[Biopython-dev] New Homepage - "Brute force" effort of Community?

Tiago Antao tra at popgen.net
Fri Apr 22 15:07:30 UTC 2016

Sorry for the delay. I will do mine today.

On April 20, 2016 1:10:27 AM MDT, Markus Piotrowski <Markus.Piotrowski at ruhr-uni-bochum.de> wrote:
>Should we start?
>OK, I had hoped that we could agree on a checklist, nevertheless I have
>the feeling that the "brute force" effort has at least some supporters.
>One additional advantage to work "page-wise" will be that we don't
>time on things that others are already addressing.
>Although Tiago and Lenna are willing to do 20 pages, I suggest to start
>with 10 pages and look if there are some issues that need 
>feedback/coordination/etc. If everything is fine we just do another 10.
>@Tiago:  From "65-bit_Windows_Biopython.md" to "Biopython_md"
>@Lenna: From "Building_a_release.md" to "Coordinate_mapping.md"
>@me: From "Create_an_Article_to_this_category.md" to "GSOC2010_Joao.md"
>@Vincent: ready/willing to join in this approach?
>@Peter:  OK?
>Should we move to github.com/biopython/biopython.github.io/issues for 
>Am 19.04.2016 um 14:25 schrieb Markus Piotrowski:
>> Here is draft of a checklist, open for discussion:
>> Checklist:
>> 1. Title
>> - The title in the markdown file may be changed into something more 
>> user friendly 
>> (https://github.com/biopython/biopython.github.io/issues/22)
>> - Take care that the title is not repeated in the main text (like 
>> here: http://biopython.org/wiki/Documentation)
>> 2. Is the text up-to-date? (Python versions etc)
>> 3. Formatting
>> - Suggestion: Python/Biopython commands, keywords, module/function 
>> names should be formatted as inline-code with single backticks, e.g. 
>> `Bio.SeqIO`           ??? Or bold???
>> - If applicable, they can also serve as links to the respective Wiki
>> - Code output and command-line examples should be formatted as block 
>> code with three backticks instead of several single line inline-code 
>> statements.
>> - Check block code for trailing white spaces, which may result in the
>> addition of an (unnecessary) horizontal scrollbars as here: 
>> http://biopython.org/wiki/ACE_contig_to_alignment.
>> 4. Code
>> - Code should be checked for a minimum of PEP8 compliance.
>> - The code should work (as it is) under Biopython 1.66
>> - Since we are recommending Python 3.5 as environment, the code
>> work under Python 3.5      ???
>> 5. Links
>> - Check all links
>> - 'Repair' broken links
>> Try to find a link that's more likely to be stable. E.g. for papers I
>> think that dx.doi.org references (or Pubmed references) are more 
>> stable than linking to a special page of the respective journal or 
>> private or institutional homepages. With 
>> http://www.crossref.org/SimpleTextQuery/ you can do a reverse doi 
>> lookup for a given paper.
>> - Links with anchors (.../some_page#jump_here) may have issues with 
>> upper/lowercase formatting 
>> (https://github.com/biopython/biopython.github.io/issues/13)
>> - Are the links up-to-date? E.g. in 
>> http://biopython.org/wiki/Getting_Started the Python Quick Reference 
>> links to Python 2.5
>> 6. References
>> - Some pages used a PubMed plugin under MediaWiki to display 
>> references 
>> (https://github.com/biopython/biopython.github.io/issues/12). Since 
>> it's unlikely (?) to have a functional replacement, I would suggest
>> convert them to simple links.
>> 7. RSS feeds
>> - As above, embedding an existing RSS feed seems hard 
>> (https://github.com/biopython/biopython.github.io/issues/4), again I 
>> would suggest replace with a link pointing to the RSS feed
>> -Markus
>> Am 17.04.2016 um 13:40 schrieb Markus Piotrowski:
>>> Dear Biopythoneers,
>>> It's great that the Biopython project has a working homepage again. 
>>> Great job, Peter!
>>> There is still much to do, many things (especially links) are broken
>>> due to the moving, however some things were broken before or 
>>> outdated. And most of these issues must be addressed manually.
>>> I want to suggest a "brute force" effort of the community to get
>>> of the issues repaired quickly and have a fairly up-to-date
>>> Actually there are approx. 120 markdown files in the wiki folder. If
>>> we find 10 - 12 people willing to participate then we could assign
>>> files to each person (e.g. file 1 - 10, from "64-bit_Windows...md" 
>>> to  "Biopython.md", etc.). Each person then checks his pages 
>>> completely for all issues (title, content, up-to-dateness, links, 
>>> formatting, functionality of example code, Python 2/3, etc). We
>>> design a checklist with suggested solutions to aid in this process.
>>> I think that this "per page" effort is more effective than to tackle
>>> the things "per issue". Also, having someone looking at a page who 
>>> hasn't written it, may be advantageous in finding problems.
>>> What do you think?
>>> -Markus
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>>> Biopython-dev at mailman.open-bio.org
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