Hi Vicent,

  XML format like HTML uses "<" and ">" characters as part of its basic syntax.  The solution is ugly bug you use &lt; to represent "<" and &gt; to represent ">" just as is done in HTML format.

https://stackoverflow.com/questions/1091945/what-characters-do-i-need-to-escape-in-xml-documents

  Tom


On Jun 24, 2024, at 5:25 AM, Vincent Mallet via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Tom,

A potential user of my CrAI plugin struggles to install it, and I think his problem comes from a certain version of pytorch (2.3.0) that is buggy on Windows. For this reason, I tried to impose torch<2.2 in the dependencies, in a similar fashion to the one used in Seqcrow.  

However, the parser used by Chimerax=1.5 is not happy with the "<" present in <Dependency name="ChimeraX-Core" version=">=1.3, <=1.7"/> (as you suggested above).
$chimerax --nogui --cmd "devel install . ; exit"
>>>lxml.etree.XMLSyntaxError: Unescaped '<' not allowed in attributes values, line 40, column 43

Do you have an idea on how to solve this?

Best,
Vincent

On Tue, Oct 24, 2023 at 10:33 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Vincent,

  The cripser PyPi package requires compiled code.  On Windows or Mac users won't usually have a compiler so you won't be able to distribute your ChimeraX tool if it requires installing cripser from source code.  So your best hope is to convince the developer of cripser to provide binary wheels on PyPi for Python 3.11.  Currently the binary wheels from cripser are only for Python 3.9 and 3.10.  If you still want to know why the compile fails and ChimeraX is not reporting a useful error message use ChimeraX menu Help / Report a Bug... so we know all the details of what you tried.

  The ChimeraX help command takes the name of a command, not the name of a bundle.  Look at the documentation


When you register a command you call register() and give it a CmdDesc argument that takes a URL to your html help.  Here is the documentation


  If you want to know about Python volume data objects they are in the programming documentation.  Look at Volume Data under Python Modules


or probably easier look at the ChimeraX Recipes web site to see simple examples of how to use Python with ChimeraX


  Tom


On Oct 24, 2023, at 7:34 AM, Vincent Mallet via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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.


            <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.


I'll made a ticket to add some documentation for that.


  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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