Missing surface in event.rupture when parsing the flatfile

.travis.yml

@@ -4,6 +4,8 @@ language: python
 
 python:
  - "2.7"
+# - "3.5"
+# - "3.6"
 
 addons:
   apt:
@@ -16,11 +18,12 @@ install:
   # Make sure pip is up-to-date and has support for wheels
   - pip -q install -U pip
   # Install oq-engine dependencies
-  - pip -q install -r oq-engine/requirements-py27-linux64.txt
-  - pip -q install -e oq-engine/
-  # Install HMTK extra dependencies
-  - pip -q install -r requirements-py27-linux64.txt
-  - pip -q install -e .
+  - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then pip install -r oq-engine/requirements-py27-linux64.txt;
+    elif [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then pip install -r oq-engine/requirements-py35-linux64.txt; 
+    elif [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then pip install -r oq-engine/requirements-py36-linux64.txt; 
+    else echo "Python not supported" && exit 1; fi
+  - pip install -e oq-engine/
+  - pip install -e .
 
 script:
   - nosetests -vx tests

README.md

@@ -1,5 +1,6 @@
 gmpe-smtk
 =========
+[![Build Status](https://travis-ci.org/GEMScienceTools/gmpe-smtk.svg?branch=master)](https://travis-ci.org/GEMScienceTools/gmpe-smtk)
 
 Python and OpenQuake-based Toolkit for Analysis of Strong Motions and Interpretation of GMPEs
 
@@ -16,7 +17,7 @@ License as published by the Free Software Foundation, either version
 3 of the License, or (at your option) any later version. Please take 
 a minute of your time to read the disclaimer below.
 
-Copyright (c) 2014-2017 GEM Foundation
+Copyright (c) 2014-2018 GEM Foundation
 
 
 Disclaimer
@@ -50,73 +51,31 @@ The GEM Foundation, and the authors of the software, assume no
 liability for use of the software.
 
 
-dependencies
+Installation
 ============
 
-The gmpe-smtk currently requires the following dependencies:
+The gmpe-smtk is built on top of the [OpenQuake-engine](https://github.com/gem/oq-engine).
 
+To install the toolkit, and ensure that it is aligned with the OpenQuake-engine
+we recommend to install the OpenQuake-engine according to the instructions
+given for your specific operating system. The full installation instructions for
+OpenQuake can be found here: [https://github.com/gem/oq-engine](https://github.com/gem/oq-engine).
 
-* OpenQuake Hazard Library ([oq-hazardlib](https://github.com/gem/oq-hazardlib))
-* Numpy (1.6.1 or later) (installed with oq-hazardlib)
-* Scipy (0.11.0 or later) (installed with oq-hazardlib)
-* Shapely (installed with oq-hazardlib)
-* Matplotlib (1.3.x or later)
-* h5py (2.2.0 or later)
-
-installation
-============
-
-* Windows
-
-Windows users should install the PythonXY software package (https://code.google.com/p/pythonxy/), which will install all of the dependencies except oq-hazardlib 
-To install oq-hazardlib it is recommended to install MinGW or Github for Windows.
-
-If using Github for Windows simply open a bash shell, clone the oq-hazardlib
-repository using:
-
-```bash
-git clone https://github.com/gem/oq-hazardlib.git
-```
-
-Then type
-
-```bash
-cd oq-hazardlib
-python setup.py install
-```
-
-To install the gmpe-smtk simply download the zipped code from the repository,
-unzip it to a location of your choice then add the directory path to
-the Environment Variables found in:
-
-My Computer -> Properties -> System Properties -> Advanced -> Environment Variables
-
-In the Environment Variables you will see a list of System Variables. Select
-"Path" and then "Edit". Then simply add the directory of the gmpe-smtk to the
-list of directories.
-
-* OSX/Linux
-
-To install oq-hazardlib simply clone the oq-hazardlib repository into a folder
-of your choice.
-
+Once the OpenQuake-engine is installed, the gmpe-smtk repository is cloned by:
 ```bash
-git clone https://github.com/gem/oq-hazardlib.git
+git clone https://github.com/GEMScienceTools/gmpe-smtk
 ```
 
-Then run
-
+Then:
 ```bash
-cd oq-hazardlib
+cd gmpe-smtk
 python setup.py install
 ```
 
-Matplotlib and h5py can both be installed from the native package managers,
-although it is recommended to use pip for this purpose.
+For users interested in developing new features or contributing code to the
+repository we strongly recommend to install the OpenQuake-engine according to
+the instructions for [installing OpenQuake for development](https://github.com/gem/oq-engine/blob/master/doc/installing/development.md).
 
-To install the gmpe-smtk, clone the code from the repository and then
-add the following line to your bash or profile script:
+The gmpe-smtk is currently written in Python 2.7 and work is now underway to
+port this to Python 3.5.
 
-```bash
-export PYTHONPATH=/path/to/gmpe-smtk/:$PYTHONPATH
-```

smtk/hazard/conditional_simulation.py

@@ -141,13 +141,13 @@ def conditional_simulation(known_sites, residuals, unknown_sites, imt, nsim,
     unknown_sites.depths = np.zeros_like(unknown_sites.depths)
     cov_kk = correlation_model._get_correlation_matrix(known_sites, imt).I
     cov_uu = correlation_model._get_correlation_matrix(unknown_sites, imt)
-    d_k_uk = np.zeros([known_sites.total_sites, unknown_sites.total_sites],
+    d_k_uk = np.zeros([len(known_sites), len(unknown_sites)],
                        dtype=float)
-    for iloc in range(0, known_sites.total_sites):
-        d_k_uk[iloc, :] = geodetic_distance(known_sites.lons[iloc],
-                                            known_sites.lats[iloc],
-                                            unknown_sites.lons,
-                                            unknown_sites.lats)
+    for iloc in range(len(known_sites)):
+        d_k_uk[iloc, :] = geodetic_distance(known_sites.array["lons"][iloc],
+                                            known_sites.array["lats"][iloc],
+                                            unknown_sites.array["lons"],
+                                            unknown_sites.array["lats"])
     cov_ku = correlation_model._get_correlation_model(d_k_uk, imt)
     mu = cov_ku.T * cov_kk * np.matrix(residuals).T
     stddev = cov_uu - (cov_ku.T * cov_kk * cov_ku)

smtk/intensity_measures.py

@@ -186,7 +186,7 @@ def get_response_spectrum(acceleration, time_step, periods, damping=0.05,
                                         periods, 
                                         damping,
                                         units)
-    spectrum, time_series, accel, vel, disp = response_spec.evaluate()
+    spectrum, time_series, accel, vel, disp = response_spec()
     spectrum["PGA"] = time_series["PGA"]
     spectrum["PGV"] = time_series["PGV"]
     spectrum["PGD"] = time_series["PGD"]
@@ -231,7 +231,7 @@ def geometric_mean_spectrum(sax, say):
         Dictionary of response spectrum outputs from y-component
     """
     sa_gm = {}
-    for key in sax.keys():
+    for key in sax:
         if key == "Period":
             sa_gm[key] = sax[key]
         else:
@@ -243,7 +243,7 @@ def arithmetic_mean_spectrum(sax, say):
     Returns the arithmetic mean of the response spectrum
     """
     sa_am = {}
-    for key in sax.keys():
+    for key in sax:
         if key == "Period":
             sa_am[key] = sax[key]
         else:
@@ -255,7 +255,7 @@ def envelope_spectrum(sax, say):
     Returns the envelope of the response spectrum
     """
     sa_env = {}
-    for key in sax.keys():
+    for key in sax:
         if key == "Period":
             sa_env[key] = sax[key]
         else: