fixed introduced bug in oceanography and improved RTOFS test

examples/soundspeed/ex_read_and_write.py

@@ -27,18 +27,24 @@
 
 # test readers/writers
 logger.info('test: *** START ***')
-filters = ["valeport", ]
+filters = ["aml", ]
 formats = ["caris", "csv", "elac", "hypack", "ixblue", "asvp/ssp", "qps", "sonardyne", "unb", ]
 data_outputs = dict()
 for format in formats:
     data_outputs[format] = data_output
 tests = testing.input_dict_test_files(inclusive_filters=filters)
 # print(tests)
 
+reduced_testing = True
+
 # import each identified file
 for idx, testfile in enumerate(tests.keys()):
     logger.info("test: * New profile: #%03d *" % idx)
 
+    if reduced_testing and (os.path.basename(testfile)[0] != "_"):
+        logger.debug("Skip!")
+        continue
+
     # import
     lib.import_data(data_path=testfile, data_format=tests[testfile].name)
 

hyo2/ssm2/lib/profile/oceanography.py

@@ -28,7 +28,8 @@ class Oceanography:
     # ### PRESSURE/DEPTH METHODS ###
 
     @classmethod
-    def p2d(cls, p, lat: float = 30.0, dyn_height: int | None = None, debug: bool = False) -> float:
+    def p2d(cls, p: float | np.ndarray, lat: float = 30.0, dyn_height: int | None = None, debug: bool = False) \
+            -> float | np.ndarray:
         """Convert pressure to depth"""
         try:
             return cls.p2d_gsw(p=p, lat=lat, dyn_height=dyn_height)
@@ -39,25 +40,25 @@ def p2d(cls, p, lat: float = 30.0, dyn_height: int | None = None, debug: bool =
             return cls.p2d_backup(p=p, lat=lat)
 
     @classmethod
-    def p2d_gsw(cls, p, lat: float, dyn_height: int | None) -> float:
+    def p2d_gsw(cls, p: float | np.ndarray, lat: float, dyn_height: int | None) -> float | np.ndarray:
 
         if not isinstance(p, np.ndarray):
             p = np.array(p, ndmin=1, copy=False)
 
         if dyn_height is None:
             depth = -gsw.conversions.z_from_p(p=p, lat=lat)
-            return depth[0]
+            return depth
 
         depth = -gsw.conversions.z_from_p(p=p, lat=lat, geo_strf_dyn_height=dyn_height)
         for val in depth:
             if np.isnan(val):
                 logger.info("nan in gsw.conversions.z_from_p with dyn_height")
                 return -gsw.conversions.z_from_p(p=p, lat=lat)
 
-        return depth[0]
+        return depth
 
     @classmethod
-    def p2d_backup(cls, p, lat: float) -> float:
+    def p2d_backup(cls, p: float | np.ndarray, lat: float) -> float | np.ndarray:
         """Convert pressure to depth
 
         If the latitude is not passed, a default value of 30.0 is used.
@@ -84,7 +85,8 @@ def p2d_backup(cls, p, lat: float) -> float:
         return d / g
 
     @classmethod
-    def d2p(cls, d, lat: float = 30.0, dyn_height: int | None = None, debug: bool = False) -> float:
+    def d2p(cls, d: float | np.ndarray, lat: float = 30.0, dyn_height: int | None = None, debug: bool = False) \
+            -> float | np.ndarray:
         """Convert pressure to depth"""
         try:
             return cls.d2p_gsw(d=d, lat=lat, dyn_height=dyn_height)
@@ -95,25 +97,25 @@ def d2p(cls, d, lat: float = 30.0, dyn_height: int | None = None, debug: bool =
             return cls.d2p_backup(d=d, lat=lat)
 
     @classmethod
-    def d2p_gsw(cls, d, lat: float, dyn_height: int | None) -> float:
+    def d2p_gsw(cls, d: float | np.ndarray, lat: float, dyn_height: int | None) -> float | np.ndarray:
 
         if not isinstance(d, np.ndarray):
             d = np.array(d, ndmin=1, copy=False)
 
         if dyn_height is None:
             pressure = gsw.conversions.p_from_z(z=-d, lat=lat)
-            return pressure[0]
+            return pressure
 
         pressure = gsw.conversions.p_from_z(z=-d, lat=lat, geo_strf_dyn_height=dyn_height)
         for val in pressure:
             if np.isnan(val):
                 logger.info("nan in gsw.conversions.p_from_z with dyn_height")
                 return gsw.conversions.p_from_z(z=-d, lat=lat)
 
-        return pressure[0]
+        return pressure
 
     @classmethod
-    def d2p_backup(cls, d, lat: float) -> float:
+    def d2p_backup(cls, d: float | np.ndarray, lat: float) -> float | np.ndarray:
         """Convert depth to pressure
 
         ref: Leroy and Parthiot(1998)

hyo2/ssm2/lib/profile/profile.py

@@ -840,6 +840,8 @@ def insert_sis_speed(self, depth, speed, src=Dicts.sources['user'], temp=None, c
         user_invalid = self.sis.flag == Dicts.flags['user']  # user-invalidate samples
         possible = np.logical_or(valid, user_invalid)  # possible samples
         ip = np.indices(self.sis.flag.shape)[0][possible]  # indices of possible samples
+        if len(ip) < 2:
+            raise RuntimeError("Too few valid samples: %d! Check cast direction" % len(ip))
 
         # find depth index both in the valid and in the possible samples
         try:

tests/soundspeed/atlas/test_rtofs.py

@@ -1,6 +1,4 @@
 import unittest
-import os
-import shutil
 import logging
 
 from hyo2.ssm2.lib.atlas.rtofs import Rtofs
@@ -11,26 +9,15 @@
 
 class TestSoundSpeedAtlasRtofs(unittest.TestCase):
 
-    def setUp(self):
-        self.cur_dir = os.path.abspath(os.path.dirname(__file__))
-
-    def tearDown(self):
-        dir_items = os.listdir(self.cur_dir)
-        for item in dir_items:
-            if item.split('.')[-1] == 'db':
-                os.remove(os.path.join(self.cur_dir, item))
-            if item == 'atlases':
-                shutil.rmtree(os.path.join(self.cur_dir, item))
-
     def test_creation_of_Rtofs(self):
-        prj = SoundSpeedLibrary(data_folder=self.cur_dir)
+        prj = SoundSpeedLibrary()
         rtofs = Rtofs(data_folder=prj.rtofs_folder, prj=prj)
         self.assertTrue('rtofs' in rtofs.data_folder)
         self.assertFalse(rtofs.is_present())
         prj.close()
 
     def test_download_db_from_Rtofs(self):
-        prj = SoundSpeedLibrary(data_folder=self.cur_dir)
+        prj = SoundSpeedLibrary()
         rtofs = Rtofs(data_folder=prj.data_folder, prj=prj)
         rtofs.download_db(server_mode=True)