Fixed merge conflict

.readthedocs.yml

@@ -21,4 +21,5 @@ formats: all
 python:
   version: 3.7
   install:
+    - requirements: docs/pre_requirements.txt
     - requirements: docs/requirements.txt

docs/conf.py

@@ -139,8 +139,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'passive-seismic.tex', 'passive-seismic Documentation',
-     'Fei Zhang, Rakib Hassan, etc', 'manual'),
+    (master_doc, 'passive-seismic.tex', 'HiPerSeis Documentation',
+     'F. Zhang, A. Medlin, R. Hassan, A. Gorbatov, B. Hejrani', 'manual'),
 ]
 
 
@@ -149,7 +149,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'passive-seismic', 'passive-seismic Documentation',
+    (master_doc, 'passive-seismic', 'HiPerSeis Documentation',
      [author], 1)
 ]
 
@@ -160,7 +160,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'passive-seismic', 'passive-seismic Documentation',
+    (master_doc, 'passive-seismic', 'HiPerSeis Documentation',
      author, 'passive-seismic', 'One line description of project.',
      'Miscellaneous'),
 ]
@@ -201,7 +201,10 @@
     # 'obspy.geodetics.base' ,'obspy.clients.fdsn.client',
     # 'obspy.core.inventory',
     # 'obspy.clients.nrl',
-    'osgeo'
+    'osgeo',
+    'mpi4py', 'mpi4py.MPI',
+    'rf',
+    'tqdm','tqdm.auto'
 ]
 
 import mock

docs/pre_requirements.txt

@@ -0,0 +1,3 @@
+numpy
+cython
+pyproj

docs/requirements.txt

@@ -1,28 +1,23 @@
 sphinx>=1.8
-numpy==1.16.4
+pytest>=4.2.0
+click
+scipy
 pandas
-#pyproj==1.9.6
+geopandas
 h5py
 pyasdf
 obspy==1.1.0
 obspyh5
 shapely
 geographiclib
-#cartopy
 pytables==3.5.2; sys_platform=="win32"
 tables==3.5.2; sys_platform!="win32"
-mpi4py
 psutil
-#geopandas
-pytest>=4.2.0
 joblib
-click
 netcdf4
 ujson
 deprecated
 pyyaml
 requests
-Cython  # On NCI, use module load
-#mpi4py # On NCI, use module load
-tqdm
-rf==0.8.0
+#cartopy install failure rf==0.8.0
+#mpi4py

docs/seismic.rst

@@ -1,5 +1,5 @@
 =================
-Package Seismic
+HiPerSeis Package: Seismic
 =================
 
 **Earth 3D Grid Model**
@@ -44,7 +44,7 @@ Package Seismic
 .. automodule:: seismic.xcorqc.correlator
 	:members:
 
-.. automodule:: seismic.xcorqc.notebooks.xcorr_station_clock_analysis
+.. automodule:: seismic.xcorqc.xcorr_station_clock_analysis
 	:members:
 
 

requirements.txt

@@ -9,7 +9,7 @@ obspy==1.1.0
 obspyh5
 shapely
 geographiclib
-cartopy
+#cartopy
 pytables==3.5.2; sys_platform=="win32"
 tables==3.5.2; sys_platform!="win32"
 mpi4py
@@ -18,7 +18,7 @@ psutil
 pytest>=4.2.0
 joblib
 click
-netcdf4
+netcdf4==1.4.0
 ujson
 deprecated
 pyyaml

seismic/receiver_fn/rf_3dmigrate.py

@@ -431,6 +431,9 @@ def main(rf_h5_file, output_folder, start_lat_lon, azimuth, dimensions, num_cell
         python rf_3dmigrate.py --start-lat-lon -17.4 132.9 --azimuth 80 --dimensions 1000 450 75 \
             --num-cells 100 45 375 /g/data/ha3/am7399/shared/OA-ZRT-R-cleaned.h5 /g/data/ha3/am7399/shared/OA_piercing
 
+    The script produces text data files which are converted to visualization using experimental
+    ipython notebook `sandbox/plot_3dmigrate.ipynb`.
+
     :param rf_h5_file: Source file containing receiver functions
     :type rf_h5_file: str or Path
     :param output_folder: Folder in which to output results

seismic/traveltime/sort_rays.py

@@ -11,6 +11,7 @@
 
 Developer:
     fei.zhang@ga.gov.au
+
 """
 from __future__ import print_function, absolute_import
 
@@ -78,8 +79,9 @@ def sort(input_file, sorted_file, residual_cutoff):
     """
     Sort and filter the arrivals based on the source and station block number.
     There are two stages of filtering:
-        - Filter based on the arrival time residual value: defult value for the cutoff is 5 for P-Wave, 10 for S-Wave
-        - Filter based on median of observed travel time.
+
+    - Filter based on the arrival time residual value: defult value for the cutoff is 5 for P-Wave, 10 for S-Wave
+    - Filter based on median of observed travel time.
 
     If there are multiple source and station block combinations, we keep the
     row corresponding to the median observed travel time (observed_tt).
@@ -156,11 +158,8 @@ def sort(input_file, sorted_file, residual_cutoff):
 def sort2(input_file, sorted_file, residual_cutoff):
     """
     Sort and filter the arrivals based on the source and station block number.
-    There are two stages of filtering:
-        - Filter based on the time residual
-        - Filter based on best Signal to Noise Ratio of the seismic wave:
-
     If there are multiple source and station block combinations, the row corresponding to the highest SNR value is kept.
+    (This function is for experiment only, not used.)
 
     :param input_file: output file from the gather stage (eg, outfile_P.csv)
     :param sorted_file: str, optionaloptional sorted output file path. Default: sorted.csv.