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analysiscenter / cardio

CardIO is a library for data science research of heart signals
https://analysiscenter.github.io/cardio/
Apache License 2.0
247 stars 78 forks source link

Installation Failed ( pyEDFlib requires a version of NumPy, even for setup ) #28

Closed Shlyankin closed 5 years ago

Shlyankin commented 5 years ago

Привет. Не получается установить библиотеку cardIO. Пробовал устанавливать через pipenv, pip и через python setup.py install. В всех случаях ругается на pyEDFlib и NumPy. Лог прилагается.

Hello. I am having a problem installing the cardIO library using pipenv or pip. Maybe the problem is in setup.py or pyEDFlib?

It is log: Microsoft Windows [Version 6.1.7601] (c) Корпорация Майкрософт (Microsoft Corp.), 2009. Все права защищены.

C:\Users\user>pipenv install git+https://github.com/analysiscenter/cardio.git#eg g=cardio Creating a virtualenv for this project: Pipfile: C:\Users\user\Pipfile Using c:\python\python.exe (3.7.4) to create virtualenv: [ =] Creating virtual environment...Already using interpreter c:\python\python .exe Using base prefix 'c:\python' New python executable in C:\Users\user.virtualenvs\user-KgVmIwbj\Scripts\python .exe Installing setuptools, pip, wheel... done.

Successfully created virtual environment! Virtualenv location: C:\Users\user.virtualenvs\user-KgVmIwbj Creating a Pipfile for this project: Installing git+https://github.com/analysiscenter/cardio.git#egg=cardio: Warning: You installed a VCS dependency in non-editable mode. This will work fin e, but sub-dependencies will not be resolved by $ pipenv lock. To enable this sub-dependency functionality, specify that this dependency is e ditable. Collecting cardio from git+https://github.com/analysiscenter/cardio.git#egg=card io Cloning https://github.com/analysiscenter/cardio.git to c:\users\user\appdata local\temp\pip-install-g2sfymp2\cardio Collecting numpy>=1.13.1 (from cardio) Downloading https://files.pythonhosted.org/packages/26/26/73ba03b2206371cdef62 afebb877e9ba90a1f0dc3d9de22680a3970f5a50/numpy-1.17.0-cp37-cp37m-win_amd64.whl ( 12.8MB) Collecting scipy>=0.19.1 (from cardio) Downloading https://files.pythonhosted.org/packages/50/eb/defa40367863304e1ef0 1c6572584c411446a5f29bdd9dc90f91509e9144/scipy-1.3.1-cp37-cp37m-win_amd64.whl (3 0.3MB) Collecting pandas>=0.21.1 (from cardio) Downloading https://files.pythonhosted.org/packages/c1/cf/58ccaa38d5670dd4d2ae e5df90aa03d670ede3947b7148e72391c80d4f91/pandas-0.25.0-cp37-cp37m-win_amd64.whl (9.2MB) Collecting scikit-learn==0.19.1 (from cardio) Downloading https://files.pythonhosted.org/packages/f5/2c/5edf2488897cad4fb8c4 ace86369833552615bf264460ae4ef6e1f258982/scikit-learn-0.19.1.tar.gz (9.5MB) Collecting numba>=0.35.0 (from cardio) Downloading https://files.pythonhosted.org/packages/dd/89/861d76f7a677fc5ba7fa fa8085017c43b76e3880e9e365f863f8cc800a46/numba-0.45.1-cp37-cp37m-win_amd64.whl ( 2.0MB) Collecting pywavelets>=0.5.2 (from cardio) Downloading https://files.pythonhosted.org/packages/71/57/1b6c06f2b681975e5b43 ff13ba127031f668d65b592cc56fae6445b675c7/PyWavelets-1.0.3-cp37-none-win_amd64.wh l (4.2MB) Collecting matplotlib>=2.1.0 (from cardio) Downloading https://files.pythonhosted.org/packages/1a/c0/69e3f695d7384012e90b e1e16570c08953baae00fd98094179ef87c7d5a2/matplotlib-3.1.1-cp37-cp37m-win_amd64.w hl (9.1MB) Collecting dill>=0.2.7.1 (from cardio) Downloading https://files.pythonhosted.org/packages/39/7a/70803635c850e3512570 29089d38748516a280864c97cbc73087afef6d51/dill-0.3.0.tar.gz (151kB) Collecting pydicom>=0.9.9 (from cardio) Downloading https://files.pythonhosted.org/packages/fc/d5/da1fdf3b967e324ee47a 7ad9553c9b94c1193b6b98afd9eeda0efb76b9f7/pydicom-1.3.0-py2.py3-none-any.whl (7.1 MB) Collecting pyedflib>=0.1.11 (from cardio) Downloading https://files.pythonhosted.org/packages/a4/c1/11d90aa4d20a1d3df04e a9e1db4e03fea4b199a5b515a057cbe5e35769c0/pyEDFlib-0.1.14.tar.gz (1.1MB)

Error: An error occurred while installing git+https://github.com/analysiscenter /cardio.git#egg=cardio! b' Running command git clone -q https://github.com/analysiscenter/cardio.git ' C:\Users\user\AppData\Local\Temp\pip-install-g2sfymp2\cardio'\n Running command git submodule update --init --recursive -q\n ERROR: Command errored out with exit status 4294967295:\n command: 'c:\users\user.virtualenvs \user-kgvmiwbj\scripts\python.exe' -c 'import sys, setuptools, tokenize; sys .argv[0] = '"'"'C:\Users\user\AppData\Local\Temp\pip-instal l-g2sfymp2\pyedflib\setup.py'"'"'; file='"'"'C:\Users\user \AppData\Local\Temp\pip-install-g2sfymp2\pyedflib\setup.py'" '"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().rep lace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info\n cwd : C:\Users\user\AppData\Local\Temp\pip-install-g2sfymp2\pyedflib\n C omplete output (4 lines):\n No module named 'numpy'\n package "numpy " not found \n pyEDFlib requires a version of NumPy, even for setup.\n Please get it from http://numpy.scipy.org/ or install it through your package ma nager.\n ----------------------------------------\nERROR: Command errored out with exit status 4294967295: python setup.py egg_info Check the logs for full c ommand output.\n' This is likely caused by a bug in cardio. Report this to its maintainers. Installation Failed

roman-kh commented 5 years ago

Apparently the problem has nothing to do with cardio on its own. The thing is that you don't have numpy installed while it's required by pyedflib. The question "why python tries to install pyedflib before numpy" is a notorious example of questions hardy ever answered as there is a long-existing problem with a weird install order (e.g. https://github.com/pypa/pip/issues/24).

As a workaround, install numpy first, then install cardio.

Shlyankin commented 5 years ago

@roman-kh , I already have numpy. I think problem in the python version. I installed python 3.6.1 (instead of 3.7.4) and downloaded cardio using pipenv. It seems to work.

From this post https://github.com/holgern/pyedflib/issues/60, I think that pyEDFlib have not binaries files for python 3.7.