dbdreader 0.5.5__tar.gz → 0.5.7__tar.gz

{dbdreader-0.5.5 → dbdreader-0.5.7}/MANIFEST.in

@@ -5,7 +5,7 @@ include extension/include/*.h
 include lz4/*.c
 include lz4/include/*.h
 include tests/*.py
-include data/*.[stdem][bcl][dg]
-include data/cac/*.c[ac]c
-include data/cac_missing/*.cac
+include dbdreader/data/*.[stdem][bcl][dg]
+include dbdreader/data/cac/*.c[ac]c
+include dbdreader/data/cac_missing/*.cac
 include examples/*.py

{dbdreader-0.5.5 → dbdreader-0.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dbdreader
-Version: 0.5.5
+Version: 0.5.7
 Summary: A python module to access binary data files generated by Teledyne WebbResearch gliders
 Home-page: https://dbdreader.readthedocs.io/en/latest/
 Author: Lucas Merckelbach
@@ -18,8 +18,27 @@ License-File: COPYING
 DBDREADER
 =========
 
+Synopsis
+--------
+Slocum ocean gliders are autonomous underwater vehicles, used for
+making oceanographic measurements. The data that these devices and
+their sensors collect, are stored in binary data files. The python
+module *dbdreader* provides the utilities to extract the data from the
+binary files, so that they can be further analysed.
+
 Change log
 ----------
+
+Version 0.5.7
+
+* Drops dependency on python 3.10+, introduced in 0.5.6, and should
+  work still with python 3.9.
+
+Version 0.5.6
+
+* Moves data directory under dbdreader, making these files accessible
+  after an pip install
+
 Version 0.5.5
 
 * Makes MultiDBD's get_CTD_sync method compatible with RBR CTD data.
@@ -132,13 +151,6 @@ Version 0.4.5
 * dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.
 
 
-Synopsis
---------
-Slocum ocean gliders are autonomous underwater vehicles, used for
-making oceanographic measurements. The data that these devices and
-their sensors collect, are stored in binary data files. The python
-module *dbdreader* provides the utilities to extract the data from the
-binary files, so that they can be further analysed.
 
 Installation (linux)
 --------------------

{dbdreader-0.5.5 → dbdreader-0.5.7}/README.rst

@@ -3,8 +3,27 @@
 DBDREADER
 =========
 
+Synopsis
+--------
+Slocum ocean gliders are autonomous underwater vehicles, used for
+making oceanographic measurements. The data that these devices and
+their sensors collect, are stored in binary data files. The python
+module *dbdreader* provides the utilities to extract the data from the
+binary files, so that they can be further analysed.
+
 Change log
 ----------
+
+Version 0.5.7
+
+* Drops dependency on python 3.10+, introduced in 0.5.6, and should
+  work still with python 3.9.
+
+Version 0.5.6
+
+* Moves data directory under dbdreader, making these files accessible
+  after an pip install
+
 Version 0.5.5
 
 * Makes MultiDBD's get_CTD_sync method compatible with RBR CTD data.
@@ -117,13 +136,6 @@ Version 0.4.5
 * dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.
 
 
-Synopsis
---------
-Slocum ocean gliders are autonomous underwater vehicles, used for
-making oceanographic measurements. The data that these devices and
-their sensors collect, are stored in binary data files. The python
-module *dbdreader* provides the utilities to extract the data from the
-binary files, so that they can be further analysed.
 
 Installation (linux)
 --------------------

dbdreader-0.5.7/dbdreader/__init__.py

@@ -0,0 +1,10 @@
+__version__="0.5.7"
+
+__all__ = ['dbdreader']
+
+import os
+
+from .dbdreader import *
+
+EXAMPLE_DATA_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                                 'data'))

{dbdreader-0.5.5 → dbdreader-0.5.7}/dbdreader/dbdreader.py

@@ -1877,7 +1877,6 @@ class MultiDBD(object):
                 # get() method.
                 time_values_read_sofar+=len(t[0])
                 if method=="get" and kwds["max_values_to_read"]>0:
-                    print(f"time values read so far: {time_values_read_sofar}. Parameters {p}")
                     if time_values_read_sofar>=kwds["max_values_to_read"]:
                         break
 

{dbdreader-0.5.5 → dbdreader-0.5.7}/dbdreader.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dbdreader
-Version: 0.5.5
+Version: 0.5.7
 Summary: A python module to access binary data files generated by Teledyne WebbResearch gliders
 Home-page: https://dbdreader.readthedocs.io/en/latest/
 Author: Lucas Merckelbach
@@ -18,8 +18,27 @@ License-File: COPYING
 DBDREADER
 =========
 
+Synopsis
+--------
+Slocum ocean gliders are autonomous underwater vehicles, used for
+making oceanographic measurements. The data that these devices and
+their sensors collect, are stored in binary data files. The python
+module *dbdreader* provides the utilities to extract the data from the
+binary files, so that they can be further analysed.
+
 Change log
 ----------
+
+Version 0.5.7
+
+* Drops dependency on python 3.10+, introduced in 0.5.6, and should
+  work still with python 3.9.
+
+Version 0.5.6
+
+* Moves data directory under dbdreader, making these files accessible
+  after an pip install
+
 Version 0.5.5
 
 * Makes MultiDBD's get_CTD_sync method compatible with RBR CTD data.
@@ -132,13 +151,6 @@ Version 0.4.5
 * dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.
 
