♻️ Refactor CLI #60
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♻️ Refactor CLI #60
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Replace main.py with Click CLI module - cli.py
Change invokation of ingest so that you can do:
$ kidsfirst <cmd> <args> <options>
fiendish
suggested changes
Oct 17, 2018
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side note: If I python setup.py install and then try to run kidsfirst, I get:
Traceback (most recent call last):
File "/Users/kelmana/Documents/kids-first/kf-lib-data-ingest/venv/bin/kidsfirst", line 11, in <module>
load_entry_point('kf-lib-data-ingest==0.1', 'console_scripts', 'kidsfirst')()
File "/Users/kelmana/Documents/kids-first/kf-lib-data-ingest/venv/lib/python3.7/site-packages/pkg_resources/__init__.py", line 484, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/kelmana/Documents/kids-first/kf-lib-data-ingest/venv/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2707, in load_entry_point
return ep.load()
File "/Users/kelmana/Documents/kids-first/kf-lib-data-ingest/venv/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2325, in load
return self.resolve()
File "/Users/kelmana/Documents/kids-first/kf-lib-data-ingest/venv/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2331, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
ModuleNotFoundError: No module named 'cli'
Why does that fail but pip install -e . works?
.gitignore
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| @@ -105,3 +105,6 @@ venv.bak/ | |||
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| # mypy | |||
| .mypy_cache/ | |||
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| # Visual studio | |||
| .vscode/ | |||
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please put a newline at the end of the file so that this ugly 
symbol goes away, lol
src/cli.py
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| """ | ||
| A CLI utility for ingesting study data into the Kids First ecosystem. | ||
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| This method not need to be implemented. cli is the root group that all |
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Suggested change
| This method not need to be implemented. cli is the root group that all | |
| This method does not need to be implemented. cli is the root group that all |
src/cli.py
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| A CLI utility for ingesting study data into the Kids First ecosystem. | ||
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| This method not need to be implemented. cli is the root group that all | ||
| subcommands will implicitly be part of |
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Suggested change
| subcommands will implicitly be part of | |
| subcommands will implicitly be part of. |
fiendish
suggested changes
Oct 17, 2018
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@fiendish It looks like the failure of python setup.py install has to do with the issues here. If you click the "exhaustive tests" link on that issue page and find your way into documentation on namespace packaging, there is some info on how to make the package installable via both setup.py and pip, but do we really need to support both? I think we just need to support pip.. |
fiendish
approved these changes
Oct 17, 2018
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good to go |
Merged
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Refactor CLI to use a CLI framework in preparation for implementing additional extract, transform, load subcommands (#37)