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kushalkolar / MESmerize

Platform for Calcium Imaging analysis. DEPRECATED.
GNU General Public License v3.0
58 stars 14 forks source link

[INSTALLATION HELP] #102

Closed engineeringjoy closed 2 years ago

engineeringjoy commented 2 years ago

ISSUE WITH TRYING TO INSTALL I am trying to install mesmerize with conda (version 4.12.0) into a dedicated environment with Python 3.6 following the instructions on this page for Mac OSX [http://docs.mesmerizelab.org/en/master/user_guides/installation.html]

Conda is stuck on trying to solve the environment after I try to install caiman. I tried the normal caiman install, then used the the troubleshooting suggestion of installing a specific version of caiman and it still gets stuck. It's been trying to solve the environment for about 20 minutes.

System information

  1. Mac OSX Catalina 10.15.7
  2. Processor 2.3 GHz 8-Core Intel Core i9 / Graphics Intel UHD Graphics 630 1536 MB
  3. 16 GB 2667 MHz DDR4
  4. SSD

Copy & paste the entire output of the terminal while you were trying to install when the issue came up:

(base) nerdette@Joys-MacBook-Pro ~ % conda create --name mesmerize python=3.6
(task was completed successfully but then closed terminal so couldn't copy/paste the exact info)
(base) nerdette@Joys-MacBook-Pro ~ % source activate mesmerize          
(mesmerize) nerdette@Joys-MacBook-Pro ~ % conda install -c conda-forge caiman==1.8.5
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: \
kushalkolar commented 2 years ago

This is a common problem with conda. Can you install mamba and then try.

#in the base env
conda install -c conda-forge mamba
conda clean -a

#install caiman with same instructions, just replace conda with mamba

On Mon, May 30, 2022, 11:34 Joy Franco @.***> wrote:

Assigned #102 https://github.com/kushalkolar/MESmerize/issues/102 to @kushalkolar https://github.com/kushalkolar.

— Reply to this email directly, view it on GitHub https://github.com/kushalkolar/MESmerize/issues/102#event-6703980344, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRCZRHX5OSZCSIYDSFTVMTN2BANCNFSM5XK6OSDQ . You are receiving this because you were assigned.Message ID: @.***>

engineeringjoy commented 2 years ago

This is a common problem with conda. Can you install mamba and then try. #in the base env conda install -c conda-forge mamba conda clean -a #install caiman with same instructions, just replace conda with mamba … On Mon, May 30, 2022, 11:34 Joy Franco @.> wrote: Assigned #102 <#102> to @kushalkolar https://github.com/kushalkolar. — Reply to this email directly, view it on GitHub <#102 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRCZRHX5OSZCSIYDSFTVMTN2BANCNFSM5XK6OSDQ . You are receiving this because you were assigned.Message ID: @.>

Thank you! I ran into another issue after installing mamba. I received an error that the caiman installation couldn't be completed because ipyparallel required python >= 3.7. I deleted my original mesmerize environment, created a new one with python 3.7, and was then able to complete the installation. I launched Mesmerize successfully (or at least, I made it to the Welcome Window). Side question: is there a proper way to shut down the program? I just did command+q and confirmed closing all windows. That seemed to work, but then I received a system error that python 3.7 had shutdown unexpectedly.

kushalkolar commented 2 years ago

clicking the exit button in the title bar of the welcome window is the proper way to close it, not sure what that error is. If you post it I can take a look.

engineeringjoy commented 2 years ago

I tried to recreate the error by setting up two different test environments. When I installed caiman without specifying which version, I couldn't install mesmerize but I couldn't interpret the error message. That terminal output is attached as mesmerize_test.txt. In the second test, I specified which version of caiman to install. Then when I installed mesmerize, I got the error message below (the full terminal output is attached as mesmerize_test2).

When I set up the env with py 3.7 I was able to complete the mesmerize install without issue. ...

Confirm changes: [Y/n] y Finished astroid (00m:00s) 291 KB 1 MB/s Finished autopep8 (00m:00s) 41 KB 154 KB/s Finished hdmf (00m:00s) 96 KB 288 KB/s Finished python-lsp-server (00m:00s) 41 KB 107 KB/s Finished jsonschema (00m:00s) 54 KB 119 KB/s Finished h5py (00m:00s) 1 MB 2 MB/s Finished pynwb (00m:00s) 195 KB 395 KB/s Finished wrapt (00m:00s) 43 KB 86 KB/s Finished pylint (00m:00s) 235 KB 444 KB/s Finished caiman (00m:18s) 116 MB 29 MB/s Preparing transaction: done Verifying transaction: done Executing transaction: - Enabling notebook extension jupyter-js-widgets/extension...

