Fix testing with tox on windows (#517)

* tox: forward required env.vars to tests

* Replace filecmp.cmp by line-ending-neutral version

* Make linter happy.

tests/__init__.py

@@ -1,3 +1,4 @@
+import difflib
 import math
 from pathlib import Path
 from typing import List
@@ -128,3 +129,14 @@ def object_is_subsumed_by_member_of(obj: YAMLRoot, obj_list: List[YAMLRoot], **k
         if object_subsumed_by(o, obj, **kwargs):
             return True
     return False
+
+
+def filecmp_difflib(left_path: Path, right_path: Path) -> bool:
+    """Platfom neutral filecmp.cmp(..) function for text files
+
+    Files are read in text mode to ignore newline differences.
+    """
+    with open(left_path) as left, open(right_path) as right:
+        diff = difflib.unified_diff(left.readlines(), right.readlines())
+
+    return list(diff) == []

tests/test_implementations/test_pronto.py

@@ -1,4 +1,3 @@
-import filecmp
 import logging
 import unittest
 
@@ -37,6 +36,7 @@
     ORGANELLE_MEMBRANE,
     OUTPUT_DIR,
     VACUOLE,
+    filecmp_difflib,
 )
 from tests.test_implementations import ComplianceTester
 
@@ -377,7 +377,7 @@ def test_sort_order_no_edits(self):
         oi = ProntoImplementation(resource)
         OUTPUT_DIR.mkdir(exist_ok=True)
         oi.dump(output_path, syntax="obo")
-        self.assertTrue(filecmp.cmp(input_path, output_path))
+        self.assertTrue(filecmp_difflib(input_path, output_path))
 
     def test_reflexive_diff(self):
         self.compliance_tester.test_reflexive_diff(self.oi)

tests/test_implementations/test_simple_obo.py

@@ -1,4 +1,3 @@
-import filecmp
 import logging
 import unittest
 from copy import deepcopy
@@ -52,6 +51,7 @@
     ORGANELLE_MEMBRANE,
     OUTPUT_DIR,
     VACUOLE,
+    filecmp_difflib,
 )
 from tests.test_implementations import ComplianceTester
 
@@ -351,11 +351,11 @@ def test_sort_order_no_edits(self):
         oi = SimpleOboImplementation(resource)
         OUTPUT_DIR.mkdir(exist_ok=True)
         oi.dump(output_path, syntax="obo")
-        self.assertTrue(filecmp.cmp(input_path, output_path))
+        self.assertTrue(filecmp_difflib(input_path, output_path))
         # try ordering stanzas (but do not ordering within a stanza)
         oi.obo_document.order_stanzas()
         oi.dump(output_path, syntax="obo")
-        self.assertTrue(filecmp.cmp(input_path, output_path))
+        self.assertTrue(filecmp_difflib(input_path, output_path))
 
     @unittest.skip(
         "Currently not guaranteed same as OWLAPI: see https://github.com/owlcollab/oboformat/issues/138"
@@ -371,7 +371,7 @@ def test_sort_order_with_forced_reorder(self):
         oi.obo_document.normalize_line_order()
         OUTPUT_DIR.mkdir(exist_ok=True)
         oi.dump(output_path, syntax="obo")
-        self.assertTrue(filecmp.cmp(input_path, output_path))
+        self.assertTrue(filecmp_difflib(input_path, output_path))
 
     def test_merge(self):
         resource1 = OntologyResource(slug=TEST_ONT, directory=INPUT_DIR, local=True)

tox.ini

@@ -11,6 +11,12 @@ envlist =
     py
 
 [testenv]
+# forward env.vars to tox env for tests\test_implementations\test_sqldb.py
+passenv =
+    LNAME
+    LOGNAME
+    USER
+    USERNAME
 commands =
     coverage run -p -m pytest --durations=20 {posargs:tests}
     coverage combine