Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
On Wed, Jul 24, 2013 at 3:42 PM, Peter Cock wrote: > On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock wrote: >> On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock wrote: > On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster 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 ): ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
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 wrote: > On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster 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 > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
