jermp
CI via Github Actions
Hi @jermp, I was just wondering that it might be a good idea to include CI via Github Actions.
Fulgor is at this point a great SW, but one limitation that we as its users are constantly facing is the difficulty to reliably deploy it in essentially any real project. While some issues were of a one-time nature and could be easily fixed, e.g., the ones related to probabilistically failing index construction, others seem to be recursively reappearing (e.g., issues with compilation on different system), partially due to Fulgor's reliance on a pretty complex-to-compile stack including SSHash and GGcat and all the Rust-vs-C++ complexity.
It would extremely helpful if there could be at least basic unit / compilation / integration tests that would be executed across all officially supported platforms that could ensure that the program is compilable and works correctly correct. In addition, it would be extremely helpful if precompiled binaries could be provided (eg via Bioconda), as it's almost impossible to compile this in a reliable way on many clusters (think of an old CentOS without root even without zlib).
Hi Karel, sorry for being slow to answer. Continuous integration is a great idea; a workflow would be definitely nice to have.
On the other hand, I have no experience with distributing precompiled binaries via Bioconda. It is surely possibile if someone is willing to try that :)
One thing to mention is that Fulgor is still in active development, i.e., in the near future is going to improve even further. This means that we should also periodically update those binaries, etc., and I don't know how difficult that is.
An update on this front. I've now added a build.yml workflow. @Alessio-Campa has a docker file that allows one to use Fulgor without needing to install any dependency. He will soon add it to the repo as well.