diff --git a/src/estimagic/__init__.py b/src/estimagic/__init__.py index e0342c416..5d7fa71be 100644 --- a/src/estimagic/__init__.py +++ b/src/estimagic/__init__.py @@ -1,8 +1,8 @@ -from estimagic.estimation.estimate_ml import LikelihoodResult, estimate_ml -from estimagic.estimation.estimate_msm import MomentsResult, estimate_msm -from estimagic.estimation.msm_weighting import get_moments_cov -from estimagic.inference.bootstrap import BootstrapResult, bootstrap -from estimagic.visualization.estimation_table import ( +from estimagic.estimate_ml import LikelihoodResult, estimate_ml +from estimagic.estimate_msm import MomentsResult, estimate_msm +from estimagic.msm_weighting import get_moments_cov +from estimagic.bootstrap import BootstrapResult, bootstrap +from estimagic.estimation_table import ( estimation_table, render_html, render_latex, diff --git a/src/estimagic/inference/bootstrap.py b/src/estimagic/bootstrap.py similarity index 97% rename from src/estimagic/inference/bootstrap.py rename to src/estimagic/bootstrap.py index dcdae775e..526593cf1 100644 --- a/src/estimagic/inference/bootstrap.py +++ b/src/estimagic/bootstrap.py @@ -8,10 +8,10 @@ from pybaum import leaf_names, tree_flatten, tree_just_flatten, tree_unflatten from optimagic.batch_evaluators import joblib_batch_evaluator -from estimagic.inference.bootstrap_ci import calculate_ci -from estimagic.inference.bootstrap_helpers import check_inputs -from estimagic.inference.bootstrap_outcomes import get_bootstrap_outcomes -from estimagic.inference.shared import calculate_estimation_summary +from estimagic.bootstrap_ci import calculate_ci +from estimagic.bootstrap_helpers import check_inputs +from estimagic.bootstrap_outcomes import get_bootstrap_outcomes +from estimagic.shared_covs import calculate_estimation_summary from optimagic.parameters.block_trees import matrix_to_block_tree from optimagic.parameters.tree_registry import get_registry from optimagic.utilities import get_rng diff --git a/src/estimagic/inference/bootstrap_ci.py b/src/estimagic/bootstrap_ci.py similarity index 99% rename from src/estimagic/inference/bootstrap_ci.py rename to src/estimagic/bootstrap_ci.py index fc932935b..ad86054cf 100644 --- a/src/estimagic/inference/bootstrap_ci.py +++ b/src/estimagic/bootstrap_ci.py @@ -1,7 +1,7 @@ import numpy as np from scipy.stats import norm -from estimagic.inference.bootstrap_helpers import check_inputs +from estimagic.bootstrap_helpers import check_inputs def calculate_ci( diff --git a/src/estimagic/inference/bootstrap_helpers.py b/src/estimagic/bootstrap_helpers.py similarity index 100% rename from src/estimagic/inference/bootstrap_helpers.py rename to src/estimagic/bootstrap_helpers.py diff --git a/src/estimagic/inference/bootstrap_outcomes.py b/src/estimagic/bootstrap_outcomes.py similarity index 95% rename from src/estimagic/inference/bootstrap_outcomes.py rename to src/estimagic/bootstrap_outcomes.py index 59973dc7b..c92917426 100644 --- a/src/estimagic/inference/bootstrap_outcomes.py +++ b/src/estimagic/bootstrap_outcomes.py @@ -1,6 +1,6 @@ from optimagic.batch_evaluators import process_batch_evaluator -from estimagic.inference.bootstrap_helpers import check_inputs -from estimagic.inference.bootstrap_samples import get_bootstrap_indices +from estimagic.bootstrap_helpers import check_inputs +from estimagic.bootstrap_samples import get_bootstrap_indices def get_bootstrap_outcomes( diff --git a/src/estimagic/inference/bootstrap_samples.py b/src/estimagic/bootstrap_samples.py similarity index 100% rename from src/estimagic/inference/bootstrap_samples.py rename to src/estimagic/bootstrap_samples.py diff --git a/src/estimagic/estimation/estimate_ml.py b/src/estimagic/estimate_ml.py similarity index 99% rename from src/estimagic/estimation/estimate_ml.py rename to src/estimagic/estimate_ml.py index 608363b80..714ca76b0 100644 --- a/src/estimagic/estimation/estimate_ml.py +++ b/src/estimagic/estimate_ml.py @@ -8,14 +8,14 @@ from optimagic.differentiation.derivatives import first_derivative, second_derivative from optimagic.exceptions import InvalidFunctionError, NotAvailableError -from estimagic.inference.ml_covs import ( +from estimagic.ml_covs import ( cov_cluster_robust, cov_hessian, cov_jacobian, cov_robust, cov_strata_robust, ) -from estimagic.inference.shared