Merge pull request #1695 from obspy/various

Fixes various small issues, typos, UserWarnings, deprecations, etc.

obspy/core/tests/test_response.py

@@ -161,7 +161,7 @@ def test_segfault_after_error_handling(self):
         As long as it does not segfault the test is doing alright.
         """
         filename = os.path.join(self.data_dir,
-                                "TM.SKLT..BHZ_faulty_response.xml")
+                                "TM.SKLT.__.BHZ_faulty_response.xml")
         inv = read_inventory(filename)
 
         t_samp = 0.05
@@ -195,7 +195,7 @@ def test_response_list_stage(self):
 
         sampling_rate = 40.0
         t_samp = 1.0 / sampling_rate
-        nfft = 100.0
+        nfft = 100
 
         cpx_response, freq = inv[0][0][0].response.get_evalresp_response(
             t_samp=t_samp, nfft=nfft, output="VEL", start_stage=None,
@@ -236,7 +236,7 @@ def test_response_list_raises_error_if_out_of_range(self):
         # list.
         sampling_rate = 45.0
         t_samp = 1.0 / sampling_rate
-        nfft = 100.0
+        nfft = 100
 
         with self.assertRaises(ValueError) as e:
             inv[0][0][0].response.get_evalresp_response(

obspy/core/tests/test_trace.py

@@ -1333,13 +1333,19 @@ def test_taper_onesided(self):
         """
         data = np.ones(11)
         tr = Trace(data=data)
-        tr.taper(max_percentage=None, side="left")
+        # overlong taper - raises UserWarning - ignoring
+        with warnings.catch_warnings(record=True):
+            warnings.simplefilter("ignore", UserWarning)
+            tr.taper(max_percentage=None, side="left")
         self.assertTrue(tr.data[:5].sum() < 5.)
         self.assertEqual(tr.data[6:].sum(), 5.)
 
         data = np.ones(11)
         tr = Trace(data=data)
-        tr.taper(max_percentage=None, side="right")
+        # overlong taper - raises UserWarning - ignoring
+        with warnings.catch_warnings(record=True):
+            warnings.simplefilter("ignore", UserWarning)
+            tr.taper(max_percentage=None, side="right")
         self.assertEqual(tr.data[:5].sum(), 5.)
         self.assertTrue(tr.data[6:].sum() < 5.)
 
@@ -1349,8 +1355,11 @@ def test_taper_length(self):
 
         data = np.ones(npts)
         tr = Trace(data=data, header={'sampling': 1.})
-        # test an overlong taper request, should still work
-        tr.taper(max_percentage=0.7, max_length=int(npts / 2) + 1)
+        # test an overlong taper request, still works but raises UserWarning
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always", UserWarning)
+            tr.taper(max_percentage=0.7, max_length=int(npts / 2) + 1)
+        self.assertEqual(w[0].category, UserWarning)
 
         data = np.ones(npts)
         tr = Trace(data=data, header={'sampling': 1.})
@@ -1724,7 +1733,10 @@ def test_remove_polynomial_response(self):
         filename = os.path.join(path, 'data', 'stationxml_BK.CMB.__.LKS.xml')
         inv = read_inventory(filename, format='StationXML')
         tr.attach_response(inv)
-        tr.remove_response()
+        # raises UserWarning: Stage gain not defined - ignoring
+        with warnings.catch_warnings(record=True):
+            warnings.simplefilter("ignore", UserWarning)
+            tr.remove_response()
 
     def test_processing_info_remove_response_and_sensitivity(self):
         """

obspy/imaging/tests/test_scan.py

@@ -10,6 +10,7 @@
 import shutil
 import unittest
 from os.path import abspath, dirname, join, pardir
+import warnings
 
 from obspy import read
 from obspy.core.util.base import NamedTemporaryFile
@@ -51,7 +52,7 @@ def test_scan_main_method(self):
                 shutil.copy(filename, os.curdir)
 
             with ImageComparison(self.path, 'scan.png') as ic:
-                obspy_scan([os.curdir] + ['--output', ic.name, '--quiet'])
+                obspy_scan([os.curdir] + ['--output', ic.name])
 
     def test_scan_function_and_scanner_class(self):
         """
@@ -107,15 +108,17 @@ def test_scan_save_load_npz(self):
             for filename in self.all_files:
                 shutil.copy(filename, os.curdir)
 
-            obspy_scan([os.curdir, '--write', 'scan.npz', '--quiet'])
+            obspy_scan([os.curdir, '--write', 'scan.npz'])
             scanner.parse(os.curdir)
             scanner.save_npz('scanner.npz')
             scanner = Scanner()
-            scanner.load_npz('scanner.npz')
+            # version string of '0.0.0+archive' raises UserWarning - ignore
+            with warnings.catch_warnings(record=True):
+                warnings.simplefilter('ignore', UserWarning)
+                scanner.load_npz('scanner.npz')
 
             with ImageComparison(self.path, 'scan.png') as ic:
-                obspy_scan(['--load', 'scan.npz', '--output', ic.name,
-                            '--quiet'])
+                obspy_scan(['--load', 'scan.npz', '--output', ic.name])
         with ImageComparison(self.path, 'scan.png') as ic:
             scanner.plot(ic.name)
 
