grdfilter crashes in pygmt if GMT_IN is used #4577
Description
Currently, PyGMT opens virtual files using GMT_IN|GMT_IS_REFERENCE, and the following script works well:
import pygmt
grid = pygmt.datasets.load_earth_relief()
smooth_field = pygmt.grdfilter(grid=grid, filter="g600", distance="4")
However, if PyGMT uses GMT_IN, the above script crashes:
grdfilter [ERROR]: G->data is not NULL when memory allocation is about to happen
[Session pygmt-session (3)]: Error returned from GMT API: GMT_PTR_IS_NULL (75)
[Session pygmt-session (3)]: Error returned from GMT API: GMT_PTR_IS_NULL (75)
[Session pygmt-session (3)]: Error returned from GMT API: GMT_OBJECT_NOT_FOUND (60)
...
GMTCLibError: Failed to close virtual file '@GMTAPI@-S-I-G-M-G-N-000000'.
To reproduce the issue, please update your pygmt repository, checkout this PR (GenericMappingTools/pygmt#517), and run the above script.
It crashes with GMT 6.1.1 and GMT master, but it might work for old versions.