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tests/biobambam2: convert to new stand-alone test process (#35696)

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Tamara Dahlgren 2023-05-29 03:54:38 -07:00 committed by GitHub
parent d85a27f317
commit 212b1edb6b
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1 changed files with 6 additions and 15 deletions
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21
var/spack/repos/builtin/packages/biobambam2/package.py
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@ -30,25 +30,16 @@ def configure_args(self):
args = ["--with-libmaus2={0}".format(self.spec["libmaus2"].prefix)]
return args
def _fix_shortsort(self):
"""Fix the testshortsort.sh file copied during installation."""
test_dir = join_path(self.install_test_root, self.test_src_dir)
filter_file("../src/", "", join_path(test_dir, "testshortsort.sh"))
@run_after("install")
def cache_test_sources(self):
"""Copy the test source files after the package is installed to an
install test subdirectory for use during `spack test run`."""
self.cache_extra_test_sources(self.test_src_dir)
self._fix_shortsort()
def test(self):
"""Perform stand-alone/smoke test on installed package."""
def test_short_sort(self):
"""run testshortsort.sh to check alignments sorted by coordinate"""
test_dir = join_path(self.test_suite.current_test_cache_dir, self.test_src_dir)
self.run_test(
"sh",
["testshortsort.sh"],
expected="Alignments sorted by coordinate.",
purpose="test: checking alignments",
work_dir=test_dir,
)
with working_dir(test_dir):
sh = which("sh")
out = sh("testshortsort.sh", output=str.split, error=str.split)
assert "Alignments sorted by coordinate." in out