From 6583dcecc315b222b4e8607dbe34e59d22548f9c Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 13 Aug 2024 17:14:38 -0400 Subject: [PATCH] test: update tests for new behavior --- src/renee/util.py | 2 +- tests/test_cache.py | 2 +- tests/test_run.py | 2 +- tests/test_util.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/renee/util.py b/src/renee/util.py index 1401cad..4a6e273 100644 --- a/src/renee/util.py +++ b/src/renee/util.py @@ -7,7 +7,7 @@ def renee_base(*paths): @return abs_path """ basedir = pathlib.Path(__file__).absolute().parent.parent.parent - return basedir.joinpath(*paths) + return str(basedir.joinpath(*paths)) def get_version(): diff --git a/tests/test_cache.py b/tests/test_cache.py index 0c1c431..76d87f8 100644 --- a/tests/test_cache.py +++ b/tests/test_cache.py @@ -38,7 +38,7 @@ def test_cache_sif(): def test_cache_nosif(): - output, config = run_in_temp(f"{renee_run}") + output, config = run_in_temp(f"{renee_run} --sif-cache not/a/path") assertions = [ config["images"]["arriba"] == "docker://nciccbr/ccbr_arriba_2.0.0:v0.0.1" ] diff --git a/tests/test_run.py b/tests/test_run.py index 793a6db..a2b05be 100644 --- a/tests/test_run.py +++ b/tests/test_run.py @@ -18,7 +18,7 @@ def test_dryrun(): if get_hpcname() == "biowulf": with tempfile.TemporaryDirectory() as tmp_dir: run_args = argparse.Namespace( - input=list(glob.glob(renee_base(".tests", "*.fastq.gz"))), + input=list(glob.glob(f"{renee_base('.tests')}/*.fastq.gz")), output=tmp_dir, genome=renee_base("config", "genomes", "biowulf", "hg38_36.json"), mode="slurm", diff --git a/tests/test_util.py b/tests/test_util.py index 3b45454..17f8b5f 100644 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -17,7 +17,7 @@ def test_renee_base(): renee_bin = renee_base(os.path.join("bin", "renee")) - assert str(renee_bin).endswith("/bin/renee") and renee_bin.exists() + assert str(renee_bin).endswith("/bin/renee") and os.path.exists(renee_bin) def test_cp_safe():