[med-svn] [Git][med-team/q2-phylogeny][upstream] New upstream version 2022.8.0

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch upstream at Debian Med / q2-phylogeny


Commits:
659a7f8b by Mohammed Bilal at 2022-09-07T11:09:13+00:00
New upstream version 2022.8.0
- - - - -


4 changed files:

- ci/recipe/meta.yaml
- q2_phylogeny/_version.py
- q2_phylogeny/plugin_setup.py
- q2_phylogeny/tests/test_iqtree.py


Changes:

=====================================
ci/recipe/meta.yaml
=====================================
@@ -18,16 +18,15 @@ requirements:
 
   run:
     - python {{ python }}
-    - scikit-bio
+    - scikit-bio {{ scikit_bio }}
     - qiime2 {{ qiime2_epoch }}.*
     - q2-types {{ qiime2_epoch }}.*
     - q2-alignment {{ qiime2_epoch }}.*
-    # fasttree pinned because newer versions don't include fasttreemp on osx:
-    # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/fasttree/build.sh
-    - fasttree ==2.1.10=0
+    - fasttree
     - raxml
-    - iqtree >=1.6.4
-    - pytest
+    - iqtree
+    # this isn't a direct dependency, but it helps convince conda to do the right thing
+    - h5py
 
 test:
   requires:


=====================================
q2_phylogeny/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
     # setup.py/versioneer.py will grep for the variable names, so they must
     # each be defined on a line of their own. _version.py will just call
     # get_keywords().
-    git_refnames = " (tag: 2022.2.0)"
-    git_full = "527838b0abdd3754b1fd98709e9cb97e262e6059"
-    git_date = "2022-02-18 19:38:00 +0000"
+    git_refnames = " (tag: 2022.8.0)"
+    git_full = "2474e0992e445460e758284a0c66116592b5f464"
+    git_date = "2022-08-23 17:49:14 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 


=====================================
q2_phylogeny/plugin_setup.py
=====================================
@@ -289,7 +289,6 @@ plugin.methods.register_function(
                  '(http://www.iqtree.org/) with automatic model selection.'),
     citations=[citations['Minh2020iqtree'],
                citations['Kalyaanamoorthy2017modelfinder']],
-    deprecated=True
 )
 
 plugin.methods.register_function(
@@ -399,7 +398,6 @@ plugin.methods.register_function(
                citations['Kalyaanamoorthy2017modelfinder'],
                citations['Minh2013ultrafastbootstrap'],
                citations['Hoang2017ultrafastbootstrap2']],
-    deprecated=True
 )
 
 T1 = TypeMatch([Frequency, RelativeFrequency, PresenceAbsence])
@@ -648,7 +646,6 @@ plugin.pipelines.register_function(
                  'q2-alignment methods, and both the rooted and unrooted '
                  'phylogenies from q2-phylogeny methods.'
                  ),
-    deprecated=True
 )
 
 plugin.pipelines.register_function(


=====================================
q2_phylogeny/tests/test_iqtree.py
=====================================
@@ -6,11 +6,13 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+from itertools import zip_longest
+import math
 import os
-import unittest
-import skbio
 import tempfile
+import unittest
 
+import skbio
 from qiime2.plugin.testing import TestPluginBase
 from qiime2.util import redirected_stdio
 from q2_types.feature_data import AlignedDNAFASTAFormat
@@ -332,9 +334,20 @@ class IqtreeTests(TestPluginBase):
         exp_tree = skbio.TreeNode.read(self.get_data_path('test5.tre'))
         exp_supp = [node.name for node in exp_tree.non_tips()]
 
-        self.assertEqual(set(obs_supp), set(exp_supp))
-        self.assertEqual(len(obs_supp[0].split('/')), 4)  # should be 4 values
-        self.assertEqual(len(exp_supp[0].split('/')), 4)  # should be 4 values
+        # iter through all support values for each node and check if they
+        # are at least within 1 support unit away from each other
+        zipped = zip_longest(obs_supp, exp_supp)
+        for (branch_sup_obs, branch_sup_exp) in zipped:
+            obs_sl = [float(n) for n in branch_sup_obs.split("/")]
+            exp_sl = [float(n) for n in branch_sup_exp.split("/")]
+            for (obs_f, exp_f) in zip_longest(obs_sl, exp_sl):
+                if math.isclose(obs_f, exp_f, abs_tol=1):
+                    continue
+                else:
+                    raise ValueError(
+                        "Observed branch support values \'{}\' are not equal "
+                        "to the expected values \'{}\'.".format(
+                                            branch_sup_obs, branch_sup_exp))
 
     def test_iqtree_ultrafast_bootstrap_safe_allnni(self):
         # Test that output tree is made.



View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/commit/659a7f8b1e5fe5b87d07174d6fe140da55ff2d6d

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View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/commit/659a7f8b1e5fe5b87d07174d6fe140da55ff2d6d
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