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Develop CLI #27

Merged
merged 5 commits into from
Jan 15, 2024
Merged

Develop CLI #27

merged 5 commits into from
Jan 15, 2024

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eivindtostesen
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@eivindtostesen eivindtostesen commented Jan 4, 2024 •
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Goal:

Develop a Command Line Interface.

Wanted features:

  • A CLI for a python package (invoke using the -m flag)
  • A tool (do one thing and do it well)
  • CSV input and CSV output (to work in pipes with other CLI tools)
  • Use argparse (to parse arguments and options)
  • Options: help, version, valleys, circular, long, maxsize, delimiter

Solution:

  • New package called peakoscope
  • Renamed modules and classes: NumSlice -> Scope, SliceStr - > Region
  • From standard library: sys, argparse, csv
  • CSV input, but text output
  • implemented options: help, valleys, delimiter, field
  • Dropped option maxsize (it would be two tools)

@eivindtostesen
feat: add command line interface
a236535 
Create cli.py that gets data from file or stdin and prints a tree of peak regions.
@eivindtostesen eivindtostesen linked an issue Jan 4, 2024 that may be closed by this pull request
CLI #26
Closed
@eivindtostesen
feat: add optional command-line arguments
35611ed 
In the CLI, add optional arguments: for help (-h, --help) and for targeting valleys instead of peaks (-v, --valleys).
@eivindtostesen
feat: add csv options from the CLI
d8e8315 
In the CLI, add a csv reader with new options (delimiter and field) from the command line.
@eivindtostesen
feat: create package
921ab64 
Create peakoscope package with new namespace: peakoscope/__init__.py. Rename cli.py -> peakoscope/__main__.py to get CLI when running package.
Move all modules (.py) to peakoscope/. Modify imports in all modules (.py) and notebooks (.ipynb).
@eivindtostesen
refactor: rename
b2e0f04 
Rename modules: peaky_data.py -> data.py, strings.py -> formats.py, peaks_in_matplotlib.py -> interface_matplotlib.py, peaks_in_polars.py -> interface_polars.py, peaks_in_pandas.py -> interface_pandas.py, peaks_and_valleys.py -> peaks.py.
Rename classes: NumSlice -> Scope, SliceStr -> Region.
@eivindtostesen eivindtostesen marked this pull request as ready for review January 15, 2024 08:52
@eivindtostesen eivindtostesen merged commit dc39dec into main Jan 15, 2024
@eivindtostesen eivindtostesen deleted the 26-dev-cli branch January 15, 2024 08:58
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