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Package version #175

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zodieusz opened this issue Feb 7, 2025 · 3 comments · May be fixed by #176
Open

Package version #175

zodieusz opened this issue Feb 7, 2025 · 3 comments · May be fixed by #176

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@zodieusz
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zodieusz commented Feb 7, 2025 •
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So after following the installation guide for MAErec, I get a lot of issue regarding package version. For example, the rxd part using numpy legacy code. Then if I downgrade numpy to access the legacy code, I get error with other package that are relying on numpy more recent version.... anyways, Could I get a working/compatible list of package/library with their version ? thanks in advance

Current setting :
windows 10
python 3.9 ( I don't mind changing)

The rest of my package I tried a lot of different version but here are some (I tried to reinstall them all on a fresh environment)
olorama==0.4.6
contourpy==1.2.0
cycler==0.12.1
Cython==3.0.11
fonttools==4.55.8
h5py==3.12.1
importlib_resources==6.5.2
kiwisolver==1.4.7
LFPy==2.3.5
LFPykit==0.5.1
matplotlib==3.8.0
MEAutility==1.5.2
NEURON==7.8
numpy==1.26.4
packaging==24.2
pillow==11.1.0
pyparsing==3.2.1
python-dateutil==2.9.0.post0
PyYAML==6.0.2
scipy==1.13.1
six==1.17.0
tqdm==4.67.1
zipp==3.21.0
@alejoe91 alejoe91 linked a pull request Feb 7, 2025 that will close this issue
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@zodieusz
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zodieusz commented Feb 7, 2025 •
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So, It does seem to work somewhat now. However, I am currently getting an error that i know how to fix (kind of) but i would love too have feedback on why is it happening ? and maybe this is a fixable issue. I know this issues was reported and never "fixed" .

error message:

Intracellular simulation: C:\Users\antoi\.config\mearec\1.9.1\cell_models\bbp\L5_BTC_bAC217_1
Mechanisms already loaded from path: C:\Users\antoi\.config\mearec\1.9.1\cell_models\bbp\mods.  Aborting.
NEURON: bAC217_biophys : a template cannot be redefined
 in biophysics.hoc near line 33
 begintemplate bAC217_biophys
                            ^
        xopen("biophysics.hoc")
      execute1("{xopen("bi...")
    load_file(1, "biophysics.hoc")
NEURON: Can't open  synapsessynapses.hoc
 in biophysics.hoc near line 1
 {xopen("synapsessynapses.hoc")}
                                ^
        xopen("synapsessy...")
      execute1("{xopen("sy...")
    load_file(1, "synapses\s...")
        1
        1
        1
NEURON: synapses_160272643a is not a template
 in template.hoc near line 136
     synapses = new synapses_160272643a()
                                        ^
        xopen("template.hoc")
      execute1("{xopen("te...")
    load_file(1, "template.hoc")
template bAC217_L5_BTC_160272643a exist already

So for some reason, the "path" is suppose to be "synapses\synapses.hoc" but it appears as "synapsessynapses.hoc". my quick fix is to copy the synapse.hoc file and put it as "synapsessynapses.hoc" in his parent folder. This way the "synapsessynapses.hoc" file exist.

@alejoe91
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alejoe91 commented Feb 8, 2025

Mmm it might be a problem here:
https://github.com/SpikeInterface/MEArec/blob/main/src/MEArec/simulate_cells.py#L143

If you installed from source, can you try to play around with that line? It looks ok for me, but it's clearly misbehaving for windows...

@zodieusz
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zodieusz commented Feb 9, 2025 •
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So it was kind of the line you mentioned. The real problem come with h.load_file() on line161 but is caused by the path formatting (your code return the "path 3 formmating"). See the script (purely for testing) and the outcome bellow .

from neuron import h

print("using path 1 : simulatedData/h.hoc")
h.load_file(1, "simulatedData/h.hoc")

print("\n\nusing path 2 : simulatedData//h.hoc")
h.load_file(1, "simulatedData//h.hoc")

print("\n\nusing path 3 : simulatedData\\h.hoc")
h.load_file(1, "simulatedData\\h.hoc")

using path 1 : simulatedData/h.hoc
NEURON: String is not a template
 in h.hoc near line 87
         mtype_name_string = new String(mtype_name)
                                                  ^
        xopen("h.hoc")
      execute1("{xopen("h....")
    load_file(1, "simulatedD...")


using path 2 : simulatedData//h.hoc
NEURON: synapses_d0cc8d7615 : a template cannot be redefined
 in h.hoc near line 31
 begintemplate synapses_d0cc8d7615
                                 ^
        xopen("h.hoc")
      execute1("{xopen("h....")
    load_file(1, "simulatedD...")


using path 3 : simulatedData\h.hoc
NEURON: Can't open  simulatedDatah.hoc
 in h.hoc near line 1
 {xopen("simulatedDatah.hoc")}
                              ^
        xopen("simulatedD...")
      execute1("{xopen("si...")
    load_file(1, "simulatedD...")

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Fixes for numpy 2.0 SpikeInterface/MEArec
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@alejoe91 @zodieusz