Convert the mat file to v6 from inside Python

Call the Matlab script from the Python script. We cannot do this with
subprocess because Matlab requires a terminal. With subprocess, the
Matlab script complains: "inappropriate ioctl for device". Note that
we cannot test that the Matlab script worked normally because it exit
with code 0 regardless: the exit instruction returns code 0.

The idea here is that we do not want to store the converted v6 mat files.

Convert_Matlab/inst_eddies_v6.py

 #!/usr/bin/env python3
 
-"""Converts adt_YYYY-MM-DD_v6.mat files to a triplet of
-    shapefiles. The mat files should be in v6 format. The data in each
-    input file is the set of detected instantaneous eddies at a given
-    date.
+"""Converts adt_YYYY-MM-DD.mat files to a triplet of shapefiles. The
+    mat files are assumed to be in v7.3 (HDF5) format and will be
+    converted to v6 format before being read. The data in each input
+    file is the set of detected instantaneous eddies at a given date.
 
 """
 
@@ -14,6 +14,8 @@ import scipy.io as sio
 import datetime
 import f90nml
 import sys
+import pty
+import os
 
 def define_fields(writers):
     """writers is a dictionary of shapefile.Writer objects."""
@@ -91,7 +93,7 @@ def write(writers, cell, cyclone):
 
 adt_file = sys.argv[1]
 dirname, basename = path.split(adt_file)
-my_date = datetime.datetime.strptime(basename, "adt_%Y-%m-%d_v6.mat").date()
+my_date = datetime.datetime.strptime(basename, "adt_%Y-%m-%d.mat").date()
 
 if len(sys.argv) == 3:
     final_date = datetime.datetime.strptime(sys.argv[2], "%Y-%m-%d").date()
@@ -122,8 +124,11 @@ for f in factories:
     file = path.join(f["SHP_coll"], "ishape_last.txt")
     f["writers"]["ishape_last"] = open(file, "w")
     
+
 while True:
-    matlab_data = sio.loadmat(adt_file, squeeze_me = True,
+    os.symlink(adt_file, "adt.mat")
+    pty.spawn(["matlab", "-nojvm", "-r", "inst_eddies"])
+    matlab_data = sio.loadmat("adt_v6.mat", squeeze_me = True,
                               variable_names = ("date_num", "X", "Y",
                                                 "Anticyclonic_Cell",
                                                 "Cyclonic_Cell", "ADT"))
@@ -136,9 +141,10 @@ while True:
     for f in factories:
         write(f["writers"], matlab_data[f["cell_name"]], f["cyclone"])
     
+    os.remove("adt.mat")
     my_date += datetime.timedelta(1)
     if my_date > final_date: break
-    basename = my_date.strftime("adt_%Y-%m-%d_v6.mat")
+    basename = my_date.strftime("adt_%Y-%m-%d.mat")
     adt_file = path.join(dirname, basename)
     
 nml = f90nml.Namelist()
@@ -149,3 +155,5 @@ nml["grid_nml"] = dict(corner_deg = [matlab_data["X"][0], matlab_data["Y"][0]],
 for f in factories:
     nml.write(path.join(f["SHP_coll"], "grid_nml.txt"), force = True)
     for k, v in f["writers"].items(): v.close()
+
+os.remove("adt_v6.mat")

Tests/short_tests.json

@@ -1097,8 +1097,10 @@
 	"command":
 	[
 	    "$src_dir/Convert_Matlab/inst_eddies_v6.py",
-	    "$src_dir/Tests/Input/Eurec4A_OA/adt_2019-12-15_v6.mat"
-	]
+	    "/data/lmd-oce/EUREC4A_OA/DATA_SAT_NewExport_Atalante/TOEddies/Eddies/adt_2019-12-15.mat",
+	    "2019-12-16"
+	],
+	"required": ["$src_dir/Convert_Matlab/inst_eddies.m"]
     },
     {
 	"title": "Plot_eddy_contours",