Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg@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
Hi peter, I've made this change in 10254:e22f360cda13, so now only those readme files whose file anme ends in .rst will be rendered as such. Thanks! Greg Von kuster On Jul 23, 2013, at 12:24 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg@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
On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg@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/e22f360cda1363d0c93a86d6... 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 ):
On Wed, Jul 24, 2013 at 3:42 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg@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/e22f360cda1363d0c93a86d6...
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/528bee4dd14addc5db2b59a0... 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/9b5cd13... 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
participants (2)
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Greg Von Kuster -
Peter Cock