diff --git a/libensemble/alloc_funcs/fast_alloc.py b/libensemble/alloc_funcs/fast_alloc.py index dd7322a57..c8595207b 100644 --- a/libensemble/alloc_funcs/fast_alloc.py +++ b/libensemble/alloc_funcs/fast_alloc.py @@ -9,8 +9,8 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): is told to call the generator function, provided this wouldn't result in more than ``gen_specs['user']['num_active_gen']`` active generators. - :See: - ``/libensemble/tests/regression_tests/test_fast_alloc.py`` + .. seealso:: + `test_fast_alloc.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/fast_alloc_and_pausing.py b/libensemble/alloc_funcs/fast_alloc_and_pausing.py index 6bcc9ffec..c4115f669 100644 --- a/libensemble/alloc_funcs/fast_alloc_and_pausing.py +++ b/libensemble/alloc_funcs/fast_alloc_and_pausing.py @@ -21,8 +21,8 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): alloc_specs['user']['stop_partial_fvec_eval']: True --- after the value returned from combine_component_func is larger than a known upper bound on the objective. - :See: - ``/libensemble/tests/regression_tests/test_chwirut_uniform_sampling_one_residual_at_a_time.py`` + .. seealso:: + `test_chwirut_uniform_sampling_one_residual_at_a_time.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/fast_alloc_to_aposmm.py b/libensemble/alloc_funcs/fast_alloc_to_aposmm.py index 3a260a6c0..94ed90c79 100644 --- a/libensemble/alloc_funcs/fast_alloc_to_aposmm.py +++ b/libensemble/alloc_funcs/fast_alloc_to_aposmm.py @@ -12,8 +12,8 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): more than ``gen_specs['user']['num_active_gen']`` active generators. Also allows for a 'batch_mode'. - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_aposmm_LD_MMA.py`` + .. seealso:: + `test_6-hump_camel_aposmm_LD_MMA.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/give_pregenerated_work.py b/libensemble/alloc_funcs/give_pregenerated_work.py index c64a6609d..4da5edb72 100644 --- a/libensemble/alloc_funcs/give_pregenerated_work.py +++ b/libensemble/alloc_funcs/give_pregenerated_work.py @@ -6,8 +6,8 @@ def give_pregenerated_sim_work(W, H, sim_specs, gen_specs, alloc_specs, persis_i This allocation function gives (in order) entries in alloc_spec['x'] to idle workers. It is an example use case where no gen_func is used. - :See: - ``/libensemble/tests/regression_tests/test_fast_alloc.py`` + .. seealso:: + `test_fast_alloc.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/give_sim_work_first.py b/libensemble/alloc_funcs/give_sim_work_first.py index 8525706c1..54a25aaa1 100644 --- a/libensemble/alloc_funcs/give_sim_work_first.py +++ b/libensemble/alloc_funcs/give_sim_work_first.py @@ -20,8 +20,8 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): This is the default allocation function if one is not defined. - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_uniform_sampling.py`` + .. seealso:: + `test_6-hump_camel_uniform_sampling.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/persistent_aposmm_alloc.py b/libensemble/alloc_funcs/persistent_aposmm_alloc.py index df0586274..5a87850c3 100644 --- a/libensemble/alloc_funcs/persistent_aposmm_alloc.py +++ b/libensemble/alloc_funcs/persistent_aposmm_alloc.py @@ -13,8 +13,8 @@ def persistent_aposmm_alloc(W, H, sim_specs, gen_specs, alloc_specs, persis_info This function assumes that one persistent APOSMM will be started and never stopped (until some exit_criterion is satisfied). - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_persistent_aposmm.py`` + .. seealso:: + `test_6-hump_camel_persistent_aposmm.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/start_only_persistent.py b/libensemble/alloc_funcs/start_only_persistent.py index 4b3543b60..3d832de45 100644 --- a/libensemble/alloc_funcs/start_only_persistent.py +++ b/libensemble/alloc_funcs/start_only_persistent.py @@ -10,8 +10,8 @@ def only_persistent_gens(W, H, sim_specs, gen_specs, alloc_specs, persis_info): the persistent generator have been returned from the simulation evaluation, then this information is given back to the persistent generator. - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_persistent_uniform_sampling.py`` + .. seealso:: + `test_6-hump_camel_persistent_uniform_sampling.py `_ """ Work = {} diff --git a/libensemble/alloc_funcs/start_persistent_local_opt_gens.py b/libensemble/alloc_funcs/start_persistent_local_opt_gens.py index a56b49906..698f158b9 100644 --- a/libensemble/alloc_funcs/start_persistent_local_opt_gens.py +++ b/libensemble/alloc_funcs/start_persistent_local_opt_gens.py @@ -20,8 +20,8 @@ def start_persistent_local_opt_gens(W, H, sim_specs, gen_specs, alloc_specs, per evaluated (oldest first). - If no points are left, call the generation function. - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_uniform_sampling_with_persistent_localopt_gens.py`` + .. seealso:: + `test_6-hump_camel_uniform_sampling_with_persistent_localopt_gens.py `_ """ Work = {} diff --git a/libensemble/gen_funcs/aposmm.py b/libensemble/gen_funcs/aposmm.py index 009411429..d83112f33 100644 --- a/libensemble/gen_funcs/aposmm.py +++ b/libensemble/gen_funcs/aposmm.py @@ -133,11 +133,12 @@ def aposmm_logic(H, persis_info, gen_specs, _): active runs, order of points in each run, etc. The allocation function must ensure it's always given. - :See: - ``libensemble/tests/regression_tests/test_branin_aposmm.py`` + .. seealso:: + `test_branin_aposmm_nlopt_and_then_scipy.py `_ for basic APOSMM usage. - :See: - ``libensemble/tests/regression_tests/test_chwirut_aposmm_one_residual_at_a_time.py`` + + .. seealso:: + `test_chwirut_aposmm_one_residual_at_a_time.py `_ for an example of APOSMM coordinating multiple local optimization runs for an objective with more than one component. """ @@ -371,8 +372,8 @@ def update_history_dist(H, n, gen_specs, c_flag): """ Updates distances/indices after new points that have been evaluated. - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ updated_inds = set() @@ -766,8 +767,8 @@ def decide_where_to_start_localopt(H, r_k, mu=0, nu=0, gamma_quantile=1): Indices where a local opt run should be started - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ if nu > 0: @@ -890,8 +891,8 @@ def initialize_APOSMM(H, gen_specs): """ Computes common values every time that APOSMM is reinvoked - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ user_specs = gen_specs['user'] diff --git a/libensemble/gen_funcs/persistent_aposmm.py b/libensemble/gen_funcs/persistent_aposmm.py index 7b085afd9..fea4c2f7b 100644 --- a/libensemble/gen_funcs/persistent_aposmm.py +++ b/libensemble/gen_funcs/persistent_aposmm.py @@ -141,11 +141,12 @@ def aposmm(H, persis_info, gen_specs, libE_info): active runs, order of points in each run, etc. The allocation function must ensure it's always given. - :See: - ``libensemble/tests/regression_tests/test_branin_aposmm.py`` + .. seealso:: + `test_branin_aposmm_nlopt_and_then_scipy.py `_ for basic APOSMM usage. - :See: - ``libensemble/tests/regression_tests/test_chwirut_aposmm_one_residual_at_a_time.py`` + + .. seealso:: + `test_chwirut_aposmm_one_residual_at_a_time.py `_ for an example of APOSMM coordinating multiple local optimization runs for an objective with more than one component. """ @@ -671,8 +672,8 @@ def update_history_dist(H, n): """ Updates distances/indices after new points that have been evaluated. - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ new_inds = np.where(~H['known_to_aposmm'])[0] @@ -803,8 +804,8 @@ def decide_where_to_start_localopt(H, n, n_s, rk_const, ld=0, mu=0, nu=0): Indices where a local opt run should be started - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ r_k = calc_rk(n, n_s, rk_const, ld) @@ -895,8 +896,8 @@ def initialize_APOSMM(H, user_specs, libE_info): """ Computes common values every time that APOSMM is reinvoked - :See: - ``/libensemble/alloc_funcs/start_persistent_local_opt_gens.py`` + .. seealso:: + `start_persistent_local_opt_gens.py `_ """ n = len(user_specs['ub']) diff --git a/libensemble/gen_funcs/persistent_uniform_sampling.py b/libensemble/gen_funcs/persistent_uniform_sampling.py index ed51ec599..6f3a826ce 100644 --- a/libensemble/gen_funcs/persistent_uniform_sampling.py +++ b/libensemble/gen_funcs/persistent_uniform_sampling.py @@ -9,8 +9,8 @@ def persistent_uniform(H, persis_info, gen_specs, libE_info): This generation function always enters into persistent mode and returns ``gen_specs['gen_batch_size']`` uniformly sampled points. - :See: - ``libensemble/libensemble/tests/regression_tests/test_6-hump_camel_persistent_uniform_sampling.py`` + .. seealso:: + `test_6-hump_camel_persistent_uniform_sampling.py `_ """ ub = gen_specs['user']['ub'] lb = gen_specs['user']['lb'] diff --git a/libensemble/gen_funcs/sampling.py b/libensemble/gen_funcs/sampling.py index bc045edbe..06b35c118 100644 --- a/libensemble/gen_funcs/sampling.py +++ b/libensemble/gen_funcs/sampling.py @@ -12,8 +12,8 @@ def uniform_random_sample_with_different_nodes_and_ranks(H, persis_info, gen_spe ``gen_specs['user']['lb']``. Also randomly requests a different ``number_of_nodes`` and ``ranks_per_node`` to