Merge branch 'master' into quant

.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

@@ -23,8 +23,16 @@
   `importlib.metadata` to the standard library, saving a few hundred
   milliseconds.
 
-## [0.6.1] - 2021-03-11  
+## [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.
 - `Label` column is now converted to boolean during PIN file parsing. 
   Previously, problems occurred if the `Label` column was of dtype `object`.

mokapot/confidence.py

@@ -461,7 +461,6 @@ 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

@@ -207,7 +207,6 @@ def read_percolator(perc_file):
 
         psms = pd.concat((c for c in _parse_in_chunks(perc, cols)), copy=False)
 
-    print(psms.head())
     return psms