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))