 
-Synopsis
---------
-Slocum ocean gliders are autonomous underwater vehicles, used for
-making oceanographic measurements. The data that these devices and
-their sensors collect, are stored in binary data files. The python
-module *dbdreader* provides the utilities to extract the data from the
-binary files, so that they can be further analysed.
 
 Installation (linux)
 --------------------

dbdreader-0.5.7/dbdreader.egg-info/SOURCES.txt

@@ -0,0 +1,73 @@
+COPYING
+COPYRIGHT
+INSTALL.rst
+LICENSE
+MANIFEST.in
+README.rst
+requirements.txt
+setup.py
+dbdreader/__init__.py
+dbdreader/dbdreader.py
+dbdreader/decompress.py
+dbdreader/scripts.py
+dbdreader.egg-info/PKG-INFO
+dbdreader.egg-info/SOURCES.txt
+dbdreader.egg-info/dependency_links.txt
+dbdreader.egg-info/entry_points.txt
+dbdreader.egg-info/requires.txt
+dbdreader.egg-info/top_level.txt
+dbdreader/data/01600000.dcd
+dbdreader/data/01600000.ebd
+dbdreader/data/01600000.ecd
+dbdreader/data/01600000.mcg
+dbdreader/data/01600000.mlg
+dbdreader/data/01600001.dbd
+dbdreader/data/01600001.dcd
+dbdreader/data/01600001.ebd
+dbdreader/data/01600001.ecd
+dbdreader/data/amadeus-2014-204-05-000.dbd
+dbdreader/data/amadeus-2014-204-05-000.ebd
+dbdreader/data/amadeus-2014-204-05-000.sbd
+dbdreader/data/amadeus-2014-204-05-000.tbd
+dbdreader/data/amadeus-2014-204-05-001.sbd
+dbdreader/data/amadeus-2014-204-05-001.tbd
+dbdreader/data/amadeus-2014-204-05-002.sbd
+dbdreader/data/amadeus-2014-204-05-002.tbd
+dbdreader/data/ammonite-2008-028-01-000.mbd
+dbdreader/data/electa-2023-143-00-050.sbd
+dbdreader/data/electa-2023-143-00-050.tbd
+dbdreader/data/empty-2014-204-05-000.dbd
+dbdreader/data/invalid_encoding-2014-204-05-000.dbd
+dbdreader/data/sebastian-2014-204-05-000.dbd
+dbdreader/data/sebastian-2014-204-05-000.ebd
+dbdreader/data/sebastian-2014-204-05-001.dbd
+dbdreader/data/sebastian-2014-204-05-001.ebd
+dbdreader/data/unit_887-2021-321-3-0.sbd
+dbdreader/data/unit_887-2021-321-3-0.tbd
+dbdreader/data/cac/06a36d4e.cac
+dbdreader/data/cac/06a36d4e.ccc
+dbdreader/data/cac/093bd5ed.cac
+dbdreader/data/cac/0f682cb2.cac
+dbdreader/data/cac/468fd1be.cac
+dbdreader/data/cac/61b1780f.cac
+dbdreader/data/cac/813b137d.cac
+dbdreader/data/cac/92610b65.cac
+dbdreader/data/cac/c4ec741e.cac
+dbdreader/data/cac/d6f44165.cac
+dbdreader/data/cac/daad1b20.cac
+dbdreader/data/cac/daad1b20.ccc
+dbdreader/data/cac/dc76ebd5.cac
+dbdreader/data/cac_missing/d6f44165.cac
+examples/read_multiple_dbd_files.py
+examples/read_single_dbd_file.py
+extension/dbdreader.c
+extension/decompress.c
+extension/py_dbdreader.c
+extension/include/dbdreader.h
+extension/include/decompress.h
+lz4/lz4.c
+lz4/include/lz4.h
+tests/dbd_test.py
+tests/dbd_test_2.py
+tests/dbdreader_test.py
+tests/test_decompress.py

{dbdreader-0.5.5 → dbdreader-0.5.7}/examples/read_multiple_dbd_files.py

@@ -36,8 +36,8 @@ import dbdreader
 # open some files, using a pattern
 # Note that the default location for cache files ($HOME/.dbdreader) is
 # overriden.
-dbd=dbdreader.MultiDBD(pattern="../data/amadeus*.[st]bd",
-                       cacheDir='../data/cac')
+dbd=dbdreader.MultiDBD(pattern="../dbdreader/data/amadeus*.[st]bd",
+                       cacheDir='../dbdreader/data/cac')
 
 # print what parameters are available:
 print("we the following science parameters:")
@@ -87,7 +87,7 @@ dbd.close()
 
 pattern_selector=dbdreader.DBDPatternSelect()
 pattern_selector.set_date_format("%d %b %Y %H")
-selection=pattern_selector.select(pattern="../data/amadeus*.[st]bd",from_date="24 Jul 2014 18")
+selection=pattern_selector.select(pattern="../dbdreader/data/amadeus*.[st]bd",from_date="24 Jul 2014 18")
 
 print("full list of sbd files:")
 for i,n in enumerate(dbd.filenames):

{dbdreader-0.5.5 → dbdreader-0.5.7}/examples/read_single_dbd_file.py

@@ -4,8 +4,8 @@ import dbdreader
 # open a given file
 # Note that the default location for cache files ($HOME/.dbdreader) is
 # overriden.
-dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd",
-                  cacheDir='../data/cac')
+dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd",
+                  cacheDir='../dbdreader/data/cac')
 
