jschnab/pyms-plot

Graphical user interface for easy plotting and statistical analysis of mycorrhizal colonization data.

pyms-plot's Issues

Tag a release

This is required for JOSS (and the version should match that in the review 0.8.1) (see openjournals/joss-reviews#1125)

Add expected output to docs

openjournals/joss-reviews#1125
Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

For the docs (either in the README.md or on readthedocs) I think you should add at least one image showing the expected output for the test case example

Add to pip/conda

openjournals/joss-reviews#1125
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

I would recommend adding this package to either PyPI or anaconda (as you prefer). You might like to follow these instructions for PyPI/pip:
https://gehrcke.de/2014/02/distributing-a-python-command-line-application/
or try bioconda:
https://bioconda.github.io/contributing.html

The package meets the stated requirement in JOSS, but if you are able to add to one of these sources and automatically handle dependencies at the same time I think that would be preferable

Check references in paper

openjournals/joss-reviews#1125

References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

These look ok to me, but could you confirm whether DOIs are available for the references, and add them if they are?

You may wish to add one reference to either an example of where pyms has been used (e.g. to generate plots for a paper) or one to an example dataset of quantitative analysis of mycorrhizal fungi colonization of plant roots.
I would suggest adding both the references from the README.md to the paper too

Add further method documentation

openjournals/joss-reviews#1125

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There is a description of the statistical tests in the paper, but I believe it would be helpful to add these descriptions to either the README.md or readthedocs