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AuReMe / aucome

Automatic Comparison of Metabolism
GNU General Public License v3.0
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requirements.txt and setup.py differ on packages versions #4

Open glucksfall opened 3 years ago

glucksfall commented 3 years ago

Hello,

I tried to install aucome in a virtual environment with pip, but failed because of errors to build lxml and future. Then, I looked at the requirements.txt file that said padmed>=4.0 while there are other differences with setup.py file. After some iterations installing dependencies, I was able to install aucome.

These are the installed packages after the installation process. Hope this information is helpful. Best regards.

anyio               3.2.1    
appdirs             1.4.4    
argcomplete         1.12.3   
argh                0.26.2   
aucome              0.5      
biopython           1.79     
certifi             2021.5.30
cffi                1.14.6   
chardet             4.0.0    
charset-normalizer  2.0.1    
cobra               0.22.1   
colorama            0.4.4    
commonmark          0.9.1    
cycler              0.10.0   
depinfo             1.7.0    
diskcache           5.2.1    
docopt              0.6.2    
future              0.18.2   
gffutils            0.10.1   
h11                 0.12.0   
httpcore            0.13.6   
httpx               0.18.2   
idna                3.2      
importlib-resources 5.2.0    
Jinja2              3.0.1    
kiwisolver          1.3.1    
lxml                4.6.3    
MarkupSafe          2.0.1    
matplotlib          3.4.2    
mpmath              1.2.1    
mpwt                0.6.3    
numpy               1.21.0   
optlang             1.5.2    
padmet              5.0.1    
pandas              1.3.0    
Pillow              8.3.1    
pip                 20.0.2   
pkg-resources       0.0.0    
pycparser           2.20     
pydantic            1.8.2    
pyfaidx             0.6.1    
Pygments            2.9.0    
pyparsing           2.4.7    
python-dateutil     2.8.2    
python-libsbml      5.19.0   
pytz                2021.1   
requests            2.26.0   
rfc3986             1.5.0    
rich                10.6.0   
rpy2                3.4.5    
ruamel.yaml         0.17.10  
ruamel.yaml.clib    0.2.6    
scipy               1.7.0    
seaborn             0.11.1   
setuptools          44.0.0   
simplejson          3.17.3   
six                 1.16.0   
sniffio             1.2.0    
supervenn           0.4.1    
swiglpk             5.0.3    
sympy               1.8      
typing-extensions   3.10.0.0 
tzlocal             2.1      
urllib3             1.26.6   
zipp                3.5.0
ArnaudBelcour commented 3 years ago

Hello @glucksfall,

For the requirements of aucome there is a lot of issues coming from old dependencies that have been removed (for exemple eventlet). Sorry for the issues that you encounter and thank you for the list of dependencies associated to a correct install of aucome.

I will look at the issue with lxml/future and try to fix these dependencies issues this month.

Also aucome is still in development so there is a lot of other issues. For example the readme is not up-to-date. I will also update it this month.

Sorry for the delay to answer, Best Regards.