refactor: write get_singularity_cache_dir()

same behavior as before, just moved this from orchestrate() to its own function for the GUI to use too

src/renee/__main__.py

@@ -910,7 +910,7 @@ def parsed_arguments(name, description):
         type=lambda option: os.path.abspath(os.path.expanduser(option)),
         required=False,
         help=argparse.SUPPRESS,
-        default=get_sif_cache_dir(),
+        default=get_sif_cache_dir(hpc=get_hpcname()),
     )
 
     # Create NIDAP output folder

src/renee/cache.py

@@ -2,10 +2,18 @@
 import os
 import sys
 
-from .util import get_hpcname
+
+def get_singularity_cachedir(output_dir, cache_dir=None):
+    """Returns the singularity cache directory.
+    If no user-provided cache directory is provided,
+    the default singularity cache is in the output directory.
+    """
+    if not cache_dir:
+        cache_dir = os.path.join(output_dir, ".singularity")
+    return cache_dir
 
 
-def get_sif_cache_dir(hpc=get_hpcname()):
+def get_sif_cache_dir(hpc=None):
     sif_dir = None
     if hpc == "biowulf":
         sif_dir = "/data/CCBR_Pipeliner/SIFS"

src/renee/gui.py

@@ -13,6 +13,8 @@
     get_shared_resources_dir,
     renee_base,
     get_version,
+    get_singularity_cachedir,
+    get_hpcname,
 )
 from .cache import get_sif_cache_dir
 from .run import run_in_context
@@ -176,8 +178,10 @@ def launch_gui(sub_args, debug=True):
                 mode="slurm",
                 runmode="run",
                 dry_run=True,
-                sif_cache=get_sif_cache_dir(),
-                singularity_cache=os.environ["SINGULARITY_CACHEDIR"],
+                sif_cache=get_sif_cache_dir(hpc=get_hpcname()),
+                singularity_cache=get_singularity_cachedir(
+                    output_dir, os.environ.get("SINGULARITY_CACHEDIR", None)
+                ),
                 tmp_dir=get_tmp_dir(None, output_dir),
                 shared_resources=get_shared_resources_dir(None, output_dir),
                 star_2_pass_basic=False,

src/renee/util.py

@@ -5,6 +5,7 @@
 import shutil
 import sys
 import warnings
+from .cache import get_singularity_cachedir
 
 
 def renee_base(rel_path=""):
@@ -224,13 +225,9 @@ def orchestrate(
     # to output directory
     my_env = {}
     my_env.update(os.environ)
-    cache = os.path.join(outdir, ".singularity")
-    my_env["SINGULARITY_CACHEDIR"] = cache
 
-    if alt_cache:
-        # Override the pipeline's default cache location
-        my_env["SINGULARITY_CACHEDIR"] = alt_cache
-        cache = alt_cache
+    cache = get_singularity_cachedir(output_dir=outdir, cache_dir=alt_cache)
+    my_env["SINGULARITY_CACHEDIR"] = cache
 
     if additional_bind_paths:
         # Add Bind PATHs for outdir and tmp dir

tests/test_cache.py

@@ -3,7 +3,7 @@
 import os.path
 import subprocess
 
-from renee.src.renee.cache import get_sif_cache_dir
+from renee.src.renee.cache import get_sif_cache_dir, get_singularity_cachedir
 
 renee_run = (
     "./bin/renee run "
@@ -56,3 +56,12 @@ def test_get_sif_cache_dir():
     ]
     errors = [assertion for assertion in assertions if not eval(assertion)]
     assert not errors, "errors occurred:\n{}".format("\n".join(errors))
+
+
+def test_get_singularity_cachedir():
+    assertions = [
+        "get_singularity_cachedir('outdir') == 'outdir/.singularity'",
+        "get_singularity_cachedir('outdir', 'cache') == 'cache'",
+    ]
+    errors = [assertion for assertion in assertions if not eval(assertion)]
+    assert not errors, "errors occurred:\n{}".format("\n".join(errors))