to out_cont and speed_cont (shorter names).

Propagate change in shapelib_03: shp_append_simple_object_03 to
shp_append_object_03.

and signalling NaN so we cannot use the -ffpe-trap=invalid option.

Accept that we might not be able to compute the mean speed on the
outermost contour: there might be undefined values of velocity
around. In that case just use the contour coming from
max_speed_contour_ssh.

Add quiver_key in plot_snapshot.py.

New test for region 5.

procedure set_all_outerm. So do not define and output null max-speed
contours.

Bug fix in program test_set_all_outerm: take into account missing
values in ADT.

Make plot_snapshot.py work even if there is no max-speed contour
shapefile. So we can use plot_snapshot.py on results of program
test_set_all_outerm.

For ssh, missing value is huge(0.). We have to take a large value
because Contour_531 has an argument zmax for missing values. For
velocity, missing value is a quiet NaN. We have to take this because
we need to know if the interpolation procedure in mean_speed has not
used any missing value and we do not want to alter the interpolation
procedure itself.

In local_extrema, we accept as local extrema only points with 8 valid
values around them.

When we look for the maximum speed contour, we are hoping that good
contours do not englobe missing values. If this happens, the program
aborts.

When computing the mean speed on a contour, we are hoping that the
interpolation of speed on contour points does not use missing
values. If this happens, the program aborts.

Draw coastlines in plot_snaphot.py. At the same time, this allows the
use of any projection.

because the order is not obvious.

In test_mean_speed and test_set_max_speed, do not read primary
variables with nf95_gw_var so the primary variables are allowed to
have or not a degenerate dimension.

level max_speed_contour_ssh, take outermost contour as max-speed
contour.

set_all_outerm. Thus, we have the clearer intent(out) for argument s
of set_all_outerm. Also, this prepares a possible replacement of
set_all_outerm by a procedure from the Topology toolkit.

Create test program for procedure set_all_outerm.

with some components intent(in) and one component intent(out) was less
clear. Also, replace argument ind_targ_extr by argument i. This is
simpler both in get_1_outerm and in set_all_outerm.

There is now no need to use an eddy in test_get_1_outerm.

set_all_outerm, for clarity.

program behavior.

In plot_snapshot.py, no need to accumulate all content of shapefile
extremum_1, just process it record by record, as for other shapefiles.

remember the order of positional arguments so we rather use fixed
input file names and no arguments.

namelist input. Also, choose name of primary NetCDF variable in
namelist and read only this variable, not its coordinates. This makes
it easier to use an arbitrary NetCDF file.

In program test_set_outermost_contour, it is hard to remember the
order of positional arguments so we rather use fixed input file names
and no arguments.

In JSON input file for tests, it is simpler to use the "input" key
than creating a one-line input file, in some cases.

out-of-range index so add min when calculating urc.

Bug fix in procedure good_contour. polygon_contains_point should not
be called if polyline is not closed.

Procedure polygon_contains_point became unpure so remove pure for
procedure inside_4 too.

In program test_good_contour, read corner and step from namelist
rather than from coordinates in NetCDF file. Makes it possible to use
the same NetCDF file with different coordinates. Also read
outside_points from a file rather than standard input so there is no
need to specify in advance the number of outside points.

Take into account the possibility that no outermost contour was found
in program test_set_outermost_contour. Also, use fixed names for input
files because it is not convenient to require a particular order of
these two files on the command line.

defined. Also, allow test_set_outermost_contour to read ssh from a
NetCDF variable with a degenerate time coordinate or with no time
coordinante.

"stdout" key became optional in "tests.json" and "directory" key
became "title", with no indication of directory.

contour.

Read whole NetCDF files in program test_set_outermost_contour instead
of specifying a reading window. Simpler to prepare a file outside
the Fortran program, as in program test_local_extrema. Also, compute
step from read longitude and latitude.

contour no longer means that the eddy is interpolated.

acceptable. So define flat_extr by a strict inequality in procedure
get_snapshot.

