On Wed, Jul 24, 2013 at 3:42 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>> Hello Björn,
>>>
>>> This one has been applied in changeset 10219:a7edac403b6c, and all of
>>> your patches are now running on the test tool shed.
>>>
>>> Thanks very much,
>>>
>>> Greg Von Kuster
>>
>> Hi Greg & Björn,
>>
>> I think supporting reStructuredText is a good idea, but should not be
>> done automatically, consider:
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
>>
>> This README file is named with the extension *.txt and does not render
>> nicely if treated as *.rst, things like "System Message: ERROR" and
>> "System Message: WARNING" are shown to the user.
>>
>> I suggest that the ToolShed only render like this if the README file
>> is using the *.rst extension, but otherwise default to plain text (e.g.
>> no extension or *.txt files).
>>
>> Thanks,
>>
>> Peter
>
> Thanks Greg for doing that:
> https://bitbucket.org/galaxy/galaxy-central/commits/e22f360cda1363d0c93a86d64c17032e7507b296
>
> Here's a follow-up patch to hopefully fix the rendering of these revisions
> where I have switched to an *.rst file but the filename isn't used:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/a119cd123b2d
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/a119cd123b2d
>
> Thanks,
>
> Peter
>
> $ hg diff
> diff -r e22f360cda13 lib/tool_shed/util/metadata_util.py
> --- a/lib/tool_shed/util/metadata_util.py       Wed Jul 24 10:34:21 2013 -0400
> +++ b/lib/tool_shed/util/metadata_util.py       Wed Jul 24 15:39:44 2013 +0100
> @@ -990,6 +990,7 @@
>      valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) )
>      valid_filenames.extend( readme_files )
>      valid_filenames.append( '%s.txt' % repository_name )
> +    valid_filenames.append( '%s.rst' % repository_name )
>      return valid_filenames
>
>  def get_relative_path_to_repository_file( root, name,
> relative_install_dir, work_dir, shed_config_dict,
> resetting_all_metadata_on_repository ):

That was applied a while back, thanks Greg:

https://bitbucket.org/galaxy/galaxy-central/commits/528bee4dd14addc5db2b59a0a229e3aa441f8fda?at=default

Here are some example where it is working (repository_name.rst
for the README file), here filename seq_select_by_id.rst works etc:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/87086e8e9bb8
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/00153c4efec3
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/9b5cd13eb78b

However here are two examples where my repository_name.rst
styled README file is not being shown,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/2dedcbc5f4b6

I've tried this in another browser in case it was a caching issue.
Is there some silly difference here that I am overlooking?

Thanks,

Peter

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