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  1. 19 Dec, 2019 1 commit
  2. 12 Dec, 2019 1 commit
  3. 20 Nov, 2019 1 commit
  4. 18 Nov, 2019 1 commit
  5. 13 Nov, 2019 2 commits
    • Marek Szuba's avatar
    • Marek Szuba's avatar
      Add prototype Gitlab-CI configuration · e62eb711
      Marek Szuba authored
      What I have done here is take .gitlab-ci.yml and
      MultiTestDB.conf.gitlabci.mysql from ensembl (my own development version
      in case of the former), modify the before_script section of the former
      to account for differences in dependencies between the two projects,
      create a dependent-build trigger attempting to launch one on
      ensembl-gh-mirror/ensembl (i.e.  already on EBI Gitlab), and fix the
      declaration of same because it has turned out variable expansion
      in trigger declarations works only in the branch field, not in "project".
      Note that all of this results in a somewhat different build
      matrix than on Travis but unlike there, on GitLab we have got
      consistency between ensembl and ensembl-test.
  6. 07 Nov, 2019 3 commits
  7. 06 Nov, 2019 2 commits
  8. 04 Nov, 2019 1 commit
  9. 11 Oct, 2019 1 commit
  10. 16 Sep, 2019 1 commit
  11. 09 Jul, 2019 2 commits
  12. 08 Jul, 2019 1 commit
  13. 02 Jul, 2019 1 commit
    • Jorge Alvarez-Jarreta's avatar
      fixed bug when core db does not have contigs · 092dc80b
      Jorge Alvarez-Jarreta authored
      Removed assumption that the 3 levels of assembly are chromosome,
      supercontig and contig, as there are many other species with different
      coord_system sequence level (e.g. primary assembly, scaffold).
      A similar error might be raised in the future regarding supercontigs,
      and since 'toplevel' and 'seqlevel' are linked in the assembly table,
      that part of the code has also been removed.
  14. 25 Jun, 2019 1 commit
  15. 21 Jun, 2019 1 commit
  16. 17 Jun, 2019 1 commit
  17. 14 Jun, 2019 2 commits
  18. 24 May, 2019 1 commit
    • Marek Szuba's avatar
      Travis: Add mysql to the list of services · 35c26d8f
      Marek Szuba authored
      Ubuntu Xenial, which is now being rolled out as the default Linux distro
      for Travis builds following the end of life of Ubuntu Trusty, does not
      start services such as MySQL unless told to. We use the default distro
      in our builds so we are likely to be affected.
  19. 12 Apr, 2019 1 commit
  20. 04 Apr, 2019 1 commit
  21. 22 Mar, 2019 1 commit
  22. 20 Mar, 2019 2 commits
  23. 18 Mar, 2019 2 commits
    • Marek Szuba's avatar
      Delete scripts/README.dump_test_schema · a7d86682
      Marek Szuba authored
      It is mostly redundant now that dependencies of are
      in the cplanfile, moreover it was out of date (MooseX::App:Simple has
      since become a dependency of ensembl-test as a whole).
    • Marek Szuba's avatar
      cpanfile: add dependencies of · b8e684c7
      Marek Szuba authored
      The aforementioned script, which is used in the course of patching test
      databases, has got two additional dependencies (which in turn depend on
      quite a few other new modules), which until now were only mentioned in
      a dedicated README file in scripts/ . Put them in the cpanfile where
      they belong, wrapped in a dedicated feature so that we do not inflict
      them on people who do not want to ever patch test databases.
  24. 28 Jan, 2019 1 commit
  25. 15 Jan, 2019 1 commit
  26. 14 Jan, 2019 1 commit
    • Marek Szuba's avatar
      MultiTestDB: add an environment variable for overriding test-DB prefix · 3aa7f64b
      Marek Szuba authored
      Until now, MultiTestDB would prefix the names of test databases it
      creates with the local user name as determined by looking at the
      environment variables: LOGNAME and USER, in the order as written here.
      There are the following problems with this approach:
       - it leaks local user names to the database system and by extension to
         everyone who can access them,
       - in the event of said local user names being different from farm ones
         it makes it more difficult to identify to whom a specific database
      To address these issues the present commit introduces a new environment
      variable called ENSEMBL_TESTDB_PREFIX which when defined takes
      precedence over LOGNAME. Now anyone running tests on their local machine
      can set that variable to their farm user name.
  27. 07 Jan, 2019 1 commit
  28. 02 Jan, 2019 1 commit
  29. 21 Nov, 2018 1 commit
  30. 12 Nov, 2018 1 commit
  31. 09 Nov, 2018 1 commit
  32. 07 Nov, 2018 1 commit