Installation error with python 3.9[BUG]

[frenkiboy]

Describe the bug When I try to install pySCENIC using python version 3.9 the installation drops with an error

It works in python 3.8.

The error seems to be related to pyarrow.

Steps to reproduce the behavior

1. Command run when the error occurred:

conda create -n pyscenic python=3.9
conda activate pyscenic
pip install pyscenic

2. Error encountered:

log is attached

Expected behavior

install the package

Please complete the following information:

• pySCENIC version: [e.g. 0.10.0, use pyscenic -h at the command line]
• Installation method: pip
• Run environment: bash command line
• OS: CentOS
• Package versions: -# Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 11.2.0 h1d223b6_13 conda-forge libgomp 11.2.0 h1d223b6_13 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libzlib 1.2.11 h36c2ea0_1013 conda-forge ncurses 6.3 h9c3ff4c_0 conda-forge openssl 3.0.0 h7f98852_2 conda-forge pip 22.0.3 pyhd8ed1ab_0 conda-forge python 3.9.10 hc74c709_2_cpython conda-forge python_abi 3.9 2_cp39 conda-forge readline 8.1 h46c0cb4_0 conda-forge setuptools 60.9.3 py39hf3d152e_0 conda-forge sqlite 3.37.0 h9cd32fc_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tzdata 2021e he74cb21_0 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h36c2ea0_1013 conda-forge

gcc version 11.2.1 20210728 (Red Hat 11.2.1-1) (GCC)

...
[pyscenic-install.log](https://github.com/aertslab/pySCENIC/files/8185776/pyscenic-install.log)

[JBreunig]

Same error with pyscenic install. Can't install pyarrow on Python 3.9.

[hyang333]

I got the same issue with pyscenic install on python3.9. I tried to install pyarrow==0.16.0 separately. It seems like it requires python_version<3.7.

pip install pyarrow==0.16.0

---

Collecting pyarrow==0.16.0 Using cached pyarrow-0.16.0.tar.gz (5.7 MB) Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [3363 lines of output] Ignoring numpy: markers 'python_version < "3.7"' don't match your environment Collecting cython>=0.29 Using cached Cython-0.29.30-py2.py3-none-any.whl (985 kB) Collecting numpy==1.16.0 Using cached numpy-1.16.0.zip (5.1 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting setuptools Using cached setuptools-62.3.2-py3-none-any.whl (1.2 MB) Collecting setuptools_scm Using cached setuptools_scm-6.4.2-py3-none-any.whl (37 kB) Collecting wheel Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB) Collecting tomli>=1.0.0 Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Collecting packaging>=20.0 Using cached packaging-21.3-py3-none-any.whl (40 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB) Building wheels for collected packages: numpy Building wheel for numpy (setup.py): started Building wheel for numpy (setup.py): finished with status 'error' error: subprocess-exited-with-error

    × python setup.py bdist_wheel did not run successfully.
    │ exit code: 1
    ╰─> [3007 lines of output]
        Running from numpy source directory.
        /private/var/folders/gp/5bzl3kxn2n1f8y43zlmv135m0000gn/T/pip-install-5glxlhxn/numpy_d183a89bd265493cbda3efc9e0df1fc2/numpy/distutils/misc_util.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
          return is_string(s) and ('*' in s or '?' is s)
        blas_opt_info:
        blas_mkl_info:
        customize UnixCCompiler
          libraries mkl_rt not found in ['/opt/homebrew/Caskroom/mambaforge/base/lib', '/usr/local/lib', '/usr/lib']
          NOT AVAILABLE

...............

[GreyRockIQ]

Hello I am having same error as below with pyarrow on python 3.9., m1 Mac.

Failed to build pyarrow ERROR: Could not build wheels for pyarrow which use PEP 517 and cannot be installed directly

I have tried to get new version of pyarrow but no use.

Does anyone get it installed on python 3.9? Any suggestions?

Thanks GreyRock

[JBreunig]

Same error with pyscenic install. Can't install pyarrow on Python 3.9.

This issue is now fixed for me as install proceeded without issue adding the new ctxcore and other elements just using "pip install -U pyscenic"

[ghuls]

pySCENIC 0.12.0 is out which works with recent versions of pyarrow (>=8.0.0). Also updating pip should help as they can install binary artifacts instead of compiling pyarrow from source.