Feature: fix log formatting issues

.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

.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
-

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():

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,
             )

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"
@@ -43,23 +52,14 @@
 ]
 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()
 
 to_remove = [
     "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(