Installation in windows for dummies #628

srcfernandes · 2023-03-23T11:12:07Z

srcfernandes
Mar 23, 2023

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

Answered by jasmainak

Mar 28, 2023

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

D…

View full answer

jasmainak · 2023-03-23T14:45:51Z

jasmainak
Mar 23, 2023
Maintainer

@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 ?

0 replies

srcfernandes · 2023-03-23T15:13:57Z

srcfernandes
Mar 23, 2023
Author

Dear Mainak Jas, I installed anaconda3 (local installation). Then, I installed neuron as recommended using the precompiled installer for windows 10. I selected the anaconda3 dir as installation dir for neuron (is this correct?) Then, I opened the Anaconda Prompt and checked, as you recommended: (base) C:\Users\FML>python -c 'import neuron;' File "<string>", line 1 'import ^ SyntaxError: unterminated string literal (detected at line 1) (base) C:\Users\FML> Since it was a syntax error, I tried (base) C:\Users\FML>python -c "import neuron" Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'neuron' I did not move forward, since I was not able to check neuron installation. I am waiting for confirmation of acceptance in the Neuron forum to ask them. However, if you could help me with is, it would be great. Maybe I am missing some steps. Many thanks, best, Sofia

…

________________________________ From: Mainak Jas ***@***.***> Sent: Thursday, March 23, 2023 2:46:03 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) @srcfernandes<https://github.com/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 ? — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY5XZ6ADNL3R6VXEBPDW5RO2XANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

jasmainak · 2023-03-23T15:30:36Z

jasmainak
Mar 23, 2023
Maintainer

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 ...

0 replies

rythorpe · 2023-03-23T17:08:00Z

rythorpe
Mar 23, 2023
Maintainer

@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.

0 replies

srcfernandes · 2023-03-24T10:30:37Z

srcfernandes
Mar 24, 2023
Author

Dear Ryan I re-installed Neuron at root (the defaul) as recommended. When I open the Anaconda prompt and do, as recommended in your installation page (https://jonescompneurolab.github.io/hnn-core/stable/index.html#installation) python -c 'import neuron;' File "<string>", line 1 'import ^ SyntaxError: unterminated string literal (detected at line 1) But if I replace ' for ", it does not result in errors (base) C:\Users\FML>python -c "import neuron;" (base) C:\Users\FML> Nothing happens, is this OK? I then installed hnn_core[gui]: (base) C:\Users\FML>pip install hnn_core[gui] then, I tested and no errors were reported (base) C:\Users\FML>python -c "import hnn_core" (base) C:\Users\FML> but when I try to start the gui according to the instruction provided in the webpage, I get an error (base) C:\Users\FML>hnn-gui 'hnn-gui' is not recognized as an internal or external command, operable program or batch file. I tried other things, with the same error (base) C:\Users\FML>hnn_core 'hnn_core' is not recognized as an internal or external command, operable program or batch file. (base) C:\Users\FML>hnn 'hnn' is not recognized as an internal or external command, operable program or batch file. (base) C:\Users\FML>hnn_core[gui] 'hnn_core[gui]' is not recognized as an internal or external command, operable program or batch file. What have I missed here? I am doing this all in the Anaconda prompt. Do I need do do something like "conda activate"? I also send a text with the outputs that I get during hnn-core installation. Also, I would like to use Jupyter lab to run the scripts. What should be the steps for starting this? Thank you for all your help, best Sofia

…

________________________________ From: Ryan Thorpe ***@***.***> Sent: Thursday, March 23, 2023 5:08:11 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) @srcfernandes<https://github.com/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. — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY7AJ46XYLOEWRFFCU3W5R7PXANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***> (base) C:\Users\FML>python -c "import neuron;" (base) C:\Users\FML>pip install hnn_core[gui] Requirement already satisfied: hnn_core[gui] in c:\users\fml\appdata\roaming\python\python310\site-packages (0.3) Requirement already satisfied: numpy>=1.14 in c:\users\fml\anaconda3\lib\site-packages (from hnn_core[gui]) (1.23.5) Requirement already satisfied: scipy in c:\users\fml\anaconda3\lib\site-packages (from hnn_core[gui]) (1.10.0) Requirement already satisfied: matplotlib>=3.5.3 in c:\users\fml\anaconda3\lib\site-packages (from hnn_core[gui]) (3.7.0) Requirement already satisfied: ipympl<0.9 in c:\users\fml\appdata\roaming\python\python310\site-packages (from hnn_core[gui]) (0.8.8) Requirement already satisfied: voila<=0.3.6 in c:\users\fml\appdata\roaming\python\python310\site-packages (from hnn_core[gui]) (0.3.6) Requirement already satisfied: ipywidgets<=7.7.1 in c:\users\fml\anaconda3\lib\site-packages (from 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srcfernandes · 2023-03-24T11:08:17Z

