[GenABEL-dev] ProbABEL: Binaries without extension

[Yurii Aulchenko]

Question which probably supports Maxim's suggestion: How will this affect
existing user pipelines?

----------------------
Yurii Aulchenko
(sent from mobile device)

On Dec 11, 2013, at 13:22, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:

 Hi Lennart,

For me, it sounds reasonable to remove the file extensions.
About probabel.pl: we can provide both 'probabel.pl' and 'probabel' for the
next few revisions (if it is possible). In this case, if users run '
probabel.pl', we show a warning messages saying that they need to use
'probabel' instead of 'proabbel.pl' and that 'probabel.pl' will be removed
soon. Later, when most of users switched to 'probabel', we remove '
probabel.pl'.

best,
Maksim




On 11/12/2013 18:08, L.C. Karssen wrote:

Dear list,

While working on packaging ProbABEL for inclusion in Debian, I came
across the following warning in the Debian package check (using the
lintian program):

W: probabel: script-with-language-extension usr/bin/extIDS.pl
W: probabel: script-with-language-extension usr/bin/probabel.pl

The short explanation is this:
    When scripts are installed into a directory in the system PATH, the
    script name should not include an extension such as .sh or .pl that
    denotes the scripting language currently used to implement it. The
    implementation language may change; if it does, leaving the name the
    same would be confusing and changing it would be disruptive.


The reasoning behind this warning is the following:
There are several reasons for not having an extension in the name of a
binary/script, nicely listed in this post:
    http://lists.debian.org/debian-med/2012/04/msg00103.html
The most important one to me is:
    I do not see what actual information such extensions are
    providing to the end user.  A user expects a program to do a job.
    Fullstop.  The user does not need to care about the language a
    program is written in if it just does what it is expected to do.


So, for ProbABEL I propose the following:
- extIDS.pl is not used a lot, so we can safely remove the .pl extension
there (and update the manual, mention it in the ChangeLog and release notes)
- For probabel.pl this is different. Many people use it exclusively
instead of calling pa{linear,logist,coxph} directly and changing this
would mean breaking user experience completely. I think we do need to
remove the extension at some point in the future, but that would be in a
'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.


What do you think of this?

Lennart.


--
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L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.orghttp://blog.karssen.org
GPG key ID: A88F554A
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