search

OpenMS / pyopenms-docs

pyOpenMS readthedocs documentation, additional utilities, addons, scripts, and examples.
https://pyopenms.readthedocs.io
Other
42 stars 52 forks source link

ConsensusMap.get_metadata_df and get_intensity_df don't exist #258

Closed qingyao closed 2 years ago

qingyao commented 2 years ago

The installed version should be latest: pyopenms==2.7.0 pyopenms-nightly==2.6.0.dev20201009

jpfeuffer commented 2 years ago

Where did you get the nightly from? This is not the latest.

qingyao commented 2 years ago

I used pip install. I compared just now with the Binder: 

? consensus_map
Type:            ConsensusMapDF
String form:     <pyopenms.dataframes.ConsensusMapDF object at 0x7f3233342dc0>
File:            /srv/conda/envs/notebook/lib/python3.7/site-packages/pyopenms/dataframes.py
Docstring:       <no docstring>

And for me:

Type:           ConsensusMap
String form:    <pyopenms.pyopenms_4.ConsensusMap object at 0x7fe4bbd86910>
File:          anaconda3/envs/new_MS_pipeline_py38/lib/python3.8/site-packages/pyopenms/pyopenms_4.cpython-38-x86_64-linux-gnu.so
Docstring:     
Cython implementation of _ConsensusMap

It seems the class "ConsensusMapDF" does not exist in the installed package? There is no dataframes.py in the pyopenms package.

jpfeuffer commented 2 years ago

The nightlies cannot be obtained from pip. Either use our wheels from GitHub Actions or use conda with the openms channel.

qingyao commented 2 years ago

I just downloaded the wheel from https://github.com/OpenMS/OpenMS/actions/runs/1728028373 Now the functions are there. Thank you! PS: conda install didn't work because of conflict, but I hadn't used openms channel, but bioconda as suggested on the Conda site: https://anaconda.org/bioconda/pyopenms