Merge branch 'release/0.1.1'

Former-commit-id: 697c300232b8937ec46e3f77c0a2d441a7f262a9 [formerly 60d052f]
Former-commit-id: 9bd12fbd74a60e24961494ed1c396187f7bacce4

.travis.yml

@@ -75,6 +75,7 @@ install:
         pytest
         pytest-pep8
         opencv
+        pyflakes=0.9.0
   - source activate test-environment
   # install packages not available via conda
   # - pip install -r requirements.txt

CHANGES.md

@@ -1,3 +1,27 @@
+## 0.1.1
+* Cope with events not always having time_errors in them in eventtoSfile;
+* Convert Quakeml depths from m to km;
+* Multiple little fixes to make Sfile conversion play well with GeoNet QuakeML files;
+* Add function to convert from obspy.core.inventory.station.Station to string format
+for Seisan STATION0.HYP file;
+* Merged feature branch - hypoDD into develop, this provides mappings for the
+hypoDD location program, including generation of dt.cc files;
+* Added tests for functions in catalog_to_dd;
+* Implemented unittest tests;
+* Changed name of EQcorrscan_plotting to plotting;
+* Added depreciation warnings;
+* Changed internal structure of pre-processing to aid long-term upkeep;
+* Added warnings in docs for template_gen relating to template generation from
+set length files;
+* Updated template_creation tutorial to use day-long data;
+* Renamed Sfile_util to sfile_util, and functions there-in: will warn about name changes;
+* Updated template plotting to include pick labels;
+* Updated template_creation tutorial to download S-picks as well as P-picks;
+* Update sfile_util to cope with many possible unfilled objects;
+* Added sac_util to convert from sac headers to useful event information - note,
+does not convert all things, just origin and pick times;
+* Added from_sac function to template_gen.
+
 ## 0.1.0
 * Implimented tests for synthetic generation and match-filter functions
 * Developed new tutorials that download from GeoNet and are much clearer

MANIFEST.in

@@ -18,5 +18,6 @@ prune eqcorrscan/doc/_build/latex
 prune eqcorrscan/plot
 prune eqcorrscan/detections
 prune eqcorrscan/grid
+prune eqcorrscan/tests/test_data
 # prune eqcorrscan/stack_templates
 # prune eqcorrscan/templates

README.md

@@ -69,7 +69,7 @@ Also within this package are:
 
 We are currently hovering around 9,000 lines of code (including doc-strings) - it is probably worth
 having a look at the docs to check what functions we have.  We plan to write a series of tutorials to be
-included on the EQcorrscan API to highlight key functions, currently our tutorial only shows
+included on the EQcorrscan API to highlight key functions, currently our tutorials only show
 how to do the core matched-filter detection.
 
 # Licence
@@ -108,3 +108,4 @@ will keep us all branching in the same way.
 * Thurber, C. H., Zeng, X., Thomas, A. M., & Audet, P. (2014). [Phase‐Weighted Stacking Applied to Low‐Frequency Earthquakes](http://www.bssaonline.org/content/early/2014/08/12/0120140077.abstract), __BSSA__, doi:10.1785/0120140077.
 * Frank, W. B., & Shapiro, N. M. (2014). [Automatic detection of low-frequency earthquakes (LFEs) based on a beamformed network response](http://gji.oxfordjournals.org/content/197/2/1215.short), __Geophysical Journal International__, 197(2), 1215-1223, doi:10.1093/gji/ggu058.
 * Rubinstein, J. L., & Ellsworth, W. L. (2010). [Precise estimation of repeating earthquake moment: Example from Parkfield, California](http://www.bssaonline.org/content/100/5A/1952.short), __BSSA__, doi:10.1785/0120100007
+fa66e06971b2dd1e4bf766

eqcorrscan/__init__.py

@@ -30,10 +30,82 @@
     You should have received a copy of the GNU General Public License
     along with EQcorrscan.  If not, see <http://www.gnu.org/licenses/>.
 """
-
+import sys
+import importlib
+import warnings
 
