Merge pull request #4 from bigbio/dev

pyquantms -> quantms-utils

README.md

@@ -1,15 +1,15 @@
-# pyquantms
-[![Python application](https://github.com/bigbio/pyquantms/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/pyquantms/actions/workflows/python-app.yml)
-[![Python package](https://github.com/bigbio/pyquantms/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/pyquantms/actions/workflows/python-package.yml)
-[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/pyquantms/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
-[![PyPI version](https://badge.fury.io/py/pyquantms.svg)](https://badge.fury.io/py/pyquantms)
+# quantms-utils
+[![Python application](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml)
+[![Python package](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/quantms-utils/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![PyPI version](https://badge.fury.io/py/quantms-utils.svg)](https://badge.fury.io/py/quantms-utils)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
 
-The package is available on PyPI: [pyquantms](https://pypi.org/project/pyquantms/)
+The package is available on PyPI: [quantms-utils](https://pypi.org/project/quantms-utils/)
 ```
-pip install pyquantms
+pip install quantms-utils
 ```
 
 ## Available Scripts 
@@ -24,7 +24,7 @@ The following functionalities are available in the package:
 
 ### SDRF scripts
 
-- `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/pyquantms/blob/dev/tests/test_data/BSA_design_urls.tsv).
+- `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/quantms-utils/blob/dev/tests/test_data/BSA_design_urls.tsv).
 - `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file. 
 
 ### ms2rescore scripts
@@ -42,4 +42,4 @@ The following functionalities are available in the package:
 
 ## Contributions and issues
 
-Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/pyquantms).
+Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/quantms-utils).

quantmsutils/quantmsutilsc.py

@@ -0,0 +1,35 @@
+import click
+
+from quantmsutils.diann.dianncfg import dianncfg
+from quantmsutils.diann.diann2mztab import diann2mztab
+from quantmsutils.features.sage_feature import add_sage_feature
+from quantmsutils.rescoring.ms2rescore import ms2rescore
+from quantmsutils.mzml.mzml_statistics import mzml_statistics
+from quantmsutils.psm.psm_conversion import convert_psm
+from quantmsutils.sdrf.check_samplesheet import check_samplesheet
+from quantmsutils.sdrf.extract_sample import extract_sample_from_expdesign
+
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    pass
+
+
+cli.add_command(dianncfg)
+cli.add_command(diann2mztab)
+
+cli.add_command(add_sage_feature)
+
+cli.add_command(mzml_statistics)
+
+cli.add_command(extract_sample_from_expdesign)
+cli.add_command(check_samplesheet)
+
+cli.add_command(ms2rescore)
+
+cli.add_command(convert_psm)
+
+if __name__ == "__main__":
+    cli()

pyquantms/rescoring/ms2rescore.py → quantmsutils/rescoring/ms2rescore.py

@@ -1,6 +1,6 @@
 # Written by Jonas Scheid under the MIT license
 # Contributions by Yasset Perez-Riverol and Dai Chengxin
-# This script is part of the pyquantms package
+# This script is part of the quantmsutils package
 
 import click
 import importlib.resources

setup.py

@@ -2,7 +2,7 @@
 
 VERSION = "0.0.1"
 
-NAME = "pyquantms"
+NAME = "quantms-utils"
 LICENSE = "MIT License"
 DESCRIPTION = "Python package with scripts and helpers for the QuantMS workflow"
 AUTHOR = "Yasset Perez-Riverol, Dai Chengxin"
@@ -58,7 +58,7 @@
     packages=find_packages(),
     include_package_data=True,
     entry_points={
-        "console_scripts": ["pyquantmsc=pyquantms.pyquantmsc:main"]
+        "console_scripts": ["pyquantmsc=quantmsutils.pyquantmsc:main"]
     },
     install_requires=INSTALL_REQUIRES,
     python_requires=PYTHON_REQUIRES,

tests/test_commands.py

@@ -1,5 +1,5 @@
 from click.testing import CliRunner
-from pyquantms.pyquantmsc import cli
+from quantmsutils.quantmsutilsc import cli
 
 
 # test for the create_diann_cfg command in cli