EMBOSS: Project Meeting (Mon 26th Sep 11)
1. Minutes of the last meeting
The meeting on 19th September 2011 was cancelled. Minutes of the
meeting of 12th September 2011 are
2. Maintenance etc.
Peter has fixed bugs in the reporting by diffseq of
insertions in he first sequence. The reported positions were corrupted
by a change in EMBOSS 6.0.1 which reverses features where the start is
grater than the end, but this should be true for a feature "between"
two bases. A new feature constructor preserves this relationship.
Peter has implemented the proposed changes to header files on
the delelopers Wiki. ALl header files now have an @include block which
describes the LGPL license and includes RCS tags for CVS to report the
date, version and author of the latest version of each header file.
Peter has moved all deprecated functions to the ends of the
source files, and enclosed them in #ifdef blocks. One block is for
functions used in the book text from release 6.2.0,the main block is
for all other deprecated functions. New configure options determine
whether the book or all deprecated functions are included. By default
they are all currently ignored.
3. New developments
3.1 Reference sequences
3.2 Support for interfaces and GUIs
3.3 Data access
5. Documentation and Training
5.1 Web server
Peter would like to replace the home page with a new style that
better indicated the documentation, news, mailing lists and other
information. BioPython's home page is a good example, but is wiki
Jon has updated the user manual with corrections from the
Peter has updated the version numbers and some examples in all 3
books so that the web pages and original XML match release 6.4.0.
For the book text Peter suggested we should use names for the
pages rather than chapter and section so that we can link permanently
to, for example, functions handling translations.
6. User queries and answers
Peter is working through the remaining items on the bug
tracker list. Most were already resolved. None were serious bugs. Less
than 20 items remain.
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 8th August.