fix: lowercase SIFs dir (#23)

* fix: lowercase SIFs dir

see CCBR/RENEE#181

* refactor: make singularity_sif_dir a dynamic property

* test: sif cache logic

* test: hpc class repr

* chore: update CHANGELOG.md

* ci: 🤖 render readme

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -5,6 +5,8 @@
 - use major & minor version for docs website subdirectories. (#15, @kelly-sovacool)
 - fig bug where `nextflow.run()` did not import the correct HPC modules. (#20, @kelly-sovacool)
 - fix bug in `_get_file_mtime()`. (#21, @kelly-sovacool)
+- fix shared SIF cache directory spelling for biowulf. (#23, @kelly-sovacool)
+
 
 ## Tools 0.1.1
 

README.md

@@ -68,7 +68,7 @@ import ccbr_tools.pkg_util
 print(ccbr_tools.pkg_util.get_version())
 ```
 
-    0.1.1-dev
+    0.1.2-dev
 
 ## CLI Utilities
 
@@ -122,15 +122,15 @@ package and do not have any unit tests.
 Please cite this software if you use it in a publication:
 
 > Sovacool K., Koparde V., Kuhn S., Tandon M., Huse S. (2024). CCBR
-> Tools: Utilities for CCBR Bioinformatics Software (version v0.1.0).
+> Tools: Utilities for CCBR Bioinformatics Software (version v0.1.2).
 > DOI: 10.5281/zenodo.13377166 URL: https://ccbr.github.io/Tools/
 
 ### Bibtex entry
 
     @misc{YourReferenceHere,
     author = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},
     doi = {10.5281/zenodo.13377166},
-    month = {8},
+    month = {11},
     title = {CCBR Tools: Utilities for CCBR Bioinformatics Software},
     url = {https://ccbr.github.io/Tools/},
     year = {2024}

src/ccbr_tools/pipeline/cache.py

@@ -20,9 +20,9 @@ def get_singularity_cachedir(output_dir=None, cache_dir=None):
 
 
 def get_sif_cache_dir(hpc=None):
-    sif_dir = None
+    sif_dir = ""
     if hpc == "biowulf":
-        sif_dir = "/data/CCBR_Pipeliner/SIFS"
+        sif_dir = "/data/CCBR_Pipeliner/SIFs"
     elif hpc == "frce":
         sif_dir = "/mnt/projects/CCBR-Pipelines/SIFs"
     return sif_dir

src/ccbr_tools/pipeline/hpc.py

@@ -5,7 +5,7 @@
 which contains default attributes for supported clusters.
 """
 
-from .cache import get_singularity_cachedir
+from .cache import get_singularity_cachedir, get_sif_cache_dir
 from ..shell import shell_run
 
 
@@ -27,16 +27,22 @@ def __init__(self):
         self.env_vars = "\n".join(
             (f"export SINGULARITY_CACHEDIR={get_singularity_cachedir()}",)
         )
-        self.singularity_sif_dir = None
 
     def __repr__(self):
-        return f"{self.__class__}({self.__dict__})"
+        dict_with_props = dict(
+            self.__dict__, singularity_sif_dir=self.singularity_sif_dir
+        )
+        return f"{self.__class__}({dict_with_props})"
 
     def __bool__(self):
         return bool(self.name)
 
     __nonzero__ = __bool__
 
+    @property
+    def singularity_sif_dir(self):
+        return get_sif_cache_dir(hpc=self.name)
+
 
 class Biowulf(Cluster):
     """
@@ -64,7 +70,6 @@ def __init__(self):
                 else " ccbrpipeliner"
             ),
         }
-        self.singularity_sif_dir = "/data/CCBR_Pipeliner/SIFs"
 
 
 class FRCE(Cluster):
@@ -82,7 +87,6 @@ def __init__(self):
         super().__init__()
         self.name = "frce"
         self.modules = {"nxf": "nextflow", "smk": "snakemake/7 singularity"}
-        self.singularity_sif_dir = "/mnt/projects/CCBR-Pipelines/SIFs"
         self.env_vars = "\n".join(
             (
                 self.env_vars,

tests/test_pipeline_cache.py

@@ -0,0 +1,19 @@
+from ccbr_tools.pipeline.cache import get_sif_cache_dir, get_singularity_cachedir
+
+
+def test_get_sif_cache_dir():
+    assertions = [
+        "'CCBR_Pipeliner/SIFs' in get_sif_cache_dir('biowulf')",
+        "'CCBR-Pipelines/SIFs' in get_sif_cache_dir('frce')",
+    ]
+    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))

tests/test_hpc.py → tests/test_pipeline_hpc.py

@@ -10,6 +10,9 @@ def test_hpc_biowulf():
             hpc,
             hpc.name == "biowulf",
             hpc.singularity_sif_dir == "/data/CCBR_Pipeliner/SIFs",
+            hpc.__repr__().startswith(
+                "<class 'ccbr_tools.pipeline.hpc.Biowulf'>({'name': 'biowulf'"
+            ),
         ]
     )
 
@@ -32,4 +35,4 @@ def test_hpc_none():
 
 
 if __name__ == "__main__":
-    print(get_hpc(debug="biowulf"))
+    print(get_hpc(debug="biowulf").__repr__())