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Description: Following things:
- Renamed binaries according to the names available in our distribution
- Disabled one failing test
- Remove tests which test SSE or AVX extensions of raxml
- Modify a test to use Standard raxml rather than SSE3
Author: Nilesh Patra <nilesh@debian.org>
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 @@
self.assertTrue('raxmlHPC' in str(obs_stand_1[0]))
self.assertTrue(len(obs_stand_1) == 1)
- obs_sse3_1 = _set_raxml_version(raxml_version='SSE3', n_threads=1)
- self.assertTrue('raxmlHPC-SSE3' in str(obs_sse3_1[0]))
- self.assertTrue(len(obs_sse3_1) == 1)
-
- obs_avx2_1 = _set_raxml_version(raxml_version='AVX2', n_threads=1)
- self.assertTrue('raxmlHPC-AVX2' in str(obs_avx2_1[0]))
- self.assertTrue(len(obs_avx2_1) == 1)
-
- obs_stand_4 = _set_raxml_version(raxml_version='Standard',
- n_threads=4)
- self.assertTrue('raxmlHPC-PTHREADS' in str(obs_stand_4[0]))
- self.assertTrue('4' in str(obs_stand_4[1]))
- self.assertTrue(len(obs_stand_4) == 2)
-
- obs_sse3_4 = _set_raxml_version(raxml_version='SSE3', n_threads=4)
- self.assertTrue('raxmlHPC-PTHREADS-SSE3' in str(obs_sse3_4[0]))
- self.assertTrue('4' in str(obs_sse3_4[1]))
- self.assertTrue(len(obs_sse3_4) == 2)
-
- obs_avx2_4 = _set_raxml_version(raxml_version='AVX2', n_threads=4)
- self.assertTrue('raxmlHPC-PTHREADS-AVX2' in str(obs_avx2_4[0]))
- self.assertTrue('4' in str(obs_avx2_4[1]))
- self.assertTrue(len(obs_avx2_4) == 2)
-
def test_raxml_version(self):
# Test that an output tree is made when invoking threads.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
- obs = raxml(input_sequences, raxml_version='SSE3')
+ obs = raxml(input_sequences, raxml_version='Standard')
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# 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 @@
env.pop('OMP_NUM_THREADS', 0)
else:
env.update({'OMP_NUM_THREADS': str(n_threads)})
- cmd = ['FastTreeMP']
+ cmd = ['fasttreeMP']
cmd.extend(['-quote', '-nt', aligned_fp])
run_command(cmd, tree_fp, env=env)
--- a/q2_phylogeny/_iqtree.py
+++ b/q2_phylogeny/_iqtree.py
@@ -75,7 +75,7 @@
'-pre', str(run_prefix)]
if n_cores == 'auto' and n_cores_max:
- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]
+ cmd += ['-nt', 'AUTO', '-ntmax', '%i' % n_cores_max]
elif n_cores == 'auto' and n_cores_max is None:
cmd += ['-nt', 'AUTO']
else:
@@ -217,7 +217,7 @@
'-pre', str(run_prefix)]
if n_cores == 'auto' and n_cores_max:
- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]
+ cmd += ['-nt', 'AUTO', '-ntmax', '%i' % n_cores_max]
elif n_cores == 'auto' and n_cores_max is None:
cmd += ['-nt', 'AUTO']
else:
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