Prevent the single-node tree check from yielding "false positives" on linear trees; also fix the build

Makefile

@@ -1,6 +1,6 @@
 libbitarr.a: 
-	cd BitArray && $(MAKE)
-	make -C BitArray -f Makefile
+	cd bp/BitArray && $(MAKE)
+	make -C bp/BitArray -f Makefile
 
 build: libbitarr.a
 	python setup.py build_ext --inplace

README.md

@@ -1,6 +1,8 @@
 Improved Octo Waddle
 --------------------
 
+[![Improved Octo Waddle CI](https://github.com/biocore/improved-octo-waddle/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/biocore/improved-octo-waddle/actions/workflows/python-package-conda.yml)
+
 An implementation of the balanced parentheses tree structure as described by
 [Cordova and Navarro](http://www.dcc.uchile.cl/~gnavarro/ps/tcs16.2.pdf).
 

bp/GPL/tests/test_insert.py

@@ -31,4 +31,3 @@ def test_insert_multifurcating(self):
 
 if __name__ == '__main__':
     unittest.main()
-

bp/_io.pyx

@@ -148,16 +148,16 @@ cpdef parse_newick(unicode data):
         np.ndarray[np.double_t, ndim=1] lengths
         np.ndarray[np.int32_t, ndim=1] edges
 
-    if data.count(',') == 0:
-        raise ValueError("Only trees with more than 1 node supported")
-
     data = data.strip()
     if not data.endswith(';'):
         raise ValueError("Newick does not appear terminated with a semicolon")
 
     datalen = len(data)
     topology = _newick_to_bp(data)
 
+    if len(topology.B) <= 1:
+        raise ValueError("Only trees with more than 1 node supported")
+
     names = np.full(len(topology.B), None, dtype=object)
     lengths = np.zeros(len(topology.B), dtype=np.double)
     edges = np.full(len(topology.B), 0, dtype=np.int32) 

bp/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -339,7 +338,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    date = runner(
+        GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root
+    )[0].strip()
     # Use only the last line.  Previous lines may contain GPG signature
     # information.
     date = date.splitlines()[-1]
@@ -429,10 +430,14 @@ def render_pep440_pre(pieces):
     if pieces["closest-tag"]:
         if pieces["distance"]:
             # update the post release segment
-            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            tag_version, post_version = pep440_split_post(
+                pieces["closest-tag"]
+            )
             rendered = tag_version
             if post_version is not None:
-                rendered += ".post%d.dev%d" % (post_version+1, pieces["distance"])
+                rendered += ".post%d.dev%d" % (
+                    post_version+1, pieces["distance"]
+                )
             else:
                 rendered += ".post0.dev%d" % (pieces["distance"])
         else:

bp/tests/test_conv.py

@@ -16,7 +16,7 @@ def setUp(self):
         self.sktn = skbio.TreeNode.read(StringIO(self.tstr))
 
     def test_to_skbio_treenode_with_edge_numbers(self):
-        # from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009
+        # from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009 # noqa
         # but without edge labels
         # 0 1 2 3 4 5 6 7 8 9
         # 1 1 1 0 1 0 0 1 0 0

bp/tests/test_insert.py

@@ -7,11 +7,14 @@
 
 class InsertTests(unittest.TestCase):
     package = 'bp.tests'
+
     def setUp(self):
         self.jplacedata_multiple = \
             open(self.get_data_path('300/placement_mul.jplace')).read()
         self.final_multiple_fully_resolved = \
-            skbio.TreeNode.read(self.get_data_path('300/placement.full_resolve.newick'))
+            skbio.TreeNode.read(
+                self.get_data_path('300/placement.full_resolve.newick')
+            )
 
     def get_data_path(self, filename):
         # adapted from qiime2.plugin.testing.TestPluginBase
@@ -51,5 +54,6 @@ def test_insert_fully_resolved_multiple_placements(self):
         self.assertEqual(obs.compare_rfd(exp), 0)
         self.assertAlmostEqual(obs.compare_tip_distances(exp), 0)
 
+
 if __name__ == '__main__':
     unittest.main()

bp/tests/test_io.py

@@ -13,12 +13,13 @@
 
 class NewickTests(TestCase):
     def test_parse_newick_simple_edge_numbers(self):
-        # from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009
+        # from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009 # noqa
         # but without edge labels
         # 0 1 2 3 4 5 6 7 8 9
         # 1 1 1 0 1 0 0 1 0 0
         in_ = '((A:.01{0}, B:.01{1})D:.01{3}, C:.01{4}) {5};'
-        exp_sk = '((A:.01, B:.01)D:.01, C:.01);'  # skbio doesn't know about edge numbers
+        # skbio doesn't know about edge numbers
+        exp_sk = '((A:.01, B:.01)D:.01, C:.01);'
         obs = parse_newick(in_)
         obs_sk = to_skbio_treenode(obs)
         exp_sk = skbio.TreeNode.read([exp_sk])
@@ -82,6 +83,21 @@ def test_parse_newick_singlenode_bug(self):
         with self.assertRaises(ValueError):
             parse_newick(test)
 
+    def test_parse_newick_linear_tree(self):
+        # https://github.com/biocore/improved-octo-waddle/pull/48
+        test = '((b:3)a:2)root:1;'
+
+        # Test that we can parse these edge cases successfully, without
+        # mistaking them for single-node trees
+        topology = parse_newick(test)
+
+        # Convert the tree to a skbio TreeNode to make checking easier
+        skbio_tree = to_skbio_treenode(topology)
+        self.assertEqual(skbio_tree.name, "root")
+        self.assertEqual([n.name for n in skbio_tree.children], ["a"])
+        self.assertEqual([n.name for n in skbio_tree.non_tips()], ["a"])
+        self.assertEqual([n.name for n in skbio_tree.tips()], ["b"])
+
     def test_parse_newick_no_semicolon_bug(self):
         # https://github.com/wasade/improved-octo-waddle/issues/26
         test = "((h:1, i:1, j:1, k:1, l: 1),(e:1,f:1),(n:1,o:1,p:1))a:1"
@@ -96,7 +112,7 @@ def test_parse_newick_no_semicolon_bug(self):
     def test_write_newick_underscore_bug(self):
         test = "(((a)b)'c_foo',((d)e)f)r;"
         buf = io.StringIO()
-        obs = write_newick(parse_newick(test), buf, False)
+        write_newick(parse_newick(test), buf, False)
         buf.seek(0)
         self.assertIn("'c_foo'", test)