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 >>help mybundle, I don't know how to add the per argument documentation and go beyond typing hints.

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-data-formats )

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/971de45120b9cb1b7f1e5ff0f2cee4b998ec6cb5/bundle_info.xml#L68

<Dependencies>
<Dependency name="ChimeraX-Core" version=">=1.3, <=1.7"/>
<Dependency name="scipy"/>
<Dependency name="Send2Trash"/>
<Dependency name="psutil"/>
<Dependency name="jinja2"/>


</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-format
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
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