Rename procedure `get_slice_dir` to `get_ori_slice_dir`.

Rename type `shpc_slice_handler` to `ori_slice_handler`.

Of derived type `shpc_slice_handler`.

Replace dummy argument `grid_lon_lat` of procedure `shpc_create` by
`with_proj`.

Remove component radius4 of derived type eddy and field radius4 of
`outermost_contour.dbf`. They are not used any longer.

The attribute written was always true.

We will need this new shapefile in program `eddy_graph` only for a non
longitude-latitude grid. We add a new dummy argument `grid_lon_lat` to
procedure `shpc_create` to decide whether we create the shapefile
`extr_proj`.

We are trying to define clearly the directories and what Fortran files
they should contain:

- `Inst_eddies`: May only contain program units which make up the
program `inst_eddies`. If a program unit does not go into
`inst_eddies`, it should not be here. Not all program units going into
`inst_eddies` must be here: some could be in directory Common.

- `Inst_eddies/Tests`: Main programs of unit tests for procedures in
directory `Inst_eddies`. Plus procedures used only in these unit tests.

- `Overlap`: May only contain program units which make up the program
`eddy_graph`. If a program unit does not go into `eddy_graph`, it
should not be here. Not all program units going into `eddy_graph` must
be here: some could be in directory Common.

- `Overlap/Tests`: Main programs of unit tests for procedures in
directory `Overlap`. Plus procedures used only in these unit tests.

- Common: Procedures that are used in both programs `inst_eddies` and
`eddy_graph`.

- Common/Tests: Main programs of unit tests for procedures in
directory `Common`. Plus procedures used only in these unit
tests. Plus procedures used in unit tests of both `Inst_eddies` and
`Overlap` directories but not used in either program `inst_eddies` nor
`eddy_graph`.

Assume that a slice is in a directory
"{shpc_dir}/{orientation}/Slice_{slice}" where shpc_dir can be any
name, orientation is "Anticyclones" or "Cyclones" and slice is an
integer. Do not read or create any longer a file "orientation.txt" in
the slice directory. Add procedure `get_slice_dir`. Add dummy
arguments cyclone and slice to procedure `shpc_open`. Add dummy
argument slice to procedure `shpc_create`.

Split derived type `shpc_slice_handler` into `shpc_slice_handler` and
`shpc_slice_meta out`. Do not mix what is necessary to open, create
and close, analogous to a logical unit, with what comes from reading
the files.

Create component `unit` for `ishape_last.txt` in derived type
`shpc_slice_handler`. Open, create and close `ishape_last.txt` at the
same time we open, create and close the shapefiles. So we use
`read_opcol` instead of `read_column` when we need to read
`ishape_last.txt`.

Thus remove too component interpolated of derived type eddy and
component `extr_interp` of derived type shpc.

We now impose that all eddies in an SHPC have the same
orientation. Remove field `extr_cycl` from the derived type shpc and
add field cyclone to shpc. When reading an eddy, give it the
orientation of its SHPC. Add argument cyclone to procedure
`shpc_create`. Create a file `orientation.txt` in each SHPC. When
writing an eddy, check that its orientation matches that of the SHPC.

Rename triplet to collection, `shp_tr` to shpc, shpt to shpc in
comments, identifiers and file names.

`read_eddy.f90`, `read_field_indices.f90` and `shp_tr_open.f90` will
become common to Overlap and `Inst_eddies` because they will be used
in `Inst_eddies/Tests/test_set_max_speed.f90`. So there are now enough
common files to justify a new directory.

Rename files and identifiers: change `"shp_triplet"` to `"shp_tr"`.

Add dummy argument `shp_triplet_dir` to procedure
`shp_triplet_create`. Motivation: program `eddy_graph` needs to create
one SHP triplet per MPI process.

Rename procedure `init_shapefiles` to `shp_triplet_create`.

Use the components for field identifiers of a variable of type
`shp_triplet` instead of storing these field identifiers in variables
of modules `init_shapefiles_m` and `read_field_indices_m`. The dummy
argument hshp of procedure `read_field_indices` becomes
`intent(inout)`.

Create derived type `shp_triplet`. Motivation: we need to manipulate
two triplets of shapefiles in program `eddy_graph`. Use everywhere a
variable of type `shp_triplet` instead of the three variables
`hshp_extremum`, `hshp_outermost`, `hshp_max_speed` when all three of
them appear. Rename character variable `shp_triplet` to
`shp_triplet_dir`.

Use `SHP_triplet` instead of Snapshot for the name of the directory
containing the three shapefiles extremum, `outermost_contour` and
`max_speed_contour`. This is meant as a general name, analogous to a
new file type. Generally, the shapefiles may contain eddies at
different dates, not just a snapshot.

Use `dbf_read_attribute_03` instead of dbfreadattribute in procedure
`read_eddy`. This also allows us to avoid the intermediary real
`c_double` variable. Modify intent of hshp arguments, taking also
advantage of upgrade of `shp_read_object_03` in `Shapelib_03`.

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.

(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.

procedure so it can be used by program test_set_all_outerm.

Move dummy argument corner of set_all_outerm to last position.

Bug fix in procedure get_snapshot: urc(2) must always be lower than
nlat, even if periodic is true. Fix the same bug in procedure
set_all_outerm: llc(2) >= 1 and urc(2) <= nlat even if periodic is true.

Bug fix in procedure set_all_outerm: the lower bound of dummy argument
ssh is not always 1.

Make script examine_ssh_values.py work for a periodic domain.

Make program test_set_all_outerm work for a periodic
domain. max_radius is now chosen at run-time (we must change it for
a very coarse grid). Add a corresponding test.

In written shapefiles, replace field "area" by field "r_eq_area",
that is radius of disk of equal area. This is a smaller number so it
needs fewer characters, especially for a global coarse grid.

not six significant decimal digits.

reading and spares some disk space: we can reduce the size of the
field from 20 to 14 characters. We do not loose precision with this
reduction because the order of magnitude of the area is 1e3 km2 or
more so the decimal part of the field was 0. Accordingly, change the
are for a null contour from - 1 to - 1e6 m2.

Bug fix in program test_set_max_speed. No need for width 20 for field "speed".

validity of an eddy depending not only on its amplitude but also its
surface. (Note that, in this version, the component valid is redundant: one
can simply test the component out_cont%n_points.)

hard-coding them.

Remove component twice of type eddy, no longer needed.

init_shapefiles. This allows us to have variables for DBF field
numbers, as module variables. We avoid the burden of passing this
large number of variables as arguments to write_eddy. Safer to have
variables for DBF field numbers than relying on the order of those
fields.

Remove file_list. This was a duplication of information.

Use named constant for missing max speed value. It is used in two procedures.