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omnia-md / conda-recipes

conda build recipes for the Omnia project
http://omnia.md
MIT License
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Include recipe for Chemfiles #538

Open Luthaf opened 8 years ago

Luthaf commented 8 years ago

Chemfiles is a cross-platform, cross-language library for reading and writing chemistry data files (trajectories and topologies). It does only this (no analysis code is included), and try to do it efficiently, for multiple formats, and with a clean interface. It is built using a C++11 core library, and provide other languages bindings (Python 2&3, Julia, Fortran, C, Rust) through a C interface. It is useful for people writing analysis algorithms, and not wanting to deal with (complex) formats, or for people needing to do any kind of IO (simulations softwares, molecular builders, ...)

Would you be interested to include it in Omnia? I already have some conda recipes for it, which I can update and adapt.

Disclaimer: I am the creator and maintainer of chemfiles =)

jchodera commented 8 years ago

This looks pretty awesome! Let me look into this a bit further.

Omnia already has MDTraj for doing some of this, and there's certainly no harm in having multiple tools that do similar things (especially if they can be made more interoperable over time), but can you give a quick summary of how capabilities with MDTraj? Chemfiles seems to have a much larger variety of language bindings, for one...

rmcgibbo commented 8 years ago

+1 from me. Looks like a great library!

The only thing that I would request (we should do this for the rest of the recipes, but there's no harm in starting now), is to add your name and/or email into the meta.yaml file in an extras/maintainer section (example: http://conda.pydata.org/docs/building/meta-yaml.html#extra-section).

Luthaf commented 8 years ago

but can you give a quick summary of how capabilities with MDTraj?

I see MDTraj more like an analysis tool, and Chemfiles only as an IO provider. I support roughly the same formats as MDTraj for now, but more are planned, and specifically, all the format supported by VMD are supported by chemfiles. They are not activated, because I would like to have a test file for all supported formats.

Chemfiles seems to have a much larger variety of language bindings, for one...

The language binding is part of why I started writing Chemfiles. I am using it from two simulations tools written in C++ and Rust, and using Python for IO was a no-go for me.

Luthaf commented 8 years ago

A small update here: I am in the process of releasing the 0.6.0 version, and when I'll update the conda recipes I'll submit them here.

jchodera commented 8 years ago

Great!

Luthaf commented 7 years ago

Some update here: I have finally included chemfiles recipes on conda-forge: chemfiles, chemfiles-lib and chemfiles-python.

As you are migrating your own recipes to conda-forge, maybe this can be closed? Chemfiles could still be listed to the omnia meta package if you think this could be interesting to your users.

Let me know what you think!