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aucome's Introduction

AuReMe

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This project is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.

Docmentation

AuReMe documentation

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aucome's Issues

requirements.txt and setup.py differ on packages versions

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

Potential dependency conflicts between aucome and docopt

Hi, as shown in the following full dependency graph of aucome_, aucome requires docopt (the latest version)， while the installed version of padmet(3.2.1) requires docopt==0.6.2.

According to Pip's “first found wins” installation strategy, docopt 0.6.2 is the actually installed version.

Although the first found package version docopt 0.6.2 just satisfies the later dependency constraint （docopt==0.6.2), it will lead to a build failure once developers release a newer version of docopt.

Dependency tree------

aucome<version range:>
| +-docopt<version range:>
| +-eventlet<version range:>
| +-mpwt<version range:>
| | +-biopython<version range:>=1.70>
| | +-docopt<version range:>=0.6.2>
| | +-gffutils<version range:>=0.9>
| | | +-argcomplete<version range:>
| | | +-argh<version range:>
| | | +-pyfaidx<version range:>
| | | | +-setuptools<version range:>=0.7>
| | | | +-six<version range:>
| | | +-simplejson<version range:>
| | | +-six<version range:>
| +-padmet<version range:>
| | +-biopython<version range:==1.70>
| | +-cobra<version range:==0.14.0>
| | +-docopt<version range:==0.6.2>
| | +-python-libsbml<version range:==5.16.0>
| +-requests<version range:>

Thanks for your attention.
Best,
Neolith

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