On Mon, Sep 23, 2013 at 2:30 PM, Carlos Borroto
<carlos.borr...@gmail.com> wrote:
> On Mon, Sep 23, 2013 at 2:22 PM, John Chilton <chil...@msi.umn.edu> wrote:
>>> Hi John,
>>> First let me tell you why I think duplicating the biopython install
>>> reduces reproducibility. I have this on my tool setup.py:
>>>     install_requires=[
>>>         "docopt",
>>>         "biopython",
>>>         "python-levenshtein"
>>>     ],
>>> While I could specify versions here(ex. biopython==1.62), I feel that
>>> is not a good thing outside of Galaxy. I think pip should be free to
>>> install the latest version of these packages until I found there is an
>>> issue otherwise. I think this is the most common approach, I might be
>>> wrong thou. This leaves me with the issue that then when Galaxy
>>> installs my tool using virtualenv, it will grab the most up-to-date
>>> version of these packages, hence reducing reproducibility. Did I
>>> explain myself well enough? I'll be happy to debate about any of this.
>> I understand what you are saying and I sympathize with you here. Still
>> I think the better approach is going to be to copy these requirements
>> into the setup_virtualenv block and specify hard-coded versions. This
>> way you get reproduciblity across all packages, not just biopython.
> Hi John,
> Could you go a little further with this recommendation. How can I
> specify versions for required packages in setup_virtualenv. I now have
> this:
>         <install version="1.0">
>             <actions>
>                 <action type="setup_virtualenv">ngs-tools==0.1.6</action>
>             </actions>
>         </install>
> I tried these two without luck:
> <action type="setup_virtualenv">docopt==0.6.1
> python-levenshtein==0.10.2 biopython==1.62 ngs-tools==0.1.6</action>

So the contents is treated like a requirements.txt file. So the
whitespace becomes important (I have a plan to improve this and sort
of synchronize the syntax used for Ruby, Python, and R, but for now
its just a file).

So you want this:
<action type="setup_virtualenv">docopt==0.6.1

Newline between dependencies, and no whitespace to the left of each package.

Someday the syntax will be:
<action type="setup_virtualenv">

> <action type="setup_virtualenv">docopt==0.6.1,
> python-levenshtein==0.10.2, biopython==1.62, ngs-tools==0.1.6</action>
>> I think this slight duplication is a smaller problem then mixing
>> dependency mechanisms you described in your approach. To me it is
>> analogous to installing some python dependencies via os packages and
>> other ones via sudo pip install into /usr, it is a recipe for
>> confusion.
> While I'm getting convinced that maybe some duplication is not that
> bad after all, please notice that my plan is to install everything
> from the toolshed. I also don't like mixing install methods. In fact,
> I would like for 'install_pip' to have the best practice option of
> doing always 'pip install --no-deps'. This would force you to first
> upload everything your package needs to the toolshed.
> Thanks,
> Carlos
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