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Installation in windows for dummies #627

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srcfernandes opened this issue Mar 23, 2023 · 16 comments
Closed

Installation in windows for dummies #627

srcfernandes opened this issue Mar 23, 2023 · 16 comments

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@srcfernandes
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Dear HNN team

I am interested in local neural networks modelling.
I am familiar with other types of programming, such as matlab and just starting with python.

My main problem is to know how to make installations with anaconda, how are the steps procedures, prompts to open, paths to add and how.... all this kind of stuft. I tried to install hnn-core with a help of a friend, but it didn't work.

I kindly ask you if you could provide me a step-by-step instructions on how to install HNN core in windows, test and launch hnn-core (a kind of "installation for dummies"). If this is already in here, where should I look?

Thank you so much!

Sofia
@jasmainak
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@srcfernandes can you be a bit more explicit about "it didn't work". What/where did you fail?

Did you follow the steps here: https://jonescompneurolab.github.io/hnn-core/stable/index.html ?

@srcfernandes
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srcfernandes commented Mar 23, 2023 via email

@jasmainak
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I don't think you need to set anaconda3 as the install directory for Neuron. @rythorpe do you have any advice?

I hope they accept you in the forum soon, otherwise we can tag one of the Neuron developers here ...

@rythorpe
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@srcfernandes You should be able to install NEURON anywhere on your machine and it work with anaconda, but I'd recommend installing NEURON at root or wherever it tries to install by default.

@srcfernandes
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srcfernandes commented Mar 24, 2023 via email

@srcfernandes
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srcfernandes commented Mar 24, 2023 via email

@rythorpe
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A few things:

  1. Using single quotes vs double quotes is different depending on if you're running from a Windows cmd shell, so I think you're right that at times you need to use double quotation marks.
  2. In order to run the hnn-gui command, try calling start hnn-gui.
  3. hnn_core is a python module, not an executable, so you won't be able to call it directly outside of a python interpreter.

@rythorpe
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Oh, and it looks like your voila and/or ipywidgets modules might be the wrong versions (see our README). Try downgrading to the specified versions or starting a new conda environment.

@srcfernandes
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srcfernandes commented Mar 25, 2023 via email

@jasmainak
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jasmainak commented Mar 26, 2023 •
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@srcfernandes take a look at the conda documentation:

https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-with-commands

Something like:

$ conda create -n hnn_gui python=3.9

should do the trick. Followed by:

$ conda activate hnn_gui

I don't think you need to separately downgrade any package since the hnn_core install should automatically install the right versions of these packages using the constraints specified in setup.py. Just try redoing the install in a fresh environment and check if it works ...

@jasmainak
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jasmainak commented Mar 26, 2023 •
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Btw, it would be helpful if you could format the code blocks using markdown when asking for help. So it is more readable:

https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax#quoting-code

Also googling your warnings led me to these:

voila-dashboards/voila#1271
#585

Perhaps you can find something useful there?

@srcfernandes
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srcfernandes commented Mar 28, 2023 via email

@srcfernandes
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srcfernandes commented Mar 28, 2023 via email

@srcfernandes
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srcfernandes commented Mar 28, 2023 via email

@jasmainak
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jasmainak commented Mar 28, 2023 •
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Sofia,

You need to follow the instructions exactly as provided here. These are the instructions we have tested ... any other variation may not work.

What is happening is that you are doing:

pip install hnn_core

and that does not install voila. If you try to install it on your own, you will end up installing the wrong version. You need to do:

pip install hnn_core[gui]

to ensure that it installs the right version of voila. So, let's try again in a fresh environment:

conda create -n hnn_gui2 python=3.9

then:

conda activate hnn_gui2

After this, no need to uninstall anything. The Neuron installation stays as it is. Just do:

pip install hnn_core[gui]

Finally to start the GUI, just do:

hnn-gui

Does this work? If not, what error do you get?

@srcfernandes
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srcfernandes commented Mar 28, 2023 via email

@jonescompneurolab jonescompneurolab locked and limited conversation to collaborators Mar 28, 2023
@jasmainak jasmainak converted this issue into discussion #628 Mar 28, 2023

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@jasmainak @rythorpe @srcfernandes