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Author Topic: lib/readme inscorect URL  (Read 386 times)

Offline edeveaud

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lib/readme inscorect URL
« on: February 12, 2019, 04:32:18 am »
Hello,

lib/README says that trollrop should be downloaded from http://gitorious.org/trollop/mainline/blobs/raw/master/lib/trollop.rb,
while post http://forum.x3dna.org/md-simulations/ruby-scripts-for-the-analysis-of-md-simulation-trajectories/msg538/#msg538 says from http://trollop.rubyforge.org/

trollrop is available from https://rubygems.org/gems/trollop/versions/

any recommendation about specific version to use ? v1.16.2 or newer version will fit the requirements ?

Eric

Offline xiangjun

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Re: lib/readme inscorect URL
« Reply #1 on: February 12, 2019, 11:56:53 am »
Hi Eric,

Thank you so much for reporting the inconsistency issues with trollop.rb in 3DNA.

Quote
lib/README says that trollrop should be downloaded from http://gitorious.org/trollop/mainline/blobs/raw/master/lib/trollop.rb,

The note was intended for myself, that I downloaded trollrop 1.16.2 using wget from that URL. The trollop.rb script is cleaned up (see below) and distributed with 3DNA, so users do not need a separate download.

Code: [Select]
# Note from Xiang-Jun Lu (3dna.lu@gmail.com) -- some minor revisions:
#     o   reformatted the code, 4 spaces indent, split long lines
#     o   corrected '-h' or '--version' to '-v'
#     o   corrected 'In thise case' to 'this'
#     o   removed '=> e' to avoid warning on unsed variable
#     o   refined FLOAT_RE to allow for + before the number
#     o   added [INTEGER_RE = /^[+-]?\d+$/] to allow for negative integer

To avoid confusions, the README file has been removed in the updated distribution of 3DNA v2.4.

Quote
while post http://forum.x3dna.org/md-simulations/ruby-scripts-for-the-analysis-of-md-simulation-trajectories/msg538/#msg538 says from http://trollop.rubyforge.org/

trollrop is available from https://rubygems.org/gems/trollop/versions/

The post was dated on January 19, 2011, the URL for trollop was at the specific URL at that time. As you noticed, the URL for trollop has been changed again. Trollop may be relocated to yet another place (e.g., github) in the future.

Also, note that the 'trollop' gem has been deprecated and has been replaced by 'optimist'. In the 3DNA v2.4 distribution, the lib/trollop.rb single file is not a Rubygem dependency. It is a standalone "commandline option parser for Ruby that just gets out of your way." (http://manageiq.github.io/optimist/) It was for this simplicity that I initially picked up trollop from several other options. I've been happily using trollop since then in my Ruby scripts.

Quote
any recommendation about specific version to use ? v1.16.2 or newer version will fit the requirements ?

The slightly revised version of trollop v1.16.2 distributed with 3DNA has been working well, as far as I am aware.

Best regards,

Xiang-Jun


PS. Did you tried 3DNA v2.4.1 with zsh and confirm that the x3dna_setup script works as expected, or otherwise?
« Last Edit: February 12, 2019, 12:39:22 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.