…s into single file (and objective function), fixed some test errors, fixed issue where trapping algorithm Qijk piece was slightly off (and reran notebooks).

…e pytest issues.

…ing.

…nch in a moment.

…lambda machine. Rerunning the 9 mode von karman example is too intensive for my computer.

…tial fix for Von Karman street

…so cleaned up the linting in trapping_sr3.py

…sindy into trapping_extended

…sindy into trapping_extended

…aping format needs to be fortran style. Added some of the examples from the dysts database, some of which dont seem to quite be behaving -- need to look closer at these. Importantly, added functionality in the code and in the example for including a bias (constant) term in the dynamical equations.

…the repository

Also: move m0 initialization to __init__, fix _objective calc

Trapping extended jake

Merge changes from master into trapping_extended

May need to adjust correct way of testing inequality constraints

In Trapping algorithm, gradient (non-accelerated) descent
was stepping from the previous point.  However, this is
incorrect, and as the problem is nonconvex, was causing a lack of
convergence.

1. test that constraint implies PQW symmetry
2. test that PQW symmetry implies constraint
3. test that constraint matrix is full rank
4. add test for just the mixed double constraints

Currently, not all double constraints are being created, meaning that
2 is passing, but 1 and 3 are not.  4 is passing but for the rank test

…me code for computing PW now. Removed the option for accelerated prox grad descent since this seemed not to work very well anyways. Updated the trapping paper examples script. Everything now looks good except the constraint matrix is not quite right for the MHD case.

…solves the constraint breaking in the MHD case. The problem with the MHD case is the matrix is super ill conditioned.

Currently the enstrophy seems wrong.  Global trapping with enstrophy seems off,
and local trapping with enstrophy gives nonnegative As

Also gitignore some pdf outputs