be used in the evaluation of the generated point. - :See: - ``libensemble/tests/regression_tests/test_6-hump_camel_with_different_nodes_uniform_sample.py`` + .. seealso:: + `test_6-hump_camel_with_different_nodes_uniform_sample.py `_ """ ub = gen_specs['user']['ub'] lb = gen_specs['user']['lb'] @@ -46,8 +46,8 @@ def uniform_random_sample_obj_components(H, persis_info, gen_specs, _): and ``gen_specs['user']['lb']`` but requests each ``obj_component`` be evaluated separately. - :See: - ``libensemble/tests/regression_tests/test_chwirut_uniform_sampling_one_residual_at_a_time.py`` + .. seealso:: + `test_chwirut_uniform_sampling_one_residual_at_a_time.py `_ """ ub = gen_specs['user']['ub'] lb = gen_specs['user']['lb'] @@ -74,8 +74,8 @@ def uniform_random_sample(H, persis_info, gen_specs, _): Generates ``gen_specs['user']['gen_batch_size']`` points uniformly over the domain defined by ``gen_specs['user']['ub']`` and ``gen_specs['user']['lb']``. - :See: - ``libensemble/tests/regression_tests/test_6-hump_camel_uniform_sampling.py`` + .. seealso:: + `test_6-hump_camel_uniform_sampling.py `_ """ ub = gen_specs['user']['ub'] lb = gen_specs['user']['lb'] diff --git a/libensemble/gen_funcs/uniform_or_localopt.py b/libensemble/gen_funcs/uniform_or_localopt.py index 53342f15c..a2830832a 100644 --- a/libensemble/gen_funcs/uniform_or_localopt.py +++ b/libensemble/gen_funcs/uniform_or_localopt.py @@ -15,8 +15,8 @@ def uniform_or_localopt(H, persis_info, gen_specs, libE_info): ``libE_info['persistent']`` isn't ``True``). Otherwise, the generation function a persistent nlopt local optimization run. - :See: - ``libensemble/tests/regression_tests/test_6-hump_camel_uniform_sampling_with_persistent_localopt_gens.py`` + .. seealso:: + `test_6-hump_camel_uniform_sampling_with_persistent_localopt_gens.py `_ """ if libE_info.get('persistent'): diff --git a/libensemble/sim_funcs/chwirut1.py b/libensemble/sim_funcs/chwirut1.py index 59c205b33..856ebbaa0 100644 --- a/libensemble/sim_funcs/chwirut1.py +++ b/libensemble/sim_funcs/chwirut1.py @@ -260,11 +260,13 @@ def chwirut_eval(H, persis_info, sim_specs, _): component of the objective will be evaluated. Otherwise, all 214 components are evaluated and returned in the ``'fvec'`` field. - :See: - ``/libensemble/tests/regression_tests/test_chwirut_pounders.py`` for an example where the entire fvec is computed. + .. seealso:: + `test_chwirut_pounders.py `_ + for an example where the entire fvec is computed each call. - :See: - ``/libensemble/tests/regression_tests/test_chwirut_aposmm_one_residual_at_a_time.py`` + .. seealso:: + `test_chwirut_aposmm_one_residual_at_a_time.py `_ + for an example where one component of fvec is computed per call """ batch = len(H['x']) diff --git a/libensemble/sim_funcs/one_d_func.py b/libensemble/sim_funcs/one_d_func.py index 07201eb19..f0dadb2ec 100644 --- a/libensemble/sim_funcs/one_d_func.py +++ b/libensemble/sim_funcs/one_d_func.py @@ -10,8 +10,8 @@ def one_d_example(x, persis_info, sim_specs, _): """ Evaluates the six hump camel function for a single point ``x``. - :See: - ``/libensemble/libensemble/tests/regression_tests/test_fast_alloc.py`` + .. seealso:: + `test_fast_alloc.py `_ """ O = np.zeros(1, dtype=sim_specs['out']) diff --git a/libensemble/sim_funcs/six_hump_camel.py b/libensemble/sim_funcs/six_hump_camel.py index 7f51e14d8..69a44a3e1 100644 --- a/libensemble/sim_funcs/six_hump_camel.py +++ b/libensemble/sim_funcs/six_hump_camel.py @@ -15,8 +15,8 @@ def six_hump_camel_with_different_ranks_and_nodes(H, persis_info, sim_specs, lib performs a system call with a given number of nodes and ranks per node using a machinefile (to show one way of evaluating a compiled simulation). - :See: - ``/libensemble/tests/regression_tests/test_6-hump_camel_with_different_nodes_uniform_sample.py`` + .. seealso:: + `test_6-hump_camel_with_different_nodes_uniform_sample.py `_ """ from mpi4py import MPI @@ -60,8 +60,8 @@ def six_hump_camel(H, persis_info, sim_specs, _): ``sim_specs['out']`` and pauses for ``sim_specs['user']['pause_time']]`` if defined. - :See: - ``/libensemble/libensemble/tests/regression_tests/test_6-hump_camel_aposmm_LD_MMA.py`` + .. seealso:: + `test_6-hump_camel_aposmm_LD_MMA.py `_ """ batch = len(H['x']) @@ -83,8 +83,8 @@ def six_hump_camel_simple(x, persis_info, sim_specs, _): """ Evaluates the six hump camel function for a single point ``x``. - :See: - ``/libensemble/libensemble/tests/regression_tests/test_fast_alloc.py`` + .. seealso:: + `test_fast_alloc.py `_ """ O = np.zeros(1, dtype=sim_specs['out'])