import ( +from estimagic.shared_covs import ( FreeParams, calculate_ci, calculate_estimation_summary, diff --git a/src/estimagic/estimation/estimate_msm.py b/src/estimagic/estimate_msm.py similarity index 99% rename from src/estimagic/estimation/estimate_msm.py rename to src/estimagic/estimate_msm.py index aaf56e649..1c807118c 100644 --- a/src/estimagic/estimation/estimate_msm.py +++ b/src/estimagic/estimate_msm.py @@ -12,10 +12,10 @@ from pybaum import leaf_names, tree_just_flatten from optimagic.differentiation.derivatives import first_derivative -from estimagic.estimation.msm_weighting import get_weighting_matrix +from estimagic.msm_weighting import get_weighting_matrix from optimagic.exceptions import InvalidFunctionError -from estimagic.inference.msm_covs import cov_optimal, cov_robust -from estimagic.inference.shared import ( +from estimagic.msm_covs import cov_optimal, cov_robust +from estimagic.shared_covs import ( FreeParams, calculate_ci, calculate_estimation_summary, @@ -33,7 +33,7 @@ from optimagic.parameters.conversion import Converter, get_converter from optimagic.parameters.space_conversion import InternalParams from optimagic.parameters.tree_registry import get_registry -from estimagic.sensitivity.msm_sensitivity import ( +from estimagic.msm_sensitivity import ( calculate_actual_sensitivity_to_noise, calculate_actual_sensitivity_to_removal, calculate_fundamental_sensitivity_to_noise, diff --git a/src/estimagic/estimation/__init__.py b/src/estimagic/estimation/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/src/estimagic/estimation/estimation_summaries.py b/src/estimagic/estimation_summaries.py similarity index 100% rename from src/estimagic/estimation/estimation_summaries.py rename to src/estimagic/estimation_summaries.py diff --git a/src/estimagic/visualization/estimation_table.py b/src/estimagic/estimation_table.py similarity index 100% rename from src/estimagic/visualization/estimation_table.py rename to src/estimagic/estimation_table.py diff --git a/src/estimagic/inference/__init__.py b/src/estimagic/inference/__init__.py deleted file mode 100644 index 9d1a7c32b..000000000 --- a/src/estimagic/inference/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -from estimagic.inference.bootstrap import bootstrap # noqa: F401 -from estimagic.inference.bootstrap_outcomes import get_bootstrap_outcomes # noqa: F401 -from estimagic.inference.bootstrap_samples import ( - get_bootstrap_indices, # noqa: F401 - get_bootstrap_samples, # noqa: F401 -) diff --git a/src/estimagic/visualization/lollipop_plot.py b/src/estimagic/lollipop_plot.py similarity index 100% rename from src/estimagic/visualization/lollipop_plot.py rename to src/estimagic/lollipop_plot.py diff --git a/src/estimagic/inference/ml_covs.py b/src/estimagic/ml_covs.py similarity index 99% rename from src/estimagic/inference/ml_covs.py rename to src/estimagic/ml_covs.py index 54a6a6cbb..a641b147c 100644 --- a/src/estimagic/inference/ml_covs.py +++ b/src/estimagic/ml_covs.py @@ -4,7 +4,7 @@ import pandas as pd from optimagic.exceptions import INVALID_INFERENCE_MSG -from estimagic.inference.shared import process_pandas_arguments +from estimagic.shared_covs import process_pandas_arguments from optimagic.utilities import robust_inverse diff --git a/src/estimagic/inference/msm_covs.py b/src/estimagic/msm_covs.py similarity index 97% rename from src/estimagic/inference/msm_covs.py rename to src/estimagic/msm_covs.py index 6aa2d61ef..13155f53a 100644 --- a/src/estimagic/inference/msm_covs.py +++ b/src/estimagic/msm_covs.py @@ -1,7 +1,7 @@ import pandas as pd from optimagic.exceptions import INVALID_INFERENCE_MSG -from estimagic.inference.shared import process_pandas_arguments +from estimagic.shared_covs import process_pandas_arguments from optimagic.utilities import robust_inverse diff --git a/src/estimagic/sensitivity/msm_sensitivity.py b/src/estimagic/msm_sensitivity.py similarity index 99% rename from src/estimagic/sensitivity/msm_sensitivity.py rename to src/estimagic/msm_sensitivity.py index ae9a32ef1..8b695bcc9 100644 --- a/src/estimagic/sensitivity/msm_sensitivity.py +++ b/src/estimagic/msm_sensitivity.py @@ -11,8 +11,8 @@ import numpy as np import pandas as pd from optimagic.exceptions import INVALID_SENSITIVITY_MSG -from estimagic.inference.msm_covs