tests: Use pytest.fixture for better readability

tests/test_utils.py

@@ -8,6 +8,7 @@
  from io import StringIO
 
 import pandas as pd
+import pytest
 
 from xena_gdc_etl import utils
 
@@ -20,43 +21,40 @@ def test_mkdir_p():
  os.rmdir(input_)
 
 
+@pytest.fixture
 @patch("sys.stdout", new_callable=StringIO)
 def test_equal_matrices(mocked_print):
- utils.equal_matrices(
- "tests/fixtures/df1.csv",
- "tests/fixtures/df2.csv",
- )
- utils.equal_matrices(
- "tests/fixtures/df1.csv",
- "tests/fixtures/df3.csv",
- )
+ utils.equal_matrices("df1.csv", "df2.csv")
+ utils.equal_matrices("df1.csv", "df3.csv")
  assert mocked_print.getvalue() == "Not equal.\nEqual.\n"
 
 
+@pytest.fixture
 @patch.object(utils, 'time', Mock(wraps=time))
 def test_metadata():
  utils.time.gmtime.return_value = time.struct_time(
  (2019, 4, 28, 0, 0, 0, 0, 0, 0)
  )
- path_to_df = "tests/fixtures/HTSeq-FPKM-UQ.csv"
+ path_to_df = "HTSeq-FPKM-UQ.csv"
  utils.metadata(path_to_df, "htseq_fpkm-uq")
- with open("tests/fixtures/HTSeq-FPKM-UQ.csv.json", "r") as actual:
+ with open("HTSeq-FPKM-UQ.csv.json", "r") as actual:
  actual = json.load(actual)
- os.unlink("tests/fixtures/HTSeq-FPKM-UQ.csv.json")
- with open("tests/fixtures/HTSeq-FPKM-UQ.json", "r") as expected:
+ os.unlink("HTSeq-FPKM-UQ.csv.json")
+ with open("HTSeq-FPKM-UQ.json", "r") as expected:
  expected = json.load(expected)
  assert actual == expected
 
 
+@pytest.fixture
 def test_merge_xena():
- path = "tests/fixtures/"
  name = "merged_GDC_TARGET-CCSK.tsv"
- filelists = [path + "merge-xena1.csv", path + "merge-xena2.csv"]
+ filelists = ["merge-xena1.csv", "merge-xena2.csv"]
  cohort = "GDC TARGET-CCSK"
  datatype = "GDC_phenotype"
+ path = "tests/fixtures"
  outdir = path
  utils.handle_merge_xena(name, filelists, cohort, datatype, outdir)
- with open(path + "MergedCohort04292019.GDC_phenotype.tsv", "r") as actual:
+ with open("MergedCohort04292019.GDC_phenotype.tsv", "r") as actual:
  actual = pd.read_csv(actual)
  with open(path + name, "r") as expected:
  expected = pd.read_csv(expected)

xena_gdc_etl/main.py

@@ -1,7 +1,6 @@
 from __future__ import print_function
 import argparse
 from datetime import date
-import os
 
 from .utils import equal_matrices, metadata, handle_merge_xena
 from .gdc_check_new import gdc_check_new