Bug:
david2905 opened this issue · 2 comments
david2905 commented
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):
- 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 commented
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