 __all__ = ['core', 'utils', 'par']
-__version__ = '0.1.0'
+
+__version__ = '0.1.1'
+
+# Cope with changes to name-space to remove most of the camel-case
+_import_map = {
+    "eqcorrscan.utils.catalogue2DD": "eqcorrscan.utils.catalog_to_dd",
+    "eqcorrscan.utils.EQcorrscan_plotting": "eqcorrscan.utils.plotting"
+}
+
+
+class EQcorrscanDeprecationWarning(UserWarning):
+    """
+    Force pop-up of warnings.
+    """
+    pass
+
+
+class EQcorrscanRestructureAndLoad(object):
+    """
+    Path finder and module loader for transitioning
+    """
+    def find_module(self, fullname, path=None):
+        # Compatibility with namespace paths.
+        if hasattr(path, "_path"):
+            path = path._path
+
+        if not path or not path[0].startswith(__path__[0]):
+            return None
+
+        for key in _import_map.keys():
+            if fullname.startswith(key):
+                break
+        else:
+            return None
+        return self
+
+    def load_module(self, name):
+        # Use cached modules.
+        if name in sys.modules:
+            return sys.modules[name]
+        # Otherwise check if the name is part of the import map.
+        elif name in _import_map:
+            new_name = _import_map[name]
+        else:
+            new_name = name
+            for old, new in _import_map.items():
+                if not new_name.startswith(old):
+                    continue
+                new_name = new_name.replace(old, new)
+                break
+            else:
+                return None
+
+        # Don't load again if already loaded.
+        if new_name in sys.modules:
+            module = sys.modules[new_name]
+        else:
+            module = importlib.import_module(new_name)
+
+        # Warn here as at this point the module has already been imported.
+        warnings.warn("Module '%s' is deprecated and will stop working "
+                      "with the next EQcorrscan version. Please import module "
+                      "'%s' instead." % (name, new_name),
+                      EQcorrscanDeprecationWarning)
+        sys.modules[new_name] = module
+        sys.modules[name] = module
+        return module
+
+
+sys.meta_path.append(EQcorrscanRestructureAndLoad())
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod(exclude_empty=True)

eqcorrscan/core/bright_lights.py

@@ -573,7 +573,7 @@ def brightness(stations, nodes, lags, stream, threshold, thresh_type,
     from obspy.core.event import EventDescription, CreationInfo, Comment
     import obspy.Stream
     import matplotlib.pyplot as plt
-    from eqcorrscan.utils import EQcorrscan_plotting as plotting
+    from eqcorrscan.utils import plotting
     # Check that we actually have the correct stations
     realstations = []
     for station in stations:
@@ -659,7 +659,7 @@ def brightness(stations, nodes, lags, stream, threshold, thresh_type,
         del energy, indeces
     else:
         print('Reading the temp files and computing network response')
-        node_splits = len(nodes) // num_cores
+        node_splits = int(len(nodes) // num_cores)
         indeces = [range(node_splits)]
         for i in range(1, num_cores - 1):
             indeces.append(range(node_splits * i, node_splits * (i + 1)))

eqcorrscan/core/match_filter.py

@@ -401,12 +401,12 @@ def match_filter(template_names, template_list, st, threshold,
     import matplotlib.pyplot as plt
     plt.ioff()
     import copy
-    from eqcorrscan.utils import EQcorrscan_plotting
+    from eqcorrscan.utils import plotting
     from eqcorrscan.utils import findpeaks
     from obspy import Trace
     import time
 
-    # Copy the stream here because we will fuck about with it
+    # Copy the stream here because we will muck about with it
     stream = st.copy()
     templates = copy.deepcopy(template_list)
     # Debug option to confirm that the channel names match those in the
@@ -517,19 +517,19 @@ def match_filter(template_names, template_list, st, threshold,
             cccsum_hist = cccsum_plot.copy()
             cccsum_hist = cccsum_hist.decimate(int(stream[0].stats.
                                                    sampling_rate / 10)).data
-            cccsum_plot = EQcorrscan_plotting.chunk_data(cccsum_plot, 10,
-                                                         'Maxabs').data
+            cccsum_plot = plotting.chunk_data(cccsum_plot, 10,
+                                              'Maxabs').data
             # Enforce same length
             stream_plot.data = stream_plot.data[0:len(cccsum_plot)]
             cccsum_plot = cccsum_plot[0:len(stream_plot.data)]
             cccsum_hist = cccsum_hist[0:len(stream_plot.data)]
-            EQcorrscan_plotting.triple_plot(cccsum_plot, cccsum_hist,
-                                            stream_plot, rawthresh, True,
-                                            plotdir + '/cccsum_plot_' +
-                                            template_names[i] + '_' +
-                                            stream[0].stats.starttime.
-                                            datetime.strftime('%Y-%m-%d') +
-                                            '.' + plot_format)
+            plotting.triple_plot(cccsum_plot, cccsum_hist,
+                                 stream_plot, rawthresh, True,
+                                 plotdir + '/cccsum_plot_' +
+                                 template_names[i] + '_' +
+                                 stream[0].stats.starttime.
+                                 datetime.strftime('%Y-%m-%d') +
+                                 '.' + plot_format)
             if debug >= 4:
                 print(' '.join(['Saved the cccsum to:', template_names[i],
                                 stream[0].stats.starttime.datetime.