[med-svn] [Git][med-team/q2-phylogeny][master] 9 commits: Autopkgtest for all supported Python3 versions
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 18 14:25:19 GMT 2024
Andreas Tille pushed to branch master at Debian Med / q2-phylogeny
Commits:
d3d270f9 by Andreas Tille at 2024-02-18T15:15:27+01:00
Autopkgtest for all supported Python3 versions
- - - - -
2af927ae by Andreas Tille at 2024-02-18T15:15:50+01:00
New upstream version 2024.2.0
- - - - -
0b185afe by Andreas Tille at 2024-02-18T15:15:50+01:00
routine-update: New upstream version
- - - - -
ed7c0486 by Andreas Tille at 2024-02-18T15:15:50+01:00
Update upstream source from tag 'upstream/2024.2.0'
Update to upstream version '2024.2.0'
with Debian dir 6f80f340a4bd6d3840cf77c90c5b78cc9bc4f102
- - - - -
60047784 by Andreas Tille at 2024-02-18T14:15:53+00:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
- - - - -
44101509 by Andreas Tille at 2024-02-18T14:15:53+00:00
Remove unnecessary Team Upload line in changelog.
Changes-By: lintian-brush
- - - - -
b442b1a6 by Andreas Tille at 2024-02-18T15:16:24+01:00
routine-update: Regenerate debian/control from debian/control.in
- - - - -
6cf64aad by Andreas Tille at 2024-02-18T15:21:08+01:00
Refresh patches
- - - - -
8e0e5957 by Andreas Tille at 2024-02-18T15:22:54+01:00
Upload to unstable
- - - - -
14 changed files:
- .github/workflows/ci-dev.yaml
- README.md
- debian/changelog
- debian/control
- debian/patches/fix-tests-and-binary-names-and-options.patch
- debian/patches/iqtree2.patch
- debian/tests/control
- debian/tests/run-unit-test
- q2_phylogeny/_fasttree.py
- q2_phylogeny/_iqtree.py
- q2_phylogeny/_raxml.py
- q2_phylogeny/_version.py
- q2_phylogeny/plugin_setup.py
- q2_phylogeny/tests/test_iqtree.py
Changes:
=====================================
.github/workflows/ci-dev.yaml
=====================================
@@ -9,4 +9,4 @@ jobs:
ci:
uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml at dev
with:
- distro: core
\ No newline at end of file
+ distro: amplicon
\ No newline at end of file
=====================================
README.md
=====================================
@@ -1,5 +1,5 @@
# q2-phylogeny
-
+
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+q2-phylogeny (2024.2.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * Autopkgtest for all supported Python3 versions
+ * Regenerate debian/control from debian/control.in (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Feb 2024 15:21:19 +0100
+
q2-phylogeny (2023.9.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -28,8 +28,8 @@ Depends: ${shlibs:Depends},
iqtree,
mafft,
raxml,
- q2-types (>= 2023.9),
- q2-alignment (>= 2023.9)
+ q2-types (>= 2024.2),
+ q2-alignment (>= 2024.2)
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 @@
+@@ -88,37 +88,13 @@ class RaxmlTests(TestPluginBase):
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 @@
+@@ -42,7 +42,7 @@ def fasttree(alignment: AlignedDNAFASTAF
env.pop('OMP_NUM_THREADS', 0)
else:
env.update({'OMP_NUM_THREADS': str(n_threads)})
@@ -60,21 +60,21 @@ 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 @@
- '-pre', str(run_prefix)]
+@@ -81,7 +81,7 @@ def _build_iqtree_command(
+ cmd += ['-nt', '%i' % n_cores]
- 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_max is not None and n_cores_max > 0:
+- cmd += ['--threads-max', '%i' % n_cores_max]
++ cmd += ['-ntmax', '%i' % n_cores_max]
