Merge pull request #1 from bigbio/dev

second biggest commit.

.github/workflows/python-app.yml

@@ -46,4 +46,4 @@ jobs:
         wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML
     - name: Test percolator ms2rescore
       run: |
-        quantmsutilsc ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05
+        rescoring ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05

.github/workflows/python-package.yml

@@ -43,4 +43,4 @@ jobs:
         pytest
     - name: Test commandline tool
       run: |
-        quantmsutilsc --help
+        rescoring --help

README.md

@@ -1,4 +1,10 @@
 # quantms-rescoring
+
+[![Build Status](https://travis-ci.com/compomics/quantms-rescoring.svg?branch=main)](https://travis-ci.com/compomics/quantms-rescoring)
+[![codecov](https://codecov.io/gh/compomics/quantms-rescoring/branch/main/graph/badge.svg?token=3ZQZQ2ZQ2D)](https://codecov.io/gh/compomics/quantms-rescoring)
+[![PyPI version](https://badge.fury.io/py/quantms-rescoring.svg)](https://badge.fury.io/py/quantms-rescoring)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
 quantms-rescoring is a Python tool for rescoring peptide-spectrum matches (PSMs) in idXML files. It is part of the quantms ecosystem package and leverages the MS²Rescore framework to improve identification confidence in proteomics data analysis.
 
 ## Features
@@ -10,7 +16,8 @@ quantms-rescoring is a Python tool for rescoring peptide-spectrum matches (PSMs)
 - Seamless Integration: Built to integrate into proteomics workflows.
 
 ## Installation
-To use quantms-ms2rescore, ensure the following dependencies are installed:
+
+To use quantms-rescoring, ensure the following dependencies are installed:
 
 - Python 3.8+
 - click

pyproject.toml

@@ -48,7 +48,7 @@ Quantms = "https://quantms.org"
 LICENSE = "https://github.com/bigbio/quantms-rescoring/blob/main/LICENSE"
 
 [tool.poetry.scripts]
-quantmsutilsc = "quantmsrescore.rescoring:main"
+rescoring = "quantmsrescore.rescoring:main"
 
 [tool.isort]
 profile = "black"

recipe/meta.yaml

@@ -10,7 +10,7 @@ build:
   entry_points:
     - rescoring=quantmsrescore.rescoring:main
   run_exports:
-    - {{ pin_subpackage('quantms-utils', max_pin="x.x") }}
+    - {{ pin_subpackage('quantms-rescoring', max_pin="x.x") }}
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   number: 0
   noarch: python