@@ -133,8 +136,7 @@ def test_scan_times(self):
                            ['--start-time', '2004-01-01'] +
                            ['--end-time', '2004-12-31'] +
                            ['--event-time', '2004-03-14T15:09:26'] +
-                           ['--event-time', '2004-02-07T18:28:18'] +
-                           ['--quiet'])
+                           ['--event-time', '2004-02-07T18:28:18'])
 
     def test_multiple_sampling_rates(self):
         """

obspy/io/mseed/tests/test_mseed_reading_and_writing.py

@@ -136,7 +136,11 @@ def test_read_and_write_traces(self):
                         temp_file = tf.name
                         _write_mseed(this_stream, temp_file, encoding=encoding,
                                      byteorder=byteorder, reclen=reclen)
-                        new_stream = _read_mseed(temp_file)
+                        # some files raise "UserWarning: Record contains a
+                        # fractional seconds" - ignore
+                        with warnings.catch_warnings(record=True):
+                            warnings.simplefilter('ignore', UserWarning)
+                            new_stream = _read_mseed(temp_file)
                     # Assert the new stream still has the chosen attributes.
                     # This should mean that writing as well as reading them
                     # works.
@@ -733,7 +737,7 @@ def test_all_data_types_and_endians_in_multiple_files(self):
         of the read method. Only the data part is verified.
         """
         file = os.path.join(self.path, "data",
-                            "BW.BGLD.__.EHE.D.2008.001.first_record")
+                            "BW.BGLD.__.EHE.D.2008.001.second_record")
         # Read the data and copy them
         st = read(file)
         data_copy = st[0].data.copy()
@@ -1313,8 +1317,12 @@ def test_libmseed_test_cases(self):
         """
         def assert_valid(filename, reference, test_type):
             if test_type == "data":
+                # some files raise "UserWarning: Record contains a fractional
+                # seconds" - ignore
+                with warnings.catch_warnings(record=True):
+                    warnings.simplefilter('ignore', UserWarning)
+                    st = read(filename)
 
-                st = read(filename)
                 self.assertEqual(len(st), 1, msg=filename)
                 tr = st[0]
 

obspy/io/mseed/tests/test_mseed_util.py

@@ -1121,19 +1121,20 @@ def test_set_flags_in_fixed_header_with_blockette_100(self):
             tf.close()
             shutil.copy(os.path.join(self.path, 'data', 'test.mseed'),
                         tf.name)
-            # No flags set.
-            flags = util.get_timing_and_data_quality(tf.name)
-            self.assertEqual(flags["data_quality_flags"], [0] * 8)
-            # Set flags.
+            # No data quality flags set.
+            flags = util.get_flags(tf.name)['data_quality_flags_counts']
+            self.assertEqual(max(flags.values()), 0)
+            # Set  data quality flags.
             util.set_flags_in_fixed_headers(tf.name, {
                 "NL.HGN.00.BHZ": {"data_qual_flags": {
                     'glitches_detected': True,
                     'time_tag_questionable': True}}})
             # Flags are set now.
-            flags = util.get_timing_and_data_quality(tf.name)
+            flags = util.get_flags(tf.name)['data_quality_flags_counts']
             # 2 because file contains two records.
-            self.assertEqual(flags["data_quality_flags"],
-                             [0, 0, 0, 2, 0, 0, 0, 2])
+            self.assertEqual(sum(flags.values()), 4)
+            self.assertEqual(flags['glitches'], 2)
+            self.assertEqual(flags['suspect_time_tag'], 2)
 
     def _check_values(self, file_bfr, trace_id, record_numbers, expected_bytes,
                       reclen):

obspy/io/nordic/core.py

@@ -287,8 +287,12 @@ def _readheader(f):
     ksta = Comment(text='Number of stations=' + topline[49:51].strip())
     new_event.origins[0].comments.append(ksta)
     if _float_conv(topline[51:55]) is not None:
-        new_event.origins[0].time_errors['Time_Residual_RMS'] = \
-            _float_conv(topline[51:55])
+        # raises "UserWarning: Setting attribute "Time_Residual_RMS" which is
+        # not a default attribute"
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', UserWarning)
+            new_event.origins[0].time_errors['Time_Residual_RMS'] = \
+                _float_conv(topline[51:55])
     # Read in magnitudes if they are there.
     for index in [59, 67, 75]:
         if not topline[index].isspace():
@@ -488,11 +492,11 @@ def _read_picks(f, new_event):
     pickline = []
     # Set a default, ignored later unless overwritten
     snr = None
-    for lineno, line in enumerate(f):
+    for _lineno, line in enumerate(f):
         if line[79] == '7':
             header = line
             break
-    for lineno, line in enumerate(f):
+    for _lineno, line in enumerate(f):
         if len(line.rstrip('\n').rstrip('\r')) in [80, 79] and \
            line[79] in ' 4\n':
             pickline += [line]
@@ -756,7 +760,7 @@ def write_select(catalog, filename, userid='OBSP', evtype='L',
          way as the events in the catalog.
     """
     if not wavefiles:
-        wavefiles = ['DUMMY' for i in range(len(catalog))]
+        wavefiles = ['DUMMY' for _i in range(len(catalog))]
     with open(filename, 'w') as fout:
         for event, wavfile in zip(catalog, wavefiles):
             select = io.StringIO()