 # print what parameters are available:
 

{dbdreader-0.5.5 → dbdreader-0.5.7}/setup.py

@@ -1,6 +1,8 @@
 import sys
 import os
 
+import glob
+
 import setuptools
 
 with open("dbdreader/__init__.py", "r") as fh:
@@ -95,7 +97,7 @@ else:
     sources += ["lz4/lz4.c"]
     libraries = []
     include_dirs += ['lz4/include']
-    
+
 setuptools.setup(
     name="dbdreader",
     version=VERSION,
@@ -106,6 +108,8 @@ setuptools.setup(
     long_description_content_type="text/x-rst",
     url='https://dbdreader.readthedocs.io/en/latest/',
     packages=['dbdreader'],
+    package_data = {'dbdreader': glob.glob("dbdreader/data/*")},
+    include_package_data=True,
     py_modules=[],
     entry_points = {'console_scripts':['dbdrename=dbdreader.scripts:dbdrename',
                                         'cac_gen=dbdreader.scripts:cac_gen'],

{dbdreader-0.5.5 → dbdreader-0.5.7}/tests/dbdreader_test.py

@@ -13,25 +13,25 @@ class Dbdreader_DBD_test(unittest.TestCase):
     
     def test_open(self):
         print("Open")
-        v=self.get("../data/amadeus-2014-204-05-000.sbd","m_depth")
+        v=self.get("../dbdreader/data/amadeus-2014-204-05-000.sbd","m_depth")
         self.assertTrue(len(v)==2 and len(v[0])>0)
     
     def test_get_non_existing_variable(self):
         print("get_non_existing_variable")
-        v=self.get("../data/amadeus-2014-204-05-000.sbd","sci_water_pressure")
+        v=self.get("../dbdreader/data/amadeus-2014-204-05-000.sbd","sci_water_pressure")
         self.assertTrue(len(v)==2 and len(v[0])==0 and len(v[1])==0)
 
     def test_get_sync_non_existing_variable(self):
         print("get_sync_non_existing_variable")
         v = self.get_method("sync",
-                          "../data/amadeus-2014-204-05-000.sbd",
+                          "../dbdreader/data/amadeus-2014-204-05-000.sbd",
                             "m_depth",'sci_water_pressure','m_lon')
         self.assertTrue(len(v)==4 and len(v[2])==len(v[1]) and np.all(np.isnan(v[2])))
 
     def test_get_non_valid_variable(self):
         print("get_non_valid_variable")
         with self.assertRaises(dbdreader.DbdError) as e:
-            v=self.get("../data/amadeus-2014-204-05-000.sbd","M_LON")
+            v=self.get("../dbdreader/data/amadeus-2014-204-05-000.sbd","M_LON")
         # We expect an exception when an non-existing parameter is being requested.
         self.assertTrue(e.exception.value==dbdreader.DBD_ERROR_NO_VALID_PARAMETERS)
 
@@ -39,41 +39,41 @@ class Dbdreader_DBD_test(unittest.TestCase):
     def test_get_sync(self):
         print("get_sync")
         self.get_method("sync",
-                        "../data/amadeus-2014-204-05-000.sbd",
+                        "../dbdreader/data/amadeus-2014-204-05-000.sbd",
                         "m_depth",'m_lat','m_lon')
 
     def test_get_sync_obselete(self):
         print("get_sync_obselete")
-        dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
+        dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd")
         x = dbd.get_sync("m_depth", ['m_lat','m_lon'])
 
     def test_get_xy(self):
         print("get_xy")
         self.get_method("xy",
-                        "../data/amadeus-2014-204-05-000.sbd",
+                        "../dbdreader/data/amadeus-2014-204-05-000.sbd",
                         'm_lat','m_lon')
 
     def test_get_list(self):
         print("get_list")
-        dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
+        dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd")
         x, y = dbd.get_list("m_lat", "m_lon")
 
 
     def test_file_open_time(self):
         print("file_open_time")
-        dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
+        dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd")
         t=dbd.get_fileopen_time()
         self.assertEqual(t,1406221414)
 
     def test_get_mission_name(self):
         print("get_mission_name")
-        dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd")
+        dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd")
         t=dbd.get_mission_name()
         self.assertEqual(t,"micro.mi")
 
     def test_non_standard_cache_dir(self):
         print("non_standard_cache_dir")
-        dbd=dbdreader.DBD("../data/amadeus-2014-204-05-000.sbd", cacheDir='../data/cac')
+        dbd=dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.sbd", cacheDir='../dbdreader/data/cac')
         depth = dbd.get("m_depth")
         self.assertEqual(len(depth), 2)
 
@@ -82,50 +82,50 @@ class Dbdreader_DBD_test(unittest.TestCase):
         print("non_standard_cache_dir_generated_cachefile")
         # this should create a cache file. Remove it if already present.
         try:
-            os.unlink('../data/cac/(813b137d.cac')
+            os.unlink('../dbdreader/data/cac/(813b137d.cac')
         except FileNotFoundError:
             pass
-        dbd=dbdreader.DBD("../data/ammonite-2008-028-01-000.mbd", cacheDir='../data/cac')
+        dbd=dbdreader.DBD("../dbdreader/data/ammonite-2008-028-01-000.mbd", cacheDir='../dbdreader/data/cac')
         depth = dbd.get("m_depth")
         self.assertEqual(len(depth), 2)
 
