ResolutionTooDeep (pip v21.2.4)

[arturomarin]

Description

Hi,

I have been trying to install the program dms_tools2, but after several hours pip gives me an error:

pip._vendor.resolvelib.resolvers.ResolutionTooDeep: 2000000

error_3.txt

Expected behavior

Install the dms_tools2 software using pip.

pip version

21.2.4

Python version

3.8.5 (miniconda3)

OS

macOS 10.15.7

How to Reproduce

1. create an environment with miniconda3: conda create -n avidd python=3.8.5
2. using pip to install dms_tools2: pip3 install dms_tools2 --user --verbose

Output

No response

Code of Conduct

• I agree to follow the PSF Code of Conduct.

[notatallshaw]

If you read your error output you will see that weblogo requires numpy to be installed to run it's setup.py, this is very bad practice but you need to take it up with them:

Collecting weblogo<3.6,>=3.4
  Using cached weblogo-3.5.0.tar.gz (434 kB)
    Running command python setup.py egg_info
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/lv/0sfjrh0s669f8k0kd8d1_qgm0000gn/T/pip-install-ltw0mubd/weblogo_90963a40a69446f5b8bbe5e600475f88/setup.py", line 12, in <module>
        from weblogolib import __version__
      File "/private/var/folders/lv/0sfjrh0s669f8k0kd8d1_qgm0000gn/T/pip-install-ltw0mubd/weblogo_90963a40a69446f5b8bbe5e600475f88/weblogolib/__init__.py", line 102, in <module>
        from numpy import array, asarray, float64, ones, zeros, any, int32, all, shape
    ModuleNotFoundError: No module named 'numpy'
WARNING: Discarding https://files.pythonhosted.org/packages/86/32/bb72ad056f186e68a8518ca34eef85494dd564238945c6f29522e463a57e/weblogo-3.5.0.tar.gz#sha256=84e39ee7c4f70efea55d6a92b3efdc4d2602b3d32a793f98865bca35e6bd1133 (from https://pypi.org/simple/weblogo/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

If you install your numpy requirements first:

python -m pip install "numpy<1.20,>=1.16"

Then your installation should work fine:

python -m pip install dms_tools2
...
Successfully installed dms-tools2 attrs biopython IPython jedi jupyter matplotlib cycler kiwisolver mizani natsort numpy pandas parso pexpect phydms cython plotnine descartes patsy prompt-toolkit ptyprocess pyparsing PyPDF2 pysam pystan python-dateutil pytz pyvolve regex scipy seaborn six statsmodels sympy mpmath traitlets umi-tools weblogo backcall decorator future ipykernel debugpy jupyter-client jupyter-core matplotlib-inline nest-asyncio pyzmq tornado entrypoints ipython-genutils ipywidgets jupyterlab-widgets nbformat jsonschema pyrsistent widgetsnbextension notebook Send2Trash terminado argon2-cffi cffi jinja2 MarkupSafe jupyter-console nbconvert mistune nbclient pandocfilters pygments bleach defusedxml jupyterlab-pygments packaging palettable pickleshare prometheus-client pybktree pycparser qtconsole qtpy testpath wcwidth webencodings setuptools

[arturomarin]

Hi,

now pip installs dms_tools2 without problems on Linux and macOS. Thanks for your help.