BioSystemsUM/troppo

Implement Table/Excel formatted task file reader

vvvieira opened this issue · 3 comments

vvvieira commented

A new reader should be added to the task_io module with the ability to read task lists such as those feature on Human-GEM and HMR.

Ideally this should be generic for any kind of tabular format, but reading directly from XLS(X) files would be nice.

aschluter commented

Hi skapur,

I think in relation whith this I get the error "ImportError: cannot import name 'ExcelTaskIO'" when running reconstruction_pipeline_comparison.py from human_ts_models. It is possible that task.io is not implemented with this function?

python reconstruction_pipeline_comparison.py
Python 3.6.9 (default, Jan 26 2021, 15:33:00)
[GCC 8.4.0] on linux
Traceback (most recent call last):
File "reconstruction_pipeline_comparison.py", line 17, in
from projects.breast_mcf7.scripts.human1.models import get_human1_model
File "/home/agatha/python-virtual-environments/env/human_ts_models/projects/breast_mcf7/scripts/human1/models.py", line 3, in
from troppo.tasks.task_io import ExcelTaskIO
ImportError: cannot import name 'ExcelTaskIO'

thank you in advance,

Agatha

vvvieira commented

Hello Agatha,

Thanks for pointing this out. The scripts you are testing require some features currently in a development version of this tool which we haven't yet released to PyPI. I am no longer actively maintaining the tool so you might have to wait for a proper fix (sorry!)

However, you can make this work by removing the current version of troppo and installing the latest version using the following commands in your command line/Python environment:

  • pip remove troppo
  • pip install git+https://github.com/BioSystemsUM/troppo.git@dev

I also recommend that you do the same for cobamp:

  • pip remove cobamp
  • pip install git+https://github.com/BioSystemsUM/cobamp.git@dev.

Sorry for the inconvenience and I hope this solves it!

aschluter commented