upgrade github actions (#24)

* changes resulting from upgrading black formatter

* change setup-python@v4 to setup-python@v5

* update upload-artifact@v4 and download-artifact@v4 to v5

* update changelog

Author: bmx8177

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -27,7 +27,7 @@ jobs:
       run: |
         python -m build --sdist --wheel .
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -47,7 +47,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/

crema/__init__.py

@@ -1,4 +1,5 @@
 """Initialize the crema package."""
+
 try:
     from importlib.metadata import version, PackageNotFoundError
 

crema/confidence.py

@@ -1,6 +1,7 @@
 """The :py:class:`Confidence` class is used to define a collection of
 peptide-spectrum matches with calculated false discovery rates (FDR) and q-values.
 """
+
 import logging
 import numpy as np
 import pandas as pd

crema/crema.py

@@ -1,6 +1,7 @@
 """
 This is the command line interface for crema
 """
+
 import os
 import sys
 import time

crema/dataset.py

@@ -1,6 +1,7 @@
 """The :py:class:`PsmDataset` class is used to define a collection of
 peptide-spectrum matches.
 """
+
 import logging
 
 from .confidence import TdcConfidence

crema/params.py

@@ -1,6 +1,7 @@
 """The :py:class:`Params` class is used to define the details and arguments
 necessary for running crema from the command line.
 """
+
 import argparse
 import textwrap
 from . import __version__

crema/parsers/comet.py

@@ -1,4 +1,5 @@
 """A parser for Comet output"""
+
 import re
 import logging
 

crema/parsers/msamanda.py

@@ -1,4 +1,5 @@
 """A parser for the MSAmanda tab-delimited format"""
+
 import re
 import logging
 

crema/parsers/msfragger.py

@@ -1,4 +1,5 @@
 """A parser for the MSFragger tab-delimited format"""
+
 import re
 import logging
 

crema/parsers/msgf.py

@@ -1,4 +1,5 @@
 """A parser for the MSGF+ tab-delimited format"""
+
 import re
 import logging
 

crema/parsers/mztab.py

@@ -1,4 +1,5 @@
 """This module contains the parser for PSMs in mzTab format"""
+
 import logging
 
 import pandas as pd

crema/parsers/pepxml.py

@@ -2,6 +2,7 @@
 This module contains the parser for PSMs in pepXML format.
 This code is heavily based on Will Fondrie's Mokapot pepxml parser code
 """
+
 import logging
 from lxml import etree
 from functools import partial

crema/parsers/tide.py

@@ -1,4 +1,5 @@
 """A parser for the Tide tab-delimited format"""
+
 import re
 import logging
 

crema/parsers/txt.py

@@ -1,4 +1,5 @@
 """A parser for generic delmited text files."""
+
 import logging
 
 import pandas as pd

crema/qvalues.py

@@ -1,6 +1,7 @@
 """
 This module estimates q-values.
 """
+
 import logging
 
 import numpy as np

crema/utils.py

@@ -1,4 +1,5 @@
 """Utility functions that are used in multiple modules"""
+
 import pandas as pd
 import logging
 

crema/writers/txt.py

@@ -1,4 +1,5 @@
 """Writer to save results in a tab-delmited format"""
+
 from pathlib import Path
 from collections import defaultdict
 

docs/CHANGELOG.md

@@ -3,7 +3,8 @@
 ## [Unreleased]
 ### Fixed
 
-## [0.0.10] - 2024-02-01
+## [0.0.10] - 2024-02-21
+- Upgraded Github action versions
 - Updated CLI documentation
 - Removed protein field requirement from create\_pairing\_from\_file function
 

setup.py

@@ -1,6 +1,7 @@
 """
 Setup the crema package.
 """
+
 import setuptools
 
 setuptools.setup()

tests/conftest.py

@@ -1,4 +1,5 @@
 """Fixtures that are used in multiple tests"""
+
 from pathlib import Path
 
 import pytest

tests/system_tests/test_cli.py

@@ -1,4 +1,5 @@
 """These tests verify that the crema CLI works as expected."""
+
 from pathlib import Path
 import subprocess
 

tests/system_tests/test_crux_tdc.py

@@ -1,4 +1,5 @@
 """These tests verify that confidence estimates are correctly produced via tdc through various parsers"""
+
 import unittest
 
 import numpy as np

tests/unit_tests/test_confidence.py

@@ -1,6 +1,7 @@
 """
 These tests verify the confidence implementations function as expected
 """
+
 import pytest
 import numpy as np
 

tests/unit_tests/test_dataset.py

@@ -1,6 +1,7 @@
 """
 These are unit tests for the PSM Dataset Class:
 """
+
 import pytest
 import numpy as np
 import pandas as pd

tests/unit_tests/test_parsers.py

@@ -1,6 +1,7 @@
 """
 These are unit tests for functions within parsers.py:
 """
+
 import pytest
 import pandas as pd
 

tests/unit_tests/test_qvalues.py

@@ -1,6 +1,7 @@
 """
 These tests verify that our q-value calculations are correct.
 """
+
 import logging
 
 import pytest