Updates code to work with latest dependencies.

.travis.yml

@@ -1,17 +1,43 @@
-language: python
-python:
-  - "2.7"
-virtualenv:
-  system_site_packages: true
+language: generic
+os:
+  - linux
+env:
+  matrix:
+    - DEP_VERSIONS="oldest"
+    - DEP_VERSIONS="latest"
 before_install:
-  - pip uninstall -y numpy
-  - sudo apt-add-repository -y ppa:octave/stable
+  - if [[ $DEP_VERSIONS == "oldest" ]]; then
+      sudo apt-get install -y -qq python-pip python-setuptools python-numpy python-scipy python-matplotlib python-tables python-nose python-coverage python-pandas python-sphinx python-mock python-numpydoc python-yaml;
+      sudo pip install --no-deps oct2py==2.4.2 DynamicistToolKit==0.4.0;
+    elif [[ $DEP_VERSIONS == "latest" ]]; then
+      MINICONDA_URL="https://repo.continuum.io/miniconda";
+      MINICONDA_FILE="Miniconda3-latest-Linux-x86_64.sh";
+      curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}";
+      bash $MINICONDA_FILE -b;
+      source ~/miniconda3/bin/activate root;
+      conda config --set always_yes yes;
+      conda update -q conda;
+      conda env create -f env-dev-latest.yml;
+      source activate gaitanalysis-dev-latest;
+      sudo apt-add-repository -y ppa:octave/stable;
+    fi
   - sudo apt-get update
-  - sudo apt-get install -y -qq python-setuptools python-numpy python-scipy python-matplotlib python-tables python-nose python-coverage octave
-  - pip install pandas==0.12.0 pyyaml oct2py==1.2.0 DynamicistToolKit==0.4.0
-  - pip freeze
-  - octave --version
+  - sudo apt-get install -y -qq octave
 install:
-  - python setup.py install
-script: nosetests -v --with-coverage --cover-package=gaitanalysis
-after_success: coveralls
+  - if [[ $DEP_VERSIONS == "oldest" ]]; then
+      sudo pip install --no-deps -e .;
+    elif [[ $DEP_VERSIONS == "latest" ]]; then
+      python setup.py install;
+    fi
+before_script:
+  - octave --version
+  - if [[ $DEP_VERSIONS == "oldest" ]]; then
+      pip freeze;
+    elif [[ $DEP_VERSIONS == "latest" ]]; then
+      conda info;
+      conda list;
+    fi
+script:
+  - nosetests -v --with-coverage --cover-package=gaitanalysis
+  - cd docs
+  - make html

RELEASE.txt

@@ -2,6 +2,6 @@
 2. Bump the version in gaitanalysis/version.py, for example 0.1.0dev to 0.1.0.
 3. Commit changes.
 4. git tag -a vX.X.X -m "Version X.X.X"
-5. python setup.py regsiter sdist upload
+5. python setup.py register sdist upload
 6. Make sure the latest version is available on readthedocs.org
 7. Bump the version in the git repo to one with "dev" appended.

env-dev-latest.yml

@@ -0,0 +1,18 @@
+name: gaitanalysis-dev-latest
+channels:
+  - conda-forge
+dependencies:
+  - python =2.7.*
+  - numpy
+  - scipy
+  - matplotlib
+  - pytables
+  - pandas
+  - pyyaml
+  - dynamicisttoolkit
+  - oct2py
+  - nose
+  - sphinx
+  - coverage
+  - mock
+  - numpydoc

env-dev-oldest.yml

@@ -0,0 +1,20 @@
+name: gaitanalysis-dev-oldest
+channels:
+  - defaults
+  - moorepants
+dependencies:
+  - python =2.7.*
+  - numpy =1.9.1
+  - scipy =0.14.0
+  - matplotlib =1.4.2
+  - pytables =3.1.1
+  - pandas =0.15.1
+  - pyyaml =3.11
+  - nose
+  - sphinx
+  - coverage
+  - mock
+  - numpydoc
+  - pip:
+    - dynamicisttoolkit==0.3.5
+    - oct2py==2.4.2

gaitanalysis/gait.py

@@ -5,11 +5,13 @@
 import os
 
 # external libraries
+from pkg_resources import parse_version
 import numpy as np
 from scipy.integrate import simps
 import matplotlib.pyplot as plt
 import pandas
 from dtk import process
+import oct2py
 from oct2py import octave
 
