Merge pull request #163 from CCBR/iss-162

fix: correct renee base path for cache subcommand

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 - New contributing guide available on GitHub and the documentation website. (#159, @kelly-sovacool)
 - New `renee debug` subcommand to determine the base directory for debugging purposes. (#159, @kelly-sovacool)
+- Fix `renee cache` subcommand to correctly read the container images config file. (#163, @kelly-sovacool)
 
 ## RENEE 2.6.0
 

src/renee/__main__.py

@@ -418,8 +418,7 @@ def cache(sub_args):
     """
     sif_cache = sub_args.sif_cache
     # Get absolute PATH to templates in renee git repo
-    repo_path = os.path.dirname(os.path.abspath(__file__))
-    images = os.path.join(repo_path, "config", "containers", "images.json")
+    images = os.path.join(RENEE_PATH, "config", "containers", "images.json")
 
     # Create image cache
     if not os.path.exists(sif_cache):
@@ -462,7 +461,7 @@ def cache(sub_args):
             username = os.environ.get("USER", os.environ.get("USERNAME"))
             masterjob = subprocess.Popen(
                 "sbatch --parsable -J pl:cache --time=10:00:00 --mail-type=BEGIN,END,FAIL "
-                + str(os.path.join(repo_path, "resources", "cacher"))
+                + str(os.path.join(RENEE_PATH, "resources", "cacher"))
                 + " slurm "
                 + " -s '{}' ".format(sif_cache)
                 + " -i '{}' ".format(",".join(pull))

tests/test_cache.py

@@ -61,3 +61,10 @@ def test_get_singularity_cachedir():
     ]
     errors = [assertion for assertion in assertions if not eval(assertion)]
     assert not errors, "errors occurred:\n{}".format("\n".join(errors))
+
+
+def test_cache_in_temp():
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        outdir = os.path.join(tmp_dir, "testout")
+        output = shell_run(f"./bin/renee cache --sif-cache {outdir} --dry-run")
+    assert "Image will be pulled from" in output