Ausbeth reinstall

[Ausbeth]

reinstall functionality

[Ausbeth]

shpc reinstall software # reinstall all installed versions of that software (achieved)
shpc reinstall software:version # reinstall only that version (achieved)
shpc reinstall --all # reinstall all installed versions of all software (achieved)

By default, shpc reinstall software will keep the current container of that software.

User can type --complete flagger to override that:
shpc reinstall software --complete/shpc reinstall software:version --complete #remove the current container and reinstall

Note - User cannot type:

   shpc reinstall software --all

[gq1]

shpc reinstall
You must specify a recipe to reinstall or use --all to reinstall all installed modules.

$ shpc reinstall -h
usage: shpc reinstall [-h] [--complete] [--all] [--keep-path] [--no-view] [--force] [--module-sys {lmod,tcl}] [--container-tech {singularity,podman,docker}]
                      [reinstall_recipe] [container_image]

Reinstall a module. Containers are kept by default

  # Reinstall a specific version of a module
  $ shpc reinstall python:3.12-rc

  # Reinstall the all versions of a module
  $ shpc reinstall python

  # Completely reinstall a module without keeping the container
  $ shpc reinstall python --complete

  # Reinstall all installed modules
  $ shpc reinstall python --all

positional arguments:
  reinstall_recipe      recipe to reinstall
  container_image       path to an existing container image for this software

options:
  -h, --help            show this help message and exit
  --complete, --c       do not keep the container image file, when uninstall or reinstall
  --all, --a            reinstall all installed modules
  --keep-path           if installing a local container, do not copy the container - use the provided path.
  --no-view             skip installing to the default view, if defined in settings.
  --force, -f           replace existing symlinks
  --module-sys {lmod,tcl}
                        module system to use (defaults to lmod)
  --container-tech {singularity,podman,docker}
                        container technology to use to override settings.yaml

$ shpc reinstall quay.io/biocontainers/samtools
You currently don't have 'quay.io/biocontainers/samtools' installed.
Try: shpc install

$ shpc reinstall quay.io/biocontainers/samtools
Reinstalling all versions of quay.io/biocontainers/samtools...
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
/nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/views/tol/samtools/1.20--h50ea8bc_0 has been removed.
singularity pull --name /nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/container_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/quay.io-biocontainers-samtools-1.20--h50ea8bc_0-sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc.sif docker://quay.io/biocontainers/samtools@sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc
INFO:    Using cached SIF image
Module quay.io/biocontainers/samtools:1.20--h50ea8bc_0 was created.
Creating link $module_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/module.tcl -> $views_base/tol/samtools/1.20--h50ea8bc_0
Successfully reinstalled all versions of quay.io/biocontainers/samtools.

shpc reinstall quay.io/biocontainers/samtools:1.20--h50ea8bc_0
Reinstalling quay.io/biocontainers/samtools:1.20--h50ea8bc_0...
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
/nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/views/tol/samtools/1.20--h50ea8bc_0 has been removed.
singularity pull --name /nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/container_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/quay.io-biocontainers-samtools-1.20--h50ea8bc_0-sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc.sif docker://quay.io/biocontainers/samtools@sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc
INFO:    Using cached SIF image
Module quay.io/biocontainers/samtools:1.20--h50ea8bc_0 was created.
Creating link $module_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/module.tcl -> $views_base/tol/samtools/1.20--h50ea8bc_0
Successfully reinstalled of quay.io/biocontainers/samtools:1.20--h50ea8bc_0.

$ shpc reinstall --all
Reinstalling all installed modules...
Reinstalling all versions of quay.io/biocontainers/samtools...
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
/nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/views/tol/samtools/1.20--h50ea8bc_0 has been removed.
singularity pull --name /nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/container_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/quay.io-biocontainers-samtools-1.20--h50ea8bc_0-sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc.sif docker://quay.io/biocontainers/samtools@sha256:d0ebd10e887e3ddd02d071f1ca7b649dc90dc6fb99a5ffd0f5ebf8611a1f92cc
INFO:    Using cached SIF image
Module quay.io/biocontainers/samtools:1.20--h50ea8bc_0 was created.
Creating link $module_base/quay.io/biocontainers/samtools/1.20--h50ea8bc_0/module.tcl -> $views_base/tol/samtools/1.20--h50ea8bc_0
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
Container was kept but template will be overwritten upon reinstall
/nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/views/tol/samtools/1.19.2--h50ea8bc_1 has been removed.
singularity pull --name /nfs/users/nfs_g/gq2/workdir/ausbeth/shpc2/ausbeth-reinstall/container_base/quay.io/biocontainers/samtools/1.19.2--h50ea8bc_1/quay.io-biocontainers-samtools-1.19.2--h50ea8bc_1-sha256:9cd15e719101ae8808e4c3f152cca2bf06f9e1ad8551ed43c1e626cb6afdaa02.sif docker://quay.io/biocontainers/samtools@sha256:9cd15e719101ae8808e4c3f152cca2bf06f9e1ad8551ed43c1e626cb6afdaa02
INFO:    Using cached SIF image
Module quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1 was created.
Creating link $module_base/quay.io/biocontainers/samtools/1.19.2--h50ea8bc_1/module.tcl -> $views_base/tol/samtools/1.19.2--h50ea8bc_1
Successfully reinstalled all versions of quay.io/biocontainers/samtools.
All modules reinstalled.

[muffato]

Hi @Ausbeth . Here are some comments on your code, mainly going into two categories:

• the current implementation
• options/modes we haven't talked much about so far, like views, container paths, etc.

[muffato]

Almost nothing left from me. Good job

[muffato]

Thank you @Ausbeth for those changes 👍🏼 .
pytest works for me locally, but I only run tcl and singularity. There seems to be an error on GitHub CI. Can you take a look ? That's the only reason why I'm not approving the PR yet

[Ausbeth]

Hi @muffato, yes, the issue is that the tests are not working with podman for some reason. I have been trying to solve it, but I don't know how to at the moment