Python packaging & repo structure

[GemmaTuron]

Hi @miquelduranfrigola

As this is organised now, it basically uses three modules:

• Docking (code embedded within the repository)
• Conformer generation (either from the embedded code in the repo with OpenBabel or via the smiles-to-3d package)
• 3D Shape analysis (via the repo vsflow-ligand-based-3d-screening)

Q1: since both smiles-to3d and vsflow-... are very small repos, is this the right structure or we should embed the code within THIS repository?

Q2 (maybe for @DhanshreeA ) I've given up on the python packages. Both repositories, smiles-to-3d and vsflow-ersilia have a setup.py and in principle should be pip installable from the repo, but unless I clone the repo and do pip install . from the cloned repos it does not work, what am I doing wrong?

[miquelduranfrigola]

Hello @GemmaTuron

RE:

• Q1: I do think we should embed the code within this repository. Good idea.
• Q2: I don't know what may be going wrong, possibly some package data not being installed, or package paths not being specified correctly? Since those repos were just quick tests, I did not work on packaging them nicely via the setup.py. I can have a deeper look but, on a quick look, @DhanshreeA, can you spot what may be going on?

[DhanshreeA]

@miquelduranfrigola I'd spent some time on this last week and it's not about package data, for some strange reason, Python is unable to find the installed module (smiles3d). The only way we could get it to work was going from the src layout to flat layout.

[miquelduranfrigola]

Oh OK, so is it solved?

[GemmaTuron]

mmm not really I think

I've added the necessary code from VSFlow so we only need to make sure smiles-to-3d is pip installable

[miquelduranfrigola]

all right. let's have a look together and make smiles-to-3d pip-installable