ReproNim / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers
https://www.repronim.org/neurodocker/
Apache License 2.0
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Add mamba option to miniconda #562

Closed Shotgunosine closed 1 year ago

Shotgunosine commented 1 year ago

We're having trouble getting conda to install pandas in a timely fashion over in the freesurfer bids app: https://github.com/bids-apps/freesurfer/pull/67

Adding an option to use the mamba solver with miniconda would solve that for us.

Shotgunosine commented 1 year ago

Thanks, @stebo85, any ideas why the linters check is failing? Something about not being able to access the user site-packages directory? Seems like the same error as #561.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 97.43% and no project coverage change.

Comparison is base (a77bcc1) 88.63% compared to head (65cedc2) 88.63%. Report is 22 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #562 +/- ## ======================================= Coverage 88.63% 88.63% ======================================= Files 11 11 Lines 1021 1021 ======================================= Hits 905 905 Misses 116 116 ``` | [Files Changed](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim) | Coverage Δ | | |---|---|---| | [neurodocker/cli/minify/\_prune.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvY2xpL21pbmlmeS9fcHJ1bmUucHk=) | `0.00% <0.00%> (ø)` | | | [neurodocker/cli/generate.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvY2xpL2dlbmVyYXRlLnB5) | `91.59% <100.00%> (ø)` | | | [neurodocker/cli/minify/trace.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvY2xpL21pbmlmeS90cmFjZS5weQ==) | `84.09% <100.00%> (ø)` | | | [neurodocker/reproenv/renderers.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvcmVwcm9lbnYvcmVuZGVyZXJzLnB5) | `93.06% <100.00%> (ø)` | | | [neurodocker/reproenv/state.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvcmVwcm9lbnYvc3RhdGUucHk=) | `97.29% <100.00%> (ø)` | | | [neurodocker/reproenv/template.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvcmVwcm9lbnYvdGVtcGxhdGUucHk=) | `93.51% <100.00%> (ø)` | | | [neurodocker/reproenv/types.py](https://app.codecov.io/gh/ReproNim/neurodocker/pull/562?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReproNim#diff-bmV1cm9kb2NrZXIvcmVwcm9lbnYvdHlwZXMucHk=) | `100.00% <100.00%> (ø)` | |

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Remi-Gau commented 1 year ago

@stebo85 Do you think that we want to add a test of installing conda on the list of all the "containers" we test? It feels a bit silly to just install conda with no packages but if something start failing with a given distro, at least we may hear about it.

stebo85 commented 1 year ago

yes, that's a good idea. I haven't seen any issues with miniconda / mamba across different base systems, but a test for it would be nice