- 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:
+ if seed:
+ cmd += ['-seed', '%i' % seed]
+@@ -224,7 +224,7 @@ def _build_iqtree_ufbs_command(
+ cmd += ['-nt', '%i' % n_cores]
+
+ if n_cores_max is not None and n_cores_max > 0:
+- cmd += ['--threads-max', '%i' % n_cores_max]
++ cmd += ['-ntmax', '%i' % n_cores_max]
+
+ if seed:
+ cmd += ['-seed', '%i' % seed]
=====================================
debian/patches/iqtree2.patch
=====================================
@@ -3,9 +3,9 @@ Author: Andreas Tille <tille at debian.org>
Forwarded: not-needed
Last-Update: Wed, 20 Jul 2022 14:54:54 +0200
---- q2-phylogeny.orig/q2_phylogeny/_iqtree.py
-+++ q2-phylogeny/q2_phylogeny/_iqtree.py
-@@ -66,7 +66,7 @@
+--- a/q2_phylogeny/_iqtree.py
++++ b/q2_phylogeny/_iqtree.py
+@@ -66,7 +66,7 @@ def _build_iqtree_command(
lbp: int = _iqtree_defaults['lbp'],
safe: bool = _iqtree_defaults['safe']):
@@ -14,7 +14,7 @@ Last-Update: Wed, 20 Jul 2022 14:54:54 +0200
cmd += ['-st', str(dtype),
'--runs', '%i' % n_runs,
-@@ -208,7 +208,7 @@
+@@ -210,7 +210,7 @@ def _build_iqtree_ufbs_command(
# This is a separate command becuase there are several
# bootstrap specific options.
@@ -23,9 +23,9 @@ Last-Update: Wed, 20 Jul 2022 14:54:54 +0200
cmd += ['-st', str(dtype),
'--runs', '%i' % n_runs,
---- q2-phylogeny.orig/q2_phylogeny/tests/test_iqtree.py
-+++ q2-phylogeny/q2_phylogeny/tests/test_iqtree.py
-@@ -414,7 +414,7 @@
+--- a/q2_phylogeny/tests/test_iqtree.py
++++ b/q2_phylogeny/tests/test_iqtree.py
+@@ -414,7 +414,7 @@ class IqtreeRunCommandTests(TestPluginBa
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtree')
@@ -34,7 +34,7 @@ Last-Update: Wed, 20 Jul 2022 14:54:54 +0200
'-m', 'HKY',
'-seed', '1723',
'-s', aligned_fp,
-@@ -444,7 +444,7 @@
+@@ -444,7 +444,7 @@ class IqtreeRunCommandTests(TestPluginBa
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot')
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest-cov
+Depends: @, python3-pytest-cov, python3-all
Restrictions: allow-stderr, skip-not-installable
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,4 +18,7 @@ if [ ! -f /usr/lib/python3/dist-packages/pytest_cov/__init__.py ] ; then
fi
# Run build-time tests
-py.test-3 --cov=${pkg}
+for py in $(py3versions -s 2> /dev/null)
+do
+ ${py} -m pytest -v --cov=${pkg}
+done
=====================================
q2_phylogeny/_fasttree.py
=====================================
@@ -38,7 +38,7 @@ def fasttree(alignment: AlignedDNAFASTAFormat,
cmd = ['FastTree']
else:
env = os.environ.copy()
- if n_threads == 'auto':
+ if n_threads == 0:
env.pop('OMP_NUM_THREADS', 0)
else:
env.update({'OMP_NUM_THREADS': str(n_threads)})
=====================================
q2_phylogeny/_iqtree.py
=====================================
@@ -74,13 +74,15 @@ def _build_iqtree_command(
'-m', str(substitution_model),
'-pre', str(run_prefix)]
- if n_cores == 'auto' and n_cores_max:
- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]
- elif n_cores == 'auto' and n_cores_max is None:
+ if n_cores == 0:
cmd += ['-nt', 'AUTO']
else:
+ print('n cores', n_cores)
cmd += ['-nt', '%i' % n_cores]
+ if n_cores_max is not None and n_cores_max > 0:
+ cmd += ['--threads-max', '%i' % n_cores_max]
+
if seed:
cmd += ['-seed', '%i' % seed]
@@ -216,13 +218,14 @@ def _build_iqtree_ufbs_command(
'-m', str(substitution_model),
'-pre', str(run_prefix)]
- if n_cores == 'auto' and n_cores_max:
- cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max]
