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doc link to old version #190

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osallou opened this issue Feb 9, 2020 · 1 comment
Open

doc link to old version #190

osallou opened this issue Feb 9, 2020 · 1 comment

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@osallou
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osallou commented Feb 9, 2020

doc link in README link to https://pbcommand.readthedocs.io/en/latest/

it shows version 1.7.0 (???) and shows old API. In gather_tool_contract for example:

from pbcommand.models import get_gather_pbparser, FileTypes

which is not present anymore

@smoe
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smoe commented Mar 22, 2020

The README.md has example code

from pbcommand.cli import pbparser_runner

that triggers

    from pbcommand.cli import pbparser_runner
ImportError: cannot import name 'pbparser_runner' from 'pbcommand.cli' (/usr/lib/python3/dist-packages/pbcommand/cli/__init__.py)

The problem is that https://github.com/PacificBiosciences/kineticsTools executes the very same:

$ grep -r pbparser_runner .
./kineticsTools/tasks/gather_kinetics_h5.py:from pbcommand.cli import pbparser_runner
./kineticsTools/tasks/gather_kinetics_h5.py:    return pbparser_runner(argv[1:],
./kineticsTools/ipdSummary.py:from pbcommand.cli import pbparser_runner
./kineticsTools/ipdSummary.py:        return pbparser_runner(
./kineticsTools/summarizeModifications.py:from pbcommand.cli import pbparser_runner
./kineticsTools/summarizeModifications.py:    return pbparser_runner(

Seen nicer via https://github.com/PacificBiosciences/kineticsTools/search?q=pbparser_runner&unscoped_q=pbparser_runner

Is there anything you can suggest to help kineticsTools out?

Many thanks
Steffen

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