srcfernandes
Mar 24, 2023
Author

Dear Ryan, Meanwhile, I follow some indications I get from Sara Piersigilli (she already contacted you) and did pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master It runned fine. I then did (base) C:\Users\FML>python -c "import hnn_core" and got nothing (so it must be OK) and did (base) C:\Users\FML>hnn-gui Here, it started the hnn_widget but it was empthy. There were several errors in the prompt, I send all the outputs in attachment. Can you help me? Many thanks, best, Sofia

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________________________________ From: Sofia Fernandes Sent: Friday, March 24, 2023 10:29:59 AM To: jonescompneurolab/hnn-core; jonescompneurolab/hnn-core Cc: Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) Dear Ryan I re-installed Neuron at root (the defaul) as recommended. When I open the Anaconda prompt and do, as recommended in your installation page (https://jonescompneurolab.github.io/hnn-core/stable/index.html#installation) python -c 'import neuron;' File "<string>", line 1 'import ^ SyntaxError: unterminated string literal (detected at line 1) But if I replace ' for ", it does not result in errors (base) C:\Users\FML>python -c "import neuron;" (base) C:\Users\FML> Nothing happens, is this OK? I then installed hnn_core[gui]: (base) C:\Users\FML>pip install hnn_core[gui] then, I tested and no errors were reported (base) C:\Users\FML>python -c "import hnn_core" (base) C:\Users\FML> but when I try to start the gui according to the instruction provided in the webpage, I get an error (base) C:\Users\FML>hnn-gui 'hnn-gui' is not recognized as an internal or external command, operable program or batch file. I tried other things, with the same error (base) C:\Users\FML>hnn_core 'hnn_core' is not recognized as an internal or external command, operable program or batch file. (base) C:\Users\FML>hnn 'hnn' is not recognized as an internal or external command, operable program or batch file. (base) C:\Users\FML>hnn_core[gui] 'hnn_core[gui]' is not recognized as an internal or external command, operable program or batch file. What have I missed here? I am doing this all in the Anaconda prompt. Do I need do do something like "conda activate"? I also send a text with the outputs that I get during hnn-core installation. Also, I would like to use Jupyter lab to run the scripts. What should be the steps for starting this? Thank you for all your help, best Sofia

