Fix test warnings and a new failure from #36

biocommons · May 4, 2022 · 22b5556 · 22b5556
1 parent ed6eaf6
commit 22b5556
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Showing 2 changed files with 18 additions and 20 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -69,9 +69,13 @@ exclude =
 dev =
     ipython>=7.5
     jupyter>=1.0
+    pytest
+    pytest-cov
+    pytest-optional-tests
     pyyaml
     restview
     tox
+    vcrpy
     yapf
 docs =
     sphinx
@@ -102,14 +106,16 @@ max-complexity = 10
 ignore = E129,E221,E241,E251,E303,W291
 
 [tool:pytest]
-addopts = --cov-config=setup.cfg --cov-report term-missing --cov=bioutils   --doctest-modules --doctest-glob='*.rst'  --strict
-collect_ignore = setup.py
+addopts = --cov-config=setup.cfg --cov-report term-missing --cov=bioutils   --doctest-modules --doctest-glob='*.rst'  --strict-markers
+# collect_ignore = setup.py
 doctest_optionflags = ALLOW_UNICODE ALLOW_BYTES ELLIPSIS IGNORE_EXCEPTION_DETAIL NORMALIZE_WHITESPACE
 norecursedirs =
   _data
   dist
   build
   .tox
 testpaths = src tests
-optional_tests =
-  network: run network tests
+markers =
+    network
+#optional_tests =
+#  network: run network tests
diff --git a/tests/test_sequences.py b/tests/test_sequences.py
@@ -1,6 +1,6 @@
 import pytest
 from bioutils.sequences import translate_cds
-from src.bioutils.sequences import TranslationTable
+from bioutils.sequences import TranslationTable
 
 
 def test_translate_examples():
@@ -29,21 +29,13 @@ def test_translate_examples():
 def test_translate_selenoproteins():
     """unit test for sec codon"""
     assert translate_cds("AUGTGATAA") == "M**"
-    assert (
-        translate_cds("AUGTGATAA", translation_table=TranslationTable.standard) == "M**"
-    )
-    assert (
-        translate_cds("AUGTGATAA", translation_table=TranslationTable.selenocysteine)
-        == "MU*"
-    )
-    assert (
-        translate_cds(
-            "AUGTGATA",
-            translation_table=TranslationTable.selenocysteine,
-            full_codons=False,
-        )
-        == "MU*"
-    )
+    assert (translate_cds("AUGTGATAA", translation_table=TranslationTable.standard) == "M**")
+    assert (translate_cds("AUGTGATAA", translation_table=TranslationTable.selenocysteine) == "MU*")
+    assert (translate_cds(
+        "AUGTGATA",
+        translation_table=TranslationTable.selenocysteine,
+        full_codons=False,
+    ) == "MU*")
 
     with pytest.raises(ValueError):
         translate_cds("AUGTGATA", translation_table=TranslationTable.selenocysteine)