ms2pip - npm Package Compare versions

Comparing version 4.1.1 to 4.1.2

ms2pip.egg-info/PKG-INFO

 Metadata-Version: 2.4
 Name: ms2pip
-Version: 4.1.1
+Version: 4.1.2
 Summary: MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction.
@@ -5,0 +5,0 @@ Author: Sven Degroeve, Ana Sílvia C. Silva

ms2pip/__init__.py

 # isort: skip_file
 """MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction."""
 
-__version__ = "4.1.1"
+__version__ = "4.1.2"
 
@@ -6,0 +6,0 @@ from warnings import filterwarnings

ms2pip/__main__.py

@@ -7,4 +7,4 @@ import logging
 import click
+import rich
 from psm_utils.io import READERS
-from rich.console import Console
 from rich.logging import RichHandler
@@ -21,3 +21,2 @@ from werkzeug.utils import secure_filename
 
-console = Console()
 logger = logging.getLogger(__name__)
@@ -57,6 +56,6 @@
         handlers=[
-            RichHandler(rich_tracebacks=True, console=console, show_level=True, show_path=False)
+            RichHandler(rich_tracebacks=True, show_level=True, show_path=False)
         ],
     )
-    console.print(build_credits())
+    rich.print(build_credits())
 
@@ -84,3 +83,3 @@
     # Write output
-    console.print(build_prediction_table(predicted_spectrum))
+    rich.print(build_prediction_table(predicted_spectrum))
     write_spectra(output_name, [result], output_format)
@@ -87,0 +86,0 @@ if plot:

ms2pip/_utils/xgb_models.py

@@ -99,3 +99,7 @@ """Utilities for handling XGBoost model files within the MS²PIP prediction framework."""
     logger.info(f"Downloading {model} to {filename}...")
-    urllib.request.urlretrieve(f"https://zenodo.org/records/13270668/files/{model}", filename)
+    try:
+        urllib.request.urlretrieve(f"https://genesis.ugent.be/uvpublicdata/ms2pip/{model}", filename)
+    except Exception:
+        logger.warning("Falling back to Zenodo for model downloads.")
+        urllib.request.urlretrieve(f"https://zenodo.org/records/13270668/files/{model}", filename)
     if not _check_model_integrity(filename, model_hash):
@@ -102,0 +106,0 @@ raise InvalidXGBoostModelError()

ms2pip/core.py

@@ -199,3 +199,2 @@ #!/usr/bin/env python
     ):
-        logging.disable(logging.CRITICAL)
         yield predict_batch(
@@ -209,3 +208,2 @@ search_space.filter_psms_by_mz(PSMList(psm_list=list(batch))),
         )
-        logging.disable(logging.NOTSET)
 
@@ -212,0 +210,0 @@

PKG-INFO

 Metadata-Version: 2.4
 Name: ms2pip
-Version: 4.1.1
+Version: 4.1.2
 Summary: MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction.
@@ -5,0 +5,0 @@ Author: Sven Degroeve, Ana Sílvia C. Silva

pyproject.toml

@@ -97,5 +97,5 @@ [project]
 # Prevent building from source for packages with complex C/C++ dependencies
-environment = { PIP_ONLY_BINARY = "pyarrow,pandas,numpy,lxml,xgboost" }
+environment = { PIP_ONLY_BINARY = "pyarrow,pandas,numpy,lxml,xgboost,scipy" }
 
 [tool.cibuildwheel.macos]
 before-all = "brew install libomp"

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