Incompatible packages reinstalling Minian

[anna-teruel]

Hi all! I have a couple of questions/issues to discuss over here (I need help!!!!).

The first question is quite simple. I have been using Minian and already got some results (A, C, S matrix). However, I don't get what matrix A is representing. Could anybody briefly explain what each row and column in matrix A is representing?

Secondly, although Minian was perfectly working on my laptop, I decided to format my laptop and reinstall everything again. I had no issues installing conda, nor with other envs such as DeepLabCut. But, when I try to install Minian I get the following conflicts:

A) If I try to install the env using conda:

(minian) annateruel@MacBook-MacBook-Pro-de-Anna minian % conda install -y -c conda-forge minian

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: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - minian

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

B) If I install from source: too long to post, I attach a file.

error.docx

Information about my laptop: it's a 'macOS-13.0-arm64-arm-64bit' M1, thus I installed Anaconda3-2022.10-MacOSX-arm64.sh. I first tried to create the env with miniconda but then decided to change to anaconda just in case. But I get the same error anyway. I have been checking similar issues in other forums but I didn't get the right thing to make it work.

Could anybody help me? Perhaps it's a simple question, but I don't know what it's going on. THANK YOU!

[anna-teruel]

Update: I know little about this, but I assume the problem is due to arm64. I assume the minian package is only included in the conda-forge channel for 64x, not in conda-forge/osx-arm64.

Is there an easy and not time consuming way to update this and include the minian package in osx-arm64 for M1 users like me? Although I am new to this, I am willing to help.

I look forward to a answer. Thank you!

[nikolaskaralis]

Same issue here (in most systems I tried). Note: I am trying on Intel PCs, not M1 mac.

Some more info: conda takes infinite time for resolving the environment. I tried with mamba, which is much faster and more informative.

I believe there is an issue/incompatibility with the dependencies.

Any clue?

See the log below:

Looking for: ['minian']

pkgs/main/noarch [====================] (00m:00s) Done pkgs/r/win-64 [====================] (00m:00s) Done pkgs/msys2/noarch [====================] (00m:00s) Done pkgs/r/noarch [====================] (00m:00s) Done pkgs/msys2/win-64 [====================] (00m:00s) Done pkgs/main/win-64 [====================] (00m:01s) Done conda-forge/noarch [====================] (00m:04s) Done conda-forge/win-64 [====================] (00m:08s) Done

Pinned packages:

• python 3.9.*

Encountered problems while solving:

• package minian-0.2.5-py38_0 requires python >=3.8,<3.9.0a0, but none of the providers can be installed

[anna-teruel]

Hi @nikolaskaralis In the end, I managed to solve it. In my case, I installed two versions of miniconda (for arm64 and x86-64) and run minian in x86-64. I also noticed it took very long time following installation instructions from minian readthedocs. Thus I installed it with Mamba. I asked Federico, from Miniscope team, and he suggested running following steps:

1. conda create -y -n minainWorkshop python=3.8.5
2. conda activate minainWorkshop
3. conda install -y -c conda-forge mamba
4. mamba install -y -c conda-forge minian
5. pip install jinja2==2.11.2

I am not sure if you have tried this already, but it worked for me. Good luck!

[nikolaskaralis]

HI @anna-teruel ,

thanks a lot for your response. So based on this, I managed to get it to work.

For those reading this thread in the future, the problem is the following: It seems there is a strong dependency on the particular python version. So the trick is to indeed specify python=3.8.5 I had tried earlier the same with python=3.8 and it doesn't work.

The last command about jinja2 doesn't work for me (dependency issue). I will see if it is necessary.

And mamba helps a lot (it is a drop-in replacement for conda that is much faster).

[droumis]

If you are on an M1 (osx-arm64) system and need to install minian (only available for osx-64), here is one solution:

conda create -n osx-64 # create empty env for non-native platform
conda activate osx-64
conda config --env --set subdir osx-64 # set this environment to only install osx-64 packages (not osx-arm64)
conda install minian

An alternative would be to manage two (osx-64, osx-arm64) versions of miniconda on the same system.

Hopefully, a project maintainer will build an osx-arm64 version of minian in the future, but the pins definitely need to be adjusted.