James Marshall

icon indicating a website link http://staffwww.dcs.shef.ac.uk/people/J.Marshall/james.html

icon company Opteran Technologies icon location Chief Scientific Officer at Opteran Technologies / Professor of Theoretical and Computational Biology at University of Sheffield

Results 39 comments of James Marshall

Test suite: run all notebooks in one or more dirs rather than explicitly named notebooks

I'm happy with that - stick it on the second release milestone for now I think...

Test suite: run all notebooks in one or more dirs rather than explicitly named notebooks

I think this could be a sensible suggestion since it could also solve another problem, of how to publish new notebooks which are linked from readthedocs, without needing to tag...

Test suite: run all notebooks in one or more dirs rather than explicitly named notebooks

OK, this is getting overcomplicated IMO - maybe we should revert to keeping the notebooks as is... but if those to be run as tests need to be explicitly included,...

Do not suppress tracebacks when running 'test' notebooks via nbval

I think this is `setVerbose()`? Add this to test notebooks if it's not there already?

Do not suppress tracebacks when running 'test' notebooks via nbval

OK - maybe run it last? It's good to test the user manual of course, but most of the functionality should have been tested if the other notebooks complete...

Consider DOI release assignment strategy

So as of https://github.com/DiODeProject/MuMoT/milestone/3 I think this should be left as is...

Muticontroller plot warning

This issue is specific to nested multicontrollers - unfortunately following the solution proposed by the warning breaks multicontroller nesting, and puts all component plots at the same level. For now...

Greek letters should be used consistently in all functions

Please could you provide a code snippet to illustrate - presumably this refers to partial controllers but, for example, is the problem manifest when using `params`, `initWidgets`, both?

Update contributors

Actually I think readthedocs still needs updating - then this issue can be moved back to the second release milestone...

Clean exceptions

(quoted from #318) > I changed my old print("Warning message") with > raise exceptions.MuMoTWarning("Warning message") (as indicated in #352), however this stops the program. Instead, the desired behaviour is to...