install failure

[josenimo]

hello, I followed instructions and conda install failed:

git clone https://github.com/computational-cell-analytics/patho-sam
Cloning into 'patho-sam'...
remote: Enumerating objects: 439, done.
remote: Counting objects: 100% (220/220), done.
remote: Compressing objects: 100% (161/161), done.
remote: Total 439 (delta 115), reused 82 (delta 59), pack-reused 219 (from 3)
Receiving objects: 100% (439/439), 347.59 KiB | 4.57 MiB/s, done.
Resolving deltas: 100% (170/170), done.
❯ cd patho-sam
❯ conda env create -f environment.yaml
Retrieving notices: ...working... done
Collecting package metadata (repodata.json): / WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
done
Solving environment: \ Assertion failed: (glue <= MAXGLUE), function add_simplified_clause, file ./picosat.c, line 2419.

I am working on MacOs 14, M2 chip.

[anwai98]

Hi @josenimo,

Thanks for your interest in patho-sam.

Hmm seems like the solver is broken for some reason. We can try two things:

1. Since the environment.yaml installs a few packages, you could simply try: conda create -n micro-sam -c conda-forge python=3.11 micro_sam. And then install patho-sam package from source using pip install -e .
2. The robust solution here would be to opt for newer solvers (seems like your conda manager is still using old solvers). In case the solution 1. does not work, I'd suggest switching to micromamba (https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html). The package manager is kinda lightweight and the installation is only a few commands.

Let me know if one of the two solutions above work for you, or if you have any other questions!

[josenimo]

ok, I like that better, I will try it sometime this week, sorry this is a little side adventure :)
will report what happens.
I can highly suggest uv if possible :) it is quite a fast and capable solver.

[anwai98]

will report what happens.

No worries. Let us know how it goes!

I can highly suggest uv if possible :) it is quite a fast and capable solver.

Unfortunately, our primary dependent package micro_sam is deployed only in conda-forge, due to some technical hurdles. And from what I am aware of, uv does not have conda support. We have this in mind for a while, but we plan to make some progress in the coming months!

For now, conda-forge (with a latest package manager having libmamba solver) is the way-to-go.