Run bigscape v2

[adraismawur]

#216
This implements running BiG-SCAPE 2.

I opted for keeping the run_bigscape function the same and changing how the arguments are built up to avoid a large amount of duplicated code. Let me know if a separate run_bigscape_v2 function is still desired.

The installation of BiG-SCAPE 2 will likely change in time. I have now fixed it to a reliable development version by commit, mirroring the BiG-SCAPE 1 installation. It's limited to low blob filesizes so should only minimally impact the installation time.

When we package BiG-SCAPE 2 we should be able to easily change this installation.

[adraismawur]

Seems like a few unrelated tests aren't passing? Let me know if I broke something.

[CunliangGeng]

The changes look good to me. A few small things need to be updated. But please first solve the conflict to get the latest codebase before addressing my comments.

[CunliangGeng]

There is not unit tests for the rubbigscape.py. It'd great to add them with some simple input data.

[adraismawur]

Sorry this took a while, getting the structure of BiG-SCAPE right to be a normal package was a bit of a hassle.

This should now cover all the issues.

[sonarcloud]

Quality Gate failed

Failed conditions
0.0% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud

[CunliangGeng]

Thanks, the new commits look good to me.

The unit tests are still missing for testing the run_bigscape function, could you add that?

[adraismawur]

I've added some very rudimentary tests, they add --help as an argument so that the process returns successfully quickly.

I also tried adding some where the actual run is tested by inputting some files and checking for the existence of the expected output files, but I am seeing that it takes a relatively long time for v1 to finish, and for some reason v2 doesn't finish at all.

If wanted, I can still try adding this, but in theory the important code is covered with only these fast tests.

[CunliangGeng]

I just killed the github actions to stop the unit tests.

[adraismawur]

Thanks for the update! Almost there.

I see the unit tests (github action) have been running for two hours ;-) Is it possible to have a lot more smaller antismash input (e.g. fake and mini gbk files) to make sure the running of bigscape complete within 2 mins? If it's not possible, I would prefer discarding these unit tests.

Oh no, they should already complete within two minutes...
I can check if it works with only two gbk files, or maybe I can make them very minimal by trimming the files themselves.
Otherwise I think we unfortunately need to remove those tests.

[adraismawur]

Okay it looks like this test just refuses to complete on the worker. I don't understand why; this is a very small sample.

[CunliangGeng]

OK, let's skip the test on CI, but keep running it on local computer, it's really fast.

A few more comments to address. After that, I think we are ready to release a new version of NPlinker.

[CunliangGeng]

Last two comments about docstring.

🎉 then you can directly merge the PR!

[sonarcloud]

Quality Gate failed

Failed conditions
73.2% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud