fix: avoid "Admin" prompt when using conda on windows #1046
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At least on Windows, some packages will try to install start-menu shortcuts which require admin rights. This prevent an unattended installation of the conda environment. There is a "--no-shortcuts" for "conda create", but that doesn't work for "conda env create" See: conda/conda#9474 Conda build handles the problem by creating environments prefixed with an underscore "_<env-name>", which also cause conda to skip environment creation.
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For this to work I need help updating the docker image: "docker://quay.io/snakemake/containerize-testimage:1.0" I have updated the docker file, and all that is needed is for someone to make a new version of the test image and upload it. |
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For this to work I need help updating the docker image: "docker://quay.io/snakemake/containerize-testimage:1.0" I have updated the docker file, and all that is needed is for someone to make a new version of the test image and upload it. |
snakemake/deployment/conda.py
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| get_path = lambda h: os.path.join(env_dir, h) | ||
| # The underscore prefix cause the conda to skip shortcut installation so | ||
| # no admin prevleges are needed for windows. | ||
| get_path = lambda h: os.path.join(env_dir, "_" + h) |
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Mhm, I don't like to change a path just to work around some conda behavior. How does this relate to the --no-shortcuts flag below? How will this affect linux? Is this also an issue when using mamba instead of conda for the archive based installation?
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@johanneskoester: Yes, I understand why this is a bit ugly. But it seems like this is only way at the moment, and it is also what conda-build does when programmatically creating build and test environments.
The --no-shortcuts flag is only available for conda create and not for conda env create.
Maybe Mike Sarahan (@msarahan) can help clarify. Is prepending the environment name with a underscore still the only reliable way to prevent menu installation?
Is this also an issue when using mamba instead of conda for the archive based installation?
Mamba uses conda implementation here. So it should be fine. For micro-mamba the menuinst feature is beeing added right now: mamba-org/mamba#923 (comment)
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Ok, understood. If that is kind of the intended behavior and the underscore is the desired semantic meaning here, then I'm fine with it. Will it also prevent envs to be listed when running conda env list (which would be desired because that always annoyed me)?
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No. Unfortunately not. But it would be a good idea. I find that annoying as well.
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The only thing I could think of is adding something like:
sed -i "/_[^/]*$/d" ~/.conda/environments.txt
in you .bachrc to clean you environment listing every time you start a shell. That will remove environments from you listing starting with underscore. They environments will get re-added once they are activated again. But it is the only workaround I can think of.
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johanneskoester
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| hash_candidates = [ | ||
| hash[:8], | ||
| hash, | ||
| hash + "_", # activate no-shortcuts behavior (so that no admin rights are needed on win) |
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@johanneskoester, Maybe I misunderstand the code here, but I think the environment name should be prefixed with an underscore "_". I am not sure that postfix does the same thing.
`conda create --no-shortcuts` is only valid on windows. The option does not exist on other OSes. This fixes the regression introduced in snakemake#1046
`conda create --no-shortcuts` is only valid on windows. The option does not exist on other OSes. This fixes the regression introduced in snakemake#1046
`conda create --no-shortcuts` is only valid on windows. The option does not exist on other OSes. This fixes the regression introduced in snakemake#1046
#1046) (#1916) `conda create --no-shortcuts` is only valid on windows. The option does not exist on other OSes. This fixes the regression introduced in #1046 See https://github.com/conda/conda/blob/32b958df05e5fab04254ed2af9044ea99f5f13f1/conda/cli/conda_argparse.py#L1827-L1837
🤖 I have created a release *beep* *boop* --- ## [7.16.1](v7.16.0...v7.16.1) (2022-10-18) ### Bug Fixes * conda create --no-shortcuts absent on Linux/MacOS (regression from [#1046](#1046)) ([#1916](#1916)) ([8a86a1e](8a86a1e)) * fix typo in line display of exceptions ([#1912](#1912)) ([55e38a6](55e38a6)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
snakemake#1046) (snakemake#1916) `conda create --no-shortcuts` is only valid on windows. The option does not exist on other OSes. This fixes the regression introduced in snakemake#1046 See https://github.com/conda/conda/blob/32b958df05e5fab04254ed2af9044ea99f5f13f1/conda/cli/conda_argparse.py#L1827-L1837
🤖 I have created a release *beep* *boop* --- ## [7.16.1](snakemake/snakemake@v7.16.0...v7.16.1) (2022-10-18) ### Bug Fixes * conda create --no-shortcuts absent on Linux/MacOS (regression from [snakemake#1046](snakemake#1046)) ([snakemake#1916](snakemake#1916)) ([8a86a1e](snakemake@8a86a1e)) * fix typo in line display of exceptions ([snakemake#1912](snakemake#1912)) ([55e38a6](snakemake@55e38a6)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Description
This fixes a problem where
--use-condacan sometimes trigger an ´admin rights` prompt on Windows.The reason is that some conda packages will try to install start-menu shortcuts, and thus trigger an admin prompt.
There is a
conda create --no-shortcutsargument. But, unfortunately, the same doesn't exist forconda env createSee: conda/conda#9474
conda buildhandles the problem by creating environments prefixed with an underscore "_", which also cause conda to skip environment creation.This PR prefixes an underscore to the conda environments created in ".snakemake/conda"
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).