def test_or__check_version__insufficient_number_of_values():
def _do_or_check_num_values(obj_1, obj_2):
obj = versions.Or(obj_1, obj_2)
assert_raises(ValueError, obj, (1, 3))
yield _do_or_check_num_values, versions.GE(1, 2, 2), versions.LT(2, 0)
yield _do_or_check_num_values, versions.GE(1, 2, 2), versions.LT(2, 0, 1)
def test_or__str__two_items__first_is_operator():
obj_1 = versions.Or(versions.GE(1, 2), versions.LT(2, 0))
obj_2 = versions.LT(3, 4)
obj = versions.Or(obj_1, obj_2)
assert_equal(str(obj),
"(at least v1.2.x or prior to v2.0.x) or prior to v3.4.x")
def test_or__check_version__truncated():
def _do_or_check_truncated(obj_1, obj_2):
obj = versions.Or(obj_1, obj_2)
assert obj((1, 3, 3))
yield _do_or_check_truncated, versions.GE(1, 2), versions.LT(2, 0)
yield _do_or_check_truncated, versions.GE(1, 2, 2), versions.LT(2, 0)
yield _do_or_check_truncated, versions.GE(1, 2), versions.LT(2, 0, 1)
def test_or__str__two_items__second_is_operator():
obj_1 = versions.GE(1, 2)
obj_2 = versions.And(versions.GE(2, 0), versions.LT(3, 4))
obj = versions.Or(obj_1, obj_2)
assert_equal(str(obj),
"at least v1.2.x or (at least v2.0.x and prior to v3.4.x)")
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))
def test_lt__str__one_value():
obj = versions.LT(1)
assert_equal(str(obj), "prior to v1.x")
def test_or__check_version__insufficient_number_of_values__is_lazy():
obj_1 = versions.GE(1, 2)
obj_2 = versions.LT(2, 0, 1)
obj = versions.Or(obj_1, obj_2)
assert obj((1, 3))
def test_or__check_version__neither_true():
obj_1 = versions.And(versions.GE(1, 2), versions.LT(2, 0))
obj_2 = versions.And(versions.GE(2, 3), versions.LT(3, 0))
obj = versions.Or(obj_1, obj_2)
assert not obj((2, 2))
def test_lt__str__two_values():
obj = versions.LT(2, 1)
assert_equal(str(obj), "prior to v2.1.x")
def test_lt__check_values__not_less_than():
obj = versions.LT(2, 3)
assert not obj((2, 3))
assert not obj((2, 4))
def test_or__check_version__second_true():
obj_1 = versions.And(versions.GE(1, 2), versions.LT(2, 0))
obj_2 = versions.And(versions.GE(2, 3), versions.LT(3, 0))
obj = versions.Or(obj_1, obj_2)
assert obj((2, 3))
def test_requirement__new_obj_if_checks_differ():
obj1 = versions.Requirement("echo", "", versions.GE(1))
obj2 = versions.Requirement("echo", "", versions.LT(1))
assert_is_not(obj1, obj2)
# SOFTWARE.
#
import os
from pypeline.node import CommandNode
from pypeline.atomiccmd.command import AtomicCmd
from pypeline.common.fileutils import reroot_path, swap_ext
import pypeline.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.And(versions.GE(0, 1, 18),
versions.LT(0, 2, 0))
SAMTOOLS_VERSION = versions.Requirement(call=("samtools",),
search=_VERSION_REGEX,
checks=_COMMON_CHECK)
BCFTOOLS_VERSION \
= versions.Requirement(call=("bcftools",),
search=_VERSION_REGEX,
checks=_COMMON_CHECK)
TABIX_VERSION = versions.Requirement(call=("tabix",),
search=_VERSION_REGEX,
checks=versions.GE(0, 2, 5))
def test_or__init__non_check_value():
assert_raises(ValueError, versions.Or, versions.LT(2), None)
def test_or__str__two_items():
obj_ge = versions.GE(1, 2)
obj_lt = versions.LT(3, 4)
obj = versions.Or(obj_ge, obj_lt)
assert_equal(str(obj), "at least v1.2.x or prior to v3.4.x")
def test_and__check_version__first_true():
obj_1 = versions.And(versions.GE(1, 2), versions.LT(2, 0))
obj_2 = versions.And(versions.GE(2, 3), versions.LT(3, 0))
obj = versions.And(obj_1, obj_2)
assert not obj((1, 3))
def test_lt__check_values__not_less_than_too_few_values():
obj = versions.LT(2, 3)
assert_raises(ValueError, obj, (3,))
def test_lt__check_values__less_than_truncated():
obj = versions.LT(2, 3)
assert obj((2, 2, 1))
assert obj((2, 1, 2))
def test_requirement__obj_is_cached_for_same_values():
obj1 = versions.Requirement("echo", "", versions.LT(1))
obj2 = versions.Requirement("echo", "", versions.LT(1))
assert_is(obj1, obj2)
def test_or__check_version__both_true():
obj_1 = versions.GE(1, 2)
obj_2 = versions.LT(2, 0)
obj = versions.Or(obj_1, obj_2)
assert obj((1, 3))
def test_requirement__new_obj_if_search_differ():
obj1 = versions.Requirement("echo", r"(\d+)", versions.LT(1))
obj2 = versions.Requirement("echo", "", versions.LT(1))
assert_is_not(obj1, obj2)
def test_lt__check_values__less_than():
obj = versions.LT(2, 3)
assert obj((2, 2))
assert obj((1, 9))
def test_requirement_highest_priority_retained():
obj1 = versions.Requirement("echo", "", versions.LT(1), priority=5)
assert_equal(obj1.priority, 5)
obj2 = versions.Requirement("echo", "", versions.LT(1), priority=0)
assert_is(obj1, obj2)
assert_equal(obj2.priority, 5)
from pypeline.atomiccmd.command import AtomicCmd
from pypeline.atomiccmd.builder import \
AtomicCmdBuilder, \
use_customizable_cli_parameters, \
create_customizable_cli_parameters
from pypeline.atomiccmd.sets import ParallelCmds
from pypeline.nodes.samtools import SAMTOOLS_VERSION
import pypeline.common.versions as versions
BWA_VERSION = versions.Requirement(call=("bwa", ),
search=r"Version: (\d+)\.(\d+)\.(\d+)",
checks=versions.Or(
versions.And(versions.GE(0, 5, 9),
versions.LT(0, 6, 0)),
versions.GE(0, 7, 5)))
# Required by safeSam2Bam for 'PG' tagging support / known good version
# Cannot be a lambda due to need to be able to pickle function
def _get_pysam_version():
return __import__("pysam").__version__
PYSAM_VERSION = versions.Requirement(name="module 'pysam'",
call=_get_pysam_version,
search=r"(\d+)\.(\d+)\.(\d+)",
checks=versions.GE(0, 7, 4))
