to a more central location at Bio::DB::IndexedBase, from where its used by Bio::DB::Fasta and Bio::DB::Qual. Also made a small tweak to nhx.t and updated Changes.
…don't remove the returns
… is used.
…ocument better Build.PL: add Inline::C recommended dependency. .gitignore: ignore _Inline directories that Inline::C creates.
…urns and line feeds (\n) and (\r).
the page or a mirror returns in the future), since its purpose was to test a server
(*.ibcp.fr) is now defunct (not responding and verified that it does not appear in name server records anymore)
reported connection status appears as COMPLETED instead of TERMINATED_BY_ERROR (used GOR4 module code as reference)
…m 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data.
moved special 'Strict' table to ID 0, so it don't interfere with new tables in the future. Deleted a dead link and updated other tables according to the latest definitions. Since ID 0 now exists and is used by 'Strict', the 'id' subroutine now returns 1 (standard table) for invalid specified ids (besides the warning). Also fixed some indentations. CodonTable.t: Added tests to cover all the changes plus a few extras to improve code coverage after looking Coveralls report.
which generates an error status. Nevertheless, the coverage report is now available at https://coveralls.io/r/bioperl/bioperl-live, so I'm deactivating it for now but leaving the badge on the README.
the 4 main metrics (statement, branch, condition or path). This is the last try. If it can't finish before 50 minutes, we probably would need a Travis-CI pro account (120 minutes allowed per job) to make it work... Or Devel::Cover author help, but he has not replied my email yet.
an unneeded step for cover. Also, change 'statement' option to 'pod', which I hope will be faster.
"-coverage,subroutine", but I have confirmed that "subroutine" will cause an error if used alone. This is very tricky...
if -subs_only fixes the "Can't find digest for" error from last commit.
in time (10-15 more minutes would be needed). Adjusting to only test 'subroutine' and skip other options for now.
but the test suite was executed twice and that's why it reached the 50 minutes limit. Taking out '- PERL5OPT' will make it run only once and should finally finish. Hope this is the final test.
not Devel::Cover. I hope this time it will be easier on Travis
not enough to complete the process under 50 minutes in Travis-CI. The feature looks useful but it's really slow. I'll leave the code commented for now.
in massive slowdown of the test suite from ~6 min to >50 min, so Travis-CI aborted the build. Commenting until I can find if it can be run faster to allow Travis-CI to complete tests.
that currently works (HSFOS)
to tests where needed