Add new script for benchmarking

[HealthyPear]

Requirements

• Merge Improve data scripts output and update analysis default settings #165
• Merge Update the entire benchmark suite #166

Description

This PR adds a script that can be called as protopipe-BENCHMARK which has 2 commands,

• list, which lists all available benchmark notebooks under docs/contribute/benchmarks,
• launch, that allows to launch 1 notebook via papermill (which is here added as a development dependency) and produce not only its executed version but also an HTML page.

Using papermill allows to have default variables for input and optimizations, but the script can also read them from a configuration file bechmarks.yaml which should be copied with all the other ones by the interface (under testing in this PR).
Variables can be also overwritten on the go via the CLI flag --kwargs.

At the time of the first launch, a Jupyter Book template is filled, which pages are the single notebooks.
Such books are supposed to populate the new repository for the storage of performances.

TODO

• Update documentation
• Test with Jupyter Book
• Take care of Add analysis book template #172
• Fix merge conflicts

[codecov]

Codecov Report

Merging #157 (2e300aa) into master (f5827fc) will decrease coverage by 1.90%.
The diff coverage is 1.09%.

@@            Coverage Diff             @@
##           master     #157      +/-   ##
==========================================
- Coverage   64.95%   63.05%   -1.91%     
==========================================
  Files          27       28       +1     
  Lines        2802     2885      +83     
==========================================
- Hits         1820     1819       -1     
- Misses        982     1066      +84     

Impacted Files	Coverage Δ
protopipe/scripts/data_training.py	91.83% <ø> (ø)
protopipe/scripts/launch_benchmark.py	0.00% <0.00%> (ø)
protopipe/scripts/write_dl2.py	80.76% <ø> (ø)
protopipe/pipeline/utils.py	48.06% <100.00%> (+1.25%)	⬆️

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[kosack]

looks good