Simple example case fails

[Akkete]

Hi, I'm getting nonsensical on just the simplest example.

I'm on a computer with macOS Sonoma 14.7.6

I use a fresh Conda environment and the following environment.yml:

name: ripser-test
channels:
  - conda-forge
dependencies:
  - python=3.13 
  - numpy
  - ripser

This installs the latest version of ripser 0.6.12

Then I try to run the simple example from the documentation:

test.py

import numpy as np
from ripser import Rips

np.random.seed(1)

rips = Rips()
data = np.random.random((100,2))
diagrams = rips.fit_transform(data)
rips.plot(diagrams, show=True)

conda env create -n ripser-test -f environment.yml
conda activate ripser-test
python test.py

The outputs for seeds 1, 2, 3 and 8 look like this:

Importantly, there is never a death time at infinity, instead the death time is zero in cases where it shouldn't be.

[catanzaromj]

Woah @Akkete that is pretty weird. Unfortunately, I don't have a mac to test it on. Can you see if the same behavior replicates by installing ripser through pypi rather than conda-forge? I.e. remove the ripser dependency from environment.yml and then after installing and activating the environment, try pip install ripser==0.6.12. I'm going to be updating the github actions to build python 3.14 wheels shortly and I'm wondering if I need to modify something with the conda-forge build as well.

[Akkete]

Yes, installing through pypi instead of conda-forge removed the issue.

conda create -n ripser-test2 python==3.13
conda activate ripser-test2
pip install numpy ripser
python test.py

This installed Ripser 0.6.12 and the results look as expected.

[Akkete]

And just to confirm, I tested the original setup on a Linux system and it worked without problem. So far the problem only appeared with the macOS and conda-forge combo.

[catanzaromj]

Thanks so much for the helpful debugging! I'll look into this shortly. Hopefully it's not too much trouble to use the pypi version before we fix the conda-forge macOS release.

[bdice]

Hi! I am not very active with the ripser project but I have helped with conda-forge packaging in the past. I filed conda-forge/ripser-feedstock#36 to add tests to conda-forge. The CI on that pull request indicates that osx_64 is affected but osx_arm64, Linux, and Windows platforms appear to be passing tests.

It might be helpful to get confirmation about whether this is being observed only on Intel macOS or ARM-based OSX.

I don't have a macOS system so someone else will have to identify and fix the root problem, but hopefully we can enable tests in conda-forge after the problem is fixed.