Take into account new policy in `filter.py`: the names of the three
shapefiles are always the same and form a unit in a snaphot directory.

Rename `compil_prod_dir`to `build_dir` in JSON test files. Add a test
of `successive_overlap` with global grid, normal resolution.

`test_successive_overlap`.

`settings.mk` in GNUmakefile.

Bug fix in procedure `dispatch_snapshot`: an isolated eddy is a valid eddy.

In script `plot_snapshot.py`, in function snaphot, replace argument ax
with argument `new_figure` so the user does not have to call figure
and `axes(projection = projection)`. Add argument light to function
snapshot so we can call snapshot with light set to False for a second
snapshot. Add a test to only read `h.nc` when we need it.

In script `read_overlap.py`, print more information: number of nodes,
number of edges, number of nodes with at least one successor, number
of nodes with at least one predecessor, splitting events, merging
events.

In script `stat.py`, use the convention that shapefiles are grouped in
a directory instead of identifying a set of shapefiles by the end of
their basename.

In main program `test_successive_overlap`, we know that `delta_in` for
snapshot 1 and `delta_out` for snapshot 2 are `huge(0)` so do not test
this. Print eddy identifiers in a single line. Add the printing of
identifiers of isolated eddies.

splitting and merging.

`snapshot`. Also, move calls to `ax.gridlines` and `ax.coastlines`
inside function `snapshot`. These changes allow us to call `snapshot`
in a new figure.

Move `Region4/2006_01_01` to `Region4_2006_01_01` and
`Region4/2006_01_02` to `Region4_2006_01_02`.

Add a test of `successive_overlap` for a larger region, for which the
identifying numbers of the connected eddies are not the same for all
edges. Add corresponding input files.

Bug fix in main program `test_successive_overlap`.

snapshots in the same figure: useful for visualizing overlaps. So move
lines plotting a snapshot inside a new function called
snapshot and add option `--dashed`.

Remove the option `-e` of `plot_snaphot.py` and add directory argument
instead. The idea is that we now consider the three shapefiles as a
whole, they should always be alone in a dedicated directory.

Move the three shapefiles of `Tests/Input/Region_4/2006_01_02` to a
dedicated directory.

In `plot_snapshot.py`, netCDF variables for wind are now expected to be
called ugos and vgos.

Add a test for overlap of two different snapshots.

files, that make up a snapshot into a directory that contains only
these files. We hope that this will ease the handling of
snapshots. For now, this is useful in program
test_successive_overlap. So, in program extraction_eddies, create the
shapefiles in a directory called Snapshot. As we cannot create the
directory from Fortran (in Fortran 2003, it becomes possible in
Fortran 2008), we have to wrap the Fortran executable in a shell
script "extraction_eddies.sh". In the same way, read from a directory
Snapshot_old in programs test_read_eddy and test_read_snapshot and
create scripts "test_read_eddy.sh" and "test_read_snapshot.sh".

Reference the shell scripts "extraction_eddies.sh",
"test_read_eddy.sh" and "test_read_snapshot.sh" in JSON test files.

In program test_successive_overlap, finally read two snapshots, from
directories Snapshot_1 and Snapshot_2. Pass to successive_overlap the
date of the second snapshot. Use new variables corner_deg and step_deg
to avoid converting to rad twice.

Create directory Snapshot in Tests/Input/Region_4/2006_01_01.

overlap, we will have to read a set of three shapefiles, extremum,
outermost_contour and max_speed_contour, containing several
snapshots. We do not want to re-read field indices for each snapshot.

Rename u, v to ugos, vgos in NetCDF files.

vgos, lon to longitude, lat to latitude.

Add a test for successive_overlap with periodic grid.

Add snapshot for region 4 at a different date, in input files, for a
new test of successive_overlap.

read_snapshot and successive_overlap instead of a named constant of
module successive_overlap_m.

Bug fix in main programs test_read_snapshot and
test_successive_overlap: take into account that step is in degrees.

not sure about this. I will stay on the safe side for now.

Support periodic grid in successive_overlap.

eddies at date "j" in a new function candidate_overlap. This reduces
the number of nested constructs from 8 to 5. Incidentally, we can now
avoid defining needlessly polyline_1 if there is no candidate at date
"j". Also the function candidate_overlap should also be called by
non_successive_overlap.

Add argument periodic to procedure successive_overlap.

In main unit test_successive_overlap, pass to successive_overlap the
date subscript returned by read_snapshot instead of an arbitrary
value. Only print delta_in and delta_out if they are /= huge.

Tests/CMakeLists.txt. This is more concise since we can merge them
with target_sources.

Bug fix: missing source file successive_overlap.f90 for target
test_read_snapshot.

0ce6b1b4.

Write extr_map in test_read_snapshot since extr_map has been
defined. So create a procedure write_extr_map because now we want to
write extr_map both in test_local_extrema and in test_read_snapshot.

Preparing to take into account periodicity in successive_overlap: add
argument periodic to read_snapshot and extend s%extr_map in longitude
if periodic.

In program extraction_eddies, constraint on max_radius(1) is necessary
only if periodic.

Make read_snapshot more general: add argument step.

In procedure get_snapshot, remove definition of s%number_eddies
because this is already done in read_snapshot.

Promote dist_lim from local constant of successive_overlap to constant
of module successive_overlap_m because we need it in read_snapshot
(and test_successive_overlap and test_read_snapshot).

(instead of date_index = 1). This is the value read from the NetCDF
files. We have to increase the width of field date_index to 5 digits
(4 digits would only allow approximately 30 years since 1950).

In procedure read_snapshot, check that all input eddies have the same
date index, and return it as an additional argument.

Assume that the input NetCDF files contain a single date.

In program test_set_all_outerm, do not write file
"isolated_nodes_1.csv". Since s is defined by set_all_outerm only, all
the eddies are necessarily isolated.

targetted a single main program.

In script plot_snapshot.py, with option --light, do not plot invalid
outermost contours.

longer a test program).

unit test_get_snapshot. get_snapshot reads from shapefiles instead of
netCDF files.

Bug fix: programs test_get_snapshot and test_read_snapshot do not need
dispatch_snapshot.f and send_snapshot.f.

Procedures dispatch_snapshot, get_snapshot, send_snapshot and
receive_snapshot are no longer referenced, for now. They will be
called by the overlap program.

spherical_polygon_area to spher_polygon_area.

In procedure max_speed_contour_ssh, instead of aborting when the speed
is not defined, continue with missing_ssh. Found such a case in
November 29th, 2015 data. Added corresponding test. In procedure
set_max_speed, if max_speed_contour_ssh returns missing_ssh then we
just take the outermost contour as max-speed contour.

order to take missing value attribute into account.

input NetCDF files rather than selecting a window. Clearer and easier
to set up new tests.

extraction of eddies and overlapping.

Procedure dispatch_snapshot will be called by the overlap program and
will not write eddies. So remove the calls to write_eddy from
dispatch_snapshot and move them to test_get_snapshot and
test_read_snapshot.

Do not create files isolated_nodes_1.csv and number_eddies_1.csv in
test_get_snapshot and test_read_snapshot, that will be done by the
overlap program.

distribution_function. This allows to plot comparisons of various
combinations of runs.

Update plot_snapshot.py to work with version 2 of pyshp.

script distribution_function.py. Return dictionary instead of tuple:
easier to use.

In script plot_snapshot.py, move definition of readers to the
beginning so there is no risk of entering the window for nothing if we
forgot the end_filename option. Also, enter the four values defining
the window in a single input: easier to copy and paste.

distribution_function.py. Plot two distribution functions and two
histograms for positive speed and absolute value of negative speed.