[med-svn] [Git][med-team/q2-phylogeny][master] 6 commits: routine-update: New upstream version
Mohd Bilal (@rmb)
gitlab at salsa.debian.org
Wed Sep 7 12:23:52 BST 2022
Mohd Bilal pushed to branch master at Debian Med / q2-phylogeny
Commits:
9a349ddd by Mohammed Bilal at 2022-09-07T11:09:08+00:00
routine-update: New upstream version
- - - - -
659a7f8b by Mohammed Bilal at 2022-09-07T11:09:13+00:00
New upstream version 2022.8.0
- - - - -
04ea1445 by Mohammed Bilal at 2022-09-07T11:09:15+00:00
Update upstream source from tag 'upstream/2022.8.0'
Update to upstream version '2022.8.0'
with Debian dir 62c879c1e20471c3e6f821f5bdbe54a809bc2ee2
- - - - -
61801c90 by Mohammed Bilal at 2022-09-07T11:13:40+00:00
Refresh patch
- - - - -
de2d751e by Mohammed Bilal at 2022-09-07T11:14:23+00:00
Update dependency on qiime/q2-* >= 2022.8.0
- - - - -
3509d73a by Mohammed Bilal at 2022-09-07T11:15:12+00:00
Upload to unstable
- - - - -
7 changed files:
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/patches/fix-tests-and-binary-names-and-options.patch
- 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:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-phylogeny (2022.8.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 2022.8.0
+ * Refresh patch
+ * Update dependency on qiime/q2-* >= 2022.8.0
+
+ -- Mohammed Bilal <mdbilal at disroot.org> Wed, 07 Sep 2022 11:14:28 +0000
+
q2-phylogeny (2022.2.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -25,8 +25,8 @@ Depends: ${shlibs:Depends},
iqtree,
mafft,
raxml,
- q2-types (>= 2022.2.0),
- q2-alignment (>= 2022.2.0)
+ q2-types (>= 2022.8.0),
+ q2-alignment (>= 2022.8.0)
Description: QIIME 2 plugin for phylogeny
QIIME 2 plugin for phylogenetic reconstruction, and operations on
phylogenetic trees.
=====================================
debian/patches/fix-tests-and-binary-names-and-options.patch
=====================================
@@ -8,7 +8,7 @@ Forwarded: not-needed
Last-Update: 2021-07-18
--- a/q2_phylogeny/tests/test_raxml.py
+++ b/q2_phylogeny/tests/test_raxml.py
-@@ -88,37 +88,13 @@ class RaxmlTests(TestPluginBase):
+@@ -88,37 +88,13 @@
self.assertTrue('raxmlHPC' in str(obs_stand_1[0]))
self.assertTrue(len(obs_stand_1) == 1)
@@ -49,7 +49,7 @@ Last-Update: 2021-07-18
# load the resulting tree and test that it has the right number of
--- a/q2_phylogeny/_fasttree.py
+++ b/q2_phylogeny/_fasttree.py
-@@ -42,7 +42,7 @@ def fasttree(alignment: AlignedDNAFASTAF
+@@ -42,7 +42,7 @@
env.pop('OMP_NUM_THREADS', 0)
else:
env.update({'OMP_NUM_THREADS': str(n_threads)})
@@ -60,7 +60,7 @@ Last-Update: 2021-07-18
run_command(cmd, tree_fp, env=env)
--- a/q2_phylogeny/_iqtree.py
+++ b/q2_phylogeny/_iqtree.py
-@@ -75,7 +75,7 @@ def _build_iqtree_command(
+@@ -75,7 +75,7 @@
'-pre', str(run_prefix)]
if n_cores == 'auto' and n_cores_max:
@@ -69,7 +69,7 @@ Last-Update: 2021-07-18
elif n_cores == 'auto' and n_cores_max is None:
cmd += ['-nt', 'AUTO']
else:
-@@ -217,7 +217,7 @@ def _build_iqtree_ufbs_command(
+@@ -217,7 +217,7 @@
'-pre', str(run_prefix)]
if n_cores == 'auto' and n_cores_max:
@@ -78,13 +78,3 @@ Last-Update: 2021-07-18
elif n_cores == 'auto' and n_cores_max is None:
cmd += ['-nt', 'AUTO']
else:
---- a/q2_phylogeny/tests/test_iqtree.py
-+++ b/q2_phylogeny/tests/test_iqtree.py
-@@ -332,7 +332,6 @@ 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
-
=====================================
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/-/compare/f3a98d8cedb46a8a66c83ecb182cc909a02534ff...3509d73a3481484fc0e28570782f7b7270f48ef3
--
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/f3a98d8cedb46a8a66c83ecb182cc909a02534ff...3509d73a3481484fc0e28570782f7b7270f48ef3
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