diff --git a/.travis.yml b/.travis.yml index dfe47fe6fb9..018720eb1ae 100644 --- a/.travis.yml +++ b/.travis.yml @@ -27,7 +27,6 @@ env: - BUILD_CMD="pip install -v package/ && pip install testsuite/" - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats" - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1" - - PIP_DEPENDENCIES="" - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable diff --git a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py index 70c15b8795d..6a5bd82f9ab 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py @@ -423,6 +423,7 @@ def solve(self, p_guess=None): Initial guess for the leastsq fit, must match the shape of the expected coefficients + Continuous defition results are fitted to a double exponential with :func:`scipy.optimize.leastsq`, intermittent definition are fit to a triple exponential. diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index 4b91ca9261b..62d302211dd 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -409,26 +409,27 @@ def hausdorff(P, Q): still has to calculate the *symmetric* Hausdorff distance as `max(directed_hausdorff(P, Q)[0], directed_hausdorff(Q, P)[0])`. + References ---------- .. [Huttenlocher1993] D. P. Huttenlocher, G. A. Klanderman, and W. J. Rucklidge. Comparing images using the Hausdorff distance. IEEE Transactions on Pattern Analysis and Machine Intelligence, 15(9):850–863, 1993. - .. [Taha2015] A. A. Taha and A. Hanbury. An efficient algorithm for calculating the exact Hausdorff distance. IEEE Transactions On Pattern Analysis And Machine Intelligence, 37:2153-63, 2015. - SeeAlso - ------- + + See Also + -------- scipy.spatial.distance.directed_hausdorff """ N, axis = get_coord_axes(P) d = get_msd_matrix(P, Q, axis=axis) - return ( max( np.amax(np.amin(d, axis=0)), \ - np.amax(np.amin(d, axis=1)) ) / N )**0.5 + return (max(np.amax(np.amin(d, axis=0)), + np.amax(np.amin(d, axis=1))) / N)**0.5 def hausdorff_wavg(P, Q): diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index a23ad59a094..aff0ff6f11d 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -118,18 +118,18 @@ def test_triangular_matrix(): incremented_triangular_matrix = triangular_matrix + scalar assert_equal(incremented_triangular_matrix[0,1], expected_value + scalar, - err_msg="Error in TriangularMatrix: addition of scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: addition of scalar gave" + "inconsistent results") triangular_matrix += scalar assert_equal(triangular_matrix[0,1], expected_value + scalar, - err_msg="Error in TriangularMatrix: addition of scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: addition of scalar gave" + "inconsistent results") multiplied_triangular_matrix_2 = triangular_matrix_2 * scalar assert_equal(multiplied_triangular_matrix_2[0,1], expected_value * scalar, - err_msg="Error in TriangularMatrix: multiplication by scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: multiplication by scalar gave" + "inconsistent results") triangular_matrix_2 *= scalar assert_equal(triangular_matrix_2[0,1], expected_value * scalar,