moved duplicate code in testing files to common import

pepmatch/tests/test_discontinuous_search.py

@@ -1,18 +1,11 @@
 #!/usr/bin/env python3
 
-import pytest
 import pandas as pd
 import pandas.testing as pdt
-from pathlib import Path
-
+from common_features import *
 from pepmatch import Matcher
 
 
-@pytest.fixture
-def proteome_path() -> Path:
-  return Path(__file__).parent / 'data' / 'proteome.fasta'
-
-
 @pytest.fixture
 def expected_path() -> Path:
   return Path(__file__).parent / 'data' / 'discontinuous_expected.csv'

pepmatch/tests/test_mismatching.py

@@ -1,29 +1,12 @@
 #!/usr/bin/env python3
 
 import os
-import pytest
 import pandas as pd
 import pandas.testing as pdt
-from pathlib import Path
-
+from common_features import *
 from pepmatch import Preprocessor, Matcher
 
 
-@pytest.fixture
-def proteome_path() -> Path:
-  return Path(__file__).parent / 'data' / 'proteome.fasta'
-
-
-@pytest.fixture
-def query_path() -> Path:
-  return Path(__file__).parent / 'data' / 'mismatching_query.fasta'
-
-
-@pytest.fixture
-def expected_path() -> Path:
-  return Path(__file__).parent / 'data' / 'mismatching_expected.csv'
-
-
 def test_mismatching(proteome_path, query_path, expected_path):
   """Test mismatching of query peptides to a proteome. The query is various peptides
   with different mismatches searched in the Dugbe virus proteome (isolate ArD44313)."""

pepmatch/tests/test_ouptput_files.py

@@ -9,7 +9,7 @@
 from pepmatch.matcher import VALID_OUTPUT_FORMATS
 
 @pytest.fixture
-def match(proteome_path, query_path, expected_path):
+def match(proteome_path, query_path):
     return Matcher(
             query=query_path,
             proteome_file=proteome_path,
@@ -18,6 +18,8 @@ def match(proteome_path, query_path, expected_path):
             output_format='csv'
         )
 
+
+# fixtures and supporting
 @pytest.fixture
 def simple_dataframe():
     return DF(data={"col1" : [1, 2], "col2": [3, 4]})
@@ -29,7 +31,10 @@ def _creation_calls(_matcher, _path, _df):
     _matcher.output_name = _path
     _matcher._output_matches(_df)
 
+
+# Actual tests
 def test_local_creation(match, simple_dataframe):
+    """Test creation given the local path"""
     local_location = Path("local_result.csv")
 
     _creation_calls(match, local_location, simple_dataframe)
@@ -39,6 +44,7 @@ def test_local_creation(match, simple_dataframe):
 
 
 def test_relative_creation(match, simple_dataframe):
+    """Tests for creation given a relative path"""
     relative_location = Path(f"../PEPMatch/relative.csv")
 
     _creation_calls(match, relative_location, simple_dataframe)
@@ -48,16 +54,19 @@ def test_relative_creation(match, simple_dataframe):
 
 
 def test_absolute_creation(match, simple_dataframe):
+    """Tests creation given an absolute path"""
     absolute_location = Path("absolute.csv").absolute()
 
     _creation_calls(match, absolute_location, simple_dataframe)
 
     assert absolute_location.exists()
     remove(absolute_location.__str__())
 
-def test_type_creation(match, simple_dataframe):
 
-    # tests .csv, .tsv, and xlsx
+def test_type_creation(match, simple_dataframe):
+    """Tests Matcher's ability to convert all supported types
+    into the expected file's output and format
+    """
     for accepted_type in VALID_OUTPUT_FORMATS[1:]:
         location = Path(f"test_output.{accepted_type}")
         if location.exists():

pepmatch/tests/test_parallel_match.py

@@ -1,28 +1,11 @@
 #!/usr/bin/env python3
 
 import os
-import pytest
 import pandas as pd
 import pandas.testing as pdt
-from pathlib import Path
-
+from common_features import *
 from pepmatch import Preprocessor, ParallelMatcher
 
-
-@pytest.fixture
-def proteome_path() -> Path:
-  return Path(__file__).parent / 'data' / 'proteome.fasta'
-
-
-@pytest.fixture
-def query_path() -> Path:
-  return Path(__file__).parent / 'data' / 'mismatching_query.fasta'
-
-
-@pytest.fixture
-def expected_path() -> Path:
-  return Path(__file__).parent / 'data' / 'mismatching_expected.csv'
-
 
 def test_mismatching(proteome_path, query_path, expected_path):
   """Test mismatching of query peptides to a proteome. The query is various peptides