Merge bf7d0c5 into 54970c7

.coveragerc

@@ -4,12 +4,13 @@ branch = True
 source =
     seismic
     convert_logs
+    legacy
 omit =
-    # omit everything in
-    # seismic/tasks/*
-    # omit these files
-    seismic/pslog.py
-    seismic/scripts/event.py
+    legacy/engdahl/*
+    seismic/inventory/legacy/*
+    seismic/receiver_fn/c_sippl_reference/*
+    # Exclude file that requires seiscomp3, not supported in testing runtime environment:
+    seismic/inventory/fdsnxml_convert.py
 concurrency = multiprocessing
 parallel = True
 
@@ -44,5 +45,5 @@ exclude_lines =
 
 ignore_errors = True
 
-# [html]
-# rectory = coverage_html_report
+[html]
+directory = coverage_html_report

.gitignore

@@ -77,3 +77,11 @@ seismic/xcorqc/*refdata.h5
 seismic/gps_corrections/**/*.png
 seismic/xcorqc/**/*.pdf
 seismic/xcorqc/**/*.png
+seismic/gps_corrections/**/*.csv
+seismic/inventory/INVENTORY_*.txt
+seismic/inventory/INVENTORY_*.xml
+seismic/receiver_fn/DATA/*
+seismic/xcorqc/**/*.nc
+seismic/xcorqc/**/*.cfg
+seismic/xcorqc/**/*.pbs
+**/junk.*

.travis.yml

@@ -2,17 +2,24 @@ dist: trusty
 sudo: required  # use VM instead of docker
 
 language: python
-virtualenv:
-  system_site_packages: true
+
 python:
 - '2.7'
+- '3.5'
+- '3.6'
+
+before_install:
+- pip install Cython --install-option="--no-cython-compile"
+- pip install pytest-cov
+- pip install coveralls
+
 install:
 - pip install -r requirements.txt
+- pip install -r tests/requirements.txt
+
 script:
-- pytest  tests/test_dum_success.py
-- pytest  -v tests/test_event.py
-- pytest  -v tests/test_config.py
-# - coverage run test/test_operations.py
+- pytest --cov
+
 after_success: coveralls
 
 #after_script: cd ~

README.rst

@@ -1,7 +1,7 @@
 HiPerSeis: High Performance Software Package for Seismology Data/Metadata Processing and Analysis
 =================================================================================================
 
-|Build Status|  |Documentation Status|
+|Build Status| |Coverage Status| |Documentation Status|
 
 
 Overview
@@ -36,19 +36,32 @@ System Requirements
 - Python 2.7
 - Python 3.5 or higher
 
+
 Setup Guide for Developers
 ==========================
 
 1. Install Python environment and dependency packages. See Wiki Pages: https://github.com/GeoscienceAustralia/hiperseis/wiki
 
-
 2. Obtain the source code from https://github.com/GeoscienceAustralia/hiperseis
 
 -  ``git clone https://github.com/GeoscienceAustralia/hiperseis.git``
 - ``cd hiperseis``
+- ``git submodule init``
+- ``git submodule update``
 
    - ``pip install -v --user -e .`` (into user's own home ~/.local/lib/python2.7/site-packages/)
-
+
+To subsequently update submodule folders to latest remote version, run:
+
+- ``git submodule update --remote``
+
+and if any updates are made, re-run the pip install step.
+
+If you are using the library without ``pip install``-ing it, then make sure the ``hiperseis`` folder
+is in your ``PYTHONPATH`` environment variable.  E.g. in bash shell, if ``~/dev/hiperseis`` is where
+``hiperseis`` was checked out:
+
+- ``export PYTHONPATH=~/dev/hiperseis:$PYTHONPATH``
 
 
 License
@@ -61,10 +74,9 @@ HiPerSeis is licensed under the GPL version 3
 .. |Build Status| image:: https://travis-ci.org/GeoscienceAustralia/hiperseis.svg?branch=develop
    :target: https://travis-ci.org/GeoscienceAustralia/hiperseis
 
-.. |Coverage Status| image:: https://coveralls.io/repos/github/GeoscienceAustralia/hiperseis/badge.svg?branch=develop
-   :target: https://coveralls.io/github/GeoscienceAustralia/hiperseis?branch=develop
+.. |Coverage Status| image:: https://coveralls.io/repos/github/GeoscienceAustralia/hiperseis/badge.svg
+   :target: https://coveralls.io/github/GeoscienceAustralia/hiperseis
 
 .. |Documentation Status| image:: https://readthedocs.org/projects/hiperseis/badge/?version=develop
    :target: http://hiperseis.readthedocs.io/en/develop/
 
-

legacy/cluster/cluster.py

@@ -29,9 +29,9 @@
 from obspy.geodetics import locations2degrees, gps2dist_azimuth
 from obspy.geodetics.base import WGS84_A as RADIUS
 from seismic.traveltime import pslog
-from seismic import mpiops
+from seismic.traveltime import mpiops
 import ellipcorr
-from seismic.inventory.parse_inventory import read_all_stations
+from seismic.inventory.legacy.parse_inventory import read_all_stations
 
 DPI = asin(1.0) / 90.0
 R2D = 90. / asin(1.)

requirements.txt

@@ -1,11 +1,18 @@
 sphinx>=1.8
+numpy>=1.14.2
+pytables; sys_platform=="win32"
+tables; sys_platform!="win32"
 obspy==1.1.0
 pyasdf
 #geopandas
-pytest
+pytest>=4.2.0
 joblib
-pytest
 click
 pandas
+h5py
 deprecated
-
+pyyaml
+requests
+Cython  # On NCI, use module load
+#mpi4py # On NCI, use module load
+tqdm

seismic/gps_corrections/relative_tt_residuals_plotter.py

@@ -638,7 +638,9 @@ def analyze_target_relative_to_ref(df_picks, ref_stn, target_stns, batch_options
               help='Filter out events with magnitude value less than this. '
                    '(Only applies when pick quality stats are all zero.)')
 @click.option('--strict-filtering/--no-strict-filtering', default=DEFAULT_STRICT_FILTERING, show_default=True,
-              help='Whether to strictly apply quality filters to reference station.')
+              help='Whether to apply quality filters to picks of the station being analyzed/plotted.'
+                   'If False, quality filters are still applied to the reference station picks, but'
+                   'not to the target station, resulting in a larger number of plotted events per station.')
 @click.option('--show-deployments', is_flag=True, default=False, show_default=True,
               help='Show temporary deployments time durations on the plots.')
 @click.option('--show-historical/--no-show-historical', default=True, show_default=True,