0.5.0
github-actions
released this
31 May 19:32
·
92 commits
to refs/heads/master
since this release
New Features
--venv
parameter available inkbatch
andkrun
, allowing preloading of a venv. This is especially useful for scripts.kpy export venv <name> --path <path>
allows the export of kpy venvs to any path.kapp
is a new family of commands to download and manage singularity containers. Full details can be found in the docs- Containers are pulled by name, but resolved to their content hash. This means that if you, for instance, pull both the
:latest
image and the specific version:latest
points to, no the image won't be pulled twice. On the other hand, if you pull:latest
a second time after the container is updated, the newly updated latest image will be pulled. - Containers are downloaded and built safely, regardless of size. For large containers, a job is scheduled on an interactive node to build the container.
- Containers can be aliased, providing easy access to commonly used apps
- kapp has light wrappers around singularity shell, run, and exec, allowing for easy consumption of kapp managed containers. For complete flexibility,
kapp path <container_uri_or_alias>
returns the resolved path of the container - All containers are automatically aliased in a snakemake readable format. Calling
kapp snakemake
returns a path you can pass to snakemake via the CLI param--singularity-prefix
, allowing snakemake to seamlessly consume any kapp managed container.
- Containers are pulled by name, but resolved to their content hash. This means that if you, for instance, pull both the
Fixes and Improvements
- When kjupyter is called with a
--venv
provided, it attempts to install jupyter-lab if not already installed - Escaped quotes in kbatch and krun commands are properly preserved
- kbatch properly runs sbatch scripts:
#SBATCH directives
will be properly parsed - The venv prompt name properly updates when calling
kpy load
. An asterisk (*) appears beside the venv name when modified (e.g. a new package is installed) - Better error messages
Changes
- Print scheduled time for batch @pvandyken (#33)
- kapp @pvandyken (#35)
🐛 Bug Fixes
- Fix kbatch treatment of scripts and in-job krun @pvandyken (#34)
- Improve quoting of commands @pvandyken (#32)
- Jupyter autoinstall @pvandyken (#31)