Overhall CLI

[je-cook]

Description

Rewrites the CLI to use click and orchestrates all cli modules under the process cli function

Closes #4011

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 21.32196% with 1107 lines in your changes missing coverage. Please review.
✅ Project coverage is 49.44%. Comparing base (1a9dd1c) to head (96c9094).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
process/core/io/plot/stress_tf.py	0.00%	265 Missing ⚠️
process/core/io/vary_run/config.py	28.23%	211 Missing ⚠️
process/core/io/plot/sankey.py	11.60%	160 Missing ⚠️
process/core/io/plot/scans.py	3.26%	89 Missing ⚠️
process/core/io/plot/cli.py	0.00%	63 Missing ⚠️
process/core/io/plot/costs/costs_bar.py	0.00%	52 Missing ⚠️
process/core/io/in_dat/create.py	0.00%	45 Missing ⚠️
process/core/io/plot/costs/cli.py	0.00%	40 Missing ⚠️
process/core/io/mfile/cli.py	0.00%	30 Missing ⚠️
process/core/io/mfile/comparison.py	21.21%	26 Missing ⚠️
... and 8 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4105      +/-   ##
==========================================
+ Coverage   48.08%   49.44%   +1.36%     
==========================================
  Files         144      149       +5     
  Lines       30243    29802     -441     
==========================================
+ Hits        14541    14737     +196     
+ Misses      15702    15065     -637     

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[chris-ashe]

Just a few requests.

• Can we add -h as a shortcut for --help as this was a legacy option?
• In some of the plotting options you have to specify -f before the MFILE's while in some the value is positional.
• In the Sankey plot section there is no option to plot the interactive plotly option. Only the old Matplotlib one is there.

[timothy-nunn]

• process
• process --version
• process -i IN.DAT
• process -i IN.DAT --solver my_solver
• process -i IN.DAT --full-output
• process -i large_tokamak_eval.IN.DAT --update-obsolete
• process -i large_tokamak_eval.IN.DAT --mfile my.MFILE.DAT
• process -i large_tokamak_eval.IN.DAT --mfile my.MFILE.DAT --full-output
• process indat
• process indat -f large_tokamak_nof.MFILE.DAT -i large_tokamak_nof.IN.DAT (including -fpi 0, 1, -1)
• process mfile convert -f my.MFILE.DAT -fmt json (including --scan 0, -1)
• process mfile convert -f my.MFILE.DAT -fmt csv
• process mfile convert -f my.MFILE.DAT -fmt toml
• process mfile compare my2.MFILE.DAT my.MFILE.DAT (with --save)
• process plot costs bar my.MFILE.DAT
• process plot costs pie my.MFILE.DAT
• process plot sankey -f my.MFILE.DAT
• process plot scans scan_example_file_MFILE.DAT -yv rmajor
• process plot scans scan_example_file_MFILE.DAT -yv rmajor -yv2 qstar
  • --x-axis-percent
  • --y-axis-percent
  • --y-axis2-percent
• process plot summary -f my.MFILE.DAT
• process plot tf-stress -f my.SIG_TF.json

[je-cook]

Just a few requests.

• Can we add -h as a shortcut for --help as this was a legacy option?

Yeah I can do that

• In some of the plotting options you have to specify -f before the MFILE's while in some the value is positional.

the costs ones are positional (I think thats the only case where its an arg) because you can specify lots of files

• In the Sankey plot section there is no option to plot the interactive plotly option. Only the old Matplotlib one is there.

process plot sankey -fmt html does that I thought?

[timothy-nunn]

Half way through my review and only comments so far are around filenames. Will post them now so they don't get lost over Easter.

[je-cook]

Ive also moved all the process config process funcs into a vary run folder because they were only used there and essentially is io for vary run.

There is also a fix for #4011

[timothy-nunn]

The --mfile fix is only half working. If I run:
process -i large_tokamak_nof.IN.DAT --mfile my.MFILE.DAT --full-output then it fails because it looks for my.SIG_TF.json... I would suggest propagating the mfile prefix to the OUT.DAT, SIG_TF.json, and the .log file.

[timothy-nunn]

Still also getting errors for the two commands not ticked in #4105 (comment)