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

[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 page
- 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 should 
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 to 
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 most 
> of the issues repaired quickly and have a fairly up-to-date homepage:
> Actually there are approx. 120 markdown files in the wiki folder. If 
> we find 10 - 12 people willing to participate then we could assign 10 
> 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 could 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
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev

-- 
_________________________________
Dr. Markus Piotrowski
Privatdozent/Akademischer Rat
Lehrstuhl für Pflanzenphysiologie
ND 3/49
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