test: update tests for new behavior

src/renee/util.py

@@ -7,7 +7,7 @@ def renee_base(*paths):
     @return abs_path <str>
     """
     basedir = pathlib.Path(__file__).absolute().parent.parent.parent
-    return basedir.joinpath(*paths)
+    return str(basedir.joinpath(*paths))
 
 
 def get_version():

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"
     ]

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",

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():