[med-svn] [Git][med-team/augur][upstream] New upstream version 13.0.2
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Oct 19 12:27:22 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / augur
Commits:
56d7c1d2 by Nilesh Patra at 2021-10-19T16:50:14+05:30
New upstream version 13.0.2
- - - - -
6 changed files:
- − .travis.yml
- CHANGES.md
- augur/__version__.py
- augur/tree.py
- setup.py
- tests/functional/tree.t
Changes:
=====================================
.travis.yml deleted
=====================================
@@ -1,45 +0,0 @@
-version: ~> 1.0
-language: generic
-
-# See <https://docs.travis-ci.com/user/build-stages/> for more information on
-# how build stages work.
-stages:
- - test
-
- # See <https://docs.travis-ci.com/user/conditions-v1> for more on the "if" syntax.
- - name: deploy
- if: branch = release and type != pull_request
-
-jobs:
- include:
- - &test
- stage: test
- language: python
- python: 3.6
- before_install:
- - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- - bash miniconda.sh -b -p $HOME/miniconda
- - export PATH="$HOME/miniconda/bin:$PATH"
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
- - conda info -a
- - conda create -n augur -c bioconda python=$TRAVIS_PYTHON_VERSION mafft raxml fasttree iqtree vcftools pip
- - source activate augur
- install:
- - pip install -e .[dev]
- script:
- - (pytest -c pytest.python3.ini --cov-report= --cov=augur)
- - (cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t)
- - (bash tests/builds/runner.sh)
- after_success:
- # upload to codecov
- - bash <(curl -s https://codecov.io/bash) -f "!*.gcov" -X gcov -e TRAVIS_PYTHON_VERSION -y ci/codecov.yml|| echo "Codecov did not collect coverage reports"
-
- - <<: *test
- python: 3.7
- - <<: *test
- python: 3.8
-
- - stage: deploy
- script: ./devel/travis-rebuild-docker-image
=====================================
CHANGES.md
=====================================
@@ -3,6 +3,16 @@
## __NEXT__
+## 13.0.2 (12 October 2021)
+
+### Bug Fixes
+
+* dependencies: Support latest versions of BioPython. [#777][] (@huddlej)
+* tree: Allow users to specify arbitrary IQ-TREE models. [#776][] (@huddlej)
+
+[#776]: https://github.com/nextstrain/augur/pull/776
+[#777]: https://github.com/nextstrain/augur/pull/777
+
## 13.0.1 (1 October 2021)
### Bug Fixes
=====================================
augur/__version__.py
=====================================
@@ -1,4 +1,4 @@
-__version__ = '13.0.1'
+__version__ = '13.0.2'
def is_augur_version_compatible(version):
=====================================
augur/tree.py
=====================================
@@ -191,19 +191,19 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt
file=sys.stderr
)
- if substitution_model.lower() != "none":
+ if substitution_model.lower() != "auto":
call = [iqtree, *fast_opts, "-nt", str(nthreads), "-s", shquote(tmp_aln_file),
"-m", substitution_model, tree_builder_args, ">", log_file]
else:
- call = [iqtree *fast_opts, "-nt", str(nthreads), "-s", shquote(tmp_aln_file), tree_builder_args, ">", shquote(log_file)]
+ call = [iqtree, *fast_opts, "-nt", str(nthreads), "-s", shquote(tmp_aln_file), tree_builder_args, ">", shquote(log_file)]
cmd = " ".join(call)
print("Building a tree via:\n\t" + cmd +
"\n\tNguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies."
"\n\tMol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300\n")
- if substitution_model.lower() == "none":
- print("Conducting a model test... see iqtree.log for the result. You can specify this with --substitution-model in future runs.")
+ if substitution_model.lower() == "auto":
+ print(f"Conducting a model test... see '{shquote(log_file)}' for the result. You can specify this with --substitution-model in future runs.")
try:
run_shell_command(cmd, raise_errors = True)
@@ -216,10 +216,6 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt
n.name = tmp_name
#this allows the user to check intermediate output, as tree.nwk will be
if clean_up:
- #allow user to see chosen model if modeltest was run
- if substitution_model.lower() == 'none':
- shutil.copyfile(log_file, out_file.replace(out_file.split('/')[-1],"iqtree.log"))
-
if os.path.isfile(tmp_aln_file):
os.remove(tmp_aln_file)
@@ -344,8 +340,8 @@ def register_arguments(parser):
parser.add_argument('--alignment', '-a', required=True, help="alignment in fasta or VCF format")
parser.add_argument('--method', default='iqtree', choices=["fasttree", "raxml", "iqtree"], help="tree builder to use")
parser.add_argument('--output', '-o', type=str, help='file name to write tree to')
- parser.add_argument('--substitution-model', default="GTR", choices=["HKY", "GTR", "HKY+G", "GTR+G", "GTR+R10"],
- help='substitution model to use. Specify \'none\' to run ModelTest. Currently, only available for IQTREE.')
+ parser.add_argument('--substitution-model', default="GTR",
+ help='substitution model to use. Specify \'auto\' to run ModelTest. Currently, only available for IQTREE.')
parser.add_argument('--nthreads', type=nthreads_value, default=1,
help="number of threads to use; specifying the value 'auto' will cause the number of available CPU cores on your system, if determinable, to be used")
parser.add_argument('--vcf-reference', type=str, help='fasta file of the sequence the VCF was mapped to')
=====================================
setup.py
=====================================
@@ -48,7 +48,7 @@ setuptools.setup(
python_requires = '>={}'.format('.'.join(str(n) for n in min_version)),
install_requires = [
"bcbio-gff >=0.6.0, ==0.6.*",
- "biopython >=1.67, <=1.76",
+ "biopython >=1.67, !=1.77, !=1.78",
"jsonschema >=3.0.0, ==3.*",
"packaging >=19.2",
"pandas >=1.0.0, ==1.*",
=====================================
tests/functional/tree.t
=====================================
@@ -20,6 +20,15 @@ Try building a tree with IQ-TREE with more threads (4) than there are input sequ
> --nthreads 4 > /dev/null
WARNING: more threads requested than there are sequences; falling back to IQ-TREE's `-nt AUTO` mode.
+Try building a tree with IQ-TREE using its ModelTest functionality, by supplying a substitution model of "auto".
+
+ $ ${AUGUR} tree \
+ > --alignment tree/aligned.fasta \
+ > --method iqtree \
+ > --substitution-model auto \
+ > --output "$TMP/tree_raw.nwk" \
+ > --nthreads 1 > /dev/null
+
Clean up tree log files.
$ rm -f tree/*.log
View it on GitLab: https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325
--
View it on GitLab: https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325
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