def test_check__can_pickle():
def _do_test_can_pickle(obj):
pickle.dumps(obj)
yield _do_test_can_pickle, versions.EQ(1, 2, 3)
yield _do_test_can_pickle, versions.GE(1, 2, 3)
yield _do_test_can_pickle, versions.LT(1, 2, 3)
yield _do_test_can_pickle, versions.Any()
yield _do_test_can_pickle, versions.And(versions.EQ(1, 2, 3))
yield _do_test_can_pickle, versions.Or(versions.GE(1, 2, 3))
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
import os
from paleomix.node import CommandNode
from paleomix.atomiccmd.command import AtomicCmd
from paleomix.atomiccmd.sets import SequentialCmds
from paleomix.common.fileutils import reroot_path, swap_ext
import paleomix.common.versions as versions
_VERSION_REGEX = r"Version: (\d+)\.(\d+)(?:\.(\d+))?"
# v0.2.0 was the pre-release version of v1.0, and lacks required features
_COMMON_CHECK = versions.Or(versions.EQ(0, 1, 19), versions.GE(1, 0, 0))
SAMTOOLS_VERSION = versions.Requirement(call=("samtools", ),
search=_VERSION_REGEX,
checks=_COMMON_CHECK)
SAMTOOLS_VERSION_1x = versions.Requirement(call=("samtools", ),
search=_VERSION_REGEX,
checks=versions.GE(1, 0, 0))
SAMTOOLS_VERSION_0119 = versions.Requirement(call=("samtools", ),
search=_VERSION_REGEX,
checks=versions.EQ(0, 1, 19))
BCFTOOLS_VERSION_0119 \
= versions.Requirement(call=("bcftools",),
use_customizable_cli_parameters, \
create_customizable_cli_parameters
from paleomix.atomiccmd.sets import ParallelCmds
from paleomix.nodes.samtools import SAMTOOLS_VERSION
from paleomix.common.fileutils import \
describe_paired_files, \
missing_files
import paleomix.common.versions as versions
import paleomix.tools.factory as factory
BWA_VERSION = versions.Requirement(call=("bwa",),
search=r"Version: (\d+)\.(\d+)\.(\d+)",
checks=versions.Or(versions.EQ(0, 5, 9),
versions.EQ(0, 5, 10),
versions.EQ(0, 6, 2),
versions.GE(0, 7, 9)))
BWA_VERSION_07x = versions.Requirement(call=("bwa",),
search=r"Version: (\d+)\.(\d+)\.(\d+)",
checks=versions.GE(0, 7, 9))
class BWAIndexNode(CommandNode):
def __init__(self, input_file, prefix=None, dependencies=()):
prefix = prefix if prefix else input_file
builder = _get_bwa_template(("bwa", "index"), prefix, iotype="OUT",
IN_FILE=input_file,
TEMP_OUT_PREFIX=os.path.basename(prefix),
def test_eq__check_values__not_equal():
obj = versions.EQ(2, 3)
assert not obj((1, 3))
assert not obj((2, 2))
assert not obj((1, 4))
def test_eq__check_values__equal():
obj = versions.EQ(2, 3)
assert obj((2, 3))
def test_eq__str__two_values():
obj = versions.EQ(2, 1)
assert str(obj) == "v2.1.x"
def test_eq__str__one_value():
obj = versions.EQ(1)
assert str(obj) == "v1.x"
def test_eq__check_values__not_equal_too_few_values():
obj = versions.EQ(2, 3)
with pytest.raises(ValueError):
obj((1, ))
def test_eq__check_values__equal_truncated():
obj = versions.EQ(2, 3)
assert obj((2, 3, 1))
checks=versions.GE(1, 1),
name="test#1",
)
try:
obj()
assert False # pragma: no coverage
except versions.VersionRequirementError as error:
assert str(error) == expected
###############################################################################
###############################################################################
# Pickling of checks
_CAN_PICKLE_VALUES = (
versions.EQ(1, 2, 3),
versions.GE(1, 2, 3),
versions.LT(1, 2, 3),
versions.Any(),
versions.And(versions.EQ(1, 2, 3)),
versions.Or(versions.GE(1, 2, 3)),
)
@pytest.mark.parametrize("obj", _CAN_PICKLE_VALUES)
def test_check__can_pickle(obj):
pickle.dumps(obj)
###############################################################################
###############################################################################
def test_eq__str__two_values():
obj = versions.EQ(2, 1)
assert_equal(str(obj), "v2.1.x")
def test_eq__str__one_value():
obj = versions.EQ(1)
assert_equal(str(obj), "v1.x")
def test_eq__check_values__not_equal_too_few_values():
obj = versions.EQ(2, 3)
assert_raises(ValueError, obj, (1, ))