Procedure set_outermost_contour no longer has a dummy argument
noise_around. We no longer call outermost_possible_level so we do not
have an artificial discontinuity of results with and without maximum
amplitude. We abandon the idea of reducing the amplitude of initial
level_good compared to innermost_level: problem of consistence with
get_snapshot, and it does not seem worth the trouble, just abandon
those problematic extrema. Allow for null outermost_contour instead of
aborting.

In procedure get_snapshot, s%list_vis(i)%suff_amp is first defined
only if flat_extr(i). Also we are no longer sure that
set_outermost_contour finds an outermost contour so we have to test
this to define s%list_vis(i)%suff_amp. noise_around is now defined
only for flat_extr(i) and s%list_vis(i)%suff_amp. Also, since we may
not find an outermost contour even if not flat_extr(i), we update
s%extr_map after the second call to set_outermost_contour.

In procedure local_extrema, we use the mask diff_center instead of
mask_center. So we no longer need procedure construct_mask_center. In
procedure local_extrema, we ignore one in two adjacent degenerate
extrema instead of aborting.

In plot_snapshot.py, color extrema and allow for null outermost
contour.

Synthesize output in test_local_extrema.py.

procedure inside was used in previous commits, but inside_4 is based
on polygon_contains_point.

In procedure set_max_speed, extend the search for radius beyond the
value provided by polygon_point_dist_2d. We are now certain that
ind_extr + radius is outside. We recover the value of radius that was
computed by inside assuming no degeneracy.

degenerate cases. Also, in procedure set_max_speed, I do not like
changing algorithms and results when going to min_amp = 0, and there
is no real meaning for this change.

Make program test_good_contour more general.

sufficient amplitude.

outermost_possible_level. This is especially important if the extremum
is one point away from the last point.

Bug fix. In procedure set_outermost_contour, take level_good a little
bit closer to ssh_extremum than innermost_level because of border
points. Contour_531 will not close a contour passing at a point on the
border. So if innermost_level corresponds to a point on the border,
good_contour at innermost_level finds nothing.

Make the program test_good_contour more general: read a NetCDF file
instead of calling define_example_reg.

low-amplitude threshold, min_amp.

Add component suff_amp to derived type eddy. Write this component in
extremum_$m.dbf.

In shapefiles, write positions of vertices in degrees rather than
radians.

test_get_snapshot reads the whole domain of input NetCDF files instead
of selecting a window through a namelist. This is clearer and more
convenient. Same in test_get_snapshot.py, test_local_extrema and
test_local_extrema.py.

In test_get_snapshot.py, annotate extrema instead of inserting a
legend.

More correct names: radian_per_degree to deg_over_rad,
degree_per_radian to rad_over_deg.

test_good_contour has more general input.

test_inside tests only inside, no loop on radius.

procedure get_eddy), with corresponding test.

Take into account the fact that derived type polygon became polyline
in library Contour_531.

Use new procedure null_polyline from library Contour_531.

Correct a sneaky bug in mean_speed: the last point in the polygon
array is a duplicate of the first point, do not take the last point
into account when averaging (and interpolating). Discovered this bug
because the mean speed was not exactly the same for equivalent
polygons with circular permutation.

Change philosophy for the tests: read whole NetCDF variables, prepare
different NetCDF files for different geographical regions if needed;
read all data from file or namelist; read names of files on command
line.

Use generic test_program.sh (which is out of this project) instead of
the specific tests_detection_eddies.sh.

input depending on noise_around. So it is clearer to compute radius
outside of max_speed_contour_ssh. Thus, we simplify
max_speed_contour_ssh. radius is an input argument. The case where
radius == 1 must now be processed also outside of
max_speed_contour_ssh.

test_set_outermost_contour are in degrees.

but reads extr_map from a file.

call only one procedure per test, and read all the required
data. (Also: there was much duplication of code between
test_set_outermost_contour and test_max_speed_contour_ssh.)