  • Validating: OK

done (mesmerize_test2) nerdette@Joys-MacBook-Pro ~ % pip install mesmerize
Collecting mesmerize Using cached mesmerize-0.8.0-py3-none-any.whl (1.2 MB) Requirement already satisfied: ipyparallel>=6.3 in ./anaconda3/envs/mesmerize_test2/lib/python3.6/site-packages (from mesmerize) (8.3.0) ERROR: Package 'ipyparallel' requires a different Python: 3.6.15 not in '>=3.7' (mesmerize_test2) nerdette@Joys-MacBook-Pro ~ %

mesmerize_test.txt mesmterize_test2.txt

kushalkolar commented 2 years ago

Looks like bokeh is giving issues, anyways you do have an environment in which you've successfully installed mesmerize?

On Wed, Jun 1, 2022, 00:02 Joy Franco @.***> wrote:

I tried to recreate the error by setting up two different test environments. When I installed caiman without specifying which version, I couldn't install mesmerize but I couldn't interpret the error message. That terminal output is attached as mesmerize_test.txt. In the second test, I specified which version of caiman to install. Then when I installed mesmerize, I got the error message below (the full terminal output is attached as mesmerize_test2).

When I set up the env with py 3.7 I was able to complete the mesmerize install without issue. ...

Confirm changes: [Y/n] y Finished astroid (00m:00s) 291 KB 1 MB/s Finished autopep8 (00m:00s) 41 KB 154 KB/s Finished hdmf (00m:00s) 96 KB 288 KB/s Finished python-lsp-server (00m:00s) 41 KB 107 KB/s Finished jsonschema (00m:00s) 54 KB 119 KB/s Finished h5py (00m:00s) 1 MB 2 MB/s Finished pynwb (00m:00s) 195 KB 395 KB/s Finished wrapt (00m:00s) 43 KB 86 KB/s Finished pylint (00m:00s) 235 KB 444 KB/s Finished caiman (00m:18s) 116 MB 29 MB/s Preparing transaction: done Verifying transaction: done Executing transaction: - Enabling notebook extension jupyter-js-widgets/extension...

  • Validating: OK

done (mesmerize_test2) @. ~ % pip install mesmerize Collecting mesmerize Using cached mesmerize-0.8.0-py3-none-any.whl (1.2 MB) Requirement already satisfied: ipyparallel>=6.3 in ./anaconda3/envs/mesmerize_test2/lib/python3.6/site-packages (from mesmerize) (8.3.0) ERROR: Package 'ipyparallel' requires a different Python: 3.6.15 not in '>=3.7' (mesmerize_test2) @. ~ %

mesmerize_test.txt https://github.com/kushalkolar/MESmerize/files/8810943/mesmerize_test.txt mesmterize_test2.txt https://github.com/kushalkolar/MESmerize/files/8810944/mesmterize_test2.txt

— Reply to this email directly, view it on GitHub https://github.com/kushalkolar/MESmerize/issues/102#issuecomment-1143091909, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRHWYC3KZM3EPX2OOF3VM3OFVANCNFSM5XK6OSDQ . You are receiving this because you were mentioned.Message ID: @.***>

esfahany commented 2 years ago

conda install -c conda-forge mamba

I'm having the same issue as described by @engineeringjoy, where the caiman install gets stuck at "Solving environment" indefinitely. However, this command to install mamba also appears to get stuck indefinitely, so I'm unable to proceed using this solution.

System information

  1. Mac OSX Monterey 12.2
  2. Apple M1
  3. 16 GB 2667 MHz DDR4
  4. SSD

Installation method

  1. Are you using anaconda, python virtual environments, or something else? Anaconda, conda version : 4.13.0

  2. If you're installing mesmerize through pip, what version of pip is installed in the environment? n/a

  3. Are you trying to install in developer mode from the repo? n/a

  4. What is the python version in the environment you're trying to install mesmerize in? tried 3.6 and 3.7

  5. Information if you're using some other installation method.

kushalkolar commented 2 years ago

I've only tried installation on the M1 once. I think I used python 3.8 or 3.9 and the current master branch in GitHub (there are a lot of old deps that don't work on the M1)

On Wed, Jun 1, 2022, 07:27 Kathleen Esfahany @.***> wrote:

conda install -c conda-forge mamba

I'm having the same issue as described by @engineeringjoy https://github.com/engineeringjoy, where the caiman install gets stuck at "Solving environment" indefinitely. However, this command to install mamba also appears to get stuck indefinitely, so I'm unable to proceed using this solution.

System information

  1. Mac OSX Monterey 12.2
  2. Apple M1
  3. 16 GB 2667 MHz DDR4
  4. SSD

Installation method

1.

Are you using anaconda, python virtual environments, or something else? Anaconda, conda version : 4.13.0 2.

If you're installing mesmerize through pip, what version of pip is installed in the environment? n/a 3.

Are you trying to install in developer mode from the repo? n/a 4.

What is the python version in the environment you're trying to install mesmerize in? tried 3.6 and 3.7 5.

Information if you're using some other installation method.

— Reply to this email directly, view it on GitHub https://github.com/kushalkolar/MESmerize/issues/102#issuecomment-1143481626, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRERWHXJ25ZA3N55S6TVM5CIXANCNFSM5XK6OSDQ . You are receiving this because you were mentioned.Message ID: @.***>

snMousavi commented 2 years ago

I'm facing issues also posted above.

Some issues I've faced: