Hi Vincent, ChimeraX bundles can list dependencies on PyPi packages. Here's an example of PyPi dependencies in bundle_info.xml of the SEQCROW ChimeraX plugin. ChimeraX will install these when the bundle is installed. https://github.com/QChASM/SEQCROW/blob/971de45120b9cb1b7f1e5ff0f2cee4b998ec6... <Dependencies> <Dependency name="ChimeraX-Core" version=">=1.3, <=1.7"/> <Dependency name="scipy"/> <Dependency name="Send2Trash"/> <Dependency name="psutil"/> <Dependency name="jinja2"/> <!-- bse is large and may fail to install with bad internet <Dependency name="basis-set-exchange"/> --> <!-- wait for numpy to fix fortran stuff in python 3.8 I've tried installing this with just gfortran on windows, but no luck <Dependency name="stripy"/> --> </Dependencies> With PyTorch I don't know if the PyPi packages include CUDA support or how the CUDA version is handled. Maybe they are CPU-only unless compiled from source on the install machine, which of course would require a compiler that only Linux (not Windows) would likely have installed. We should have some documentation on how to handle PyPi dependencies. I don't see anything useful about how to include them in the bundle_info.xml or pyproject.toml documentation for ChimeraX. https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html#bundle-for... https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/pyproject.html I'll made a ticket to add some documentation for that. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10036 Tom
On Oct 20, 2023, at 4:58 AM, Vincent Mallet via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file.
I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace...
I am hoping you can help me, thanks in advance for the help !
Best, Vincent _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/