     def test_G3S_data_file(self):
         print("Reading a G3S data file for which the byte order needs to be swapped.")
-        dbd = dbdreader.DBD("../data/unit_887-2021-321-3-0.sbd",
-                            cacheDir='../data/cac')
+        dbd = dbdreader.DBD("../dbdreader/data/unit_887-2021-321-3-0.sbd",
+                            cacheDir='../dbdreader/data/cac')
         tm, depth = dbd.get("m_depth")
         self.assertAlmostEqual(depth.max(),34.5, delta=0.1)
         
     def test_missing_cache_file(self):
         print("Throw an error when cache file is missing...")
         with self.assertRaises(dbdreader.DbdError) as e:
-            dbd = dbdreader.DBD("../data/unit_887-2021-321-3-0.sbd")
+            dbd = dbdreader.DBD("../dbdreader/data/unit_887-2021-321-3-0.sbd")
             #tm, depth = dbd.get("m_depth")
 
     def test_donottest_non_standard_cache_dir_fail(self):
         print("non_standard_cache_dir_fail")
-        kwds = dict(cacheDir='../data/not_there')
-        self.assertRaises(dbdreader.DbdError, dbdreader.DBD, "../data/amadeus-2014-204-05-000.sbd", **kwds)
+        kwds = dict(cacheDir='../dbdreader/data/not_there')
+        self.assertRaises(dbdreader.DbdError, dbdreader.DBD, "../dbdreader/data/amadeus-2014-204-05-000.sbd", **kwds)
 
     def test_missing_cache_file_data_feature(self):
         print("Throw an error when cache file is missing, and check who is missing.")
         try:
-            dbd = dbdreader.DBD("../data/unit_887-2021-321-3-0.sbd")
+            dbd = dbdreader.DBD("../dbdreader/data/unit_887-2021-321-3-0.sbd")
         except dbdreader.DbdError as e:
             data = e.data
             for k,v in data.missing_cache_files.items():
-                assert k == 'd6f44165' and v[0] == "../data/unit_887-2021-321-3-0.sbd"
+                assert k == 'd6f44165' and v[0] == "../dbdreader/data/unit_887-2021-321-3-0.sbd"
 
 
     def test_handling_inf(self):
-        dbd = dbdreader.DBD("../data/amadeus-2014-204-05-000.dbd",
-                            cacheDir="../data/cac")
+        dbd = dbdreader.DBD("../dbdreader/data/amadeus-2014-204-05-000.dbd",
+                            cacheDir="../dbdreader/data/cac")
 
         t, v = dbd.get("m_time_til_wpt", return_nans =True)
         t = t[:24]
         v = v[:24]
         # Now read the output by dbd2asc
-        with open("../data/dbd2asc_output.txt") as fp:
+        with open("../dbdreader/data/dbd2asc_output.txt") as fp:
             lines = fp.readlines()
         lines.pop(0) # remark
         tp = np.zeros_like(t)
@@ -143,7 +143,7 @@ class Dbdreader_DBD_test(unittest.TestCase):
 
     def test_get_sync_on_parameter_without_values(self):
         print("Reads in a parameter to sync that has no values.")
-        dbd = dbdreader.DBD("../data/sebastian-2014-204-05-001.dbd")
+        dbd = dbdreader.DBD("../dbdreader/data/sebastian-2014-204-05-001.dbd")
         _, _, x = dbd.get_sync("m_depth", "u_dbd_sensor_list_xmit_control")
         assert np.all(np.isfinite(x)==False)
 
@@ -151,23 +151,23 @@ class Dbdreader_DBD_test(unittest.TestCase):
     def test_get_reading_initial_data_line(self):
         print("Tests whether initial data line can be read if requested.")
         
-        dbd = dbdreader.DBD("../data/sebastian-2014-204-05-001.dbd")
+        dbd = dbdreader.DBD("../dbdreader/data/sebastian-2014-204-05-001.dbd")
         t0, v0 = dbd.get("m_depth")
-        dbd = dbdreader.DBD("../data/sebastian-2014-204-05-001.dbd", skip_initial_line=False)
+        dbd = dbdreader.DBD("../dbdreader/data/sebastian-2014-204-05-001.dbd", skip_initial_line=False)
         t1, v1 = dbd.get("m_depth")
         assert len(v0) == len(v1) - 1
         
 
     def test_get_reading_limited_values(self):
         print("Test whether we can read in only 10 depth values from a file.")
-        dbd = dbdreader.DBD("../data/sebastian-2014-204-05-001.dbd")
+        dbd = dbdreader.DBD("../dbdreader/data/sebastian-2014-204-05-001.dbd")
         t0, v0 = dbd.get("m_depth", max_values_to_read=10)
         assert len(t0)==len(v0) and len(t0)==10
         
     def test_get_reading_limited_values_requesting_multiple_parameters(self):
         print("Test whether reading a limited number of values from multiple values fails.")
         with self.assertRaises(ValueError):
-            dbd = dbdreader.DBD("../data/sebastian-2014-204-05-001.dbd")
+            dbd = dbdreader.DBD("../dbdreader/data/sebastian-2014-204-05-001.dbd")
             result = dbd.get("m_depth", "m_pitch", max_values_to_read=10)
         
     def get(self,fn,x):
@@ -196,7 +196,7 @@ class Dbdreader_DBD_test(unittest.TestCase):
 class Dbdreader_MultiDBD_test(unittest.TestCase):
 
     def setUp(self):
-        self.pattern="../data/amadeus-2014-*.[st]bd"
+        self.pattern="../dbdreader/data/amadeus-2014-*.[st]bd"
 
