So if listing mdtraj as a dependency fails with the ChimeraX 1.6 release candidate, we'd like to know.  It should work.   There were bugs in earlier versions of ChimeraX for handling source code package dependencies.   And they might not all be gone.

So back to the fact that mdtraj is a source code distribution.  It has the added complication that a C computer is required on the destination computer to install it.  That is rarely true on Windows.   And is not guaranteed  to work on Linux and macOS.  You need to say, that a C compiler is required, very prominently near the beginning of the description of your bundle.  If there is no C compiler, there will be lots of installation errors that ChimeraX can't handle.

So it would be much better that you included a precompiled version of mdtaj with your bundle.  And distributed binary versions for Windows, Linux, and macOS.  We can help you with that if need be.

    -- Greg

Hello,

I am developing a chimerax plugin. My code will have some interaction with mdtraj. I need mdtraj to be installed in the python that ships with chimerax. I tried "chimerax -m pip install mdtraj" but I get all kinds of error dialogs popping up in the chimerax instance that gets launched during the installation. I terminate all the error dialogs and then exit chimerax (as the python install seems frozen) and then it indeed says installation has failed and gives unusual error messages (like setuptools was less than version 48.0.0 while chimerax reports it to be 65.x.y and even 66.x.y after upgrading).

Can someone tell me the correct syntax to use to install mdtraj in chimerax's python? Thank you.

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