From 57bfade587ee8f3fdc2a8d3ff6d3e256db2d6722 Mon Sep 17 00:00:00 2001
From: Andy <22140743+bmx8177@users.noreply.github.com>
Date: Wed, 21 Feb 2024 21:40:09 -0800
Subject: [PATCH] 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
---
 .github/workflows/publish.yml       | 6 +++---
 crema/__init__.py                   | 1 +
 crema/confidence.py                 | 1 +
 crema/crema.py                      | 1 +
 crema/dataset.py                    | 1 +
 crema/params.py                     | 1 +
 crema/parsers/comet.py              | 1 +
 crema/parsers/msamanda.py           | 1 +
 crema/parsers/msfragger.py          | 1 +
 crema/parsers/msgf.py               | 1 +
 crema/parsers/mztab.py              | 1 +
 crema/parsers/pepxml.py             | 1 +
 crema/parsers/tide.py               | 1 +
 crema/parsers/txt.py                | 1 +
 crema/qvalues.py                    | 1 +
 crema/utils.py                      | 1 +
 crema/writers/txt.py                | 1 +
 docs/CHANGELOG.md                   | 3 ++-
 setup.py                            | 1 +
 tests/conftest.py                   | 1 +
 tests/system_tests/test_cli.py      | 1 +
 tests/system_tests/test_crux_tdc.py | 1 +
 tests/unit_tests/test_confidence.py | 1 +
 tests/unit_tests/test_dataset.py    | 1 +
 tests/unit_tests/test_parsers.py    | 1 +
 tests/unit_tests/test_qvalues.py    | 1 +
 26 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 226f246..9b37b5b 100644
--- a/.github/workflows/publish.yml
+++ b/.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/
diff --git a/crema/__init__.py b/crema/__init__.py
index cdcccf3..1acd42f 100644
--- a/crema/__init__.py
+++ b/crema/__init__.py
@@ -1,4 +1,5 @@
 """Initialize the crema package."""
+
 try:
     from importlib.metadata import version, PackageNotFoundError
 
diff --git a/crema/confidence.py b/crema/confidence.py
index a583698..cc45d9f 100644
--- a/crema/confidence.py
+++ b/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
diff --git a/crema/crema.py b/crema/crema.py
index 3071bcd..60b1116 100644
--- a/crema/crema.py
+++ b/crema/crema.py
@@ -1,6 +1,7 @@
 """
 This is the command line interface for crema
 """
+
 import os
 import sys
 import time
diff --git a/crema/dataset.py b/crema/dataset.py
index 42bd7bc..da89481 100644
--- a/crema/dataset.py
+++ b/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
diff --git a/crema/params.py b/crema/params.py
index 23bd83e..b209de0 100644
--- a/crema/params.py
+++ b/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__
diff --git a/crema/parsers/comet.py b/crema/parsers/comet.py
index e532015..86f59c5 100644
--- a/crema/parsers/comet.py
+++ b/crema/parsers/comet.py
@@ -1,4 +1,5 @@
 """A parser for Comet output"""
+
 import re
 import logging
 
diff --git a/crema/parsers/msamanda.py b/crema/parsers/msamanda.py
index dfe6d83..8e01c0f 100644
--- a/crema/parsers/msamanda.py
+++ b/crema/parsers/msamanda.py
@@ -1,4 +1,5 @@
 """A parser for the MSAmanda tab-delimited format"""
+
 import re
 import logging
 
diff --git a/crema/parsers/msfragger.py b/crema/parsers/msfragger.py
index 9cc6f0d..17b8af4 100644
--- a/crema/parsers/msfragger.py
+++ b/crema/parsers/msfragger.py
@@ -1,4 +1,5 @@
 """A parser for the MSFragger tab-delimited format"""
+
 import re
 import logging
 
diff --git a/crema/parsers/msgf.py b/crema/parsers/msgf.py
index 5f3bc7d..d848003 100644
--- a/crema/parsers/msgf.py
+++ b/crema/parsers/msgf.py
@@ -1,4 +1,5 @@
 """A parser for the MSGF+ tab-delimited format"""
+
 import re
 import logging
 
