Need to reinstall planemo every time after using it #1078
Description
Here is what I did to setup planemo
- I created a conda environment with only Python 3.6 (
conda create -n planemo python=3.6) - I installed Planeno in it with pip (
pip install planemo)
When I run Planeno for test (planemo test --galaxy_python_version 3.6 --galaxy_branch release_20.05 .), it works fine the 1st time (installing Galaxy, running the Galaxy and the tests). But if I run it a 2nd time, I got this error:
Traceback (most recent call last):
File "~/miniconda3/envs/planemo/bin/planemo", line 5, in <module>
from planemo.cli import planemo
File "~/miniconda3/envs/planemo/lib/python3.6/site-packages/planemo/cli.py", line 11, in <module>
from planemo.galaxy import profiles
File "~/miniconda3/envs/planemo/lib/python3.6/site-packages/planemo/galaxy/__init__.py", line 5, in <module>
from .config import galaxy_config
File "~/miniconda3/envs/planemo/lib/python3.6/site-packages/planemo/galaxy/config.py", line 52, in <module>
from .workflows import (
File "~/miniconda3/envs/planemo/lib/python3.6/site-packages/planemo/galaxy/workflows.py", line 12, in <module>
from gxformat2.normalize import inputs_normalized, outputs_normalized
ImportError: cannot import name 'outputs_normalized'
If I reinstall Planeno with pip, it works again. And then the next time, same error. Need to reinstall Planeno.
It seems that a different version of gxformat2 is reinstalled:
Installing collected packages: bioblend, gxformat2
Attempting uninstall: bioblend
Found existing installation: bioblend 0.13.0
Uninstalling bioblend-0.13.0:
Successfully uninstalled bioblend-0.13.0
Attempting uninstall: gxformat2
Found existing installation: gxformat2 0.11.3
Uninstalling gxformat2-0.11.3:
Successfully uninstalled gxformat2-0.11.3
Successfully installed bioblend-0.14.0 gxformat2-0.15.
Is it an expected behavior? Are Galaxy and Planemo using different versions of gxformat2 and gxformat2 is overwriting when Galaxy is installed during planemo test?