Merge pull request #57 from eqcorrscan/develop

Update for version 0.1.4

.travis.yml

@@ -19,10 +19,6 @@ matrix:
 
 sudo: false
 
-env:
-  global:
-    - OBSPY_VERSION=1.0.1
-
 install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
       export OS="MacOSX";
@@ -57,16 +53,19 @@ install:
         PYFLAKES="pyflakes=0.9.0"
       fi
   - echo $PYTHON_VERSION
-  - |
-      if [[ "$OS" == "MacOSX" ]]; then
-          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
-      elif [[ "$py" == "3.5" ]]; then
-          conda create -q -n test-environment --file $env_file
-      elif [[ "$py" == "2.7" ]]; then
-          conda create -q -n test-environment --file $env_file
-      else
-          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
-      fi
+  - conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
+#  - |
+#      if [[ "$OS" == "MacOSX" ]]; then
+#          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
+#      elif [[ "$py" == "3.5" ]]; then
+#          conda create -q -n test-environment --file $env_file
+#      elif [[ "$py" == "2.7" ]]; then
+#          conda create -q -n test-environment --file $env_file
+#      elif [[ "$py" == "3.4" ]]; then
+#          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib=1.5.1 obspy flake8 mock coverage opencv3
+#      else
+#          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
+#      fi
   - source activate test-environment
   - conda install $PYFLAKES
   - conda install pyproj
@@ -83,20 +82,16 @@ install:
   - pip install geographiclib
   - pip install https://github.com/megies/PyImgur/archive/py3.zip
   - pip install pep8-naming
-  - pip install pytest
-  - pip install pytest-cov
+  - pip install pytest pytest-cov pytest-pep8
   - pip install Cython
-  #  - pip install obspy==$OBSPY_VERSION
   - pip freeze
   - conda list
   # done installing dependencies
   - git version
   - python setup.py install
 
 script:
-  # Need to ignore the files in current directory to ensure we find the
-  # installed version of EQcorrscan with compiled code.
-  - python setup.py test
+  - travis_wait 50 python setup.py test
 
 after_success:
   # Check how much code is actually tested and send this report to coveralls

CHANGES.md

@@ -1,3 +1,28 @@
+## 0.1.4
+* Bug-fix in plot_repicked removed where data were not normalized
+properly;
+* Bug-fix in lag_calc where data were missing in the continuous data 
+fixed (this led to incorrect picks, **major bug!**);
+* Output cross-channel correlation sum in lag-calc output;
+* Add id to DETECTION objects, which is consistent with the events
+within DETECTION objects and catalog output, and used in lag_calc to
+allow linking of detections to catalog events;
+* Add lots of logging and error messages to lag-calc to ensure user 
+understands limits;
+* Add error to day-proc to ensure user is aware of risks of padding;
+* Change utils.pre_processing.process to accept different length of 
+data enforcement, not just full day (allow for overlap in processing,
+which might be useful for reducing day start and end effects);
+* Bug-fix in mag_calc.amp_pick_event, broke loop if data were missing;
+* Lots of docs adjustment to sort order of doc-strings and hyper-links;
+* Allow multiple uses of the same channel in templates (e.g. you can
+now use a template with two windows from the same channel, such as a P
+and an S);
+* Add evaluation mode filter to utils.catalog_utils.filter_picks;
+* Update subspace plot to work when detector is not partitioned;
+* Make tests run a little faster;
+* Add pep8 testing for all code.
+
 ## 0.1.3
 * Now testing on OSX (python 2.7 and 3.5) - also added linux python 3.4;
 * Add lag-calculation and tests for it;

CONTRIBUTORS.md

@@ -0,0 +1,5 @@
+Calum John Chamberlain
+Chet Hopp
+Emily Warren-Smith
+Konstantinos Michailos
+Shanna Chu

README.md

@@ -7,6 +7,7 @@
 [![Coverage Status](https://coveralls.io/repos/github/eqcorrscan/EQcorrscan/badge.svg?branch=master)](https://coveralls.io/github/eqcorrscan/EQcorrscan?branch=master)
 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.59976.svg)](http://dx.doi.org/10.5281/zenodo.59976)
 [![DocumentationStatus](http://readthedocs.org/projects/eqcorrscan/badge/?version=latest)](http://eqcorrscan.readthedocs.org/en/latest/?badge=latest)
+[![Dependency Status](https://dependencyci.com/github/eqcorrscan/EQcorrscan/badge)](https://dependencyci.com/github/eqcorrscan/EQcorrscan)
 <!--[![DOI](https://zenodo.org/badge/18852/eqcorrscan/EQcorrscan.svg)](https://zenodo.org/badge/latestdoi/18852/eqcorrscan/EQcorrscan)-->
 
