From 1c0c978d44f13101e44759cecc57474b1d336ac2 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 3 Dec 2024 11:33:17 +0000 Subject: [PATCH 1/2] second biggest commit. --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9678ee8..0869e0b 100644 --- a/README.md +++ b/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 From e52fbf10892f87ef737bb7df62c23260329c5a7a Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 3 Dec 2024 12:01:20 +0000 Subject: [PATCH 2/2] second biggest commit. --- .github/workflows/python-app.yml | 2 +- .github/workflows/python-package.yml | 2 +- pyproject.toml | 2 +- recipe/meta.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 9f25049..851a0a4 100644 --- a/.github/workflows/python-app.yml +++ b/.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 diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2249c2d..c626044 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -43,4 +43,4 @@ jobs: pytest - name: Test commandline tool run: | - quantmsutilsc --help + rescoring --help diff --git a/pyproject.toml b/pyproject.toml index 616d62e..e9abe97 100644 --- a/pyproject.toml +++ b/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" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 1e044cd..de8543f 100644 --- a/recipe/meta.yaml +++ b/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