     def test_open(self):
         print("Open")
@@ -268,24 +268,24 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
 
     def test_non_standard_cache_dir(self):
         print("non_standard_cache_dir")
-        dbd=dbdreader.MultiDBD(pattern = self.pattern, cacheDir='../data/cac')
+        dbd=dbdreader.MultiDBD(pattern = self.pattern, cacheDir='../dbdreader/data/cac')
         depth = dbd.get("m_depth")
         self.assertEqual(len(depth), 2)
 
     def test_donottest_non_standard_cache_dir_fail(self):
-        kwds = dict(pattern=self.pattern, cacheDir='../data/not_there')
+        kwds = dict(pattern=self.pattern, cacheDir='../dbdreader/data/not_there')
         self.assertRaises(dbdreader.DbdError, dbdreader.MultiDBD, **kwds)
 
     def test_get_ctd_sync(self):
         print("get_ctd_sync")
-        pattern="../data/amadeus-2014-*.[de]bd"
-        dbd=dbdreader.MultiDBD(pattern = pattern, cacheDir='../data/cac')
+        pattern="../dbdreader/data/amadeus-2014-*.[de]bd"
+        dbd=dbdreader.MultiDBD(pattern = pattern, cacheDir='../dbdreader/data/cac')
         tctd, C, T, P, depth = dbd.get_CTD_sync("m_depth")
 
     def test_get_ctd_sync_rbrCTD(self):
         print("get_ctd_sync for RBR CTDs")
-        pattern="../data/electa-2023-143-00-050.[st]bd"
-        dbd=dbdreader.MultiDBD(pattern = pattern, cacheDir='../data/cac')
+        pattern="../dbdreader/data/electa-2023-143-00-050.[st]bd"
+        dbd=dbdreader.MultiDBD(pattern = pattern, cacheDir='../dbdreader/data/cac')
         tctd, C, T, P, pressure = dbd.get_CTD_sync("m_pressure")
 
         
@@ -293,26 +293,26 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
         print("Throw an error when cache file is missing...")
         # read in a sbd and tbd file. Only the sbd's cac file is in cac_missing.
         with self.assertRaises(dbdreader.DbdError) as e:
-            dbd = dbdreader.MultiDBD(pattern="../data/unit_887-2021-321-3-0.?bd",
-                                     cacheDir='../data/cac_missing')
+            dbd = dbdreader.MultiDBD(pattern="../dbdreader/data/unit_887-2021-321-3-0.?bd",
+                                     cacheDir='../dbdreader/data/cac_missing')
         
 
     def test_open_file_with_pattern_str_as_first_argument(self):
         print("Open multidbd with just a string as first argument. Should be interpreted as a pattern")
-        dbd = dbdreader.MultiDBD("../data/amadeus-2014-*.*bd")
+        dbd = dbdreader.MultiDBD("../dbdreader/data/amadeus-2014-*.*bd")
 
     def test_open_file_with_pattern_str_as_first_argument_and_pattern(self):
         print("Open multidbd with just a string as first argument and a pattern, which should fail.")
         with self.assertRaises(dbdreader.DbdError) as e:
-            dbd = dbdreader.MultiDBD("../data/amadeus-2014-*.*bd", pattern="../data/amadeus-2014-204-05-000.?bd")
+            dbd = dbdreader.MultiDBD("../dbdreader/data/amadeus-2014-*.*bd", pattern="../dbdreader/data/amadeus-2014-204-05-000.?bd")
 
     def test_opening_empty_file(self):
         print("Ignore empty files and files with wrong encodings...")
-        dbd = dbdreader.MultiDBD(pattern = "../data/*-2014-204-05-000.dbd")
+        dbd = dbdreader.MultiDBD(pattern = "../dbdreader/data/*-2014-204-05-000.dbd")
 
     def test_opening_capitalised_files(self):
         print("Allow opening of files with capitalised extensions.")
-        dbd = dbdreader.MultiDBD(pattern = "../data/amadeus-2014-203-00-000.[ST]BD")
+        dbd = dbdreader.MultiDBD(pattern = "../dbdreader/data/amadeus-2014-203-00-000.[ST]BD")
 
     def test_problem_causing_segfault(self):
         # this test caused a segfault as a result of a bug introduced in commit eeb64d8e8c20345dafcacebf074f098fa945fd46
@@ -325,21 +325,21 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
     def test_missing_cache_file_data_feature(self):
         print("Throw an error when cache file is missing, and check who is missing.")
         try:
-            dbd = dbdreader.MultiDBD("../data/unit_887-2021-321-3-0.?bd")
+            dbd = dbdreader.MultiDBD("../dbdreader/data/unit_887-2021-321-3-0.?bd")
         except dbdreader.DbdError as e:
             data = e.data
-            assert data.missing_cache_files['c4ec741e'][0] =="../data/unit_887-2021-321-3-0.tbd"
+            assert data.missing_cache_files['c4ec741e'][0] =="../dbdreader/data/unit_887-2021-321-3-0.tbd"
 
     def test_get_sync_on_parameter_without_values(self):
         print("Reads in a parameter to sync that has no values.")
-        dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.dbd")
+        dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.dbd")
         _, _, x = dbd.get_sync("m_depth", "u_dbd_sensor_list_xmit_control")
         # x has a 2.0 as first value, but then all nans.
         assert np.all(np.isfinite(x[1:])==False) and x[0]==2.
 
