combinato installation on Windows

[lubavas]

Dear Johannes,

I’m trying to install combinato on Windows and have some problems.

I run the following code
python setup_options.py

and get the following results.
combinato\options.py exists, not doing anything.

Everything seems to go well at this point.

Then I run
python tools/test_installation.py

and get
Unable to load Combinato: No module named 'combinato' Check your PYTHONPATH and make sure to copy combinato/default_options.py to combinato/options.py Re-run after fixing problems. 'montage' from ImageMagick not found: [WinError 2] Не удается найти указанный файл Plotting continuous data will not work

I added the combinato folder to my PYTHONPATH. I don’t understand what “to copy
combinato/default_options.py to combinato/options.py” means. Could you explain what this expression means?

Could you help me with my question?

Best wishes,
Luba

[jniediek]

Hi Luba!

I can only guess that what you're seeing has to do with the fact that there is a combinato folder inside the folder that you download from Github, giving you .../combinato/combinato on you local file system. The inner folder has to be in the PYTHONPATH, this is the module that python needs to load (the outer folder is the repository, the inner folder is the combinato module for python).

As to your other question, what I mean by

to copy combinato/default_options.py to combinato/options.py

is to take the file default_options.py from the inner combinato folder and save it in the same folder under the name options.py. But it seems that you did this already, so you can ignore anything that relates to this message I think.

Best,
Johannes

[lubavas]

Dear Johannes,

Thank you for the reply!

I added the inner combinato folder to my PYTHONPATH as well as other subfolers in the combinato repository. To be on the safe side, I also saved file default_options.py as options.py in the .../combinato/combinato folder. Unfortunately, I still get the same error from my terminal. Do you have other guesses how I can improve?

Best wishes,
Luba

[jniediek]

Dear Luba,

can you run the following:

python3
>>> import sys
>>> sys.path

In my case this gives

['', '/home/johannes/Repositories/combinato', ...]

Let's try if you see combinato in this path, too!

Best,
Johannes

[jniediek]

Can I close this issue?

[lubavas]

Can I close this issue?

Dear Johannes,

Thank you for the reminder! Actually, the problem persists even after I displayed the PYTHONPATH and found the combinato folder in it. I will be able to write the exact PYTHONPATH contents tomorrow.

Do you have any suggestions on what I can try next?

Best wishes,
Luba

[jniediek]

Hi Luba,

so what happens if you do the following

python3
>>> from combinato import Combinato

Does this throw an error?

Best regards,
Johannes

[lubavas]

Hi Johannes,

I ran this command. No, it didn't retrieve and error and was waiting for new commands.

Best wishes,
Luba

[jniediek]

Hi,

have you also tried python3 tools/test_installation.py? You wrote the command without the 3.

Best,
Johannes

[AlanoudAlsubhi]

Hi,
I have been having the same exact issue. Any update on how to solve it?

Thanks,
Alanoud

[jniediek]

I would like to know where in your file system you have the dist-packages folder. One option to find this folder is to run

python3 -m site

in the command line. In my case, this gives

sys.path = [
    '/home/johannes/Repositories/combinato',
    '/usr/lib/python39.zip',
    '/usr/lib/python3.9',
    '/usr/lib/python3.9/lib-dynload',
    '/usr/local/lib/python3.9/dist-packages',
    '/usr/lib/python3/dist-packages',
]

So I have combinato explicitly in my sys.path. But I could also place combinato in /usr/lib/python3/dist-packages and it would still be found.

What's the situation at your site?

Besides this, I don't have any updates. It would be great if you could tell me which python distribution you use, and where you placed the combinato folder in your filesystem. Then I'll recreate the same situation and see if I understand the problem.

[YvesPauli]

Hi,
I had the same issue with my installation on windows.
I found a workaround by appending the path in the python code in the test_installation file.

Concretely this look like this:
sys.path.append('C:/users/your/combinato-master/location')

This solved the problem for the installation test, I have not yet found any issues with that solution.

Thank you for your help
Yves

EDIT: moved unrelated part of the answer to another issue.

[lubavas]

Hi Johannes,

have you also tried python3 tools/test_installation.py? You wrote the command without the 3.

Yes, I tried and it retrieves just Python and that's it.

I also tried python3 -m site with the 3 and nothing happens there except Python string.

Best wishes,
Luba

[jniediek]

When I try to import my own .ncs files and extract the spikes, it will find all files and directories, but it will still give another error:
File "C:\Users\PauliY\Anaconda3\lib\site-packages\scipy\signal\filter_design.py", line 2366, in iirfilter
raise ValueError("Digital filter critical frequencies ValueError: Digital filter critical frequencies must be 0 < Wn < 1

Does this error have anything to do with the previous 'solution'?

It's almost sure that there is no connection between this error and the sys.path.append that you did.

If this doesn't have anything to do with the previous problem I can open another Issue about this.

Yes, that would be great!

[jniediek]

have you also tried python3 tools/test_installation.py? You wrote the command without the 3.

Yes, I tried and it retrieves just Python and that's it.

I also tried python3 -m site with the 3 and nothing happens there except Python string.

Hi,

I'm having trouble understanding what sort of system you're using. If you tell me what python distribution (anaconda or something else?) you use and where in your system you placed combinato, I'll try to recreate the situation on my own computer to understand the problem.

[lubavas]

have you also tried python3 tools/test_installation.py? You wrote the command without the 3.

Yes, I tried and it retrieves just Python and that's it.
I also tried python3 -m site with the 3 and nothing happens there except Python string.

I'm having trouble understanding what sort of system you're using. If you tell me what python distribution (anaconda or something else?) you use and where in your system you placed combinato, I'll try to recreate the situation on my own computer to understand the problem.

Hi Johannes,

Thank you for the answer! Sure! I use a Win 10 Pro system and have 64-bit Anaconda3 installed (I used default installation path for it if this matters). I cloned combinato into C:\codes folder on my computer and Windows and Anaconda are stored on the same disk.

Best wishes,
Luba

[lubavas]

Hi Yves @YvesPauli ,

Thanks a lot for your suggestion! I tried to run sys.path.append('C:/users/your/combinato-master/location') that you proposed in my case and re-ran the installation. My shell returned the following after python tools/test_installation.py (@jniediek this may be informative for you)

Found Combinato
SPC binary not found or not executable: [WinError 87] Параметр задан неверно
Place SPC binary in a folder and set path in options.py
Re-run after fixing problems.
'montage' from ImageMagick not found: [WinError 2] Не удается найти указанный файл
Plotting continuous data will not work

At least it found combinato this time though still misses SPC.

Best wishes,
Luba

[YvesPauli]

@lubavas try rerunning the setup_options.py file.
maybe you have an old path to the SPC binary. I had the same problem and fixed it that way.
Best,
Yves
edit: of course delete the previously created options.py file first.

[lubavas]

Hi Yves @YvesPauli ,

@lubavas try rerunning the setup_options.py file.
maybe you have an old path to the SPC binary. I had the same problem and fixed it that way.
Best,
Yves
edit: of course delete the previously created options.py file first.

Thank you for your suggestions! Now the code returned the following:

Found Combinato
Found SPC binary
Your version of pytables is 3.6.1
Combinato clustering setup: no problems detected.
'montage' from ImageMagick not found: [WinError 2] Не удается найти указанный файл
Plotting continuous data will not work

This seems like the installation worked well. :)

[jniediek]

Great! I close the issue.