Remove nose from tests

tests/common.py

@@ -46,6 +46,10 @@ def __exit__(self, type, value, traceback):
             return False
 
 
+def ok_(b):
+    assert b
+
+
 def eq_(x, y, msg=None):
     if msg is None:
         assert x == y

tests/test_download_cache.py

@@ -1,33 +1,37 @@
-from nose.tools import assert_raises, ok_
-from pyensembl.download_cache import (
-    DownloadCache,
-    MissingLocalFile,
-    MissingRemoteFile
-)
-
 import os
 import tempfile
 
+from pytest import raises as assert_raises
+from pyensembl.download_cache import DownloadCache, MissingLocalFile, MissingRemoteFile
+
+
 from .data import data_path
+from .common import ok_
 
 download_cache = DownloadCache(
     reference_name="__test_reference",
     annotation_name="__test_annotation",
-    copy_local_files_to_cache=False)
+    copy_local_files_to_cache=False,
+)
+
 
 def test_download_cache_missing_local_file():
     # clear the cache
     download_cache.delete_cache_directory()
     with assert_raises(MissingLocalFile):
         download_cache.download_or_copy_if_necessary(
-            path_or_url="test_file_doesn_not_exist.file")
+            path_or_url="test_file_doesn_not_exist.file"
+        )
+
 
 def test_download_cache_missing_remote_file():
     # clear the cache
     download_cache.delete_cache_directory()
     with assert_raises(MissingRemoteFile):
         download_cache.download_or_copy_if_necessary(
-            path_or_url="ftp://NOTAURL.NOTAURL.NOTAURL")
+            path_or_url="ftp://NOTAURL.NOTAURL.NOTAURL"
+        )
+
 
 def test_download_cache_custom_location():
     test_file = "refseq.ucsc.small.gtf"
@@ -36,29 +40,27 @@ def test_download_cache_custom_location():
     print("DIR: %s" % tmp_dir)
     assert tmp_dir is not None
 
-    os.environ['PYENSEMBL_CACHE_DIR'] = tmp_dir
+    os.environ["PYENSEMBL_CACHE_DIR"] = tmp_dir
 
     # We need another instance of DownloadCache
     # that copies files over to cache folder
     download_cache = DownloadCache(
         reference_name="test_reference",
         annotation_name="test_annotation",
-        copy_local_files_to_cache=True)
+        copy_local_files_to_cache=True,
+    )
 
     # clean up
     download_cache.delete_cache_directory()
     download_cache.download_or_copy_if_necessary(
-        download_if_missing=True,
-        path_or_url=data_path(test_file))
+        download_if_missing=True, path_or_url=data_path(test_file)
+    )
 
     full_path = os.path.join(
-        tmp_dir,
-        "pyensembl",
-        "test_reference",
-        "test_annotation",
-        test_file)
+        tmp_dir, "pyensembl", "test_reference", "test_annotation", test_file
+    )
     print("FULL PATH: %s" % full_path)
     assert len(full_path) > 0
 
     ok_(os.path.exists(full_path))
-    del os.environ['PYENSEMBL_CACHE_DIR']
+    del os.environ["PYENSEMBL_CACHE_DIR"]

tests/test_ensembl_object_properties.py

@@ -5,9 +5,10 @@
 
 from __future__ import absolute_import
 
-from nose.tools import eq_
+from .common import eq_
 from pyensembl import EnsemblRelease, MAX_ENSEMBL_RELEASE
 
+
 def test_human_reference_name():
     eq_(EnsemblRelease(release=54).reference_name, "NCBI36")
     eq_(EnsemblRelease(release=74).reference_name, "GRCh37")

tests/test_gene_objects.py

@@ -1,5 +1,4 @@
-from nose.tools import eq_
-
+from .common import eq_
 from .common import run_multiple_genomes
 from .data import TP53_gene_id
 

tests/test_id_length.py

@@ -1,24 +1,25 @@
 from .common import major_releases
 
-from nose.tools import nottest
 
-@nottest
 def check_id_length(method_name):
     for release in major_releases:
         method = getattr(release, method_name)
         # only load chromosome Y to speed up tests
         idents = method(contig="Y")
         assert len(idents) > 0, "No values returned by %s" % method_name
-        assert all(len(ident) == 15 for ident in idents), \
-            "Invalid IDs for %s: %s" % (
-                method_name,
-                [ident for ident in idents if len(ident) != 15])
+        assert all(len(ident) == 15 for ident in idents), "Invalid IDs for %s: %s" % (
+            method_name,
+            [ident for ident in idents if len(ident) != 15],
+        )
+
 
 def test_gene_id_length():
-    check_id_length('gene_ids')
+    check_id_length("gene_ids")
+
 
 def test_transcript_id_length():
-    check_id_length('transcript_ids')
+    check_id_length("transcript_ids")
+
 
 def test_protein_id_length():
-    check_id_length('protein_ids')
+    check_id_length("protein_ids")

tests/test_locus.py

@@ -1,7 +1,8 @@
 from pyensembl.locus import Locus
 from pyensembl.normalization import normalize_chromosome
 
-from nose.tools import assert_raises
+from pytest import raises as assert_raises
+
 
 def test_normalize_chromosome():
     assert normalize_chromosome("X") == "X"
@@ -38,6 +39,7 @@ def test_normalize_chromosome():
     with assert_raises(ValueError):
         normalize_chromosome(0)
 
+
 def test_locus_overlaps():
     locus = Locus("1", 10, 20, "+")
     assert locus.overlaps("1", 10, 20, "+")
@@ -57,6 +59,7 @@ def test_locus_overlaps():
     # wrong strand
     assert not locus.overlaps("1", 10, 20, "-")
 
+
 def test_locus_contains():
     locus = Locus("1", 10, 20, "+")
     assert locus.contains("1", 10, 20, "+")
@@ -82,6 +85,7 @@ def test_locus_contains():
     # wrong strand
     assert not locus.contains("1", 10, 20, "-")
 
+
 def test_position_offset():
     forward_locus = Locus("1", 10, 20, "+")
     assert forward_locus.offset(10) == 0
@@ -143,6 +147,7 @@ def test_range_offset():
     with assert_raises(ValueError):
         negative_locus.offset_range(9, 10)
 
+
 def test_locus_distance():
     locus_chr1_10_20_pos = Locus("1", 10, 20, "+")
     locus_chr1_21_25_pos = Locus("1", 21, 25, "+")

tests/test_search.py

@@ -1,6 +1,5 @@
-from nose.tools import eq_
-
 from pyensembl import find_nearest_locus
+from .common import eq_
 from .common import run_multiple_genomes
 
 

tests/test_transcript_ids.py

@@ -5,8 +5,7 @@
 from __future__ import absolute_import
 
 from pyensembl import genome_for_reference_name
-from nose.tools import eq_
-
+from .common import eq_
 from .common import run_multiple_genomes
 
 grch38 = genome_for_reference_name("GRCh38")