ms2rescore 3.2.0.dev1__tar.gz → 3.2.0.dev2__tar.gz

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: ms2rescore
-Version: 3.2.0.dev1
+Version: 3.2.0.dev2
 Summary:  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications.
 Keywords: MS2Rescore,MS2PIP,DeepLC,Percolator,proteomics,mass spectrometry,peptide identification,rescoring,machine learning
 Author: Ana Sílvia C. Silva, Robbin Bouwmeester, Louise Buur
@@ -13,12 +13,13 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Development Status :: 5 - Production/Stable
+License-File: LICENSE
 Requires-Dist: cascade-config>=0.4.0
 Requires-Dist: click>=7
 Requires-Dist: customtkinter>=5,<6
 Requires-Dist: deeplc>=3.0,<3.1
 Requires-Dist: deeplcretrainer
-Requires-Dist: im2deep>=0.1.3
+Requires-Dist: im2deep>=0.3.1
 Requires-Dist: jinja2>=3
 Requires-Dist: lxml>=4.5
 Requires-Dist: mokapot==0.10
@@ -104,7 +105,7 @@ DDA-PASEF data from timsTOF instruments. TIMS²Rescore makes use of new MS²PIP
 timsTOF fragmentation and IM2Deep for ion mobility separation. Bruker .d and miniTDF spectrum
 files are directly supported through the [timsrust](https://github.com/MannLabs/timsrust) library.
 
-Checkout our [preprint](https://doi.org/10.1101/2024.05.29.596400) for more information and the
+Checkout our [paper](https://doi.org/10.1021/acs.jproteome.4c00609) for more information and the
 [TIMS²Rescore documentation][tims2rescore] to get started.
 
 ## Citing
@@ -125,7 +126,7 @@ Checkout our [preprint](https://doi.org/10.1101/2024.05.29.596400) for more info
 
 > **TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore.**
 > Arthur Declercq*, Robbe Devreese*, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R Krieger, Tharan Srikumar, George Rosenberger, Dennis Trede, Christine Carapito, Stefan Tenzer, Juliane S Walz, Sven Degroeve, Robbin Bouwmeester, Lennart Martens, and Ralf Gabriels.
-> _bioRxiv_ (2024) [doi:10.1101/2024.05.29.596400](https://doi.org/10.1101/2024.05.29.596400) <span class="__dimensions_badge_embed__" data-doi="10.1101/2024.05.29.596400" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+> _Journal of Proteome Research_ (2025) [doi:10.1021/acs.jproteome.4c00609](https://doi.org/10.1021/acs.jproteome.4c00609) <span class="__dimensions_badge_embed__" data-doi="10.1021/acs.jproteome.4c00609" data-hide-zero-citations="true" data-style="small_rectangle"></span>
 
 **Original publication describing the concept of rescoring with predicted spectra:**
 

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/README.md

@@ -46,7 +46,7 @@ DDA-PASEF data from timsTOF instruments. TIMS²Rescore makes use of new MS²PIP
 timsTOF fragmentation and IM2Deep for ion mobility separation. Bruker .d and miniTDF spectrum
 files are directly supported through the [timsrust](https://github.com/MannLabs/timsrust) library.
 
-Checkout our [preprint](https://doi.org/10.1101/2024.05.29.596400) for more information and the
+Checkout our [paper](https://doi.org/10.1021/acs.jproteome.4c00609) for more information and the
 [TIMS²Rescore documentation][tims2rescore] to get started.
 
 ## Citing
@@ -67,7 +67,7 @@ Checkout our [preprint](https://doi.org/10.1101/2024.05.29.596400) for more info
 
 > **TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore.**
 > Arthur Declercq*, Robbe Devreese*, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R Krieger, Tharan Srikumar, George Rosenberger, Dennis Trede, Christine Carapito, Stefan Tenzer, Juliane S Walz, Sven Degroeve, Robbin Bouwmeester, Lennart Martens, and Ralf Gabriels.
-> _bioRxiv_ (2024) [doi:10.1101/2024.05.29.596400](https://doi.org/10.1101/2024.05.29.596400) <span class="__dimensions_badge_embed__" data-doi="10.1101/2024.05.29.596400" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+> _Journal of Proteome Research_ (2025) [doi:10.1021/acs.jproteome.4c00609](https://doi.org/10.1021/acs.jproteome.4c00609) <span class="__dimensions_badge_embed__" data-doi="10.1021/acs.jproteome.4c00609" data-hide-zero-citations="true" data-style="small_rectangle"></span>
 
 **Original publication describing the concept of rescoring with predicted spectra:**
 

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/ms2rescore/__init__.py

@@ -1,6 +1,10 @@
-"""MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""
+"""Modular and user-friendly platform for AI-assisted rescoring of peptide identifications ."""
 
-__version__ = "3.2.0.dev1"
+__version__ = "3.2.0.dev2"
+__all__ = [
+    "parse_configurations",
+    "rescore",
+]
 
 from warnings import filterwarnings
 
@@ -12,5 +16,5 @@ filterwarnings(
     module="psims.mzmlb",
 )
 
-from ms2rescore.config_parser import parse_configurations  # noqa: F401 E402
-from ms2rescore.core import rescore  # noqa: F401 E402
+from ms2rescore.config_parser import parse_configurations  # noqa: E402
+from ms2rescore.core import rescore  # noqa: E402

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/ms2rescore/feature_generators/ms2pip.py

@@ -25,6 +25,7 @@ If you use MS²PIP through MS²Rescore, please cite:
 
 import logging
 import multiprocessing
+import os
 import warnings
 from itertools import chain
 from typing import List, Optional, Union
@@ -194,6 +195,7 @@ class MS2PIPFeatureGenerator(FeatureGeneratorBase):
                 spectrum_filename = infer_spectrum_path(self.spectrum_path, run)
                 logger.debug(f"Using spectrum file `{spectrum_filename}`")
                 try:
+                    os.environ.pop("CUDA_VISIBLE_DEVICES", None)
                     ms2pip_results = correlate(
                         psms=psm_list_run,
                         spectrum_file=str(spectrum_filename),

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/ms2rescore/gui/app.py

@@ -50,6 +50,10 @@ CITATIONS = [
         "MS²PIP: Declercq et al. NAR (2023)",
         "https://doi.org/10.1093/nar/gkad335",
     ),
+    (
+        "IM2Deep: Declercq, Devreese et al. JPR (2025)",
+        "https://doi.org/10.1021/acs.jproteome.4c00609",
+    ),
     (
         "DeepLC: Bouwmeester et al. Nat Methods (2021)",
         "https://doi.org/10.1038/s41592-021-01301-5",

{ms2rescore-3.2.0.dev1 → ms2rescore-3.2.0.dev2}/pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "customtkinter>=5,<6",
     "deeplc>=3.0,<3.1",
     "deeplcretrainer",
-    "im2deep>=0.1.3",
+    "im2deep>=0.3.1",
     "jinja2>=3",
     "lxml>=4.5",
     "mokapot==0.10",  # 0.11.0 will introduce API changes