Issue installing methylbert using conda and pip

[ggrimes]

I am trying to install methylbert using both conda and pip and get and error on the pip install methylbert part. Can you please help me.

Here is my command

mamba create -n methylbert -c conda-forge python=3.11 cudatoolkit==11.8 pip freetype-py
conda activate methylbert
pip install methylbert 2>&1 > piperror.log

error seems to be with scikit-learn

Collecting scikit-learn<1.1.0 (from methylbert)
  Using cached scikit-learn-1.0.2.tar.gz (6.7 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): still running...
  Preparing metadata (pyproject.toml): still running...
  Preparing metadata (pyproject.toml): finished with status 'error'

Here is conda env info

$ conda list --revisions
2025-01-23 09:44:48  (rev 0)
    +_libgcc_mutex-0.1 (conda-forge/linux-64)
    +_openmp_mutex-4.5 (conda-forge/linux-64)
    +bzip2-1.0.8 (conda-forge/linux-64)
    +ca-certificates-2024.12.31 (defaults/linux-64)
    +cudatoolkit-11.8.0 (conda-forge/linux-64)
    +freetype-2.12.1 (conda-forge/linux-64)
    +freetype-py-2.5.1 (conda-forge/noarch)
    +ld_impl_linux-64-2.43 (conda-forge/linux-64)
    +libexpat-2.6.4 (conda-forge/linux-64)
    +libffi-3.4.4 (defaults/linux-64)
    +libgcc-14.2.0 (conda-forge/linux-64)
    +libgcc-ng-14.2.0 (conda-forge/linux-64)
    +libgomp-14.2.0 (conda-forge/linux-64)
    +liblzma-5.6.3 (conda-forge/linux-64)
    +libnsl-2.0.1 (conda-forge/linux-64)
    +libpng-1.6.45 (conda-forge/linux-64)
    +libsqlite-3.48.0 (conda-forge/linux-64)
    +libstdcxx-14.2.0 (conda-forge/linux-64)
    +libstdcxx-ng-14.2.0 (conda-forge/linux-64)
    +libuuid-2.38.1 (conda-forge/linux-64)
    +libxcrypt-4.4.36 (conda-forge/linux-64)
    +libzlib-1.3.1 (conda-forge/linux-64)
    +ncurses-6.5 (conda-forge/linux-64)
    +openssl-3.4.0 (conda-forge/linux-64)
    +pip-24.3.1 (conda-forge/noarch)
    +python-3.11.11 (conda-forge/linux-64)
    +readline-8.2 (conda-forge/linux-64)
    +setuptools-75.8.0 (conda-forge/noarch)
    +tk-8.6.13 (conda-forge/linux-64)
    +tzdata-2025a (conda-forge/noarch)
    +wheel-0.45.1 (conda-forge/noarch)

Any help would be much appreciated

[hanyangii]

Hello @ggrimes
Thank you very much for your interest in MethylBERT!
I am trying to reproduce your error. Meanwhile, it may help you if I can share the package specs in my environment. I will get back to you as soon as I solve your issue properly. I am sorry for this inconvenience!

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
biopython                 1.84                     pypi_0    pypi
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
certifi                   2024.8.30                pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
filelock                  3.16.1                   pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
fsspec                    2024.10.0                pypi_0    pypi
huggingface-hub           0.26.2                   pypi_0    pypi
idna                      3.10                     pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.47.0               hadc24fc_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
markupsafe                3.0.2                    pypi_0    pypi
matplotlib                3.9.2                    pypi_0    pypi
methylbert                2.0.1                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
ncurses                   6.5                  he02047a_1    conda-forge
networkx                  3.4.2                    pypi_0    pypi
numpy                     2.1.1                    pypi_0    pypi
nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi
nvidia-cudnn-cu12         9.1.0.70                 pypi_0    pypi
nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi
nvidia-curand-cu12        10.3.2.106               pypi_0    pypi
nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi
nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi
nvidia-nccl-cu12          2.20.5                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.6.77                  pypi_0    pypi
nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi
openssl                   3.3.2                hb9d3cd8_0    conda-forge
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
pillow                    11.0.0                   pypi_0    pypi
pip                       24.3.1             pyh8b19718_0    conda-forge
pyparsing                 3.2.0                    pypi_0    pypi
pysam                     0.22.1                   pypi_0    pypi
python                    3.11.10         hc5c86c4_3_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
regex                     2024.11.6                pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
safetensors               0.4.5                    pypi_0    pypi
scikit-learn              1.5.1                    pypi_0    pypi
scipy                     1.14.1                   pypi_0    pypi
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sympy                     1.13.3                   pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tokenizers                0.19.1                   pypi_0    pypi
torch                     2.4.1                    pypi_0    pypi
tqdm                      4.66.5                   pypi_0    pypi
transformers              4.44.2                   pypi_0    pypi
triton                    3.0.0                    pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
urllib3                   2.2.2                    pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.13.0                   pypi_0    pypi

[ggrimes]

Thanks for the looking into this. It seems to be an issue with cython and scikit-learn for me.

[ggrimes]

I have got the pip installer to work using the following setup.py file.

However, i can only run it through python interactively

from setuptools import setup
from setuptools import find_packages

import os, glob, warnings

warnings.filterwarnings("ignore")

requirements=[
		'Bio',
		'biopython==1.84',
		'matplotlib==3.9.2',
		'numpy==2.1.1',
		'pandas==2.2.2',
		'pysam',
		'scikit_learn==1.5.1',
		#'scipy<1.7.0',
		'torch==2.4.1',
		'tqdm==4.66.5',
		'transformers==4.44.2',
		'tokenizers<0.20.0',
		'urllib3<1.27,>=1.25.4',
		'zipp==3.13.0'
	]

setup(name='methylbert',
	version='2.0.1',

	packages=find_packages("src"),
	package_dir = {"": "src"},

	install_requires = requirements,
	setup_requires = requirements,

    py_modules=[os.path.splitext(os.path.basename(path))[0] for path in glob.glob("src/*.py")]+ \
    		   [os.path.splitext(os.path.basename(path))[0] for path in glob.glob("src/methylbert/*.py")],

	test_suite="test",

	author='Yunhee Jeong',
	author_email='[email protected]',

	# cli
	entry_points={
		"console_scripts": [
			"methylbert = cli:main"
		]
	}

)