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pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

Bumb the minimal MDAnalysis version required #172

Open jbarnoud opened 6 years ago

jbarnoud commented 6 years ago

We were asking for MDAnalysis >= 0.11, but that version is ancient and the API changed rather drastically since then. I bumped the minimum required version to 0.16. The tests run fine with version 0.17 that should be preferred, especially on python 3.

@HubLot I do not know what should be done for the conda package to be rebuilt. It should now be possible to install PBxplore on python 3 with conda as MDAnalysis was the last obstacle.

pierrepo commented 6 years ago

I totally agree. We need to push toward the use of a recent version or mdanalysis.

@HubLot for conda. Could we create a quick recipe to build the package upon bioconda? This looks like the standard for bioinformatics tools.

HubLot commented 6 years ago

It's doable now since MDAnalysis is already in a conda channel. I think @jbarnoud's modifications are enough to create a conda package in a custom channel. If it succeeds, yes, we can offer a recipe for bioconda.

I can look into it next week.

pierrepo commented 6 years ago

modifications are enough to create a conda package in a custom channel.

@HubLot instead of creating our own custom conda channel, could we join bioconda channel? Their build process seems pretty robust (https://bioconda.github.io/contributing.html)?

HubLot commented 6 years ago

Yes, it is the main objective. I just wanted to try the build first before submitting to bioconda.

pierrepo commented 6 years ago

OK, as you wish. But the build process proposed by Bioconda is pretty safe (everything is build upon Travis)

jbarnoud commented 6 years ago

On 02/12/2018 02:05 PM, Pierre Poulain wrote:

OK, as you wish. But the build process proposed by Bioconda is pretty safe (everything is build upon Travis)

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For the record, the MDAnalysis conda package is on conda-forge.

HubLot commented 6 years ago

So, I retried to build a conda package from the command line but now it fails... (either on the master or this PR branch) :

see this gist: https://gist.github.com/HubLot/18da1e2063001a1a51c73916ab4adff7

It seems it's an issue on Pytest but I'm not sure. I'll try to dig more into it but I'm quite busy in the next 2 weeks.