- elif n_cores == 'auto' and n_cores_max is None:
+ if n_cores == 0:
cmd += ['-nt', 'AUTO']
else:
cmd += ['-nt', '%i' % n_cores]
+ if n_cores_max is not None and n_cores_max > 0:
+ cmd += ['--threads-max', '%i' % n_cores_max]
+
if seed:
cmd += ['-seed', '%i' % seed]
=====================================
q2_phylogeny/_raxml.py
=====================================
@@ -14,6 +14,7 @@ from random import randint
from q2_types.feature_data import AlignedDNAFASTAFormat
from q2_types.tree import NewickFormat
+from qiime2.plugin import get_available_cores
_raxml_versions = {
'Standard': '',
@@ -35,6 +36,9 @@ def run_command(cmd, verbose=True):
def _set_raxml_version(raxml_version='Standard', n_threads=1):
+ if n_threads == 0:
+ n_threads = get_available_cores()
+
if n_threads == 1:
cmd = ['raxmlHPC' + _raxml_versions[raxml_version]]
return cmd
=====================================
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: 2023.9.0, Release-2023.9)"
- git_full = "3f6beeea0d4c1510daf772f75a05d6fc95a1f37a"
- git_date = "2023-10-03 22:01:55 +0000"
+ git_refnames = " (tag: 2024.2.0, Release-2024.2)"
+ git_full = "f0ffa35ea1132d9eb7a26bb23510521a020ec463"
+ git_date = "2024-02-16 21:58:36 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_phylogeny/plugin_setup.py
=====================================
@@ -7,7 +7,7 @@
# ----------------------------------------------------------------------------
from qiime2.plugin import (Plugin, Citations, Int, Range, Str, Choices, Bool,
- Float, List, TypeMatch, Metadata)
+ Float, List, TypeMatch, Metadata, Threads)
from q2_types.tree import Phylogeny, Unrooted, Rooted
from q2_types.feature_data import FeatureData, AlignedSequence, Sequence
from q2_types.feature_table import (FeatureTable, Frequency,
@@ -104,7 +104,7 @@ plugin.methods.register_function(
plugin.methods.register_function(
function=q2_phylogeny.fasttree,
inputs={'alignment': FeatureData[AlignedSequence]},
- parameters={'n_threads': Int % Range(1, None) | Str % Choices(['auto'])},
+ parameters={'n_threads': Threads},
outputs=[('tree', Phylogeny[Unrooted])],
input_descriptions={
'alignment': ('Aligned sequences to be used for phylogenetic '
@@ -132,7 +132,7 @@ plugin.methods.register_function(
parameters={
'seed': Int,
'n_searches': Int % Range(1, None),
- 'n_threads': Int % Range(1, None),
+ 'n_threads': Threads,
'substitution_model': Str % Choices(_RAXML_MODEL_OPT),
'raxml_version': Str % Choices(_RAXML_VERSION_OPT)},
outputs=[('tree', Phylogeny[Unrooted])],
@@ -171,7 +171,7 @@ plugin.methods.register_function(
'seed': Int,
'rapid_bootstrap_seed': Int,
'bootstrap_replicates': Int % Range(10, None),
- 'n_threads': Int % Range(1, None),
+ 'n_threads': Threads,
'substitution_model': Str % Choices(_RAXML_MODEL_OPT),
'raxml_version': Str % Choices(_RAXML_VERSION_OPT)},
outputs=[('tree', Phylogeny[Unrooted])],
@@ -212,8 +212,8 @@ plugin.methods.register_function(
inputs={'alignment': FeatureData[AlignedSequence]},
parameters={
'seed': Int,
- 'n_cores': Int % Range(1, None) | Str % Choices(['auto']),
- 'n_cores_max': Int % Range(2, None),
+ 'n_cores': Threads,
+ 'n_cores_max': Threads,
'n_runs': Int % Range(1, None),
'substitution_model': Str % Choices(_IQTREE_DNA_MODELS),
'n_init_pars_trees': Int % Range(1, None),
@@ -297,8 +297,8 @@ plugin.methods.register_function(
inputs={'alignment': FeatureData[AlignedSequence]},
parameters={
'seed': Int,
