search

bebatut / enasearch

A Python library for interacting with ENA's API
http://bebatut.fr/enasearch
MIT License
22 stars 6 forks source link

Conda installation only allows Python 2 #42

Open nigiord opened 5 years ago

nigiord commented 5 years ago

When I try to install enasearch through conda, it asks me to downgrade my environment to Python 2

$ conda install -c bioconda enasearch
Solving environment: done

## Package Plan ##

  environment location: /home/giordano-n/.miniconda3/envs/test_enasearch

  added / updated specs: 
    - enasearch

The following NEW packages will be INSTALLED:

    asn1crypto:     0.24.0-py27_0                    
    biopython:      1.68-py27_0           bioconda   
    blas:           1.0-mkl                          
    cffi:           1.11.5-py27he75722e_1            
    chardet:        3.0.4-py27_1                     
    click:          7.0-py27_0                       
    configparser:   3.5.0-py27_0                     
    cryptography:   2.3.1-py27h1ba5d50_2             
    dicttoxml:      1.7.4-py27_0          conda-forge
    enasearch:      0.2.2-py27_1          bioconda   
    enum34:         1.1.6-py27_1                     
    flake8:         3.6.0-py27_0                     
    freetype:       2.9.1-h8a8886c_1                 
    idna:           2.7-py27_0                       
    intel-openmp:   2019.0-118                       
    ipaddress:      1.0.22-py27_0                    
    jpeg:           9b-h024ee3a_2                    
    libgfortran-ng: 7.3.0-hdf63c60_0                 
    libpng:         1.6.35-hbc83047_0                
    libtiff:        4.0.9-he85c1e1_2                 
    mccabe:         0.6.1-py27_1                     
    mkl:            2019.0-118                       
    mkl_fft:        1.0.6-py27h7dd41cf_0             
    mkl_random:     1.0.1-py27h4414c95_1             
    mmtf-python:    1.0.2-py27_0          bioconda   
    msgpack-python: 0.5.6-py27h6bb024c_1             
    numpy:          1.15.4-py27h1d66e8a_0            
    numpy-base:     1.15.4-py27h81de0dd_0            
    olefile:        0.46-py27_0                      
    pillow:         5.3.0-py27h34e0f95_0             
    pycodestyle:    2.4.0-py27_0                     
    pycparser:      2.19-py27_0                      
    pyflakes:       2.0.0-py27_0                     
    pyopenssl:      18.0.0-py27_0                    
    pysocks:        1.6.8-py27_0                     
    reportlab:      3.5.9-py27he686d34_0             
    requests:       2.20.0-py27_0                    
    six:            1.11.0-py27_1                    
    urllib3:        1.23-py27_0                      
    xmltodict:      0.9.2-py27_0          bioconda   

The following packages will be UPDATED:

    certifi:        2018.10.15-py37_0                 --> 2018.10.15-py27_0
    pip:            18.1-py37_0                       --> 18.1-py27_0      
    setuptools:     40.5.0-py37_0                     --> 40.5.0-py27_0    
    wheel:          0.32.2-py37_0                     --> 0.32.2-py27_0    

The following packages will be DOWNGRADED:

    python:         3.7.1-h0371630_3                  --> 2.7.15-h9bab390_4

Proceed ([y]/n)?

Installing manually via python3 setup.py installseems to work fine.

bebatut commented 5 years ago

Hi @nigiord,

Thanks for using enasearch.

This issue is known and I am sorry for that. Click (used for the command line interface) is not supported for python 3 in conda so I could not make enasearch conda package for python 3. You can do also a conda environment with python 3 and then install enasearch with pip install inside the environment. Pip package of enasearch supports python 3.

I hope it will help you

nigiord commented 5 years ago

Hi @bebatut,

Thank you for your answer. I'm confused because it seems to me Click has a Python3 version in conda: https://anaconda.org/anaconda/click/files

It can be installed using:

$ conda install -c anaconda click
Solving environment: done

## Package Plan ##

  environment location: /home/giordano-n/.miniconda3/envs/test_enasearch

  added / updated specs: 
    - click

The following packages will be downloaded:

   […]

The following NEW packages will be INSTALLED:

  […]
    click:           7.0-py37_0              anaconda
 […]

Are you sure Click is the problematic package?

This is not a big issue since, as you said, enasearch-py3 can be installed and used in a conda environment through pip and setup.py. I just think it would be cleaner to have a full conda integration for Python 3.

Cheers, Nils