import cov_robust -from estimagic.inference.shared import process_pandas_arguments +from estimagic.msm_covs import cov_robust +from estimagic.shared_covs import process_pandas_arguments from optimagic.utilities import robust_inverse diff --git a/src/estimagic/estimation/msm_weighting.py b/src/estimagic/msm_weighting.py similarity index 99% rename from src/estimagic/estimation/msm_weighting.py rename to src/estimagic/msm_weighting.py index 59105c17d..4b26a7e42 100644 --- a/src/estimagic/estimation/msm_weighting.py +++ b/src/estimagic/msm_weighting.py @@ -5,7 +5,7 @@ from pybaum import tree_just_flatten from scipy.linalg import block_diag -from estimagic.inference.bootstrap import bootstrap +from estimagic.bootstrap import bootstrap from optimagic.parameters.block_trees import block_tree_to_matrix, matrix_to_block_tree from optimagic.parameters.tree_registry import get_registry from optimagic.utilities import robust_inverse diff --git a/src/estimagic/sensitivity/__init__.py b/src/estimagic/sensitivity/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/src/estimagic/inference/shared.py b/src/estimagic/shared_covs.py similarity index 100% rename from src/estimagic/inference/shared.py rename to src/estimagic/shared_covs.py diff --git a/src/estimagic/visualization/__init__.py b/src/estimagic/visualization/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/estimagic/estimation/test_estimate_ml.py b/tests/estimagic/estimation/test_estimate_ml.py index 7cdb348db..17245517d 100644 --- a/tests/estimagic/estimation/test_estimate_ml.py +++ b/tests/estimagic/estimation/test_estimate_ml.py @@ -5,7 +5,7 @@ import pytest import scipy as sp import statsmodels.api as sm -from estimagic.estimation.estimate_ml import estimate_ml +from estimagic.estimate_ml import estimate_ml from estimagic.examples.logit import logit_derivative, logit_hessian, logit_loglike from estimagic.examples.logit import logit_loglike_and_derivative as llad from numpy.testing import assert_array_equal diff --git a/tests/estimagic/estimation/test_estimate_msm.py b/tests/estimagic/estimation/test_estimate_msm.py index 23537e21b..ee8b16070 100644 --- a/tests/estimagic/estimation/test_estimate_msm.py +++ b/tests/estimagic/estimation/test_estimate_msm.py @@ -6,7 +6,7 @@ import pandas as pd import pytest from optimagic.optimization.optimize_result import OptimizeResult -from estimagic.estimation.estimate_msm import estimate_msm +from estimagic.estimate_msm import estimate_msm from optimagic.shared.check_option_dicts import ( check_numdiff_options, check_optimization_options, diff --git a/tests/estimagic/estimation/test_estimate_msm_dict_params_and_moments.py b/tests/estimagic/estimation/test_estimate_msm_dict_params_and_moments.py index a850bbcbb..b60a97639 100644 --- a/tests/estimagic/estimation/test_estimate_msm_dict_params_and_moments.py +++ b/tests/estimagic/estimation/test_estimate_msm_dict_params_and_moments.py @@ -2,7 +2,7 @@ import numpy as np import pandas as pd -from estimagic.estimation.estimate_msm import estimate_msm +from estimagic.estimate_msm import estimate_msm from optimagic.parameters.tree_registry import get_registry from numpy.testing import assert_array_almost_equal as aaae from pybaum import tree_just_flatten diff --git a/tests/estimagic/estimation/test_msm_weighting.py b/tests/estimagic/estimation/test_msm_weighting.py index d7980b6dd..3a7408365 100644 --- a/tests/estimagic/estimation/test_msm_weighting.py +++ b/tests/estimagic/estimation/test_msm_weighting.py @@ -3,7 +3,7 @@ import numpy as np import pandas as pd import pytest -from estimagic.estimation.msm_weighting import ( +from estimagic.msm_weighting import ( _assemble_block_diagonal_matrix, get_moments_cov, get_weighting_matrix, diff --git a/tests/estimagic/inference/test_bootstrap_ci.py b/tests/estimagic/inference/test_bootstrap_ci.py index 53725185b..ebb716f46 100644 --- a/tests/estimagic/inference/test_bootstrap_ci.py +++ b/tests/estimagic/inference/test_bootstrap_ci.py @@ -3,8 +3,8 @@ import numpy as np import pandas as pd import pytest -from estimagic.inference.bootstrap_ci import calculate_ci -from estimagic.inference.bootstrap_ci import check_inputs +from estimagic.bootstrap_ci import calculate_ci +from estimagic.bootstrap_ci import check_inputs from optimagic.parameters.tree_registry