- 'n_cores': Int % Range(1, None) | Str % Choices(['auto']),
- 'n_cores_max': Int % Range(2, None),
+ 'n_cores': Threads,
+ 'n_cores_max': Threads,
'n_runs': Int % Range(1, None),
'substitution_model': Str % Choices(_IQTREE_DNA_MODELS),
'n_init_pars_trees': Int % Range(1, None),
@@ -495,7 +495,7 @@ plugin.pipelines.register_function(
'sequences': FeatureData[Sequence],
},
parameters={
- 'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
+ 'n_threads': Threads,
'mask_max_gap_frequency': Float % Range(0, 1, inclusive_end=True),
'mask_min_conservation': Float % Range(0, 1, inclusive_end=True),
'parttree': Bool,
@@ -568,7 +568,7 @@ plugin.pipelines.register_function(
'sequences': FeatureData[Sequence],
},
parameters={
- 'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
+ 'n_threads': Threads,
'mask_max_gap_frequency': Float % Range(0, 1, inclusive_end=True),
'mask_min_conservation': Float % Range(0, 1, inclusive_end=True),
'seed': Int,
@@ -659,7 +659,7 @@ plugin.pipelines.register_function(
'sequences': FeatureData[Sequence],
},
parameters={
- 'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
+ 'n_threads': Threads,
'mask_max_gap_frequency': Float % Range(0, 1, inclusive_end=True),
'mask_min_conservation': Float % Range(0, 1, inclusive_end=True),
'parttree': Bool,
=====================================
q2_phylogeny/tests/test_iqtree.py
=====================================
@@ -103,7 +103,7 @@ class IqtreeTests(TestPluginBase):
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
- obs = iqtree(input_sequences, n_cores='auto')
+ obs = iqtree(input_sequences, n_cores=0)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
@@ -122,7 +122,7 @@ class IqtreeTests(TestPluginBase):
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
- obs = iqtree(input_sequences, n_cores='auto', n_cores_max=2)
+ obs = iqtree(input_sequences, n_cores=0, n_cores_max=2)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
@@ -197,7 +197,7 @@ class IqtreeTests(TestPluginBase):
with redirected_stdio(stderr=os.devnull):
obs = _build_iqtree_command(input_sequences,
seed=1723,
- n_cores='auto',
+ n_cores=0,
n_cores_max=4,
n_runs=2,
substitution_model='MFP',
@@ -246,7 +246,7 @@ class IqtreeTests(TestPluginBase):
with redirected_stdio(stderr=os.devnull):
obs = _build_iqtree_ufbs_command(input_sequences,
seed=1723,
- n_cores='auto',
+ n_cores=0,
n_cores_max=6,
n_runs=5,
bootstrap_replicates=2000,
@@ -373,7 +373,7 @@ class IqtreeTests(TestPluginBase):
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 = iqtree_ultrafast_bootstrap(input_sequences, n_cores='auto')
+ obs = iqtree_ultrafast_bootstrap(input_sequences, n_cores=0)
obs_tree = skbio.TreeNode.read(str(obs))
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
@@ -390,7 +390,7 @@ class IqtreeTests(TestPluginBase):
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 = iqtree_ultrafast_bootstrap(input_sequences, n_cores='auto',
+ obs = iqtree_ultrafast_bootstrap(input_sequences, n_cores=0,
n_cores_max=2)
obs_tree = skbio.TreeNode.read(str(obs))
# load the resulting tree and test that it has the right number of
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/fc1fa7824ce3c6356207fe23887dc467937c6f73...8e0e5957a63f5a2853e25bc7c432499ad6574b03
--
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/compare/fc1fa7824ce3c6356207fe23887dc467937c6f73...8e0e5957a63f5a2853e25bc7c432499ad6574b03
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