Merge pull request #21 from wfondrie/rm_print

Check for debugging print statements

.github/workflows/black.yml

@@ -7,5 +7,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+
+      - name: Run black
+        uses: psf/black@stable
+
+      - name: Check for debugging print statements
+        run: |
+          if grep -rq "print(" mokapot; then
+              echo "Found the following print statements:"
+              grep -r "print(" mokapot
+              exit 1
+          fi

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog for mokapot  
 
+## [0.6.2] - 2021-03-12  
+### Added
+- Now checks to verify there are no debugging print statements in the code
+  base when linting.
+
+### Fixed  
+- Removed debugging print statements.
+
 ## [0.6.1] - 2021-03-11
 ### Fixed
 - Parsing Percolator tab-delimited files with a "DefaultDirection" line.

mokapot/confidence.py

@@ -453,7 +453,6 @@ def _assign_confidence(self, desc=True):
                     scores[targets], scores[~targets], includeDecoys=True
                 )
             except SystemExit as msg:
-                print(msg)
                 if "no decoy hits available for PEP calculation" in str(msg):
                     pep = 0
                 else:

mokapot/parsers/pin.py

@@ -87,14 +87,12 @@ def read_pin(pin_files, group_column=None, to_df=False, copy_data=False):
             raise ValueError(f"More than one '{name}' column found.")
 
     if not all([specid, peptides, proteins, labels, spectra]):
-        print([specid, peptides, proteins, labels, spectra])
         raise ValueError(
             "This PIN format is incompatible with mokapot. Please"
             " verify that the required columns are present."
         )
 
     # Convert labels to the correct format.
-    print(pin_df[labels[0]])
     pin_df[labels[0]] = pin_df[labels[0]].astype(int)
     if any(pin_df[labels[0]] == -1):
         pin_df[labels[0]] = ((pin_df[labels[0]] + 1) / 2).astype(bool)
@@ -148,7 +146,6 @@ def read_percolator(perc_file):
 
         psms = pd.concat((c for c in _parse_in_chunks(perc, cols)), copy=False)
 
-    print(psms.head())
     return psms