diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 477fcc6251185f0ea048f3015c608c4f935c2c3b..6458ae9769f0a701550abcec6f9e4f0b960939f7 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -113,7 +113,7 @@ func-test-ubuntu:
- py.test test/test_functional/test_corepers* -vx
- py.test test/test_functional/test_align-parser.py -vx
- py.test test/test_functional/test_align.py -vx
- # - py.test test/test_functional/test_tree* -vx
+ - py.test test/test_functional/test_tree* -vx
- py.test test/test_functional/test_annote-parser.py -vx
- py.test test/test_functional/test_annote.py -xv
- py.test test/test_functional/test_prepare* -vx
diff --git a/PanACoTA/subcommands/tree.py b/PanACoTA/subcommands/tree.py
index 716c233562798df1dc832e7ddbcf28dadd1f7571..b0d24abe17c96296a613a9bdf33340cb34e35cc5 100755
--- a/PanACoTA/subcommands/tree.py
+++ b/PanACoTA/subcommands/tree.py
@@ -167,26 +167,7 @@ def build_parser(parser):
parser to configure in order to extract command-line arguments
"""
import argparse
- import multiprocessing
-
- def thread_num(param):
- try:
- param = int(param)
- except Exception:
- msg = "argument --threads threads: invalid int value: {}".format(param)
- raise argparse.ArgumentTypeError(msg)
- nb_cpu = multiprocessing.cpu_count()
- if param > nb_cpu:
- msg = ("You have {} threads on your computer, you cannot ask for more: "
- "invalid value: {}").format(nb_cpu, param)
- raise argparse.ArgumentTypeError(msg)
- elif param < 0:
- msg = ("Please provide a positive number of threads (or 0 for all threads): "
- "Invalid value: {}").format(param)
- raise argparse.ArgumentTypeError(msg)
- elif param == 0:
- return nb_cpu
- return param
+ from PanACoTA import utils_argparse
# Create command-line parser for all options and arguments to give
@@ -210,7 +191,7 @@ def build_parser(parser):
"default, no bootstrap is calculated. For IQtree, it "
"will use ultrafast bootstrap (>=1000)."))
- optional.add_argument("--threads", dest="threads", default=1, type=thread_num,
+ optional.add_argument("--threads", dest="threads", default=1, type=utils_argparse.thread_num,
help=("add this option if you want to parallelize on several threads. "
"Indicate on how many threads you want to parallelize. "
"By default, it uses 1 thread. Put 0 if you want to use "
diff --git a/test/test_functional/test_tree-parser.py b/test/test_functional/test_tree-parser.py
index f70f2d8b18a39c7459c2a7a8a93c03c930b9dd2c..f598701fabb01ac31dcae3d818923d05e17afe15 100755
--- a/test/test_functional/test_tree-parser.py
+++ b/test/test_functional/test_tree-parser.py
@@ -93,7 +93,7 @@ def test_parser_quicktree_parallel(capsys):
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
with pytest.raises(SystemExit):
- tree.parse(parser, "-a align -s quicktree --threads 5 -o outdir".split())
+ tree.parse(parser, "-a align -s quicktree --threads 2 -o outdir".split())
_, err = capsys.readouterr()
assert ("You cannot run quicktree with multiple threads. Choose another software, or remove "
"the --threads option.") in err
@@ -317,14 +317,16 @@ def test_parser_threads_ok():
"""
parser = argparse.ArgumentParser(description="Tree", add_help=False)
tree.build_parser(parser)
- args = tree.parse(parser, "-a align -o outdir --threads 5".split())
+ import multiprocessing
+ nb = multiprocessing.cpu_count()
+ args = tree.parse(parser, f"-a align -o outdir --threads {nb}".split())
assert args.alignment == "align"
assert args.boot is None
assert args.outdir == "outdir"
assert args.soft == "iqtree"
assert args.model == "GTR"
assert args.write_boot is False
- assert args.threads == 5
+ assert args.threads == nb
assert args.verbose == 0
assert args.quiet == False
diff --git a/test/test_functional/test_tree.py b/test/test_functional/test_tree.py
index 6215f493d7c6881ddfe3b90d994b0b3b56bd4004..72758e21825d2d06d3062bd3e2194fea2b0ae976 100755
--- a/test/test_functional/test_tree.py
+++ b/test/test_functional/test_tree.py
@@ -33,7 +33,8 @@ def setup_teardown_module():
- remove all log files
- remove directory with generated results
"""
- os.mkdir(GENEPATH)
+ if not os.path.isdir(GENEPATH):
+ os.mkdir(GENEPATH)
print("setup")
yield
@@ -50,9 +51,10 @@ def test_main_default(capsys):
soft = "iqtree"
model = "GTR"
threads = 1
+ verbose = 3
cmd = "cmd test_main_default"
- tree.main(cmd, ALIGNMENT, outdir, soft, model, threads)
+ tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, verbose=verbose)
# Check output files
iq_log_file = os.path.join(outdir, "exp_pers4genomes.grp.aln.iqtree_tree.log")
assert os.path.isfile(iq_log_file)
@@ -73,6 +75,7 @@ def test_main_default(capsys):
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
+ print(out)
assert "Running IQtree..." in out
assert ("IQtree command: iqtree -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-nt 1 -m GTR -st DNA -pre test/data/tree/generated_by_func_tests/"
@@ -182,7 +185,7 @@ def test_main_fasttree(capsys):
threads = 1
boot = 100
cmd = "cmd: test_main_fasttree"
- tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, boot=boot)
+ tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, boot=boot, verbose=2)
# Check output files
# fastme logfile
log_file = os.path.join(outdir, "exp_pers4genomes.grp.aln.fasttree.log")
@@ -201,11 +204,12 @@ def test_main_fasttree(capsys):
# log files
logs_base = os.path.join(outdir, "PanACoTA-tree-fasttree.log")
assert os.path.isfile(logs_base)
- assert not os.path.isfile(logs_base + ".details")
+ assert os.path.isfile(logs_base + ".details")
assert not os.path.isfile(logs_base + ".debug")
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
+ print(out)
assert "Running FasttreeMP..." in out
assert ("Fasttree command: FastTreeMP -nt -gtr -noml -nocat -boot 100 "
"-log test/data/tree/generated_by_func_tests/exp_pers4genomes.grp.aln.fasttree.log "
@@ -224,7 +228,8 @@ def test_main_iqtree2_newdir(capsys):
threads = 1
cmd = "cmd test_main_default"
- tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, boot=1000, write_boot=True)
+ tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, boot=1000, write_boot=True,
+ verbose=2)
# Check output files
# Check iqtree logfile
iq_log_file = os.path.join(outdir, "exp_pers4genomes.grp.aln.iqtree_tree.log")
@@ -254,6 +259,7 @@ def test_main_iqtree2_newdir(capsys):
logs_base = os.path.join(outdir, "PanACoTA-tree-iqtree2.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".err")
+ assert os.path.isfile(logs_base + ".details")
# Check logs
out, err = capsys.readouterr()
assert "Running IQtree..." in out
@@ -278,7 +284,7 @@ def test_main_from_parse(capsys):
args.model = "HKY"
args.write_boot = False
args.threads = 1
- args.verbose = 1
+ args.verbose = 2
args.quiet = False
args.memory = False
args.fast = False