Support Bigscape v2 data

[adraismawur]

This PR enables the user to load data from a BiG-SCAPE V2 database file. The data_sqlite.db file is expected to be in the same place as the mix_clustering_[cutoff].tsv would otherwise be.

If both files are found, the loader selects the tsv file.

[CunliangGeng]

Thanks for adding the support of bigscape v2!

I left some minor comments for you.

One final comment on all files is that please remember to format all files using ruff. If you are also using vscode, the formatting could be automatic, see the guide.

[CunliangGeng]

Just merged a PR to ignore docstrings for test files. So it's ok to not have docstrings for test functions.

I'm off from now, @gcroci2 could take over this PR.

[gcroci2]

Just merged a PR to ignore docstrings for test files. So it's ok to not have docstrings for test functions.

I'm off from now, @gcroci2 could take over this PR.

Sure! @adraismawur just ask for my review again when you'll have integrated Cunliang's one :)

[adraismawur]

Alright! Changes were committed. Could you review this again?

[gcroci2]

All good :) Thanks for the contribution!

The action for checking the format needs to pass before merging. Please run ruff as explained here and then commit the format/linting fixes.

[adraismawur]

Ok I have run the formatter, but there are files outside of those I edited in this PR that fail using ruff.

Should I rebase dev onto this branch and add formatting changes of other files to this one, or should I just merge as-is and the formatting can be done elsewhere?

[gcroci2]

Ok I have run the formatter, but there are files outside of those I edited in this PR that fail using ruff.

Should I rebase dev onto this branch and add formatting changes of other files to this one, or should I just merge as-is and the formatting can be done elsewhere?

I still see:
src/nplinker/arranger.py:231:101: E501 Line too long (114 > 100)
Please make sure that the ruff checks pass on the files you edited (only) and then feel free to merge to dev. No worries about other files you didn't touch with this PR.

About the linting check failing, is this expected? @CunliangGeng If yes, I think we should exclude the checking on such files on the CI, otherwise it can be confusing for contributors.

[CunliangGeng]

@gcroci2 @adraismawur

About the linting check failing, is this expected? @CunliangGeng If yes, I think we should exclude the checking on such files on the CI, otherwise it can be confusing for contributors.

Good point! I updated the github actions to only check changed files in PR #238.