Summary of changes in this version:
New features:
- Add 'info' subcommand to print a table of configuration info (Perl and Tephra versions, and versions of all installed
external programs.
Bug fixes:
- Adjust regex for getting divergence from PAML. This is something that unfortunately needs to be adjusted with
updates to PAML. - Fixed the console messages when configuring and installing required packages so the output is much cleaner.
Misc:
- Update Perl deps when building on v5.30+ (Pod::Find).
- Add required modules for fetching muscle (and other packages) over https (Net::SSLeay and IO::Socket::SSL)
during the initial configuration. - Change how the tephra command is being called when testing the full pipeline. Now it can be tested in place rather
than expecting to be installed, which is much more desirable (avoids version conflicts and having to install the package
to test the command). - Pin genometools version to v1.6 to ensure we are working with a stable version.
- Update PAML from v4.8 to v4.10.6.
- Capture the noisy output from EMBOSS compile process. Same with HTSlib and Tephra translate program.
- Pin muscle to v3.8.31 and compile from source because the available binaries have issues in my tests.
- Remove use of Travis-CI and switch to Github Actions for CI workflow.
- Add coverage report from Codecov.
- Add test file for new 'info' subcommand to evaluate results that are returned.
- Update Docker and Github Actions to use cpm, which is much faster than to build than cpanm.
See the Changes file for more information.