Merge branch 'develop' into documentation

pyerrors/input/json.py

@@ -203,20 +203,18 @@ def dump_to_json(ol, fname, description='', indent=1, gz=True):
     fp.close()
 
 
-def load_json(fname, verbose=True, gz=True, full_output=False):
+def import_json_string(json_string, verbose=True, full_output=False):
-    """Import a list of Obs or structures containing Obs from a .json.gz file.
+    """Reconstruct a list of Obs or structures containing Obs from a json string.
 
     The following structures are supported: Obs, list, numpy.ndarray
     If the list contains only one element, it is unpacked from the list.
 
     Parameters
     ----------
-    fname : str
+    json_string : str
-        Filename of the input file.
+        json string containing the data.
     verbose : bool
         Print additional information that was written to the file.
-    gz : bool
-        If True, assumes that data is gzipped. If False, assumes JSON file.
     full_output : bool
         If True, a dict containing auxiliary information and the data is returned.
         If False, only the data is returned.
@@ -281,35 +279,22 @@ def load_json(fname, verbose=True, gz=True, full_output=False):
             ret[-1].tag = taglist[i]
         return np.reshape(ret, layout)
 
-    if not fname.endswith('.json') and not fname.endswith('.gz'):
+    prog = json_string.get('program', '')
-        fname += '.json'
+    version = json_string.get('version', '')
-    if gz:
+    who = json_string.get('who', '')
-        if not fname.endswith('.gz'):
+    date = json_string.get('date', '')
-            fname += '.gz'
+    host = json_string.get('host', '')
-        with gzip.open(fname, 'r') as fin:
-            d = json.loads(fin.read().decode('utf-8'))
-    else:
-        if fname.endswith('.gz'):
-            warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
-        with open(fname, 'r', encoding='utf-8') as fin:
-            d = json.loads(fin.read())
-
-    prog = d.get('program', '')
-    version = d.get('version', '')
-    who = d.get('who', '')
-    date = d.get('date', '')
-    host = d.get('host', '')
     if prog and verbose:
         print('Data has been written using %s.' % (prog))
     if version and verbose:
         print('Format version %s' % (version))
     if np.any([who, date, host] and verbose):
         print('Written by %s on %s on host %s' % (who, date, host))
-    description = d.get('description', '')
+    description = json_string.get('description', '')
     if description and verbose:
         print()
         print('Description: ', description)
-    obsdata = d['obsdata']
+    obsdata = json_string['obsdata']
     ol = []
     for io in obsdata:
         if io['type'] == 'Obs':
@@ -335,3 +320,37 @@ def load_json(fname, verbose=True, gz=True, full_output=False):
             ol = ol[0]
 
         return ol
+
+
+def load_json(fname, verbose=True, gz=True, full_output=False):
+    """Import a list of Obs or structures containing Obs from a .json.gz file.
+
+    The following structures are supported: Obs, list, numpy.ndarray
+    If the list contains only one element, it is unpacked from the list.
+
+    Parameters
+    ----------
+    fname : str
+        Filename of the input file.
+    verbose : bool
+        Print additional information that was written to the file.
+    gz : bool
+        If True, assumes that data is gzipped. If False, assumes JSON file.
+    full_output : bool
+        If True, a dict containing auxiliary information and the data is returned.
+        If False, only the data is returned.
+    """
+    if not fname.endswith('.json') and not fname.endswith('.gz'):
+        fname += '.json'
+    if gz:
+        if not fname.endswith('.gz'):
+            fname += '.gz'
+        with gzip.open(fname, 'r') as fin:
+            d = json.loads(fin.read().decode('utf-8'))
+    else:
+        if fname.endswith('.gz'):
+            warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
+        with open(fname, 'r', encoding='utf-8') as fin:
+            d = json.loads(fin.read())
+
+    return import_json_string(d, verbose, full_output)

tests/covobs_test.py

@@ -11,6 +11,7 @@ def test_covobs():
     name = 'Covariance'
     co = pe.cov_Obs(val, cov, name)
     co.gamma_method()
+    co.details()
     assert (co.dvalue == np.sqrt(cov))
     assert (co.value == val)
 

tests/io_test.py

@@ -41,6 +41,9 @@ def test_jsonio():
 
     os.remove(fname + '.json.gz')
 
+    for o, r in zip(ol, rl):
+        assert np.all(o == r)
+
     for i in range(len(rl)):
         if isinstance(ol[i], pe.Obs):
             o = ol[i] - rl[i]
@@ -57,6 +60,9 @@ def test_jsonio():
 
     rl = jsonio.load_json(fname, gz=False, full_output=True)
 
-    assert(description == rl['description'])
-
     os.remove(fname + '.json')
+
+    for o, r in zip(ol, rl['obsdata']):
+        assert np.all(o == r)
+
+    assert(description == rl['description'])

tests/obs_test.py

@@ -46,8 +46,9 @@ def test_Obs_exceptions():
         my_obs.gamma_method(tau_exp=2.3)
     my_obs.gamma_method()
     my_obs.details()
+    my_obs.plot_rep_dist()
 
-    my_obs += pe.Obs([np.random.rand(6)], ['name2|r1'])
+    my_obs += pe.Obs([np.random.rand(6)], ['name2|r1'], idl=[[1, 3, 4, 5, 6, 7]])
     my_obs += pe.Obs([np.random.rand(6)], ['name2|r2'])
     my_obs.gamma_method()
     my_obs.details()
@@ -475,6 +476,7 @@ def test_irregular_error_propagation():
                 pe.Obs([np.random.rand(6)], ['t'], idl=[[4, 18, 27, 29, 57, 80]]),
                 pe.Obs([np.random.rand(50)], ['t'], idl=[list(range(1, 26)) + list(range(50, 100, 2))])]
     for obs1 in obs_list:
+        obs1.details()
         for obs2 in obs_list:
             assert obs1 == (obs1 / obs2) * obs2
             assert obs1 == (obs1 * obs2) / obs2