EGTortuero / viga

De novo VIral Genome Annotator
GNU General Public License v3.0
21 stars 8 forks source link

biopython no longer supports python 2.7 #11

Closed d-yarmosh closed 1 year ago

d-yarmosh commented 1 year ago

biopython does not support python 2.7 any longer and therefore cannot be installed as a dependency, provided python2.7 remains necessary to run viga. Is a change for this in the works?

$ python2 -m pip install bcbio-gff
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Collecting bcbio-gff
  Downloading bcbio-gff-0.6.9.tar.gz (44 kB)
     |████████████████████████████████| 44 kB 70 kB/s
Collecting six
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting biopython
  Using cached biopython-1.77.tar.gz (16.8 MB)
    ERROR: Command errored out with exit status 1:
     command: python2 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-GiZhO5/biopython/setup.py'"'"'; __file__='"'"'/tmp/pip-install-GiZhO5/biopython/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-bNnmEE
         cwd: /tmp/pip-install-GiZhO5/biopython/
    Complete output (1 lines):
    Biopython requires Python 3.6 or later. Python 2.7 detected.
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
d-yarmosh commented 1 year ago

Scratch that, looked at code and it's python3. Should update the readme, though