Merge branch 'release/0.1.0'

Former-commit-id: 2c07c32e630902d795bc5f610eeaf027f876a25e [formerly be102e6]
Former-commit-id: cf329b5881331471b85c69b07e3e20bff4eb92f9

.gitignore

@@ -15,3 +15,9 @@ matcherr_*
 build
 dist
 EQcorrscan.egg-info
+*.xml
+.cache
+.eggs
+.tox
+eqcorrscan/tutorials/*.jpg
+pytest_runner*

.travis.yml

@@ -1,20 +1,28 @@
 language: python
-os: linux
+os:
+  - linux
+  # - osx  # Note, travis doesn't support python builds on osx
 python: "2.7"
-
+virtualenv:
+    system_site_packages: true
 sudo: false
 
+# Test with multiple obspy versions, allow some backwards compatability
+env:
+  - OBSPY_VERSION=0.10.2
+  - OBSPY_VERSION=1.0.0
+
 addons:
   apt:
     source:
       - lucid
     packages:
-      - python-opencv
+      # - python-opencv
+      - pandoc
 
-# before_install:
-#   - sudo apt-get update
-#   - sudo apt-get install python-opencv
-#   - sudo dpkg -L python-opencv
+# before install:
+#   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update        ; fi
+#   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pandoc; fi
 
 install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
@@ -59,33 +67,39 @@ install:
         lxml
         sqlalchemy
         mock
-        nose
         gdal
         pyproj
         docopt
         coverage
         requests
+        pytest
+        pytest-pep8
+        opencv
   - source activate test-environment
   # install packages not available via conda
   # - pip install -r requirements.txt
   - pip install coveralls
   - pip install geographiclib
+  - pip install pypandoc
   # current pyimgur stable release has a py2.6 incompatibility
   - pip install https://github.com/megies/PyImgur/archive/py26.zip
+  - pip install obspy==$OBSPY_VERSION
   - pip freeze
   - conda list
   # done installing dependencies
   - git version
   - pip install .
 script:
   # Run the tests available, more should be added
-  - python eqcorrscan/tests/runtests.py
+  # - python eqcorrscan/tests/install_test.py
+  # py.test
+  python setup.py test
 
 notifications:
     email: false
     webhooks:
       urls:
         - https://webhooks.gitter.im/e/10122f10ed5043c58ae7
-      on_success: never  # options: [always|never|change] default: always
+      on_success: change  # options: [always|never|change] default: always
       on_failure: always  # options: [always|never|change] default: always
       on_start: never     # options: [always|never|change] default: always

CHANGES.md

@@ -1,3 +1,15 @@
+## 0.1.0
+* Implimented tests for synthetic generation and match-filter functions
+* Developed new tutorials that download from GeoNet and are much clearer
+* Changed from PICK and EVENTINFO classes to obspy.core.event classes, note
+this will break some previous scripts, however wrappers are included for this,
+this ended up being the biggy, and is the reason for ceasing the 0.0.x line.
+* Added synthetic seismogram generation, very basic seismograms, but they work
+as templates for the detection of *some* seismicity.
+* Added compatibility with Obspy v.1.0.0.
+* All files now follow pep8.
+* Removed parameter files completely, and redundant scripts.
+
 ## 0.0.9
 * Working towards following pep8
 * Change how match_filter handles missing data - now remove template traces (which have been copied)

MANIFEST.in

@@ -3,19 +3,20 @@
 
 include README.md
 # include eqcorrscan/test_data/tutorial_data.tgz
-include eqcorrscan/tutorial.py
+# include eqcorrscan/tutorial.py
 recursive-include eqcorrscan/utils *.py
-recursive-include eqcorrscan/par *.py
-recursive-include eqcorrscan/scripts *.py
+# recursive-include eqcorrscan/par *.py
+# recursive-include eqcorrscan/scripts *.py
+recursive-include eqcorrscan/tutorials *.py
 recursive-include eqcorrscan/doc *
 recursive-include eqcorrscan/core *.py
 recursive-include eqcorrscan/tests *.py
 
 # exclude rules
-global-exclude *.pyc *.ms *.tgz
+# global-exclude *.pyc *.ms *.tgz
 prune eqcorrscan/doc/_build/latex
 prune eqcorrscan/plot
 prune eqcorrscan/detections
 prune eqcorrscan/grid
-prune eqcorrscan/stack_templates
-prune eqcorrscan/templates
+# prune eqcorrscan/stack_templates
+# prune eqcorrscan/templates

README.md

@@ -7,36 +7,47 @@
 [![DocumentationStatus](http://readthedocs.org/projects/eqcorrscan/badge/?version=latest)](http://eqcorrscan.readthedocs.org/en/latest/?badge=latest)
 
 # Installation
-We are now listed on pypi!  Installation has been tested on both OSX and Linux (Ubuntu) and
-is as simple as:
+Installation has been tested on both OSX and Linux (Ubuntu), we currently do not support
+Windows systems, but plan to in the future.  Installation for Linux and OS X should be as simple as:
 
-*pip install EQcorrscan*
+```pip install EQcorrscan```
 
 If upgrading from a previous version, rather than running install --upgrade, I recommend the following:
 
-*pip install -U --no-deps EQcorrscan*
+```pip install -U --no-deps EQcorrscan```
 
-This will not try to upgrade your dependencies, which is not needed for 0.0.8.
+This will not try to upgrade your dependencies, which is not needed.  You may wish
+to update your obspy version to 1.0.0 which was recently released.  We have tested
+this and support it, nevertheless, if you find any issues then let us know.
 
