Bug:

[david2905]

Describe the bug
pip install MACS3
or
pip3 install git+https://github.com/macs3-project/[email protected]
downgrade Cython to version 0.29

To Reproduce
pip install MACS3
or
pip3 install git+https://github.com/macs3-project/[email protected]

Expected behavior
dont touch Cython

-su-5.1$ pip3 install git+https://github.com/macs3-project/[email protected]
Collecting git+https://github.com/macs3-project/[email protected]
  Cloning https://github.com/macs3-project/MACS.git (to revision v3.0.0b3) to /scratch/local/pip-req-build-mhh76d2l
  Running command git clone --filter=blob:none --quiet https://github.com/macs3-project/MACS.git /scratch/local/pip-req-build-mhh76d2l
  Running command git checkout -q 076ee83c7c13ba61d570dc58e277d745dcad363f
  Resolved https://github.com/macs3-project/MACS.git to commit 076ee83c7c13ba61d570dc58e277d745dcad363f
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.19 in ./python-3.10.12-0/lib/python3.10/site-packages (from MACS3==3.0.0b3) (1.23.4)
Requirement already satisfied: hmmlearn>=0.3 in ./python-3.10.12-0/lib/python3.10/site-packages (from MACS3==3.0.0b3) (0.3.0)
Requirement already satisfied: cykhash<3.0,>=2.0 in ./python-3.10.12-0/lib/python3.10/site-packages (from MACS3==3.0.0b3) (2.0.1)
Collecting Cython~=0.29 (from MACS3==3.0.0b3)
  Obtaining dependency information for Cython~=0.29 from https://files.pythonhosted.org/packages/f8/26/ca0f1bb049b83c25cafa39f3fa5287c826a6ab36e665c906209e07f4deac/Cython-0.29.36-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata
  Using cached Cython-0.29.36-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.1 kB)
Requirement already satisfied: scikit-learn!=0.22.0,>=0.16 in ./python-3.10.12-0/lib/python3.10/site-packages (from hmmlearn>=0.3->MACS3==3.0.0b3) (1.3.0)
Requirement already satisfied: scipy>=0.19 in ./python-3.10.12-0/lib/python3.10/site-packages (from hmmlearn>=0.3->MACS3==3.0.0b3) (1.11.2)
Requirement already satisfied: joblib>=1.1.1 in ./python-3.10.12-0/lib/python3.10/site-packages (from scikit-learn!=0.22.0,>=0.16->hmmlearn>=0.3->MACS3==3.0.0b3) (1.3.2)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./python-3.10.12-0/lib/python3.10/site-packages (from scikit-learn!=0.22.0,>=0.16->hmmlearn>=0.3->MACS3==3.0.0b3) (3.2.0)
Using cached Cython-0.29.36-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Installing collected packages: Cython
  Attempting uninstall: Cython
    Found existing installation: Cython 3.0.0
    Uninstalling Cython-3.0.0:
      Successfully uninstalled Cython-3.0.0
Successfully installed Cython-0.29.36

System (please complete the following information):

• OS: [e.g. Linux, Mac OSX]
• Python version 3.10.12
• Numpy version 1.23.4
• MACS Version 3.0.0b3

Comment
commit c3c81fb create the behavior

[taoliu]

Hi @david2905, b3 can only work with cython 0.29. That's the reason behind the downgrading of cython. The next release will support Cython3. If you can't wait, you can try to install the codes in the current master branch. The patch is already there: #579

[david2905]

Hi @taoliu, thanks for the explanation. I was confuse by the version number of Cython. It looks like a downgrade for several versions, but it was just one version.
Sorry for the noise. The issue can be closed.