Python packages numpy and scipy

[jessdtate]

Users need to be able to easily use numpy and scipy. It would be best to include them with SCIRun, but we at least need documentation explaining how to do the install/ add to the path.

[jessdtate]

installing numy and scipy is very easy (for me) using pip:

cd "scirun_root"/bin/Externals/Install/Python_external/bin/ ./python3 -m pip install numpy

similar for scipy, matplotlib and other major packages.

[a-y-khan]

Which OSs did you test on?

[jessdtate]

OS X 10.10.

[a-y-khan]

Linux will probably work then. This needs testing on Windows.

[jessdtate]

There are some issues pushing matlab matrices back to scirun. They have to be converted to lists of lists, where matlab has an array format. The conversion is not as straight forward as going the opposite way (at least as far as I have found). This may be a problem with fields too.

[dcwhite]

I should be able to write a converter on the C++ side. What happens when you pass the Matlab array type to the set transient state function?

[jessdtate]

nothing. There is a null output from the module (both the interfacewithpython and pythonobjectforwarder). It doesn't seem to to be waiting around for it, like it finds the object, but can't convert it.

[dcwhite]

OK. See if there's (non-python) terminal output--I think I print a message saying the value can't be converted.

[jessdtate]

here it is:

[NOTICE] Invalid Connection request: input port is full, or ports are different datatype or same i/o type, or on the same module.

[dcwhite]

That's a different message. No worries, I can look at this Monday.

[jessdtate]

Oops, That was the one that worked (after conversion). Here is the error:

No known conversion from python object to C++ object [PYTHON] 'Transient value set'

[dcwhite]

I can't get pip working on my Windows machine. It appears that our python build is lacking required OpenSSL support. Also, we're using the flag "--with-ensurepip=no" which seems like it would explain it. Any thoughts?

[jessdtate]

I'm not sure, as I'm not an expert in python. I think that flag would just keep pip out of the default installation, but prevent subsequent installation. I have had no problems with OS X and pip.

[a-y-khan]

Turning off ensurepip was due to a Mac OS X build error in 3.4.3. I uploaded 3.4.4 for testing earlier today, since it appears to have some build fixes. OpenSSL on Windows may be tricky.

[dcwhite]

@ajanson @jessdtate I got a little bit further on Windows, but we'll probably have to modify the python external build configuration. We decided to push this one until post-IBBM since it will affect so few people.

[dcwhite]

I'll focus on getting ensurepip working after upgrading to 3.6 (see #1668).

[github-actions[bot]]

Stale issue message

[dcwhite]

Depends on Python upgrade path (gotta get off of 3.4 on Windows first, then ship 3.6 on Mac)

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This issue is stale because it has been open 120 days with no activity. Remove stale label or comment or this will be closed in 60 days.

[github-actions[bot]]

This issue is stale because it has been open 240 days with no activity. Remove the stale label or comment, or this will be closed in 60 days.

[dcwhite]

ensurepip still had problems in 3.8. Not sure why this is so difficult...

[github-actions[bot]]

This issue is stale because it has been open 240 days with no activity. Remove the stale label or comment, or this will be closed in 60 days.