Add/wrapper scripts - minor polishing #497
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marcodelapierre
changed the title
vsoch
reviewed
Feb 22, 2022
vsoch
reviewed
Feb 23, 2022
|
also, just committed some edits in the user/developer guides, only big thing is adding the description of wrapper settings in the table in the user guide, plus small edits |
vsoch
reviewed
Feb 23, 2022
|
oops, we were committing and commenting concurrently... does it make sense? otherwise we can undo the last commit and have them to be |
vsoch
reviewed
Feb 23, 2022
…-hpc into add/wrapper-scripts
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should be all good then :) |
Merged
vsoch
reviewed
Feb 23, 2022
Co-authored-by: Vanessasaurus <814322+vsoch@users.noreply.github.com>
vsoch
approved these changes
Feb 24, 2022
vsoch
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Mar 3, 2022
* reverting string to parse config params * config get: changed behaviour to work with dicts * reverting config get impl for non-dict, to try and fix tests * adding wrapper script variables * fix to updated settings.yml * new default: containers_base distinct from modules_base * 1st pass at wrapper_scripts for singularity * wrapper_script: added tcl for singularity * wrapper script: added script template for real (was in gitignore) * wrapper script: fix for add case * wrapper scripts now created as executable * wrapper scripts: templates for docker/podman * wrapper scripts: bin directory under modules * wrapper scripts: docker/podman support * reduced newlines in module templates * all shell settings nearby in settings.yml * utils/fileio: make executable using stat rather than subprocess methods * wrapper script templates: protecting argument passing * wrapper script templates: protecting argument passing for docker, too * container: defined wrapper_subdir attribute * modules: defined wrappertemplatefile property * wrapper scripts: relative PATH in modulefile templates * wrapper_scripts: new function _generate_wrapper_scripts in container/base.py * first shot at adding wrapper scripts this will support two kinds of wrapper scripts - global that live in the settings.yaml, and container.yaml specific that go alongside that file. We basically will then generate aliases for any executable names that were not created as wrappers. we will want to follow this up with a command to list wrappers, and also include descriptions for the interested user, and a flag to install to select on the fly warning - parsed_names (tool, registry, etc) are now prefixed with parsed_name.<variable> and the user will need to update settings * Add/wrapper scripts - minor polishing (#497) * fixed typos in module/templates/docs.md * minor polishing in settings.yml, wrappers_subdir * docs: edits to user and developer guides, for wrapper scripts * reverted a couple of shell occurrences (docker/podman) in modules/templates/docs.md * one more edit for shell in modules/templates/docs.md * Update docs/getting_started/user-guide.rst * adding new design for templates: bases and snippets! * wrapper/templates/bases: csh always needs "set" for variables * wrappers/templates: using variable moduleDir * modules/templates lua: moduleDir always replaces {{ module_dir }} * modules/templates tcl: moduleDir always replaces {{ module_dir }} * main/container: no more need to pass module_dir to template.render for modulefiles * registry/vanessa/salad: updated wrapper scripts with moduleDir var * registry/vanessa/salad: typo in singularity_fork.sh Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: Marco De La Pierre <marco.delapierre@gmail.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
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just minor polishing