diff --git a/crema/parsers/mztab.py b/crema/parsers/mztab.py
index 4a72c5d..2810081 100644
--- a/crema/parsers/mztab.py
+++ b/crema/parsers/mztab.py
@@ -1,4 +1,5 @@
 """This module contains the parser for PSMs in mzTab format"""
+
 import logging
 
 import pandas as pd
diff --git a/crema/parsers/pepxml.py b/crema/parsers/pepxml.py
index 742b3ee..fbac909 100644
--- a/crema/parsers/pepxml.py
+++ b/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
diff --git a/crema/parsers/tide.py b/crema/parsers/tide.py
index 18fd330..2dd3345 100644
--- a/crema/parsers/tide.py
+++ b/crema/parsers/tide.py
@@ -1,4 +1,5 @@
 """A parser for the Tide tab-delimited format"""
+
 import re
 import logging
 
diff --git a/crema/parsers/txt.py b/crema/parsers/txt.py
index 40bc6b4..4631afd 100644
--- a/crema/parsers/txt.py
+++ b/crema/parsers/txt.py
@@ -1,4 +1,5 @@
 """A parser for generic delmited text files."""
+
 import logging
 
 import pandas as pd
diff --git a/crema/qvalues.py b/crema/qvalues.py
index d17742a..8421d72 100644
--- a/crema/qvalues.py
+++ b/crema/qvalues.py
@@ -1,6 +1,7 @@
 """
 This module estimates q-values.
 """
+
 import logging
 
 import numpy as np
diff --git a/crema/utils.py b/crema/utils.py
index bd0ef98..9f4f12a 100644
--- a/crema/utils.py
+++ b/crema/utils.py
@@ -1,4 +1,5 @@
 """Utility functions that are used in multiple modules"""
+
 import pandas as pd
 import logging
 
diff --git a/crema/writers/txt.py b/crema/writers/txt.py
index 778e5a1..5eedfab 100644
--- a/crema/writers/txt.py
+++ b/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
 
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index a4ea9c3..b994b52 100644
--- a/docs/CHANGELOG.md
+++ b/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
 
diff --git a/setup.py b/setup.py
index 2865e37..77793d5 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,7 @@
 """
 Setup the crema package.
 """
+
 import setuptools
 
 setuptools.setup()
diff --git a/tests/conftest.py b/tests/conftest.py
index f4bd26e..d8088a8 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,5 @@
 """Fixtures that are used in multiple tests"""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/system_tests/test_cli.py b/tests/system_tests/test_cli.py
index 64f29f5..a0424cc 100644
--- a/tests/system_tests/test_cli.py
+++ b/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
 
diff --git a/tests/system_tests/test_crux_tdc.py b/tests/system_tests/test_crux_tdc.py
index aed05c2..8d891c8 100644
--- a/tests/system_tests/test_crux_tdc.py
+++ b/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
diff --git a/tests/unit_tests/test_confidence.py b/tests/unit_tests/test_confidence.py
index d7e83ff..c25b986 100644
--- a/tests/unit_tests/test_confidence.py
+++ b/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
 
diff --git a/tests/unit_tests/test_dataset.py b/tests/unit_tests/test_dataset.py
index 8bbe274..b3ccc33 100644
--- a/tests/unit_tests/test_dataset.py
+++ b/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
diff --git a/tests/unit_tests/test_parsers.py b/tests/unit_tests/test_parsers.py
index 5968b62..d8db01e 100644
--- a/tests/unit_tests/test_parsers.py
+++ b/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
 
diff --git a/tests/unit_tests/test_qvalues.py b/tests/unit_tests/test_qvalues.py
index e63d41d..0d631bb 100644
--- a/tests/unit_tests/test_qvalues.py
+++ b/tests/unit_tests/test_qvalues.py
@@ -1,6 +1,7 @@
 """
 These tests verify that our q-value calculations are correct.
 """
+
 import logging
 
 import pytest