
 [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2)
 [![Downloads](https://static.pepy.tech/badge/screenpro2/month)](https://pepy.tech/project/screenpro2)
-[![CodeQL](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql/badge.svg)](https://github.com/ArcInstitute/ScreenPro2/actions/workflows/github-code-scanning/codeql)
+
 # ScreenPro2
 
 ## Introduction
@@ -336,10 +338,12 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE
 by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute.  
 
 ## Citation
-If you use ScreenPro2 in your research, please cite the following paper.
+If you use ScreenPro2 in your research, please cite both the software release and the published paper.
 
-  Coming soon...
+**Final publication note**: The final ScreenPro2 publication is now available in _Nature Chemical Biology_ (2026): https://doi.org/10.1038/s41589-026-02312-z
+
+- **Software (Zenodo)**: 
+> Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467
 
-## Development
-### Testing
-Tests can be easily run using the `pytest` framework.
+- **Paper (Nature Chemical Biology)**:
+> O’Loughlin, T.A., Arab, A., et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z

{screenpro2-0.5.1 → screenpro2-0.7.0}/pyproject.toml

@@ -1,9 +1,10 @@
 [tool.poetry]
 name = "ScreenPro2"
 description = "Flexible analysis of high-content CRISPR screening"
-version = "0.5.1"
+version = "0.7.0"
 authors = [
-	"Abe Arab <abea@arcinstitute.org>"
+	"Abolfazl Arab <abolfazl.arab@ucsf.edu>",
+	"Nick Youngblut <nick.youngblut@arcinstitute.org>",
 ]
 license = "MIT"
 readme = "README.md"

{screenpro2-0.5.1 → screenpro2-0.7.0}/screenpro/assays/__init__.py

@@ -71,8 +71,8 @@ class PooledScreens(object):
         growth_factors = []
         # calculate growth factor for gamma, tau, or rho score per replicates
         for replicate in adat.obs.replicate.unique():
-            db_untreated = adat.obs.query(f'condition == "{untreated}" & replicate == {str(replicate)}')[db_rate_col][0]
-            db_treated = adat.obs.query(f'condition == "{treated}" & replicate == {str(replicate)}')[db_rate_col][0]
+            db_untreated = adat.obs.query(f'condition == "{untreated}" & replicate == {str(replicate)}')[db_rate_col].iloc[0]
+            db_treated = adat.obs.query(f'condition == "{treated}" & replicate == {str(replicate)}')[db_rate_col].iloc[0]
 
             growth_factors.append(('gamma', db_untreated, replicate, f'gamma_replicate_{replicate}'))
             growth_factors.append(('tau', db_treated, replicate, f'tau_replicate_{replicate}'))

{screenpro2-0.5.1 → screenpro2-0.7.0}/screenpro/ngs/cas9.py

@@ -154,10 +154,9 @@ def map_to_library_single_guide(df_count, library, return_type='all', verbose=Fa
         )
 
     if verbose:
-        print("% mapped reads",
-            100 * \
-            res_map.to_pandas()['count'].fillna(0).sum() / \
-            int(res.select(pl.sum("count")).to_pandas()['count'])
+        print(
+            "% mapped reads",
+            100 * res_map['count'].sum() / res["count"].sum()
         )
     
     if return_type == 'unmapped':
@@ -221,8 +220,8 @@ def map_to_library_dual_guide(df_count, library, get_recombinant=False, return_t
     if verbose:
         print("% mapped reads",
             100 * \
-            res_map.to_pandas()['count'].fillna(0).sum() / \
-            int(res.select(pl.sum("count")).to_pandas()['count'])
+            res_map['count'].sum() / \
+            res["count"].sum()
         )
     
     if get_recombinant:
@@ -230,8 +229,8 @@ def map_to_library_dual_guide(df_count, library, get_recombinant=False, return_t
         if verbose:
             print("% unmapped reads",
                 100 * \
-                res_unmap.to_pandas()['count'].fillna(0).sum() / \
-                int(res.select(pl.sum("count")).to_pandas()['count'])
+                res_unmap['count'].sum() / \
+                res["count"].sum()
             )
         
         sgRNA_table = pd.concat([
@@ -253,8 +252,8 @@ def map_to_library_dual_guide(df_count, library, get_recombinant=False, return_t
         if verbose:
             print("% fully remapped recombination events",
                 100 * \
-                res_recomb_events.drop_nulls().to_pandas()['count'].fillna(0).sum() / \
-                int(res.select(pl.sum("count")).to_pandas()['count'])
+                res_recomb_events.drop_nulls()['count'].sum() / \
+                res['count'].sum()
             )
     
     if return_type == 'unmapped':