final fixes for release

matthiaskoenig · Jul 30, 2019 · 04c8e7c · 04c8e7c
1 parent 545d5ab
commit 04c8e7c
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Showing 5 changed files with 16 additions and 24 deletions.
diff --git a/brendapy/examples.py b/brendapy/examples.py
@@ -15,7 +15,7 @@ def parse_proteins_for_ec():
 
     print(f"{len(proteins)} proteins for EC {ec} in BRENDA")
     print(f"Protein identifier: {proteins.keys()}")
-    print("-"*80)
+    print("-" * 80)
     for p in proteins.values():
         if p.organism == "Homo sapiens":
             print(p)

diff --git a/brendapy/parser.py b/brendapy/parser.py
@@ -160,7 +160,7 @@ def store_item(bid, item):
                 results[bid] = item
             elif bid in {"RN", "RE", "RT", "SN"}:
                 if isinstance(results[bid], OrderedDict):
-                    results[bid] = { item }
+                    results[bid] = {item}
                 else:
                     results[bid].add(item)
             elif bid == "RF":
@@ -311,7 +311,7 @@ def __init__(self, ec, key, data):
         """
         self.data = OrderedDict([
             ('protein_id', key),
-            ('ec',  ec),
+            ('ec', ec),
             ('organism', data['PR'][key]['data']),
         ])
         reference_ids = set(data['PR'][key]['refs'])

diff --git a/brendapy/tests/test_brenda.py b/brendapy/tests/test_brenda.py
@@ -4,6 +4,8 @@
 from brendapy import BrendaParser, BrendaProtein
 from brendapy.settings import BRENDA_FILE
 
+BRENDA_PARSER = BrendaParser()
+
 
 def test_parsing():
     brenda = BrendaParser()
@@ -19,18 +21,14 @@ def test_parsing_from_file():
 
 def test_protein1():
     """ Test the proteinBRENDA module """
-    brenda = BrendaParser()
-
     ec = "1.1.1.1"
-    proteins = brenda.get_proteins(ec)
+    proteins = BRENDA_PARSER.get_proteins(ec)
     assert proteins
     assert len(proteins) == 167
 
 
 def test_protein_detail1():
-    brenda = BrendaParser()
-    ec = "1.1.1.1"
-    proteins = brenda.get_proteins(ec)
+    proteins = BRENDA_PARSER.get_proteins(ec="1.1.1.1")
     protein = proteins[1]
 
     assert protein
@@ -40,28 +38,22 @@ def test_protein_detail1():
 
 
 def test_protein_detail2():
-    brenda = BrendaParser()
-    ec = "1.1.1.1"
-    proteins = brenda.get_proteins(ec)
+    proteins = BRENDA_PARSER.get_proteins("1.1.1.1")
     protein = proteins[4]
 
     assert protein
     assert protein.organism == "Drosophila melanogaster"
     assert 8 in protein.references
 
 
-brenda_parser = BrendaParser()
-@pytest.mark.parametrize("ec", BrendaParser().keys())
-def test_proteins_for_ec(ec):
-    proteins = brenda_parser.get_proteins(ec)
-    assert proteins is not None
-
-
 def test_info_dict():
-    brenda = BrendaParser()
     ec = "1.1.1.2"
-    ec_str = brenda.ec_text[ec]
-    d = brenda._parse_info_dict(ec, ec_str)
+    ec_str = BRENDA_PARSER.ec_text[ec]
+    d = BRENDA_PARSER._parse_info_dict(ec, ec_str)
     assert d
 
 
+@pytest.mark.parametrize("ec", BRENDA_PARSER.keys())
+def test_proteins_for_ec(ec):
+    proteins = BRENDA_PARSER.get_proteins(ec)
+    assert proteins is not None
diff --git a/brendapy/utils.py b/brendapy/utils.py
@@ -28,4 +28,4 @@ def timed(*args, **kw):
             print('%r  %2.2f ms' % (method.__name__, (te - ts) * 1000))
         return result
 
-    return timed
+    return timed
diff --git a/tox.ini b/tox.ini
@@ -12,4 +12,4 @@ skip_install = True
 deps =
     pep8
 commands =
-    pep8 --show-source brendapy
+    pep8 --show-source brendapy --ignore=E501