Better isolate the SCT conda env by using -p instead of -n during creation
#3989
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Previously, when `-n` was used, there was a risk of the conda environment being created in `$ENVS_DIRS/venv_sct`, rather than the expected `$SCT_DIR/python/envs/venv_sct`. This is because `-n` is supposed to be a *relative name* within the global conda envs dir. This global envs dir can be set by users using a `.condarc` file. But, SCT would prefer to ignore the global dir, and always create its env in $SCT_DIR. Thankfully, `-p` specifies an absolute path, rather than a relative one, so it is unaffected by the presence of `envs_dirs` in a `.condarc` file.
kousu
approved these changes
Jan 5, 2023
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@kousu, gentle ping: did you have a chance to test this fix? |
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Sorry, nope. I did not test.
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Ok, using the reproduction steps from this comment, I was able to reproduce the problem inside a Docker container running ubuntu:22.04. Then I was able to check that this branch fixes the problem. I'll go ahead and merge it. |
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Thank you @mguaypaq! |
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Description
Previously, when
-nwas used, there was a risk of thevenv_sctconda environment being created in the global$ENVS_DIRSdirectory, rather than the expected$SCT_DIR/python/envs/venv_sct. This is because-nis supposed to be a relative name within the global conda envs dir. This global envs dir can be set by users using a.condarcfile. But, SCT would prefer to ignore this global dir, and always create its env in$SCT_DIR.So instead, we use
-p, which specifies an absolute path, rather than a relative one. This means it is unaffected by the presence ofenvs_dirsin a.condarcfile.Further rationale is provided in #3982 (comment).
Linked issues
Fixes #3982.