From b984a2cdcf1e021650dad56ee29b7ff58d21405d Mon Sep 17 00:00:00 2001
From: Ralf <RalfG@hotmail.be>
Date: Thu, 7 May 2020 23:42:21 +0200
Subject: [PATCH 1/2] Fix logging string formatting issues

---
 conversion_tools/maxquant_to_peprec.py |  2 +-
 ms2pip/ms2pipC.py                      |  6 +++---
 setup.py                               | 22 +++++++++++-----------
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/conversion_tools/maxquant_to_peprec.py b/conversion_tools/maxquant_to_peprec.py
index 5393bcf3..9162cb09 100644
--- a/conversion_tools/maxquant_to_peprec.py
+++ b/conversion_tools/maxquant_to_peprec.py
@@ -149,7 +149,7 @@ def scan_mgf(peprec, mgf_folder, filename_col='raw_file', scan_num_col='scan_num
                             found = False
                     if found and line[-4:] != '0.0\n':
                         out.write(line)
-    logging.info("{}/{} spectra found and written to new MGF file.".format(count, len(peprec)))
+    logging.info("%i/%i spectra found and written to new MGF file.", count, len(peprec))
 
 
 def ArgParse():
diff --git a/ms2pip/ms2pipC.py b/ms2pip/ms2pipC.py
index 7a7bf665..a66a5cfa 100644
--- a/ms2pip/ms2pipC.py
+++ b/ms2pip/ms2pipC.py
@@ -762,8 +762,8 @@ def run(self):
                         "{}_correlations.csv".format(self.output_filename), index=True
                     )
                     logger.info(
-                        "median correlations: %f",
-                        correlations.groupby("ion")["pearsonr"].median(),
+                        "median correlations: \n%s",
+                        str(correlations.groupby("ion")["pearsonr"].median()),
                     )
         elif self.match_spectra:
             results = self._process_peptides()
@@ -822,7 +822,7 @@ def _read_peptide_information(self):
         num_pep_filtered = num_pep - len(data)
         if num_pep_filtered > 0:
             logger.info(
-                "Removed {} unsupported peptide sequences (< 3, > 99 \
+                "Removed %i unsupported peptide sequences (< 3, > 99 \
     amino acids, or containing B, J, O, U, X or Z).",
                 num_pep_filtered,
             )
diff --git a/setup.py b/setup.py
index 47929ce9..e1ff7787 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,13 @@
-VERSION = "3.6.1"
+import os
+from glob import glob
+
+from setuptools import setup
+from setuptools.extension import Extension
+from Cython.Distutils import build_ext
+import numpy
+
+
+VERSION = "3.6.2.dev"
 
 NAME = "ms2pip"
 LICENSE = "apache-2.0"
@@ -43,15 +52,6 @@
 ]
 PYTHON_REQUIRES = ">=3.6,<4"
 
-import os
-from glob import glob
-
-from setuptools import setup
-from setuptools.extension import Extension
-from Cython.Distutils import build_ext
-import numpy
-
-
 with open("README.md", "r") as fh:
     LONG_DESCRIPTION = fh.read()
 
@@ -59,7 +59,7 @@
     "ms2pip/cython_modules/ms2pip_pyx.c*",
     "ms2pip/cython_modules/ms2pip_pyx.so",
 ]
-_ = [[os.remove(f) for f in glob(pat)] for pat in to_remove]
+#_ = [[os.remove(f) for f in glob(pat)] for pat in to_remove]
 
 extensions = [
     Extension(

From 00cf360c9fd1641589f63021fba4884ff53d8f70 Mon Sep 17 00:00:00 2001
From: Ralf <RalfG@hotmail.be>
Date: Thu, 7 May 2020 23:44:03 +0200
Subject: [PATCH 2/2] Update upload-artifact action to v2

---
 .github/workflows/build_and_publish.yaml | 2 +-
 .github/workflows/test.yml               | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_and_publish.yaml b/.github/workflows/build_and_publish.yaml
index 81de795a..d1088e8c 100644
--- a/.github/workflows/build_and_publish.yaml
+++ b/.github/workflows/build_and_publish.yaml
@@ -49,7 +49,7 @@ jobs:
         twine upload wheelhouse/ms2pip*-manylinux1_x86_64.whl
         twine upload dist/*.tar.gz
 
-    - uses: actions/upload-artifact@v2-preview
+    - uses: actions/upload-artifact@v2
       with:
         name: wheels
         path: wheelhouse/ms2pip*-manylinux1_x86_64.whl
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a246e29d..9f30cf2e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -34,8 +34,7 @@ jobs:
     - name: Test with pytest
       run: |
         pytest
-    - uses: actions/upload-artifact@v2-preview
+    - uses: actions/upload-artifact@v2
       with:
         name: wheels
         path: dist/ms2pip*.whl
-  
\ No newline at end of file