Merge pull request #35 from standage/testdata/open

Add pkgdata function

setup.py

@@ -12,16 +12,16 @@
 import versioneer
 
 
+d = 'Genome annotation data analysis and management implemented in pure Python'
 setup(name='tag',
       version=versioneer.get_version(),
       cmdclass=versioneer.get_cmdclass(),
-      description='Toolkit for genome annotation data analysis',
-      url='http://github.com/standage/tag',
+      description=d,
+      url='http://tag.readthedocs.io',
       author='Daniel Standage',
       author_email='daniel.standage@gmail.com',
       license='BSD-3',
       packages=['tag'],
-      tests_require=['pytest', 'pytest-cov', 'pep8'],
       scripts=list(glob.glob('scripts/*.py')),
       classifiers=[
           'Development Status :: 4 - Beta',

tag/__init__.py

@@ -34,6 +34,11 @@ def open(filename, mode):
     return openfunc(filename, mode)
 
 
+def pkgdata(filename):
+    fullpath = '{dir}/{fn}'.format(dir='tests/testdata/', fn=filename)
+    return open(fullpath, 'r')
+
+
 def demo_feature():
     gene = feature.Feature(
         'contig1\tsnap\tgene\t1000\t7500\t.\t+\t.\tID=gene1'

tests/test_reader.py

@@ -193,7 +193,7 @@ def test_feature_out_of_range():
 
 def test_seqreg_dup():
     """Duplicated sequence-region pragma."""
-    infile = tag.open('tests/testdata/vcar-seqreg-dup.gff3.gz', 'r')
+    infile = tag.pkgdata('vcar-seqreg-dup.gff3.gz')
     reader = GFF3Reader(instream=infile)
     with pytest.raises(ValueError) as ve:
         records = [r for r in reader]
@@ -202,12 +202,12 @@ def test_seqreg_dup():
 
 def test_seqreg_outoforder():
     """sequence-region pragma declared after features on that sequence."""
-    infile = tag.open('tests/testdata/grape-cpgat-seqreg-after.gff3.gz', 'r')
+    infile = tag.pkgdata('grape-cpgat-seqreg-after.gff3.gz')
     reader = GFF3Reader(instream=infile)
     records = [r for r in reader]
     assert len(records) == 5
 
-    infile = tag.open('tests/testdata/grape-cpgat-seqreg-after.gff3.gz', 'r')
+    infile = tag.pkgdata('grape-cpgat-seqreg-after.gff3.gz')
     reader = GFF3Reader(instream=infile, assumesorted=True)
     with pytest.raises(ValueError) as ve:
         records = [r for r in reader]

tests/test_utils.py

@@ -19,7 +19,7 @@ def test_tag_open_read():
     with pytest.raises(IOError):
         fh = tag.open('tag/bogus.py', 'r')
 
-    fh = tag.open('tests/testdata/gzipdata.gff3.gz', 'r')
+    fh = tag.pkgdata('gzipdata.gff3.gz')
     line = next(fh)
     assert line == '##gff-version 3\n'