Small fixes to Blue Brain Models #4
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Resolves ValueError when writing out somatic voltages
To ensure that run.py and run_RmpRiTau.py run right out of the box, python_recordings folders were added where expected. These contain an empty .placeholder file, so that git will re-create the folder on checkout. An alternative solution would be to include .gitignore files that ignore any model output, but perhaps people want to track code there.
Revised Python code so the same things are done in the same way the two example files.
Window title now set when creating figure instead.
Create empty (but for a .placeholder file) directories so that hoc scripts also work out of the box. See 34d61e9 for details
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I don't have the rights to merge this. @wvangeit could you merge this or indicate me whom to ask for merging this? |
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I also don't have the rights. But I approve the changes though. |
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I'll take care of it later today. EBRAINS first |
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Thank you @ramcdougal |
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This PR makes a few small fixes to the code incorporated from the Blue Brain Project's NMC Portal to ensure that it works immediately and on recent versions of Python. The issues are actually in the upstream code, but it is already modified slightly in this repo, so it seems sensible to fix it here as well.
For every model directory in
cells, this PRUpdates the Python code in
run.pyandrun_RmpRiTau.pyso that they run under Python 3. First, they now build a numpy array for numpy.savetxt, instead of passing it azipbuilt from two arrays (which is not a list, and thus an array_like in Python 3). Some deprecated plotting code is replaced as well.Adds a
python_recordingsandhoc_recordingsfolder, so that the included scripts can run right out of the box (Missing directories #2). These folders were present in the original BBP code here, but seem to have been lost because git removes empty directories. These now include empty.placeholderfiles so that the directories get recreated on checkout.To do for all 25 cells, I used the attached script. This should work on the original BBP models, and I will try to get these changes incorporated there as well.
fixup.sh.txt
Closes #2 and #3