     def test_get_CTD_sync_on_parameter_without_values(self):
         print("Reads in a parameter to get_CTD_sync that has no values; Assert error.")
-        dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.dbd",
+        dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.dbd",
                                  complement_files=True)
         try:
             x = dbd.get_CTD_sync("m_depth", "u_dbd_sensor_list_xmit_control")
@@ -348,7 +348,7 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
 
     def test_get_CTD_sync_removes_empty_timestamps(self):
         print("Reads data using get_CTD_sync and empty timestamps should be removed.")
-        dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.dbd",
+        dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.dbd",
                                  complement_files=True)
         tctd, T, C, P = dbd.get_CTD_sync()
         t, tctdp = dbd.get("sci_ctd41cp_timestamp")
@@ -395,13 +395,13 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
 
     def test_get_reading_limited_values(self):
         print("Test whether we can read in only 10 depth values when reading multiple files.")
-        dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.dbd")
+        dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.dbd")
         t0, v0 = dbd.get("m_depth", max_values_to_read=10)
         assert len(t0)==len(v0) and len(t0)==10
 
     def test_get_reading_limited_values_mixed_files(self):
         print("Test whether we can read in only 10 depth values when reading multiple dbd and ebd files.")
-        dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.?bd")
+        dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.?bd")
         t0, v0 = dbd.get("sci_water_pressure", max_values_to_read=10)
         assert len(t0)==len(v0) and len(t0)==10
 
@@ -409,7 +409,7 @@ class Dbdreader_MultiDBD_test(unittest.TestCase):
     def test_get_reading_limited_values_requesting_multiple_parameters(self):
         print("Test whether reading a limited number of values from multiple values fails.")
         with self.assertRaises(ValueError):
-            dbd = dbdreader.MultiDBD("../data/sebastian-2014-204-05-00?.dbd")
+            dbd = dbdreader.MultiDBD("../dbdreader/data/sebastian-2014-204-05-00?.dbd")
             result = dbd.get("m_depth", "m_pitch", max_values_to_read=10)
 
         
@@ -434,22 +434,22 @@ class DBDPatternSelect_test(unittest.TestCase):
     def test_select_from_pattern(self):
         print("select from pattern")
         PS=dbdreader.DBDPatternSelect(date_format="%d %m %Y %H:%M")
-        fns=PS.select(pattern="../data/ama*.sbd",from_date="24 7 2014 00:00")
+        fns=PS.select(pattern="../dbdreader/data/ama*.sbd",from_date="24 7 2014 00:00")
         fns.sort()
-        self.assertEqual(fns[0],"../data/amadeus-2014-204-05-000.sbd")
-        fns=PS.select(pattern="../data/ama*.sbd",from_date="24 7 2014 18:00")
+        self.assertEqual(fns[0],"../dbdreader/data/amadeus-2014-204-05-000.sbd")
+        fns=PS.select(pattern="../dbdreader/data/ama*.sbd",from_date="24 7 2014 18:00")
         fns.sort()
-        self.assertEqual(fns[0],"../data/amadeus-2014-204-05-001.sbd")
-        fns=PS.select(pattern="../data/ama*.sbd",until_date="24 7 2014 18:00")
+        self.assertEqual(fns[0],"../dbdreader/data/amadeus-2014-204-05-001.sbd")
+        fns=PS.select(pattern="../dbdreader/data/ama*.sbd",until_date="24 7 2014 18:00")
         self.assertEqual(len(fns),1)
 
     def test_select_from_pattern_non_standard_cache_dir(self):
         print("select from pattern non standard cache dir")
         dbdreader.DBDPatternSelect.cache.clear()
-        PS=dbdreader.DBDPatternSelect(date_format="%d %m %Y %H:%M", cacheDir='../data/cac')
-        fns=PS.select(pattern="../data/ama*.sbd",from_date="24 7 2014 00:00")
+        PS=dbdreader.DBDPatternSelect(date_format="%d %m %Y %H:%M", cacheDir='../dbdreader/data/cac')
+        fns=PS.select(pattern="../dbdreader/data/ama*.sbd",from_date="24 7 2014 00:00")
         fns.sort()
-        self.assertEqual(fns[0],"../data/amadeus-2014-204-05-000.sbd")
+        self.assertEqual(fns[0],"../dbdreader/data/amadeus-2014-204-05-000.sbd")
 
 
 class DBDList_test(unittest.TestCase):

{dbdreader-0.5.5 → dbdreader-0.5.7}/tests/test_decompress.py

@@ -21,7 +21,7 @@ from dbdreader.decompress import *
 
 @fixture
 def load_verification_data():
-    filename_verify = '../data/01600000.mlg'
+    filename_verify = '../dbdreader/data/01600000.mlg'
     with open(filename_verify, 'r') as fp:
         data = fp.read()
     return data
@@ -31,7 +31,7 @@ def load_verification_data():
 #
 def test_read_file(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     data = b''
     with Decompressor(filename) as d:
         for block in d.decompressed_blocks():
@@ -43,7 +43,7 @@ def test_read_file(load_verification_data):
 #
 def test_read_file_in_memory(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     with Decompressor(filename) as d:
         data = d.decompress()
     assert data.decode('ascii') == verification_data
@@ -52,7 +52,7 @@ def test_read_file_in_memory(load_verification_data):
 # 
 #
 def test_read_file_one_block_only():
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     with Decompressor(filename) as d:
         blocks = [block for block in d.decompressed_blocks(n=1)]
     assert len(blocks) == 1
@@ -62,7 +62,7 @@ def test_read_file_one_block_only():
 # explicitly
 def test_read_file_explicit_file_opener(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     data = b''
     d = Decompressor()
     with open(filename, 'rb') as fp:
@@ -75,7 +75,7 @@ def test_read_file_explicit_file_opener(load_verification_data):
 # explicitly
 def test_read_file_in_memory_explicit_file_opener(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     d = Decompressor()
     with open(filename, 'rb') as fp:
         data = d.decompress(fp=fp)
@@ -83,7 +83,7 @@ def test_read_file_in_memory_explicit_file_opener(load_verification_data):
 
