https://github.com/m-wells/jupyterparameters.jl
Enable passing of arguments to Julia Jupyter Notebooks from the command line.
Science Score: 10.0%
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Keywords
Repository
Enable passing of arguments to Julia Jupyter Notebooks from the command line.
Basic Info
- Host: GitHub
- Owner: m-wells
- License: agpl-3.0
- Language: Julia
- Default Branch: master
- Size: 61.5 KB
Statistics
- Stars: 4
- Watchers: 2
- Forks: 1
- Open Issues: 2
- Releases: 0
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Metadata Files
README.md
JupyterParameters
Treat Jupyter notebooks as visual scripts which can be executed from the command line or from a script. JupyterParameters creates and executes a new copy of the notebook with the parameters that have been passed and preserves the original.
My main use case for JupyterParameters is for batch processes that I also want to generate inline sophiscated plots.
This essentially creates log files of my data analysis along with plots.
Running Jupyter notebooks from the command line is already possible using
jupyter nbconvert --to notebook --execute mynotebook.ipynb
The issue with using nbconvert in this fashion, is you can not pass arguments to the notebook.
Using jjnbparam provided by JupyterParameters you are able to pass variables to a notebook.
julia
using JupyterParameters
jjnbparam(["notebook_orig.ipynb","notebook_new.ipynb","--varname1","varvalue1","--varname2","varvalue2",...]
How to call jjnbparam from the shell
We can create an alias in .bashrc as
alias jjnbparam='julia -e "using JupyterParameters; jjnbparam()"'
or add the following executable script (named jjnbparam) to your PATH.
julia --color=yes -e '
try
using JupyterParameters
catch
import Pkg; Pkg.add("JupyterParameters")
using JupyterParameters
end
jjnbparam()' "$@"
The command (from the shell) becomes
jjnbparam notebook_orig.ipynb notebook_new.ipynb --varname1 varvalue1 --varname2 varvalue2 ...
The command above creates and executes a new copy of the notebook with the parameters that have been passed and preserves the original.
If one wants to overwrite the original then
jjnbparam notebook.ipynb notebook.ipynb --varname1 varvalue1 --varname2 varvalue2 ...
The target notebook needs to include a parameters cell (this does not have to be the first cell):
To create a parameters cell simply edit the cell's metadata to include the following:
json
{
"tags": [
"parameters"
]
}
It is also helpful (for the user) to have a comment inside of the cell like so
```julia
this is the parameters cell
foo = 10
bar = "hi"
``
In the cell abovefooandbar` are defined with what can be thought of as default values which will be used if the user does not replace them.
This project was inspired by papermill
Customizing Notebook Execution
The execution of the notebook can be customized with
sh
jjnbparam refnote.ipynb outnote.ipynb \
--kernel_name julia-nodeps-1.1 \
--timeout -1 \
--var1 1234 \
--var2 "abcd"
where kernel_name specifies the IJulia kernel and timeout defines the maximum time (in seconds) each notebook cell is allowed to run.
These values are passed under-the-hood to jupyter nbconvert as traitlets.
If not passed the default values for jupyter nbconvert are used (again, see traitlets).
Owner
- Name: Mark Wells
- Login: m-wells
- Kind: user
- Location: Villanova, PA
- Company: Penn State
- Repositories: 40
- Profile: https://github.com/m-wells
GitHub Events
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Last Year
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| m-wells | m****1@p****u | 78 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 4
- Total pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 5.75
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
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- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
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Top Authors
Issue Authors
- m-wells (3)
- diegozea (1)
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- JuliaTagBot (1)
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Packages
- Total packages: 1
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Total downloads:
- julia 1 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
juliahub.com: JupyterParameters
Enable passing of arguments to Julia Jupyter Notebooks from the command line.
- Documentation: https://docs.juliahub.com/General/JupyterParameters/stable/
- License: AGPL-3.0
-
Latest release: 0.1.2
published about 7 years ago