Also removes dependency on saved binary files.

Required for test_against_collect

This is needed for BOUT++'s 'collect' function to work correctly, as for
BOUT_VERSION<3.5 it was necessary to ignore the last point in the
z-grid, so collect needs to be able to check the BOUT_VERSION.

These scalar variables change from processor to processor, so are
dropped when loading a dataset and cannot be checked.

In some tests, these need to be dropped in addition to METADATA_VARS
before comparing generated and loaded datasets.

Returning 0 for an upper limit causes a bug, as the data is sliced with
slice(lower, upper), where upper=-<number of guard cells>, but -0=0 so
the slice would remove all the data.

Can then ignore it safely in the test suite.

Many tests produce a warning from xarray like:
RuntimeWarning: deallocating CachingFileManager(<class 'netCDF4._netCDF4.Dataset'>, '/tmp/pytest-of-***/<path-to-file>', mode='r', kwargs={'clobber': True, 'diskless': False, 'persist': False, 'format': 'NETCDF4'}), but file is not already closed. This may indicate a bug.
Ignore these warnings, as they do not tell us anything useful about
xBOUT.

In Python-3.6 the mayavi install fails if vtk is not available. mayavi
is a dependency of boutdata, needed for test_against_collect. As a
workaround, pip-install vtk before pip-installing boutdata.

May be needed to provide some variables that are not saved by default to
BOUT++'s output files, e.g. psixy, Rxy, Zxy.

Need to add hthe before getting toroidal coordinates, as dimension names
are changed only in the Dataset, not in the _grid member variable.

'r' coordinate is created as 1d, so selecting 'theta=0' part is an
error.

Doing this prevented the dataset being saved to netCDF file.

Also use _open_grid instead of open_boutdataset to open the grid file so
that the grid dataset does not have metadata added to the DataArray
variables. These variables are added as coordinates and become members
of the DataArrays representing simulation variables; if they have a
metadata dict, it is not possible to save them to netCDF.

...when hthe is loaded from the grid file. Variables from the grid file
do not have all the correct metadata, so cause errors when trying to
save to netCDF.

Depedency has been made optional by an update to boututils.

Depedency has been made optional by an update to boututils.

Instead use UserWarning, and in pytest.ini set a filter on the warning
message.

Test geometries

Previously, a gridfile was loaded and stored as an attribute of the
Dataset and DataArrays, then it was attempted to store the grid Dataset
as a member of the BoutDataset accessor (this does not work because
accessors are not permanent).

As of BOUT++ v4.3.0, the only information we need to load from the grid
file is some coordinates (e.g. psixy, Rxy, Zxy for 'toroidal' geometry),
so we can just open the grid file, set the coordinates and not save the
grid. This has the advantage that DataArrays inherit the coordinates
from their parent Dataset without having to do special things when
loading, or causing problems when saving to netCDF.

We no longer merge grid data from a grid file into the Dataset, so this
test is not needed.

MXG is not contained in the grid file, so needs to be passed as an
argument to _open_grid: read from the Dataset if one is being opened,
otherwise defaults to 2.

If boutdata.collect, 'old collect', is not available, then skip tests
comparing to it. Ensures users who do not install old python tools can
still run the tests.