Description

This issue will be used to track common interface option handling. This is a constant time factor so it's not the biggest deal, but I feel that we can improve some applications by reducing common latency here.

It would be helpful to have some text on how contributions should be made.
This includes how to setup the development environment and how to run the tests.

Environment: Android 6.0
NOTE: This is in the test version from #24, I have not yet tested whether this would happen in the 0.4.0 release.
Attempting to open the sketch folder from within APDE (via android's native file browser) instead opens the "Recent" list as shown in the attachment.
This applies regardless of sketchbook location.
[Link to image](https://user-images.githubusercontent.com/3

As the derivative of a given numpy array has the same size as the initial array, it could be worth mentioning how the differentiation switches between the backwards/forwards/centered scheme.

Looking at operators.diff() it uses "center" whenever it can apply it, "forward" at the left (low-index) boundary and "backward"

For hydrostatic atmospheres, we have different approaches depending on the solver. These should be documented together with the test problems.

@gaocegege -- what are the current build instructions?

CONTRIBUTING.md says "Read the README.md for build instructions" -- but it doesn't have build instructions. I'm looking through various artifacts -- docker, travis, appveyor, a build.xml for ant (eclipse?), and a set of scripts, e.g. deploy -- and trying to reconstruct a build setup for when I roll up a new release.

The current documentation can be misleading regarding which features are ready vs in-progress. I'm not sure if there's a standard practice for this, but if we can summarize the current state in this issue I'll update the README.

Relatedly, we might consider adding a header to the README that warns users that this library is still a WIP, and not to depend on it for anything critical. Again, not

https://bout-dev.readthedocs.io/en/latest/user_docs/advanced_install.html#petsc

• While we sort of support PETSc 3.4+, we definitely recommend 3.7+, and we should recommend using the latest available version
• The advice to tell PETSc to use a pre-compiled version of SUNDIALS is not great; we should recommend either using a standalone SUNDIALS or compiling PETSc with --download-sundials but

What I've noticed is that most (I didn't check all of them) PDE notebooks need to be rerun: all cells just display error messages.

E.g.:

http://benchmarks.juliadiffeq.org/html/MOLPDE/allen_cahn_spectral_wpd.html

http://benchmarks.juliadiffeq.org/html/MOLPDE/kdv_spectral_wpd.html

Things as I see them at the moment:

1. For the copyright checks of python codes, we would initially need to decide if we want to make a python-only folder to gather the source codes (which are anyway not in /src folders anyway), to make the check easier. Only then we can also see how the parsing for the checker should look like.

2. For style checks, we can enforce PEP8 style with several too

Some of @dwillcox 's Urca simulations should the grid structure imprint in the velocity field. It is possible that somewhere we are missing a ghost cell fill (e.g., after the projection, before plotfile, ...). It is most pronounced in the radial velocity field.