Closed MKoesters closed 2 years ago
Dear Manuel (@MKoesters),
Thank you for your review. We're glad that you found no major problem with ViMMS. In the master branch, we have addressed the minor issues that you found. Here's an itemised list of the minor issues and our comments:
- Contributing guidelines are available, but not properly linked in the documentation or README
We have included a Contributing guideline here, and made sure that it's now linked from the README.
- example notebooks are not working
Those notebooks were broken since the project is still in active development, and we forgot to update the notebooks. We've gone through all notebooks in the examples and demo folder and make sure they now run.
- Usage of
import *
We agree that it's generally a bad practice to use import *
, so we've made sure to eliminate them from the codebase and from the notebooks as well.
I hope these changes are satisfactory to address the minor issues above. If there's any other problem, please let me know.
Thank you,
Joe Wandy (on behalf of the ViMMS team)
Closing this since all minors are resolved!
Review checklist for @MKoesters
✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Reviewers comments
Major: None
Minor:
examples/01.\ vimms\ \(Wandy\ et\ al\ 2019\)/
dont seem to workModuleNotFoundError Traceback (most recent call last) Input In [5], in
----> 1 from vimms.DataGenerator import extract_hmdb_metabolite, get_data_source, get_spectral_feature_database
2 from vimms.MassSpec import IndependentMassSpectrometer
3 from vimms.Controller import SimpleMs1Controller
ModuleNotFoundError: No module named 'vimms.DataGenerator'
from vimms.PythonMzmine import from vimms.MassSpec import IndependentMassSpectrometer from vimms.Controller import TopNController,WeightedDEWController from vimms.PythonMzmine import
ModuleNotFoundError Traceback (most recent call last) Input In [4], in
----> 1 from vimms.PythonMzmine import *
2 from vimms.MassSpec import IndependentMassSpectrometer
3 from vimms.Controller import TopNController,WeightedDEWController
ModuleNotFoundError: No module named 'vimms.PythonMzmine'