<html><head></head><body>Sorry for the delay. I will do mine today.<br><br><div class="gmail_quote">On April 20, 2016 1:10:27 AM MDT, Markus Piotrowski <Markus.Piotrowski@ruhr-uni-bochum.de> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<pre class="k9mail">Should we start?<br />OK, I had hoped that we could agree on a checklist, nevertheless I have <br />the feeling that the "brute force" effort has at least some supporters. <br />One additional advantage to work "page-wise" will be that we don't spend <br />time on things that others are already addressing.<br />Although Tiago and Lenna are willing to do 20 pages, I suggest to start <br />with 10 pages and look if there are some issues that need <br />feedback/coordination/etc. If everything is fine we just do another 10.<br />@Tiago: From "65-bit_Windows_<a href="http://Biopython.md">Biopython.md</a>" to "Biopython_md"<br />@Lenna: From "Building_a_<a href="http://release.md">release.md</a>" to "Coordinate_<a href="http://mapping.md">mapping.md</a>"<br />@me: From "Create_an_Article_to_this_<a href="http://category.md">category.md</a>" to "GSOC2010_<a href="http://Joao.md">Joao.md</a>"<br /><br />@Vincent: ready/willing to join in this approach?<br />@Pet
er:
OK?<br /><br />Should we move to <a href="http://github.com/biopython/biopython.github.io/issues">github.com/biopython/biopython.github.io/issues</a> for <br />discussion?<br /><br />-Markus<br /><br />Am 19.04.2016 um 14:25 schrieb Markus Piotrowski:<br /><blockquote class="gmail_quote" style="margin: 0pt 0pt 1ex 0.8ex; border-left: 1px solid #729fcf; padding-left: 1ex;"> Here is draft of a checklist, open for discussion:<br /><br /> Checklist:<br /> 1. Title<br /> - The title in the markdown file may be changed into something more <br /> user friendly <br /> (<a href="https://github.com/biopython/biopython.github.io/issues/22">https://github.com/biopython/biopython.github.io/issues/22</a>)<br /> - Take care that the title is not repeated in the main text (like <br /> here: <a href="http://biopython.org/wiki/Documentation">http://biopython.org/wiki/Documentation</a>)<br /><br /> 2. Is the text up-to-date? (Python versions etc)<br /><br /> 3. Formatting<br /> - Suggestion:
Python/Biopython commands, keywords, module/function <br /> names should be formatted as inline-code with single backticks, e.g. <br /> `Bio.SeqIO` ??? Or bold???<br /> - If applicable, they can also serve as links to the respective Wiki page<br /> - Code output and command-line examples should be formatted as block <br /> code with three backticks instead of several single line inline-code <br /> statements.<br /> - Check block code for trailing white spaces, which may result in the <br /> addition of an (unnecessary) horizontal scrollbars as here: <br /> <a href="http://biopython.org/wiki/ACE_contig_to_alignment">http://biopython.org/wiki/ACE_contig_to_alignment</a>.<br /><br /> 4. Code<br /> - Code should be checked for a minimum of PEP8 compliance.<br /> - The code should work (as it is) under Biopython 1.66<br /> - Since we are recommending Python 3.5 as environment, the code should <br /> work under Python 3.5 ???<br /><br /> 5. Links<br /> - Check all li
nks<br
/> - 'Repair' broken links<br /> Try to find a link that's more likely to be stable. E.g. for papers I <br /> think that <a href="http://dx.doi.org">dx.doi.org</a> references (or Pubmed references) are more <br /> stable than linking to a special page of the respective journal or <br /> private or institutional homepages. With <br /> <a href="http://www.crossref.org/SimpleTextQuery">http://www.crossref.org/SimpleTextQuery</a>/ you can do a reverse doi <br /> lookup for a given paper.<br /> - Links with anchors (.../some_page#jump_here) may have issues with <br /> upper/lowercase formatting <br /> (<a href="https://github.com/biopython/biopython.github.io/issues/13">https://github.com/biopython/biopython.github.io/issues/13</a>)<br /> - Are the links up-to-date? E.g. in <br /> <a href="http://biopython.org/wiki/Getting_Started">http://biopython.org/wiki/Getting_Started</a> the Python Quick Reference <br /> links to Python 2.5<br /><br /> 6. References<br /> - Some pages used a
PubMed
plugin under MediaWiki to display <br /> references <br /> (<a href="https://github.com/biopython/biopython.github.io/issues/12">https://github.com/biopython/biopython.github.io/issues/12</a>). Since <br /> it's unlikely (?) to have a functional replacement, I would suggest to <br /> convert them to simple links.<br /><br /> 7. RSS feeds<br /> - As above, embedding an existing RSS feed seems hard <br /> (<a href="https://github.com/biopython/biopython.github.io/issues/4">https://github.com/biopython/biopython.github.io/issues/4</a>), again I <br /> would suggest replace with a link pointing to the RSS feed<br /><br /> -Markus<br /><br /><br /> Am 17.04.2016 um 13:40 schrieb Markus Piotrowski:<br /><blockquote class="gmail_quote" style="margin: 0pt 0pt 1ex 0.8ex; border-left: 1px solid #ad7fa8; padding-left: 1ex;"> Dear Biopythoneers,<br /><br /> It's great that the Biopython project has a working homepage again. <br /> Great job, Peter!<br /> There is still much to do, many t
hings
(especially links) are broken <br /> due to the moving, however some things were broken before or <br /> outdated. And most of these issues must be addressed manually.<br /> I want to suggest a "brute force" effort of the community to get most <br /> of the issues repaired quickly and have a fairly up-to-date homepage:<br /> Actually there are approx. 120 markdown files in the wiki folder. If <br /> we find 10 - 12 people willing to participate then we could assign 10 <br /> files to each person (e.g. file 1 - 10, from "64-bit_Windows...md" <br /> to "<a href="http://Biopython.md">Biopython.md</a>", etc.). Each person then checks his pages <br /> completely for all issues (title, content, up-to-dateness, links, <br /> formatting, functionality of example code, Python 2/3, etc). We could <br /> design a checklist with suggested solutions to aid in this process.<br /> I think that this "per page" effort is more effective than to tackle <br /> the things "per issue". Also, havi
ng
someone looking at a page who <br /> hasn't written it, may be advantageous in finding problems.<br /><br /> What do you think?<br /><br /> -Markus<br /><br /><hr /><br /> Biopython-dev mailing list<br /> Biopython-dev@mailman.open-bio.org<br /> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br /></blockquote><br /></blockquote><br /><hr /><br />Biopython-dev mailing list<br />Biopython-dev@mailman.open-bio.org<br /><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br /></pre></blockquote></div><br>
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