 # Installation

appveyor.yml

@@ -36,14 +36,15 @@ install:
   - "conda create -q --yes -n test python=%PYTHON_VERSION%"
   - "activate test"
   # Install default dependencies
-  - "conda install -q --yes pip numpy scipy opencv3 matplotlib obspy mock flake8 pytest pyflakes=0.9.0 cython h5py"
+  - "conda install -q --yes pip numpy scipy opencv3 matplotlib obspy mock flake8 pyflakes=0.9.0 cython h5py"
   # additional dependecies
   #  - "choco install opencv"
   #  - "powershell copy-item C:\\OpenCV\\opencv\\build\\python\\2.7\\x64\\cv2.pyd C:\\conda\\envs\\test\\lib\\site-packages\\."
   - "pip install pyimgur"
   - "pip install -U future"
+  - "pip install pytest"
+  - "pip install pytest-pep8"
   - "pip install pytest-cov"
-  - "pip install pytest-xdist"
   # list package versions
   - "conda list"
 

eqcorrscan/__init__.py

@@ -1,43 +1,20 @@
 #!/usr/bin/python
-r"""
-EQcorrscan is a python module designed to run match filter routines for
-seismology, within it are routines for integration to seisan and obspy.
-With obspy integration (which is necessary) all main waveform formats can be
-read in and output.
-
-This main section contains a script, LFE_search.py which demonstrates the usage
-of the built in functions from template generation from picked waveforms
-through detection by match filter of continuous data to the generation of lag
-times to be used for relative locations.
-
-The match-filter routine described here was used a previous Matlab code for the
-Chamberlain et al. 2014 G-cubed publication.  The basis for the lag-time
-generation section is outlined in Hardebeck & Shelly 2011, GRL.
-
-Code generated by Calum John Chamberlain of Victoria University of Wellington,
-2015.
-
-    EQcorrscan is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EQcorrscan is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EQcorrscan.  If not, see <http://www.gnu.org/licenses/>.
+"""
+:copyright:
+    EQcorrscan developers.
+
+:license:
+    GNU Lesser General Public License, Version 3
+    (https://www.gnu.org/copyleft/lesser.html)
 """
 import sys
 import importlib
 import warnings
 
-__all__ = ['core', 'utils']
+__all__ = ['core', 'utils', 'tutorials']
 
 
-__version__ = '0.1.3'
+__version__ = '0.1.4'
 
 
 # Cope with changes to name-space to remove most of the camel-case

eqcorrscan/core/__init__.py

@@ -1,31 +1,10 @@
-"""EQcorrscan is a python module designed to run match filter routines for \
-seismology, within it are routines for integration to seisan and obspy.
-With obspy integration (which is necessary) all main waveform formats can be
-read in and output.
-
-This main section contains a script, LFE_search.py which demonstrates the usage
-of the built in functions from template generation from picked waveforms
-through detection by match filter of continuous data to the generation of lag
-times to be used for relative locations.
-
-The match-filter routine described here was used a previous Matlab code for the
-Chamberlain et al. 2014 G-cubed publication.  The basis for the lag-time
-generation section is outlined in Hardebeck & Shelly 2011, GRL.
-
-Code generated by Calum John Chamberlain of Victoria University of Wellington,
-2015.
-
-All rights reserved.
+"""
+:copyright:
+    EQcorrscan developers.
 
-Pre-requisites:
-    gcc             - for the installation of the openCV correlation routine
-    python-joblib   - used for parallel processing
-    python-obspy    - used for lots of common seismological processing
-                    - requires:
-                        numpy
-                        scipy
-                        matplotlib
-    python-pylab    - used for plotting
+:license:
+    GNU Lesser General Public License, Version 3
+    (https://www.gnu.org/copyleft/lesser.html)
 """
 
 __all__ = ['template_gen', 'match_filter', 'bright_lights', 'lag_calc',