pymzm dependencies

[joewandy]

Convert pymzm (https://github.com/sdrogers/pymzm) into a proper package so it can be easily added as a dependency in Pipfile.

[sdrogers]

Shouldn't this be an issue on the pymzm repo? :-)

[joewandy]

yes, but easier to track if it's all here

[sdrogers]

Hi @joewandy -- I started on this, using the mass-spec-utils repo https://github.com/sdrogers/mass-spec-utils all the code that I think we use in vimms is in there. Packaged it up, and add to pypi: https://pypi.org/project/mass-spec-utils/0.0.1/ If I make a fresh venv and install this package it is all happy, but then I don't seem to be able to import it? Can you help please?

[sdrogers]

From Joe on slack...

Found two things @simon The folder structure is not correct. Need to move them into a top level mass_spec_utils or any other name you prefer In setup.py we need to specify the dependencies that this package requires. Add a install_requires section in setup.py (edited)

11:20 image.png image.png

11:20 first line shows the incorrect import. Second line fails because requests

[sdrogers]

create a folder called mass_spec_utils , add an _init__.py inside it. Then move adduct_calculator, data_import and library_matching into mass_spec_utils

[sdrogers]

Done. See mass_spec_utils