https://github.com/repronim/reproshell

Shell (bash only ATM) configuration to facilitate reproducible research
https://github.com/repronim/reproshell

Last synced: 12 months ago
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Shell (bash only ATM) configuration to facilitate reproducible research

• Host: GitHub
• URL: https://github.com/repronim/reproshell
• Owner: ReproNim
• License: apache-2.0
• Created: 2019-05-16T03:16:04.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-06-06T13:08:09.000Z (about 7 years ago)
• Last Synced: 2025-04-09T21:48:54.373Z (about 1 year ago)
• Size: 6.84 KB
• Stars: 0
• Watchers: 8
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# reproshell

Shell (bash only ATM) configuration to facilitate reproducible research

# Perspective features

Although some features are inspired by prototype implementation to be used within singularity container environments, they are applicable for any, even direct invocation.

- **Deployment**

  - [ ] could be used as a standalone configuration

  - [ ] could be "pluggable", i.e. the shell configuration to use within containers and remote sessions while "interfacing back" various session artifacts (e.g., history)

- **Features**, most of which should be configurable from outside (for "pluggable" mode of operation)

  - [ ] **infinite shell history** (unless explicitly requested to be session only, e.g. within container run)

  - [ ] **VCS support** (to show when under some VCS and in what branch/state it is)

  - **avoidance of session/execution side-effects**

   - [ ] isolated `/tmp`

   - [ ] (optionally) isolated `$HOME`? so no side-effects from `~/.local` installations etc

   - [ ] (optionally) sanitized environment variables

  - **informative and pretty (to >80% of users) prompt**

   - PS1 should should

    - [ ] show being under some container/conda/virtualenv environment

    - [ ] show full current path

    - [ ] show user (in particular when root)

    - [ ] (may be) # of commands in the history

   - additional "pluggable" indicators, such as 

    - [ ] being in a session traced by reprozip or reproman.

    - [ ] being outside of a set of "tracked" directories (e.g., within `datalad run` execution)

  - **integrations**

   - [ ] `datalad containers-run` or ReproNim/containers to replace parts of the custom .bashrc/singularity_run prototype

   - [ ] `reproman execute` and possibly `run` to provide consistent interface across wide range of resources

   - Metrics collection

    - [ ] could be the one to remind users whenever popularity-contest or our custom usage reporting facility is not enabled

   - [ ] (may be) even activate/deactivate handling for pluggable indicators etc (e.g. to enable/disable tracing)

   - [ ] could collect (and later aggregate/join) DueCredit reports from interim executions

   - [ ] may be optionally could be made persistent via starting actual session under screen or tmux.  Then could come with some custom nice .screenrc settings to visualize current load/

So, some features (infinite history, VCS integration, may be color scheme) could be provided by bundling existing 3rd party projects.  The rest more custom

## References

- Recommended .bashrc to assist in facilitating moer efficient shell and bash history use and archival:  https://github.com/ReproNim/module-reproducible-basics/pull/26

- Recording bash sessions history within git during interactive `datalad containers-run` https://github.com/ReproNim/containers/pull/9