 # using the convenience function decompress_file
 def test_convenience_function():
-    filename = '../data/01600000.dcd'
+    filename = '../dbdreader/data/01600000.dcd'
     filename_decompressed = filename.replace('dcd','dbd')
     try:
         os.unlink(filename_decompressed)
@@ -104,24 +104,24 @@ def test_extension_generator():
     fd = FileDecompressor()
     s = fd._generate_filename_for_output('01600000.dcd')
     assert s == '01600000.dbd'
-    infiles = ['../data/01600000.dcd',
-               '../data/01600000.ecd',
-               '../data/01600000.mcd',
-               '../data/01600000.mcg',
-               '../data/01600000.ncd',
-               '../data/01600000.ncg',
-               '../data/01600000.scd',
-               '../data/01600000.tcd',
-               '../data/00aa00aa.ccc']
-    outfiles = ['../data/01600000.dbd',
-               '../data/01600000.ebd',
-               '../data/01600000.mbd',
-               '../data/01600000.mlg',
-               '../data/01600000.nbd',
-               '../data/01600000.nlg',
-               '../data/01600000.sbd',
-                '../data/01600000.tbd',
-                '../data/00aa00aa.cac']
+    infiles = ['../dbdreader/data/01600000.dcd',
+               '../dbdreader/data/01600000.ecd',
+               '../dbdreader/data/01600000.mcd',
+               '../dbdreader/data/01600000.mcg',
+               '../dbdreader/data/01600000.ncd',
+               '../dbdreader/data/01600000.ncg',
+               '../dbdreader/data/01600000.scd',
+               '../dbdreader/data/01600000.tcd',
+               '../dbdreader/data/00aa00aa.ccc']
+    outfiles = ['../dbdreader/data/01600000.dbd',
+               '../dbdreader/data/01600000.ebd',
+               '../dbdreader/data/01600000.mbd',
+               '../dbdreader/data/01600000.mlg',
+               '../dbdreader/data/01600000.nbd',
+               '../dbdreader/data/01600000.nlg',
+               '../dbdreader/data/01600000.sbd',
+                '../dbdreader/data/01600000.tbd',
+                '../dbdreader/data/00aa00aa.cac']
     for a, b in zip(infiles, outfiles):
         assert fd._generate_filename_for_output(a) == b
 
@@ -137,9 +137,9 @@ def test_extension_generator_with_invalid_extension():
 # uncompressed file
 #
 def test_read_ccc_file():
-    with open('../data/cac/06a36d4e.cac', 'r') as fp:
+    with open('../dbdreader/data/cac/06a36d4e.cac', 'r') as fp:
         verification_data = fp.read()
-    filename = '../data/cac/06a36d4e.ccc'
+    filename = '../dbdreader/data/cac/06a36d4e.ccc'
     data = b''
     with Decompressor(filename) as d:
         for block in d.decompressed_blocks():
@@ -149,7 +149,7 @@ def test_read_ccc_file():
 # Using the CompressedFile object to read a compressed text file
 def test_CompressedFile(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     lines = []
     with CompressedFile(filename) as fd:
         while True:
@@ -163,7 +163,7 @@ def test_CompressedFile(load_verification_data):
 # Using the CompressedFile object to read a compressed text file, using readlines() method.
 def test_CompressedFileReadlines(load_verification_data):
     verification_data = load_verification_data
-    filename = '../data/01600000.mcg'
+    filename = '../dbdreader/data/01600000.mcg'
     with CompressedFile(filename) as fd:
         lines = fd.readlines()
         data = b"".join(lines)
@@ -173,18 +173,18 @@ def test_CompressedFileReadlines(load_verification_data):
     
 # Test reading of data/01600001.dcd and check it is identical to data/01600001.dbd
 def test_read_compressed_file_C_code():
-    compressed_filename = '../data/01600001.dcd'
-    regular_filename = '../data/01600001.dbd'
-    compressed_dbd = dbdreader.DBD(compressed_filename, cacheDir='../data/cac')
-    regular_dbd = dbdreader.DBD(regular_filename, cacheDir='../data/cac')
+    compressed_filename = '../dbdreader/data/01600001.dcd'
+    regular_filename = '../dbdreader/data/01600001.dbd'
+    compressed_dbd = dbdreader.DBD(compressed_filename, cacheDir='../dbdreader/data/cac')
+    regular_dbd = dbdreader.DBD(regular_filename, cacheDir='../dbdreader/data/cac')
     compressed_data = compressed_dbd.get("m_depth")
     regular_data = regular_dbd.get("m_depth")
     assert np.all(compressed_data[0]==regular_data[0]) and np.all(compressed_data[1]==regular_data[1])
     
 # Test reading of data/0160000?.dcd MultiDBD
 def test_read_compressed_files_C_code():
-    pattern = '../data/0160000?.dcd'
-    dbd = dbdreader.MultiDBD(pattern, cacheDir='../data/cac')
+    pattern = '../dbdreader/data/0160000?.dcd'
+    dbd = dbdreader.MultiDBD(pattern, cacheDir='../dbdreader/data/cac')
     t, d = dbd.get("m_depth")
     assert t.ptp() == pytest.approx(2511.95, 0.01)
 
