MultiTax version 1.2.1 (#11)

* v1.2.1 fix bug custom files

* tests and pep8

* docs

* travis

docs/multitax.html

@@ -209,7 +209,8 @@ <h1 class="modulename">
                     <span class="n">names</span><span class="p">[</span><span class="n">node</span><span class="p">]</span> <span class="o">=</span> <span class="n">fields</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_cols</span><span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">]]</span>
                 <span class="k">if</span> <span class="s2">&quot;rank&quot;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cols</span><span class="p">:</span>
                     <span class="n">ranks</span><span class="p">[</span><span class="n">node</span><span class="p">]</span> <span class="o">=</span> <span class="n">fields</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_cols</span><span class="p">[</span><span class="s2">&quot;rank&quot;</span><span class="p">]]</span>
-            <span class="k">return</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">ranks</span><span class="p">,</span> <span class="n">names</span>
+
+        <span class="k">return</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">ranks</span><span class="p">,</span> <span class="n">names</span>
 
     <span class="k">def</span> <span class="nf">_parse_cols</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cols</span><span class="p">):</span>
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">cols</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
@@ -468,6 +469,7 @@ <h5>Inherited Members</h5>
                         <span class="n">nodes</span><span class="p">[</span><span class="n">taxid</span><span class="p">]</span> <span class="o">=</span> <span class="n">parent_taxid</span>
                         <span class="n">names</span><span class="p">[</span><span class="n">taxid</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span>
                         <span class="n">ranks</span><span class="p">[</span><span class="n">taxid</span><span class="p">]</span> <span class="o">=</span> <span class="n">rank</span>
+
         <span class="k">return</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">ranks</span><span class="p">,</span> <span class="n">names</span>
 </pre></div>
 

docs/multitax/multitax.html

@@ -124,7 +124,7 @@ <h1 class="modulename">
 
 <span class="k">class</span> <span class="nc">MultiTax</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 
-    <span class="n">version</span> <span class="o">=</span> <span class="s2">&quot;1.2.0&quot;</span>
+    <span class="n">version</span> <span class="o">=</span> <span class="s2">&quot;1.2.1&quot;</span>
 
     <span class="n">_default_urls</span> <span class="o">=</span> <span class="p">[]</span>
     <span class="n">_default_root_node</span> <span class="o">=</span> <span class="s2">&quot;1&quot;</span>
@@ -427,7 +427,6 @@ <h1 class="modulename">
 <span class="sd">        Returns a list with the lineage of a given node.</span>
 <span class="sd">        If ranks is provided, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
-<span class="sd">        ranks and root_node are ignored if build_lineages() was used.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># If lineages were built with build_lineages() with matching params</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span> <span class="ow">and</span> <span class="n">root_node</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ranks</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -724,7 +723,7 @@ <h1 class="modulename">
             <summary>View Source</summary>
             <div class="pdoc-code codehilite"><pre><span></span><span class="k">class</span> <span class="nc">MultiTax</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 
-    <span class="n">version</span> <span class="o">=</span> <span class="s2">&quot;1.2.0&quot;</span>
+    <span class="n">version</span> <span class="o">=</span> <span class="s2">&quot;1.2.1&quot;</span>
 
     <span class="n">_default_urls</span> <span class="o">=</span> <span class="p">[]</span>
     <span class="n">_default_root_node</span> <span class="o">=</span> <span class="s2">&quot;1&quot;</span>
@@ -1027,7 +1026,6 @@ <h1 class="modulename">
 <span class="sd">        Returns a list with the lineage of a given node.</span>
 <span class="sd">        If ranks is provided, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
-<span class="sd">        ranks and root_node are ignored if build_lineages() was used.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># If lineages were built with build_lineages() with matching params</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span> <span class="ow">and</span> <span class="n">root_node</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ranks</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -1472,7 +1470,7 @@ <h1 class="modulename">
                             <div id="MultiTax.version" class="classattr">
                                             <div class="attr variable"><a class="headerlink" href="#MultiTax.version">#&nbsp;&nbsp</a>
 
