search

macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
700 stars 268 forks source link

Bug: #591

Closed david2905 closed 1 year ago

david2905 commented 1 year ago

Describe the bug pip install MACS3 or pip3 install git+https://github.com/macs3-project/MACS.git@v3.0.0b3 downgrade Cython to version 0.29

To Reproduce pip install MACS3 or pip3 install git+https://github.com/macs3-project/MACS.git@v3.0.0b3

Expected behavior dont touch Cython

-su-5.1$ pip3 install git+https://github.com/macs3-project/MACS.git@v3.0.0b3
Collecting git+https://github.com/macs3-project/MACS.git@v3.0.0b3
  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):

Comment commit c3c81fb create the behavior

taoliu commented 1 year ago

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 commented 1 year ago

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.