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pachterlab / seqspec

machine-readable file format for genomic library sequence and structure
MIT License
114 stars 17 forks source link

add "requests" package as dependency? #20

Closed chooliu closed 1 year ago

chooliu commented 1 year ago

Super minor installation issue with requests package dependency not being bundled by default in some environments?

Tested on various MacOS and Linux anaconda3/miniconda distributions (conda > 4.10.3, python 3.11.x, seqspec 967cf97).

Example:

conda create --name seqspec
conda activate seqspec

conda install pip
pip install git+https://github.com/IGVF/seqspec.git

conda list
# packages in environment at /Users/choo/opt/anaconda3/envs/seqspec:
#
# Name                    Version                   Build  Channel
attrs                     23.1.0                   pypi_0    pypi
bzip2                     1.0.8                h1de35cc_0  
ca-certificates           2023.08.22           hecd8cb5_0  
jsonschema                4.19.0                   pypi_0    pypi
jsonschema-specifications 2023.7.1                 pypi_0    pypi
libffi                    3.4.4                hecd8cb5_0  
ncurses                   6.4                  hcec6c5f_0  
newick                    1.9.0                    pypi_0    pypi
openssl                   3.0.10               hca72f7f_2  
pip                       23.2.1                   pypi_0    pypi
python                    3.11.5               hf27a42d_0  
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  hca72f7f_0  
referencing               0.30.2                   pypi_0    pypi
rpds-py                   0.10.3                   pypi_0    pypi
seqspec                   0.0.0                    pypi_0    pypi
setuptools                68.0.0                   pypi_0    pypi
sqlite                    3.41.2               h6c40b1e_0  
tk                        8.6.12               h5d9f67b_0  
tzdata                    2023c                h04d1e81_0  
wheel                     0.38.4                   pypi_0    pypi
xz                        5.4.2                h6c40b1e_0  
zlib                      1.2.13               h4dc903c_0  

seqspec --help
Traceback (most recent call last):
  File "/Users/choo/opt/anaconda3/envs/seqspec/bin/seqspec", line 5, in <module>
    from seqspec.main import main
  File "/Users/choo/opt/anaconda3/envs/seqspec/lib/python3.11/site-packages/seqspec/main.py", line 4, in <module>
    from .seqspec_format import setup_format_args, validate_format_args
  File "/Users/choo/opt/anaconda3/envs/seqspec/lib/python3.11/site-packages/seqspec/seqspec_format.py", line 1, in <module>
    from seqspec.utils import load_spec
  File "/Users/choo/opt/anaconda3/envs/seqspec/lib/python3.11/site-packages/seqspec/utils.py", line 5, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'

Fix:

pip install requests # requests 2.31.0 (pypi_0) installed
seqspec --help # launches as expected

Cheers!