-        <span class="name">version</span><span class="default_value"> = &#39;1.2.0&#39;</span>
+        <span class="name">version</span><span class="default_value"> = &#39;1.2.1&#39;</span>
     </div>
 
 
@@ -1750,7 +1748,6 @@ <h1 class="modulename">
 <span class="sd">        Returns a list with the lineage of a given node.</span>
 <span class="sd">        If ranks is provided, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
-<span class="sd">        ranks and root_node are ignored if build_lineages() was used.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># If lineages were built with build_lineages() with matching params</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span> <span class="ow">and</span> <span class="n">root_node</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ranks</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -1796,8 +1793,7 @@ <h1 class="modulename">
 
             <div class="docstring"><p>Returns a list with the lineage of a given node.
 If ranks is provided, returns only nodes annotated with such ranks.
-If root_node is provided, use it instead of default root of tree.
-ranks and root_node are ignored if build_lineages() was used.</p>
+If root_node is provided, use it instead of default root of tree.</p>
 </div>
 
 

multitax/customtx.py

@@ -46,7 +46,8 @@ def _parse(self, fhs, **kwargs):
                     names[node] = fields[self._cols["name"]]
                 if "rank" in self._cols:
                     ranks[node] = fields[self._cols["rank"]]
-            return nodes, ranks, names
+
+        return nodes, ranks, names
 
     def _parse_cols(self, cols):
         if isinstance(cols, list):

multitax/greengenestx.py

@@ -50,4 +50,5 @@ def _parse(self, fhs, **kwargs):
                         nodes[taxid] = parent_taxid
                         names[taxid] = name
                         ranks[taxid] = rank
+
         return nodes, ranks, names

multitax/multitax.py

@@ -4,7 +4,7 @@
 
 class MultiTax(object):
 
-    version = "1.2.0"
+    version = "1.2.1"
 
     _default_urls = []
     _default_root_node = "1"
@@ -307,7 +307,6 @@ def lineage(self, node: str, root_node: str = None, ranks: list = None):
         Returns a list with the lineage of a given node.
         If ranks is provided, returns only nodes annotated with such ranks.
         If root_node is provided, use it instead of default root of tree.
-        ranks and root_node are ignored if build_lineages() was used.
         """
         # If lineages were built with build_lineages() with matching params
         if node in self._lineages and root_node is None and ranks is None:

setup.py

@@ -9,7 +9,7 @@
 
 setup(
     name="multitax",
-    version="1.2.0",
+    version="1.2.1",
     url="https://www.github.com/pirovc/multitax",
     license="MIT",
     author="Vitor C. Piro",

tests/multitax/integration/test_common.py

@@ -27,7 +27,8 @@ class TestCommon(unittest.TestCase):
     taxonomies["greengenes"] = {"class": GreengenesTx,
                                 "params": {"files": [data_dir + "gg.txt.gz"]}}
     taxonomies["custom"] = {"class": CustomTx,
-                            "params": {"files": [data_dir + "custom.tsv.gz"]}}
+                            "params": {"files": [data_dir + "custom.tsv.gz",
+                                                 data_dir + "custom2.tsv.gz"]}}
 
     @classmethod
     def setUpClass(self):
@@ -59,7 +60,8 @@ def test_fail_to_download(self):
         """
         with self.assertRaises(Exception):
             with self.assertWarns(UserWarning):
-               tax = self.taxonomies["ncbi"]["class"](urls=["www.thisisnotawebsite.com/neither/a/file", "fasfafsafasfasf"])
+                tax = self.taxonomies["ncbi"]["class"](
+                    urls=["www.thisisnotawebsite.com/neither/a/file", "fasfafsafasfasf"])
 
     def test_urls_output_prefix(self):
         """

tests/multitax/integration/test_online.py

@@ -7,6 +7,7 @@
 
 sys.path.append("tests/multitax/")
 
+
 @unittest.skip('Skip online by default')
 class TestOnline(unittest.TestCase):