Mamba: could not solve for environment specs

[nynkekatinka]

Hi development team!

I have made an empty mamba environment to install cellrank into. However, I am unable to solve for the environment specs.

mamba install cellrank
warning  libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.

warning  libmamba Please make sure you understand Anaconda Terms of Services.

warning  libmamba See: https://legal.anaconda.com/policies/en/

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ cellrank =* * does not exist (perhaps a typo or a missing channel).

When specifying conda-forge as the channel, I get the following error:

mamba install -c conda-forge cellrank

conda-forge/noarch                                          Using cache
conda-forge/win-64                                          Using cache
warning  libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.

warning  libmamba Please make sure you understand Anaconda Terms of Services.

warning  libmamba See: https://legal.anaconda.com/policies/en/

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ cellrank =* * is not installable because it requires
       └─ pygpcca >=1.0.4 *, which requires
          └─ petsc >=3.13.0,!=3.14.0 *, which does not exist (perhaps a missing channel).

Adding a specific version to the command such as mamba install -c conda-forge "petsc==3.23.6" cellrank unfortunately does not solve the issue

error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ cellrank =* * is not installable because it requires
    │  └─ pygpcca >=1.0.4 *, which requires
    │     └─ petsc >=3.13.0,!=3.14.0 *, which does not exist (perhaps a missing channel);
    └─ petsc ==3.23.6 * does not exist (perhaps a typo or a missing channel).

I get the same errors when using conda rather than mamba, and independently of whether or not I am making a new environment before installing the packages or doing so simultaneously.

When going to the documentation of petsc, they only offer pypi for installation options, so that might be where things go awry. Do you perhaps have a list of all the dependencies from your conda installation that wouldn't be installed using PyPi so that I can manually add them all?

Thank you in advance for thinking along!

[Marius1311]

mh, I usually install cellrank via pip, and then petsc4py and slepc4py via mamba/conda, that works well for me. Maybe try first installing petsc4py and slepc4py via mamba, and then cellrank via mamba?

[WeilerP]

@nynkekatinka, I just double-checked, and I did not run into installation issues. Which Python version are you using?
Regarding petsc and slepc: both can be installed via conda/mamba (here and here).

[nynkekatinka]

@WeilerP I had created an empty mamba environment without a python version. I get the same errors when using eg mamba create -n newenv cellrank. When I installed cellrank using pip (i.e. without petsc4py and slepc4py) I used python=3.12.11.
I now made a new environment with python 3.12.11, i.e. mamba create -n rankedfeather python=3.12.11. After activating the environment, I still get the same error when running mamba install cellrank as I listed in my original post.

I then tried @Marius1311 suggestion to install cellrank via pip and petsc4py and slepc4py via mamba/conda. Using the installation commands from the pages listed by @WeilerP I get the same

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ slepc =* * does not exist (perhaps a typo or a missing channel).

error for both packages. It does not matter whether I first download conda or mamba, which install line I use, nor whether I first install cellrank with pip and then try to install the other two packages, whether I create a new environment without a python version installed, or whether I start from an environment with only python=3.12 installed.

For now I can start with just the pip installed cellrank, but it seems like I can't properly run the macrostate estimations without these two packages (or at least I am getting warnings I don't have them installed from running that part of your tutorial). Is it correct that that's the main thing I'm missing, or are these packages also required elsewhere?

[WeilerP]

Sorry, @nynkekatinka, I tried different Python versions and OS, and I cannot reproduce the error. The commands I am using are

mamba create -n crdebug-py312 python=3.12 --yes && mamba activate crdebug-py312
mamba install -c conda-forge cellrank --yes

1. Could you please confirm that the installation fails when you use these prompts?
2. Have you experienced issues when trying to install other packages? If so, your mamba installation may be broken.
3. Which OS are you using?

[nynkekatinka]

Hi @WeilerP, I appreciate you trying to help me out, I understand that it can be tough at times to reproduce errors.

1. When running your commands exactly, I get the error At line:1 char:49 + mamba create -n crdebug-py312 python=3.12 --yes && mamba activate crd ... The token '&&' is not a valid statement separator in this version.. If I separate the first line into two separate statements, i.e. mamba create -n crdebug-py312 python=3.12 --yes and mamba activate crdebug-py312, I confirm that the installation fails upon running mamba install -c conda-forge cellrank --yes with the same error message as before:

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ cellrank =* * is not installable because it requires
       └─ pygpcca >=1.0.4 *, which requires
          └─ petsc >=3.13.0,!=3.14.0 *, which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs

2. I deleted and reinstalled mamba about three months ago because of a white space in the root prefix, which has since been fixed. Since then I have been able to download some other packages via mamba. I did experience issues trying to install Cell2Fate via pip, but that seemed to be a common issue at the time. I don't rule out that my mamba installation could be broken, but given that I reinstalled it so recently I am not convinced it is the logical problem either.
3. I am using Windows 11 Pro with mamba=2.3.1 and pip=25.1