 # local
@@ -65,7 +67,7 @@ def find_constant_speed(time, speed, plot=False, filter_cutoff=1.0):
 
     additional_samples = sample_rate * 0.65
 
-    new_indice = indice - additional_samples
+    new_indice = indice - int(round(additional_samples))
 
     if plot is True:
         fig, ax = plt.subplots(2, 1)
@@ -237,9 +239,14 @@ def inverse_dynamics_2d(self, left_leg_markers, right_leg_markers,
             # oct2py doesn't allow multiple outputs to be stored in a tuple
             # like python, so you have to output each variable
             # independently
-            angles, velocities, moments, forces = \
-                octave.leg2d(time, marker_array, normalized_force_array,
-                             options)
+            if parse_version(oct2py.__version__) >= parse_version('4.0'):
+                angles, velocities, moments, forces = \
+                    octave.leg2d(time, marker_array, normalized_force_array,
+                                 options, nout=4)
+            else:
+                angles, velocities, moments, forces = \
+                    octave.leg2d(time, marker_array, normalized_force_array,
+                                 options)
 
             dynamics = angles, velocities, moments, forces
 

gaitanalysis/motek.py

@@ -1209,17 +1209,25 @@ def orient_accelerometer(orientation, x_prime, y_prime, z_prime):
             y_inertial = np.zeros(np.shape(y_prime))
             z_inertial = np.zeros(np.shape(z_prime))
 
-            for row, world in enumerate([x_inertial, y_inertial, z_inertial]):
-                for col, local in enumerate([x_prime, y_prime, z_prime]):
-                    world += orientation[row,col] * local
+            for col, local in enumerate([x_prime, y_prime, z_prime]):
+                x_inertial += orientation[0, col] * local
+
+            for col, local in enumerate([x_prime, y_prime, z_prime]):
+                y_inertial += orientation[1, col] * local
+
+            for col, local in enumerate([x_prime, y_prime, z_prime]):
+                z_inertial += orientation[2, col] * local
 
             return x_inertial, y_inertial, z_inertial
 
         for sensor, rot_matrix in self.meta['trial']['sensor-orientation'].iteritems():
-            data_frame[sensor + '_AccX'], data_frame[sensor + '_AccY'], \
-                data_frame[sensor + '_AccZ'] = orient_accelerometer(
-                        np.array(rot_matrix), data_frame[sensor + '_AccX'],
-                        data_frame[sensor + '_AccY'], data_frame[sensor + '_AccZ'])
+            ax, ay, az = orient_accelerometer(np.array(rot_matrix),
+                                              data_frame[sensor + '_AccX'],
+                                              data_frame[sensor + '_AccY'],
+                                              data_frame[sensor + '_AccZ'])
+            data_frame[sensor + '_AccX'] = ax
+            data_frame[sensor + '_AccY'] = ay
+            data_frame[sensor + '_AccZ'] = az
 
         return data_frame
 

gaitanalysis/octave/2d_inverse_dynamics/leg2d.m

@@ -37,6 +37,8 @@
 %	- missing marker data is interpolated *after* low pass filtering
 %	- x and y coordinates of the same marker must be either both valid or both NaN (missing)
 
+        oct_ver = strsplit(OCTAVE_VERSION, '.');
+
 	% some constants
 	Nmarkers = 6;
 	Ncoords = 2*Nmarkers;
@@ -91,9 +93,16 @@
 		maxmissing = max(diff(validsamples))-1;			% determine largest gap
 		fprintf('Marker %d: %d samples are missing, longest gap is %d samples.\n', i, missing, maxmissing);
 		[xf, xd, xdd] = myfiltfilt(validtimes, d(validsamples,:), options.freq);
-		mocap_f(:,columns) = interp1q(validtimes, xf, times);		% resample filtered signal to original time stamps
-		mocap_d(:,columns) = interp1q(validtimes, xd, times);		% resample first derivative to original time stamps
-		mocap_dd(:,columns) = interp1q(validtimes, xdd, times);		% resample second derivative to original time stamps
+		% Octave removed interp1q in version 4.2.
+		if ((str2num(oct_ver{1}) >= 4) && (str2num(oct_ver{2}) >= 2))
+			mocap_f(:,columns) = interp1(validtimes, xf, times);		% resample filtered signal to original time stamps
+			mocap_d(:,columns) = interp1(validtimes, xd, times);		% resample first derivative to original time stamps
+			mocap_dd(:,columns) = interp1(validtimes, xdd, times);		% resample second derivative to original time stamps
+		else
+			mocap_f(:,columns) = interp1q(validtimes, xf, times);		% resample filtered signal to original time stamps
+			mocap_d(:,columns) = interp1q(validtimes, xd, times);		% resample first derivative to original time stamps
+			mocap_dd(:,columns) = interp1q(validtimes, xdd, times);		% resample second derivative to original time stamps
+                end
 	end
 
 	% do the low-pass filtering on the force plate data

gaitanalysis/tests/test_gait.py

@@ -180,8 +180,8 @@ def test_grf_landmarks(self, plot=False):
         min_idx = len(self.data_frame) / 3
         max_idx = 2*len(self.data_frame) / 3
 
-        min_time = self.data_frame.index.astype(float)[min_idx]
-        max_time = self.data_frame.index.astype(float)[max_idx]
+        min_time = self.data_frame.index.values.astype(float)[min_idx]
+        max_time = self.data_frame.index.values.astype(float)[max_idx]
 
         right_strikes, left_strikes, right_offs, left_offs = \
             gait_data.grf_landmarks('Right Vertical GRF',