________________________________ From: Ryan Thorpe ***@***.***> Sent: Thursday, March 23, 2023 5:08:11 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) @srcfernandes<https://github.com/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. — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY7AJ46XYLOEWRFFCU3W5R7PXANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***> (base) C:\Users\FML>pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master Collecting https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master Downloading https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master / 532.7 kB 2.1 MB/s 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: scipy in c:\users\fml\anaconda3\lib\site-packages (from hnn-core==0.4.dev0) (1.10.0) Requirement already satisfied: matplotlib>=3.5.3 in c:\users\fml\anaconda3\lib\site-packages (from hnn-core==0.4.dev0) (3.7.0) Requirement already satisfied: numpy>=1.14 in c:\users\fml\anaconda3\lib\site-packages (from hnn-core==0.4.dev0) (1.23.5) Requirement already satisfied: cycler>=0.10 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (0.11.0) Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (1.4.4) Requirement already satisfied: fonttools>=4.22.0 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (4.25.0) Requirement already satisfied: python-dateutil>=2.7 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (2.8.2) Requirement already satisfied: pyparsing>=2.3.1 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (3.0.9) Requirement already satisfied: packaging>=20.0 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (22.0) Requirement already satisfied: pillow>=6.2.0 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (9.4.0) Requirement already satisfied: contourpy>=1.0.1 in c:\users\fml\anaconda3\lib\site-packages (from matplotlib>=3.5.3->hnn-core==0.4.dev0) (1.0.5) Requirement already satisfied: six>=1.5 in c:\users\fml\anaconda3\lib\site-packages (from python-dateutil>=2.7->matplotlib>=3.5.3->hnn-core==0.4.dev0) (1.16.0) Building wheels for collected packages: hnn-core Building wheel for hnn-core (pyproject.toml) ... done Created wheel for hnn-core: filename=hnn_core-0.4.dev0-py3-none-any.whl size=382654 sha256=3c0e743743a4f53eb49faa6e16186f32dd51b59b93d7793fae793118b149a9f1 Stored in directory: C:\Users\FML\AppData\Local\Temp\pip-ephem-wheel-cache-8x5wfn85\wheels\db\5a\bd\200eff1b2a706d65677a7f477fee0c75ce90678f615f8af985 Successfully built hnn-core Installing collected packages: hnn-core Attempting uninstall: hnn-core Found existing installation: hnn-core 0.3 Uninstalling hnn-core-0.3: Successfully uninstalled hnn-core-0.3 Successfully installed hnn-core-0.4.dev0 (base) C:\Users\FML>python -c "import hnn_core" (base) C:\Users\FML>hnn-gui [Voila] Using C:\Users\FML\AppData\Local\Temp to store connection files [Voila] Storing connection files in C:\Users\FML\AppData\Local\Temp\voila_ytw4gg6k. [Voila] Serving static files from C:\Users\FML\AppData\Roaming\Python\Python310\site-packages\voila\static. [Voila] Voilà is running at: http://localhost:8866/ [Voila] WARNING | Notebook hnn_widget.ipynb is not trusted [Voila] Kernel started: 3813c756-288d-4adc-b0cf-226fb53747e6 [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm 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[Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] 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[Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No 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handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' [Voila] WARNING | No handler found for comm target 'comm' WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 1.07ms C:\Users\FML\anaconda3\lib\site-packages\jupyter_server\base\handlers.py:197: UserWarning: The Tornado web application does not have an 'authorizer' defined in its settings. In future releases of jupyter_server, this will be a required key for all subclasses of `JupyterHandler`. For an example, see the jupyter_server source code for how to add an authorizer to the tornado settings: https://github.com/jupyter-server/jupyter_server/blob/653740cbad7ce0c8a8752ce83e4d3c2c754b13cb/jupyter_server/serverapp.py#L234-L256 warnings.warn(

0 replies

rythorpe · 2023-03-24T20:16:17Z

rythorpe
Mar 24, 2023
Maintainer

A few things:

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.
In order to run the hnn-gui command, try calling start hnn-gui.
hnn_core is a python module, not an executable, so you won't be able to call it directly outside of a python interpreter.

0 replies

rythorpe · 2023-03-24T20:22:40Z

rythorpe
Mar 24, 2023
Maintainer

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.

0 replies

srcfernandes · 2023-03-25T09:28:59Z

srcfernandes
Mar 25, 2023
Author

Dear Ryan Can you help me on how do I proceed to make the procedures you are indicating? 1) downgrading to the specific versions? 2) starting a new conda environment? I am new to anaconda and conda, so I do not know how to do this. Should the problem be because I did this first pip install hnn_core[gui] and then this pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master Thank you for all your help and attention. Best, Sofia

…

________________________________ From: Ryan Thorpe ***@***.***> Sent: Friday, March 24, 2023 8:22:50 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) Oh, and it looks like your voila and/or ipywidgets modules might be the wrong versions (see our README<https://jonescompneurolab.github.io/hnn-core/stable/index.html>). Try downgrading to the specified versions or starting a new conda environment. — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WYYPTXI2T4JEGRWRC2TW5X7BVANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

jasmainak · 2023-03-26T05:38:32Z

jasmainak
Mar 26, 2023
Maintainer

@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 ...

0 replies

jasmainak · 2023-03-26T05:39:45Z

jasmainak
Mar 26, 2023
Maintainer

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?

