help mybundle, I don't know how to add the per argument documentation and go beyond typing hints.
Hello, thanks so much for the prompt reply ! I managed to get most things flowing (I'm going to try and figure out the cuda part now). I am still struggling on a few things : 1. the install from source distribution for packages such as crispr : https://pypi.org/project/cripser/ . I contacted the author to turn his install with pip -U {url} into a regular one, and running pip install cripser on my python works. I think the compilation of the source files silently fails when installing through Chimerax, and have no idea on how to fix it 2. I don't quite understand how to play with the help API, if a user types 3. For now, I am using the name of mrc/map volume files and opening them with python, I don't know if it would be possible to directly retrieve them as python objects in my bundle ? The possibility to use volume data is mentioned in the doc, but there seems to be a missing section <https://www.cgl.ucsf.edu/chimerax/docs/devel/data_interface.html#builtin-dat...> ( https://www.cgl.ucsf.edu/chimerax/docs/devel/data_interface.html#builtin-dat... ) Maybe you can answer some of these questions, and again, thank you so much for the support ! Best, Vincent On Sat, Oct 21, 2023 at 1:37 AM Tom Goddard <goddard@sonic.net> wrote:
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/