davidnsousa / mcsd Goto Github PK

As generated using misspell:

mcsd\cells.m:25:66: "overlaping" is a misspelling of "overlapping"
mcsd\cells.m:29:13: "overlaping" is a misspelling of "overlapping"
README.md:206:260: "ouput" is a misspelling of "output"
replication_script.m:76:59: "overlaping" is a misspelling of "overlapping"
README.html:146:369: "ouput" is a misspelling of "output"
README.html:351:51: "ouput" is a misspelling of "output"

• There are currently two README files checked into the repository
• Both READMEs are identical in terms of content
• Only one README should exist (preferably the markdown version) in order to maintain a single canonical version
• If the HTML version is intended for a webpage, use a CI workflow with pandoc to generate the site

While the following statement is clear:

MCSD is a simple MATLAB/Octave tool designed to simulate diffusion processes in complex environments such as biological tissues.

It would be nice to expand on it a bit and describe why the tool is important and who or what applications it might help.

https://blog.github.com/2016-02-17-issue-and-pull-request-templates/

• Please add test cases and automated testing using CI (e.g., Travis CI, Drone, CircleCI, GitLab CI)
• The CI framework can also be used to satisfy #4 and #1

While the Details section of the README provides a high level overview, an API documentation tool (e.g., doxygen, Read The Docs, M2HTML) in conjunction with CI should be used to generate always up-to-date documentation.

Bug report

Prerequisites:

• I have read the README file, the documentation and the pdf tutorial.
• I am familiar with MCSD usage.
• I am using MATLAB with the Statistics and Machine Learning Toolbox installed / Octave.

The environment:

• MCSD version: HEAD
• Platform / OS version: Ubuntu 18
• MATLAB or Octave version: Octave 4.2.2

Steps to reproduce the problem:

cd ~/git/mcsd
octave-cli -p tests/ -p mcsd/ tests/tests.m 

Expected behaviour:

tests.m should complete in reasonable amount of time (e.g., <5min)

The problem:

How long should the test take?

Feature request

• https://github.com/davidnsousa/mcsd/settings/branch_protection_rules/new
• Require status checks to pass before merging
• Require branches to be up to date before merging
• Requires #14

Feature request

• Tests should be run by a CI service for every commit/PR
• Only passing PRs should be merged

The paper should have the following info:
Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

Bug report

Prerequisites:

• [X ] I have read the README file, the documentation and the pdf tutorial.
• [ X] I am familiar with MCSD usage.
• [X ] I am using MATLAB with the Statistics and Machine Learning Toolbox installed / Octave.

The environment:

• MCSD version:
• Platform / OS version:
• MATLAB or Octave version: Matlab R2014a

Steps to reproduce the problem:

ones(2,2,3)./ones(2,2) gives an error: matrix dimensions must agree.

In MATLAB R2018a, this syntax is supported.

This is relevant for rwalkfree.m line 27.
If backwards compatibility is needed, please generalize your code here by using repmat on dot() along the 3rd dimension.

Expected behaviour:

The problem:

Additional Information:

Feature request

Current state of the art: https://keepachangelog.com/en/1.0.0/
Or, you can use a tool such as: https://pypi.org/project/towncrier/

Feature request

• tests/tests.m shouldn't contain all the tests
  • E.g.,:
    • %% test 1: 1D Free diffusion
    • %% test 2: 2D Free diffusion
• Split the tests across several files for easier maintenance and cleaner code

https://blog.github.com/2012-09-17-contributing-guidelines/