-If you want to be kept informed about releases, bug-tracking and enhancements
-without having to keep looking on github, subscribe to our [google group](https://groups.google.com/forum/#!forum/eqcorrscan-users).
-
-You will likely need sudo permissions to run this command.  This installation
-method is quite new to the package (as of v0.0.4), so there are some things that
-are changing in the install process at the moment.  This should be smoothed out
-by v0.1.0 (maybe mid 2016).
+*You will likely need sudo permissions to run this command.*
 
 If you have any issues installing please let me know.  You will need to install openCV
-seperately using (on Linux):
+separately using (on Linux):
 
-*sudo apt-get install python-opencv*
+```apt-get install python-opencv```
 
 Or, for Mac users, this is available on Macports or other similar package managers.
 
+## Updates
+
+If you want to be kept informed about releases, bug-tracking and enhancements
+without having to keep looking on github, subscribe to our [google group](https://groups.google.com/forum/#!forum/eqcorrscan-users).
+
+# Documentation
+
 The full documentation for this package can be found here:
-[Docs](http://calum-chamberlain.github.io/EQcorrscan/) - you are also
-welcome to suggest documentation updates or update the doc in the develop branch, please
-do not work on the documentation in the gh-pages branch!
+[Docs](http://eqcorrscan.readthedocs.org/en/latest/?badge=latest).
+Any errors including typos and just missing bits can either be fixed by you,
+or flagged in the issues tab here.  We host our docs on readthedocs, which
+uses sphinx to scrape the docstrings in the codes, so it is simple to
+match the docs to the codes and change the docstrings.
+
+We also have a github-pages site [EQcorrscan](http://calum-chamberlain.github.io/EQcorrscan/),
+which uses jekyll to build the site.  Changes or additions to this site can be made on
+the gh-pages branch.
+
+# Functionality
 
 This package contains routines to enable the user to conduct match-filter earthquake
 detections using [obspy](https://github.com/obspy/obspy/wiki) bindings when reading
@@ -51,37 +62,40 @@ Also within this package are:
 * Peak finding algorithm (basic);
 * Automatic amplitude picker for local magnitude scale;
 * [Seisan](http://seisan.info/) S-file integration for database management and routine earthquake location;
+* Obspy.core.event integration, which opens up lots of other functions (Seishub, hypoDDpy etc.);
 * Stacking routines including phase-weighted stacking based on Thurber at al. (2014);
-* Brightness based template creation based on the work of Frank et al. (2014)
+* Brightness based template creation based on the work of Frank et al. (2014);
+* Singular Value Decomposition derived magnitude calculations based on Rubinstein & Ellsworth (2010).
 
-This package is written by Calum Chamberlain of Victoria University of Wellington, and
-is distributed under the LGPL GNU License, Copyright Calum Chamberlain 2015.
+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
+how to do the core matched-filter detection.
+
+# Licence
+
+This package is written by Calum Chamberlain and Chet Hopp of Victoria University of Wellington, and
+is distributed under the LGPL GNU License, Copyright Calum Chamberlain 2015, 2016.
 
-# Parameter files
-To use this package you will need to set up default parameters in the parameter
-file. Currently these are located in the source directory, this will change in
-the future, hopefully. It is recommended that you copy these default parameter
-files before adding your own to allow you to easily transfer back to other
-parameter set ups. **These are being migrated to a script directory along with all scripts
-for version 0.0.5***
 
 # Contributing
+
 Please fork this project and work on it there then create a pull request to
 merge back into develop.
 
 When you make changes please run the tests in the test directory to ensure
-everything merges with minimum effort.
+everything merges with minimum effort.  If there is not yet a test to cope
+with your changes then please write one.
 
 Please document your functions following the other documentation within the
 functions, these doc-scripts will then be built into the main documentation
 using Sphinx.
 
-We are trying to implement a better branching model, following that found here:
-http://nvie.com/posts/a-successful-git-branching-model/
+We are trying to implement a better branching model, following that found [here](http://nvie.com/posts/a-successful-git-branching-model/).
 To this end, please fork the development branch if you want to develop
 things, and flag issues in the master for us to bugfix.
 If you have a feature you want to develop please create a new branch
-of the development branch for this and work in there, we can then merge
+from the development branch and work on it there, we can then merge
 it back in to the development branch when it is stable enough.
 
 This branching model (git-flow) is pretty well established, and I would recommend
@@ -93,3 +107,4 @@ will keep us all branching in the same way.
 * CJ Chamberlain, DR Shelly, J Townend, TA Stern (2014) [Low‐frequency earthquakes reveal punctuated slow slip on the deep extent of the Alpine Fault, New Zealand](http://onlinelibrary.wiley.com/doi/10.1002/2014GC005436/full), __G-cubed__,doi:10.1002/2014GC005436
 * 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