Merge branch 'release/0.2.3'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.2
+current_version = 0.2.3
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-dev(?P<dev>\d+))?
 serialize = 
 	{major}.{minor}.{patch}-dev{dev}

.travis.yml

@@ -1,7 +1,5 @@
 language: python
 python:
-  - "3.3"
-  - "3.4"
   - "3.5"
   - "3.6"
   - "3.7"

CHANGELOG.rst

@@ -1,6 +1,14 @@
 Revision History
 ================
 
+0.2.3 2019-10-31
+
+- Refactor tests
+- Test are requiring biopython>=1.66 to run/pass
+- Fix error message for Python (3.3+) version check
+- Remove Python 3.3 and 3.4 from Travis CI config
+
+
 0.2.2 2019-10-31
 
 - Accommodate publications with no authors

README.rst

@@ -185,4 +185,4 @@ pubmed-url
     http://dx.doi.org/10.1073/pnas.1116368109
 
 
-*Version 0.2.2*
+*Version 0.2.3*

pubmed_lookup/test_pubmed_lookup.py

@@ -6,61 +6,59 @@
 from pubmed_lookup import command_line, Publication, PubMedLookup
 
 
+article_url = 'https://www.pnas.org/content/109/12/4674'
+citation = (
+    'Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF (2012). '
+    'Arabidopsis synchronizes jasmonate-mediated defense with insect '
+    'circadian behavior. Proc Natl Acad Sci U S A 109(12): 4674-7.')
+doi_url = 'http://dx.doi.org/10.1073/pnas.1116368109'
+mini_citation = 'Goodspeed D - Covington MF - 2012 - Proc Natl Acad Sci U S A'
+pmid = '22331878'
+
+
 class TestConsole(unittest.TestCase):
     """Test command-line tools."""
 
     def setUp(self):
         self.out = StringIO()
-        self.pmid = '22331878'
-
-        self.citation = (
-            'Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF '
-            '(2012). Arabidopsis synchronizes jasmonate-mediated defense with '
-            'insect circadian behavior. Proc Natl Acad Sci U S A 109(12): '
-            '4674-7.')
-        self.mini_citation = (
-            'Goodspeed D - Covington MF - 2012 - Proc Natl Acad Sci U S A')
-
-        self.article_url = 'http://www.pnas.org/content/109/12/4674'
-        self.doi_url = 'http://dx.doi.org/10.1073/pnas.1116368109'
 
     def test_pubmed_citation(self):
-        command_line.pubmed_citation([self.pmid], out=self.out)
+        command_line.pubmed_citation([pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.citation + '\n')
+        self.assertEqual(output, citation + '\n')
 
     def test_pubmed_citation_m(self):
-        command_line.pubmed_citation(['-m', self.pmid], out=self.out)
+        command_line.pubmed_citation(['-m', pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.mini_citation + '\n')
+        self.assertEqual(output, mini_citation + '\n')
 
     def test_pubmed_citation_mini(self):
-        command_line.pubmed_citation(['--mini', self.pmid], out=self.out)
+        command_line.pubmed_citation(['--mini', pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.mini_citation + '\n')
+        self.assertEqual(output, mini_citation + '\n')
 
     def test_pubmed_url(self):
-        command_line.pubmed_url([self.pmid], out=self.out)
+        command_line.pubmed_url([pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.article_url + '\n')
+        self.assertEqual(output, article_url + '\n')
 
     def test_pubmed_url_d(self):
-        command_line.pubmed_url(['-d', self.pmid], out=self.out)
+        command_line.pubmed_url(['-d', pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.doi_url + '\n')
+        self.assertEqual(output, doi_url + '\n')
 
     def test_pubmed_url_doi(self):
-        command_line.pubmed_url(['--doi', self.pmid], out=self.out)
+        command_line.pubmed_url(['--doi', pmid], out=self.out)
         output = self.out.getvalue()
-        self.assertEqual(output, self.doi_url + '\n')
+        self.assertEqual(output, doi_url + '\n')
 
 
 class TestPublication(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # Get publication record
         email = ''
-        cls.pmid = '22331878'
+        cls.pmid = pmid
         cls.lookup = PubMedLookup(cls.pmid, email)
         cls.master_record = Publication(cls.lookup)
 
@@ -93,7 +91,7 @@ def test_fields(self):
         self.assertEqual(self.record.pmid, self.pmid)
         self.assertEqual(
             self.record.pubmed_url,
-            'http://www.ncbi.nlm.nih.gov/pubmed/22331878')
+            'http://www.ncbi.nlm.nih.gov/pubmed/{}'.format(pmid))
         self.assertEqual(self.record.title, self.title)
         self.assertEqual(self.record.authors, self.authors)
         self.assertEqual(self.record.first_author, 'Goodspeed D')
@@ -116,9 +114,7 @@ def test_authors_et_al(self):
             self.record.authors_et_al(max_authors=10), self.authors)
 
     def test_cite_mini(self):
-        self.assertEqual(
-            self.record.cite_mini(),
-            'Goodspeed D - Covington MF - 2012 - Proc Natl Acad Sci U S A')
+        self.assertEqual(self.record.cite_mini(), mini_citation)
 
     def test_cite(self):
         self.assertEqual(
@@ -158,7 +154,7 @@ def test_cite_without_issue_pages_volume(self):
         "Skipping this test on Travis CI.")
     def test_doi(self):
         self.assertEqual(
-            self.record.url, 'http://www.pnas.org/content/109/12/4674')
+            self.record.url, 'https://www.pnas.org/content/109/12/4674')
 
     def test_missing_doi(self):
         del self.record.record['DOI']
@@ -168,18 +164,19 @@ def test_missing_doi(self):
     def test_invalid_doi(self):
         self.record.record.update({'DOI': 'not a valid DOI'})
         self.record.set_article_url()
-        self.assertEqual(self.record.url, '')
+        self.assertEqual(self.record.url, 'http://dx.doi.org/not a valid DOI')
 
     def test_dont_resolve_doi(self):
         record = Publication(self.lookup, resolve_doi=False)
-        self.assertEqual(record.url, 'http://dx.doi.org/10.1073/pnas.1116368109')
+        self.assertEqual(
+            record.url, doi_url)
 
 
 class TestPubMedLookup(unittest.TestCase):
     def setUp(self):
         self.email = ''
-        self.pubmed_url = 'http://www.ncbi.nlm.nih.gov/pubmed/22331878'
-        self.pmid = '22331878'
+        self.pubmed_url = 'http://www.ncbi.nlm.nih.gov/pubmed/{}'.format(pmid)
+        self.pmid = pmid
 
     def test_pmid_and_url_return_same_record(self):
         self.assertEqual(

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 if sys.version_info < (3, 3):
-    print("Sorry, djangocms-lab-publications currently requires Python 3.3+.")
+    print("Sorry, pubmed-lookup currently requires Python 3.3+.")
     sys.exit(1)
 
 # From: https://hynek.me/articles/sharing-your-labor-of-love-pypi-quick-and-dirty/
@@ -16,13 +16,13 @@ def read(*paths):
 os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
 
 install_requires = [
-    "biopython>=1.65",
+    "biopython>=1.66",
     "xmltodict>=0.9.2",
 ]
 
 setup(
     name='pubmed-lookup',
-    version='0.2.2',
+    version='0.2.3',
     packages=['pubmed_lookup'],
     test_suite='pubmed_lookup.test_pubmed_lookup',
     include_package_data=True,