Releases

From BioSQL

Jump to: navigation, search

BioSQL release v1.0.1

This is an update release of the v1.0 core BioSQL schema (code-named Tokyo), not including recent extensions.

Note: open questions are in italics. If you have thoughts or feedback on any of the below, please email them to biosql-l@lists.open-bio.org.

  1. Update INSTALL file Done. --Hilmar 05:02, 1 August 2008 (UTC)
    • Fix inconsistencies in naming of the BioSQL database instance (here and with Bioperl-db). Will name it simply biosql from now on.
    • Add note about current incompatibility with PostgreSQL v8.3+.
  2. Implement scheduled changes Done. --Hilmar 02:24, 2 August 2008 (UTC)
    • Widen column width constraint of dbxref.accession and correspondingly bioentry.accession. Will use 128 chars for now.
    • Add migration scripts at least for Pg, MySQL, and Oracle.
  3. Fix load_ncbi_taxonomy.pl to not rely on primary key and NCBI taxon ID to be identical. Done. --Hilmar 02:24, 2 August 2008 (UTC)
  4. Update Changes file. Done. --Hilmar 05:02, 1 August 2008 (UTC)
  5. Merge changes to biosql-release-1-0 branch. Done. --Hilmar 12:21, 2 August 2008 (UTC)
  6. Write release announcement. Done. --Hilmar 12:21, 2 August 2008 (UTC)
  7. Tag release with biosql-rel-1.0.1 Done. --Hilmar 13:42, 2 August 2008 (UTC)
  8. Package BioSQL for release, upload to download site (http://biosql.org/DIST) Done. --Hilmar 13:42, 2 August 2008 (UTC)
  9. Release: Done on Aug 2, except for the news post which was done by Peter Cock a few days later.
    • Add download and release link to wiki on front page.
    • Post announcement to biosql-l and news.open-bio.org.

BioSQL release v1.0.0

This is a release of the core BioSQL schema, not including recent extensions.

Note: open questions are in italics. If you have thoughts or feedback on any of the below, please email them to biosql-l@lists.open-bio.org.

  1. Update license for BioSQL and all its DDL and software scripts. Done. This is now the LGPL license for all schema files. --Hilmar 20:23, 21 February 2008 (EST)
    • The current license refers to the 'same terms as Perl' and the Perl Artistic Licence. Not only does Perl now dual-license under Artistic License v2.0 or GPL (because the original Perl Artistic License v1.0 has problems), but also there isn't a good reason to tie the BioSQL license to that of Perl.
  2. Update, fix, or remove various ancillary files that don't seem to have been touched in a long time.
    • biosql-accelerators-pg.sql Updated/fixed, and now also retired. --Hilmar 23:40, 22 February 2008 (EST)
    • biosqldb-views-pg.sql Done. --Hilmar 20:31, 21 February 2008 (EST)
  3. Rename biosql-ora to biosqldb-ora for consistency with the other schema versions Done. --Hilmar 20:31, 21 February 2008 (EST)
  4. Regenerate HTML documentation from schema DDL (using sqlt) Doesn't work, sqlt seems to be broken at present. --Hilmar 21:11, 21 February 2008 (EST)
  5. Update Changes file. Done. --Hilmar 23:41, 22 February 2008 (EST)
  6. Update documentation in the repository. Done, for Biopython (see PDF) and BioJava/Oracle. Unfortunately, realized this not before, but only after branching off, so need to merge all changes to the branch. --Hilmar 12:06, 24 February 2008 (EST)
  7. Create biosql-release-1-0 branch. Done. --Hilmar 23:43, 22 February 2008 (EST)
  8. Remove from biosql-release-1-0 branch all schema modules or versions and all scripts that aren't release-ready yet, or are not yet or no longer supported. Done. --Hilmar 23:43, 22 February 2008 (EST)
    • This includes the following:
      • phylodb module DDLs
      • phylodb ERD
      • phy* scripts (depend on phylodb, and not up-to-date)
      • load_itis_taxonomy.pl, tree-precompute.pl scripts (depend on phylodb, and not up-to-date)
      • phylodb-topo-queries.sql (depends on phylodb)
    • Can the HSQLDB version be tested by anyone for syntactic correctness and compatibility with a current revision of HSQLDB?
  9. Write release announcement. Done. --Hilmar 10:52, 5 March 2008 (EST)
  10. Tag release with biosql-rel-1.0.0 Done. --Hilmar 10:53, 5 March 2008 (EST)
  11. Package BioSQL for release, upload to download site (http://biosql.org/DIST) Done, with MD5 signatures. --Hilmar 17:07, 6 March 2008 (EST)
  12. Release: Done. --Hilmar 22:02, 6 March 2008 (EST)
    • Add download and release link to wiki on front page (also add Downloads page ot sidebar).
    • Post announcement to biosql-l and news.open-bio.org.
Retrieved from "http://biosql.org/wiki/Releases"
Personal tools