@@ -192,31 +192,31 @@ def test_read_compressed_files_C_code():
 # Test missing cac file for single dbd_label
 def test_missing_cac_file_for_single_compressed_file():
     try:
-        os.unlink('../data/cac/daad1b20.cac')
+        os.unlink('../dbdreader/data/cac/daad1b20.cac')
     except:
         pass
     
     with pytest.raises(dbdreader.DbdError):
-        dbd = dbdreader.DBD('../data/01600000.ecd', cacheDir='../data/cac')
+        dbd = dbdreader.DBD('../dbdreader/data/01600000.ecd', cacheDir='../dbdreader/data/cac')
 
 # Test missing cac file being created from ccc file for MultiDBD
 def test_missing_cac_file_for_compressed_file_multidbd():
     try:
-        os.unlink('../data/cac/daad1b20.cac')
+        os.unlink('../dbdreader/data/cac/daad1b20.cac')
     except:
         pass
     
-    dbd = dbdreader.MultiDBD('../data/0160000?.ecd', cacheDir='../data/cac')
-    assert os.path.exists('../data/cac/daad1b20.cac')
+    dbd = dbdreader.MultiDBD('../dbdreader/data/0160000?.ecd', cacheDir='../dbdreader/data/cac')
+    assert os.path.exists('../dbdreader/data/cac/daad1b20.cac')
 
 
 # Test we can open compressed flight and science files.
 def test_open_flight_and_science_files():
-    dbd = dbdreader.MultiDBD('../data/0160000?.?cd', cacheDir='../data/cac')
+    dbd = dbdreader.MultiDBD('../dbdreader/data/0160000?.?cd', cacheDir='../dbdreader/data/cac')
 
 # Test we can open compressed flight and science files.
 def test_open_flight_and_science_files_finding_complement_files():
-    dbd = dbdreader.MultiDBD('../data/0160000?.dcd', complement_files=True, cacheDir='../data/cac')
+    dbd = dbdreader.MultiDBD('../dbdreader/data/0160000?.dcd', complement_files=True, cacheDir='../dbdreader/data/cac')
 
     
 

dbdreader-0.5.5/dbdreader/__init__.py

@@ -1,5 +0,0 @@
-__version__="0.5.5"
-
-__all__ = ['dbdreader']
-
-from .dbdreader import *

dbdreader-0.5.5/dbdreader.egg-info/SOURCES.txt

@@ -1,73 +0,0 @@
-COPYING
-COPYRIGHT
-INSTALL.rst
-LICENSE
-MANIFEST.in
-README.rst
-requirements.txt
-setup.py
-data/01600000.dcd
-data/01600000.ebd
-data/01600000.ecd
-data/01600000.mcg
-data/01600000.mlg
-data/01600001.dbd
-data/01600001.dcd
-data/01600001.ebd
-data/01600001.ecd
-data/amadeus-2014-204-05-000.dbd
-data/amadeus-2014-204-05-000.ebd
-data/amadeus-2014-204-05-000.sbd
-data/amadeus-2014-204-05-000.tbd
-data/amadeus-2014-204-05-001.sbd
-data/amadeus-2014-204-05-001.tbd
-data/amadeus-2014-204-05-002.sbd
-data/amadeus-2014-204-05-002.tbd
-data/ammonite-2008-028-01-000.mbd
-data/electa-2023-143-00-050.sbd
-data/electa-2023-143-00-050.tbd
-data/empty-2014-204-05-000.dbd
-data/invalid_encoding-2014-204-05-000.dbd
-data/sebastian-2014-204-05-000.dbd
-data/sebastian-2014-204-05-000.ebd
-data/sebastian-2014-204-05-001.dbd
-data/sebastian-2014-204-05-001.ebd
-data/unit_887-2021-321-3-0.sbd
-data/unit_887-2021-321-3-0.tbd
-data/cac/06a36d4e.cac
-data/cac/06a36d4e.ccc
-data/cac/093bd5ed.cac
-data/cac/0f682cb2.cac
-data/cac/468fd1be.cac
-data/cac/61b1780f.cac
-data/cac/813b137d.cac
-data/cac/92610b65.cac
-data/cac/c4ec741e.cac
-data/cac/d6f44165.cac
-data/cac/daad1b20.cac
-data/cac/daad1b20.ccc
-data/cac/dc76ebd5.cac
-data/cac_missing/d6f44165.cac
-dbdreader/__init__.py
-dbdreader/dbdreader.py
-dbdreader/decompress.py
-dbdreader/scripts.py
-dbdreader.egg-info/PKG-INFO
-dbdreader.egg-info/SOURCES.txt
-dbdreader.egg-info/dependency_links.txt
-dbdreader.egg-info/entry_points.txt
-dbdreader.egg-info/requires.txt
-dbdreader.egg-info/top_level.txt
-examples/read_multiple_dbd_files.py
-examples/read_single_dbd_file.py
-extension/dbdreader.c
-extension/decompress.c
-extension/py_dbdreader.c
-extension/include/dbdreader.h
-extension/include/decompress.h
-lz4/lz4.c
-lz4/include/lz4.h
-tests/dbd_test.py
-tests/dbd_test_2.py
-tests/dbdreader_test.py
-tests/test_decompress.py