0 replies

srcfernandes · 2023-03-28T10:59:09Z

srcfernandes
Mar 28, 2023
Author

Dear Mainak Jas Thank you for your help. I apologize for the following question, I am really new on all these instalation procedures. I did the conda commands: $ conda create -n hnn_gui python=3.9 $ conda activate hnn_gui but when I try to run the hnn-gui in the default dir, I get the following error: (I used different combinations) (hnn_gui) C:\Users\FML>hnn-gui 'hnn-gui' is not recognized as an internal or external command, operable program or batch file. (hnn_gui) C:\Users\FML>hnn-core[gui] 'hnn-core[gui]' is not recognized as an internal or external command, operable program or batch file. (hnn_gui) C:\Users\FML>hnn_core[gui] 'hnn_core[gui]' is not recognized as an internal or external command, operable program or batch file. (hnn_gui) C:\Users\FML>hnn_gui 'hnn_gui' is not recognized as an internal or external command, operable program or batch file. Even if I try the same inside hnn_gui directory, I get the same error. I noticed that there are 2 executable files inside hnn_gui directory, "venvlauncher.exe" and "venvwlauncher.exe". When I type these, I get

> No pyvenv.cfg file

Do I need to unistall hnn-core and install it again inside this new environment? This does not apply to neuron, right? I apologize for these many questions. Thank you so much for your help. Best, Sofia

…

________________________________ From: Mainak Jas ***@***.***> Sent: Sunday, March 26, 2023 6:38:44 AM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) @srcfernandes<https://github.com/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 packages. Just try redoing the install in a fresh environment and check if it works ... — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY2PDUXX67T774GPXETW57I6JANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

srcfernandes · 2023-03-28T11:38:01Z

srcfernandes
Mar 28, 2023
Author

Dear Mainak Jas Meanwhile, I tried the following: (hnn_gui) C:\Users\FML>pip uninstall hnn_core[gui] (hnn_gui) C:\Users\FML>pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master All went fine. When I type "hnn-gui", I get the following error (hnn_gui) C:\Users\FML>hnn-gui Traceback (most recent call last): File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\FML\anaconda3\envs\hnn_gui\Scripts\hnn-gui.exe\__main__.py", line 4, in <module> File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\site-packages\hnn_core\gui\__init__.py", line 1, in <module> from .gui import HNNGUI, launch File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\site-packages\hnn_core\gui\gui.py", line 14, in <module> from IPython.display import IFrame, display ModuleNotFoundError: No module named 'IPython' Should this be a problem with PATH (to get IPython working)? Many, many thanks for all your help, best Sofia

…

________________________________ From: Mainak Jas ***@***.***> Sent: Sunday, March 26, 2023 6:38:44 AM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) @srcfernandes<https://github.com/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 packages. Just try redoing the install in a fresh environment and check if it works ... — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY2PDUXX67T774GPXETW57I6JANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

srcfernandes · 2023-03-28T12:27:10Z

srcfernandes
Mar 28, 2023
Author

Dear Mainak Jas I am going step by step and trying to find what is missing. I opened the anaconda navigator and installed IPython packages on hnn_gui environment. I am not sure that this is the procedure, I hope so. When I did "hnn-gui", it seems that only voila is missing: (hnn_gui) C:\Users\FML>hnn-gui Traceback (most recent call last): File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\FML\anaconda3\envs\hnn_gui\Scripts\hnn-gui.exe\__main__.py", line 7, in <module> File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\site-packages\hnn_core\gui\gui.py", line 1361, in launch from voila.app import main ModuleNotFoundError: No module named 'voila' I found it in a site (https://github.com/voila-dashboards/voila/archive/refs/tags/v0.3.6.zip) and use "pip install". The following error occured inside hnn_gui environment: File "C:\Users\FML\anaconda3\envs\hnn_gui\lib\subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['C:\\Users\\FML\\AppData\\Local\\Temp\\pip-build-env-v4qfubci\\overlay\\Scripts\\jlpm.EXE', 'install']' returned non-zero exit status 1. [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for voila Failed to build voila ERROR: Could not build wheels for voila, which is required to install pyproject.toml-based projects So, I did the installation on the "base" environment, which runned fine. However, I do not find voila module to install in hnn_gui env using the anaconda navigator. Maybe it is only a question of what are the voila-related packages to look for and install. Can you help me on this? It seems that it may be the only thing missing to get the gui working. Best, Sofia Message ID: ***@***.***>

0 replies

jasmainak · 2023-03-28T14:53:07Z

jasmainak
Mar 28, 2023
Maintainer

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?

