fix: use full path to conda env (#64)

* fix: use full path to conda env

* chore: update CHANGELOG.md

* test: update tests for new biowulf conda activate

* test: forgotten conda activate

Author: kelly-sovacool

CHANGELOG.md

@@ -1,3 +1,7 @@
+## Tools development version
+
+- fix `ccbr_tools install`: use the full path to the conda env on biowulf. (#64, @kelly-sovacool)
+
 ## Tools 0.3.1
 
 - Bug fixes in `ccbr_tools install`:

src/ccbr_tools/pipeline/hpc.py

@@ -70,7 +70,7 @@ class Biowulf(Cluster):
     GROUP = "CCBR_Pipeliner"
     PIPELINES_HOME = pathlib.Path("/data/CCBR_Pipeliner/Pipelines")
     TOOLS_HOME = pathlib.Path("/data/CCBR_Pipeliner/Tools")
-    CONDA_ACTIVATE = '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311'
+    CONDA_ACTIVATE = "conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311"
 
     def __init__(self):
         super().__init__()

tests/test_pipeline_hpc.py

@@ -14,7 +14,7 @@ def test_hpc_biowulf():
                 "<class 'ccbr_tools.pipeline.hpc.Biowulf'>({'name': 'biowulf'"
             ),
             hpc.CONDA_ACTIVATE
-            == '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311',
+            == "conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311",
         ]
     )
 

tests/test_software.py

@@ -42,7 +42,7 @@ def test_install():
     )
     assert (
         result
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311
+        == """conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/CHAMPAGNE.git@v0.3.0 -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
@@ -63,7 +63,7 @@ def test_install_dev():
     )
     assert (
         result
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate py311
+        == """conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/CHAMPAGNE.git@main -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
 chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev