Modified MSMLib.invert_assignments to ignore -1's in assignments (#140). Began with Project.get_random_confs_from_states to replace the old GetRandomConfsFromState (#139). Also added fix to reconcile Project.empty_traj and Trajectory.__[i]add__ (#141).
Project.get_random_confs_from_states fixes. It now does load a trajectory correctly. I still need to come up with a test to be sure that it is loading up the right conformations...
added project.get_random_confs_from_states.randomize, which will either use np.random.randint or np.random.permutation based on the kwarg replacement to generate a random sample from a particular state.
Adjusted the docstringin Project.get_random...confs as well as fixed an issue with mapping the number of conformations to find to the states list.
Modified SaveStructures.py to use the new project method to grab random structures. Also updated the SaveStructures test in test_wrappers to use the new functionality. This is a little different because the SaveStructures.run function is gone, and SaveStructures.main simply calls the project.get_random_confs_from_states and then SaveStructures.save. I do not know if this is the best way to do it.
There is a bug in msmbuilder.testing.eq. The function takes two objects and raises an error if they are not equal. Unfortunately, for dict and spmatrix types the first object was being compared to itself instead of being compared to the second object. Now three tests fail. See issue #143
Fixed typo in msmbuilder.testing (spase -> sparse). Added check for the shape of the matrices in msmbuilder.testing.assert_sparse_matrix_equal. This is the reason the BuildMSM test is failing. msmbuilder/reference/tProb.mtx is (74, 74) whereas tCounts is (100, 100). I don't know where the real tProb.mtx went...
Added ValueError when replacement=False and the state has too few conformations to sample.
Added to MSMLib.invert_assignments to notify the user that the inverse assignments will not include any -1's used to pad the trimmed states or shorter trajactories. Also added a docstring for project.get_random_confs_from_states.randomize, which is a helper function for using np.random.randint or np.random.permutation when sampling conformations
Added skipIf statement for test_msm_analysis.test_msm_acf if the statsmodels version is less than or equal to 0.4.x this is option one that @kylebeauchamp suggested to 'resolve' issue #121 I can remove this commit here if he has already fixed it elsewhere.
Docstring modifications in project.py
Merge branch 'fix_tests' of github.com:SimTk/msmbuilder into fix_tests
Changed np.dot(csr_matrix, csr_matrix) to csr_matrix.dot(csr_matrix) because np.dot does not support sparse matrix multiplication. This only occured in tpt.py
Modified MSMLib.invert_assignments to ignore -1's in assignments (#140). Began with Project.get_random_confs_from_states to replace the old GetRandomConfsFromState (#139). Also added fix to reconcile Project.empty_traj and Trajectory.__[i]add__ (#141).
Project.get_random_confs_from_states fixes. It now does load a trajectory correctly. I still need to come up with a test to be sure that it is loading up the right conformations...
added project.get_random_confs_from_states.randomize, which will either use np.random.randint or np.random.permutation based on the kwarg replacement to generate a random sample from a particular state.
Adjusted the docstringin Project.get_random...confs as well as fixed an issue with mapping the number of conformations to find to the states list.
Modified SaveStructures.py to use the new project method to grab random structures. Also updated the SaveStructures test in test_wrappers to use the new functionality. This is a little different because the SaveStructures.run function is gone, and SaveStructures.main simply calls the project.get_random_confs_from_states and then SaveStructures.save. I do not know if this is the best way to do it.
There is a bug in msmbuilder.testing.eq. The function takes two objects and raises an error if they are not equal. Unfortunately, for dict and spmatrix types the first object was being compared to itself instead of being compared to the second object. Now three tests fail. See issue #143
Fixed typo in msmbuilder.testing (spase -> sparse). Added check for the shape of the matrices in msmbuilder.testing.assert_sparse_matrix_equal. This is the reason the BuildMSM test is failing. msmbuilder/reference/tProb.mtx is (74, 74) whereas tCounts is (100, 100). I don't know where the real tProb.mtx went...