0 replies

srcfernandes · 2023-03-28T15:08:54Z

srcfernandes
Mar 28, 2023
Author

Dear Jas, It worked finally, thank you! I was doing pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master and pip install hnn_core[gui] which was probably also not helping. It still outputs some warnings when I open the hnn-gui, I hope this is not a problem: [Voila] Using C:\Users\FML\AppData\Local\Temp to store connection files [Voila] Storing connection files in C:\Users\FML\AppData\Local\Temp\voila_cabr3d8x. [Voila] Serving static files from C:\Users\FML\anaconda3\envs\hnn_gui2\lib\site-packages\voila\static. [Voila] Voilà is running at: http://localhost:8866/ [Voila] WARNING | Notebook hnn_widget.ipynb is not trusted [Voila] Kernel started: 281785cc-b7a7-4e65-87f3-bb7d50452e38 403 GET /voila/files/favicon.ico (::1): File not whitelisted 403 GET /voila/files/favicon.ico (::1) 2.00ms C:\Users\FML\anaconda3\envs\hnn_gui2\lib\site-packages\jupyter_server\base\handlers.py:197: UserWarning: The Tornado web application does not have an 'authorizer' defined in its settings. In future releases of jupyter_server, this will be a required key for all subclasses of `JupyterHandler`. For an example, see the jupyter_server source code for how to add an authorizer to the tornado settings: https://github.com/jupyter-server/jupyter_server/blob/653740cbad7ce0c8a8752ce83e4d3c2c754b13cb/jupyter_server/serverapp.py#L234-L256 warnings.warn( Thank you so much! I was trying a lot of things and even starting to change the handlers.py file... It would be nice to have these straighforward commands available to help others ones just starting as I am. Many, many thanks for all your help and kindness! Best, Sofia

…

________________________________ From: Mainak Jas ***@***.***> Sent: Tuesday, March 28, 2023 3:53:17 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Issue #627) Sofia, You need to follow the instructions exactly as provided here<https://jonescompneurolab.github.io/hnn-core/stable/index.html>. 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] Does this work? If not, what error do you get? — Reply to this email directly, view it on GitHub<#627 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY4T744NSM7NO2NTJHTW6L3N3ANCNFSM6AAAAAAWFBNRMI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

jasmainak · 2023-03-28T15:32:32Z

jasmainak
Mar 28, 2023
Maintainer

Great! I think you can safely ignore the warnings for now. If there are others seeking help, can you redirect them to the discussions page: https://github.com/jonescompneurolab/hnn-core/discussions ? I converted this issue to a discussion. We are trying to separate developer stuff (issues) from user questions (discussions). Thanks!

0 replies

srcfernandes · 2023-03-28T20:29:27Z

srcfernandes
Mar 28, 2023
Author

Yes, of course! Will I get notifications to redirect them whenever necessary?

…

________________________________ From: Mainak Jas ***@***.***> Sent: Tuesday, March 28, 2023 4:32:44 PM To: jonescompneurolab/hnn-core Cc: Sofia Fernandes; Mention Subject: Re: [jonescompneurolab/hnn-core] Installation in windows for dummies (Discussion #628) Great! I think you can safely ignore the warnings for now. If there are others seeking help, can you redirect them to the discussions page: https://github.com/jonescompneurolab/hnn-core/discussions ? I converted this issue to a discussion. We are trying to separate developer stuff (issues) from user questions (discussions). Thanks! — Reply to this email directly, view it on GitHub<#628 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6V4WY4CYQKTHIZO6CI26W3W6MABZANCNFSM6AAAAAAWKXYY2E>. You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

jasmainak · 2023-03-28T20:59:11Z

jasmainak
Mar 28, 2023
Maintainer

Just share the URL :) That should be enough!

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Installation in windows for dummies #628

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