import get_registry from pybaum import tree_just_flatten diff --git a/tests/estimagic/inference/test_bootstrap_outcomes.py b/tests/estimagic/inference/test_bootstrap_outcomes.py index e3945dc4b..5ef52ff1d 100644 --- a/tests/estimagic/inference/test_bootstrap_outcomes.py +++ b/tests/estimagic/inference/test_bootstrap_outcomes.py @@ -4,7 +4,7 @@ import pandas as pd import pytest from optimagic.batch_evaluators import joblib_batch_evaluator -from estimagic.inference.bootstrap_outcomes import ( +from estimagic.bootstrap_outcomes import ( _get_bootstrap_outcomes_from_indices, get_bootstrap_outcomes, ) diff --git a/tests/estimagic/inference/test_bootstrap_samples.py b/tests/estimagic/inference/test_bootstrap_samples.py index 6ee7987bd..ebc6f8a23 100644 --- a/tests/estimagic/inference/test_bootstrap_samples.py +++ b/tests/estimagic/inference/test_bootstrap_samples.py @@ -1,7 +1,7 @@ import numpy as np import pandas as pd import pytest -from estimagic.inference.bootstrap_samples import ( +from estimagic.bootstrap_samples import ( _convert_cluster_ids_to_indices, _get_bootstrap_samples_from_indices, get_bootstrap_indices, diff --git a/tests/estimagic/inference/test_ml_covs.py b/tests/estimagic/inference/test_ml_covs.py index 08e1923b0..2ea902e57 100644 --- a/tests/estimagic/inference/test_ml_covs.py +++ b/tests/estimagic/inference/test_ml_covs.py @@ -4,8 +4,8 @@ import numpy as np import pandas as pd import pytest -from estimagic.inference import ml_covs -from estimagic.inference.ml_covs import ( +from estimagic import ml_covs +from estimagic.ml_covs import ( _clustering, _sandwich_step, _stratification, diff --git a/tests/estimagic/inference/test_msm_covs.py b/tests/estimagic/inference/test_msm_covs.py index 9df183190..4711b78d2 100644 --- a/tests/estimagic/inference/test_msm_covs.py +++ b/tests/estimagic/inference/test_msm_covs.py @@ -3,7 +3,7 @@ import numpy as np import pandas as pd import pytest -from estimagic.inference.msm_covs import cov_optimal, cov_robust +from estimagic.msm_covs import cov_optimal, cov_robust from optimagic.utilities import get_rng from numpy.testing import assert_array_almost_equal as aaae from pandas.testing import assert_frame_equal diff --git a/tests/estimagic/inference/test_shared.py b/tests/estimagic/inference/test_shared.py index 0857dce94..f4a23f9af 100644 --- a/tests/estimagic/inference/test_shared.py +++ b/tests/estimagic/inference/test_shared.py @@ -3,7 +3,7 @@ import numpy as np import pandas as pd import pytest -from estimagic.inference.shared import ( +from estimagic.shared_covs import ( _to_numpy, calculate_estimation_summary, get_derivative_case, diff --git a/tests/estimagic/sensitivity/test_msm_sensitivity.py b/tests/estimagic/sensitivity/test_msm_sensitivity.py index ae0670fa7..3c772c581 100644 --- a/tests/estimagic/sensitivity/test_msm_sensitivity.py +++ b/tests/estimagic/sensitivity/test_msm_sensitivity.py @@ -3,8 +3,8 @@ import pytest from estimagic.config import EXAMPLE_DIR from optimagic.differentiation.derivatives import first_derivative -from estimagic.inference.msm_covs import cov_optimal -from estimagic.sensitivity.msm_sensitivity import ( +from estimagic.msm_covs import cov_optimal +from estimagic.msm_sensitivity import ( calculate_actual_sensitivity_to_noise, calculate_actual_sensitivity_to_removal, calculate_fundamental_sensitivity_to_noise, diff --git a/tests/estimagic/sensitivity/test_msm_sensitivity_via_estimate_msm.py b/tests/estimagic/sensitivity/test_msm_sensitivity_via_estimate_msm.py index bc6bc17db..994b6c526 100644 --- a/tests/estimagic/sensitivity/test_msm_sensitivity_via_estimate_msm.py +++ b/tests/estimagic/sensitivity/test_msm_sensitivity_via_estimate_msm.py @@ -2,7 +2,7 @@ import pandas as pd import pytest from estimagic.config import EXAMPLE_DIR -from estimagic.estimation.estimate_msm import estimate_msm +from estimagic.estimate_msm import estimate_msm from numpy.testing import assert_array_almost_equal as aaae from scipy import stats diff --git a/tests/estimagic/visualization/test_estimation_table.py b/tests/estimagic/visualization/test_estimation_table.py index eb28da4e6..4baa20839 100644 --- a/tests/estimagic/visualization/test_estimation_table.py +++ b/tests/estimagic/visualization/test_estimation_table.py @@ -6,7 +6,7 @@ import pytest import statsmodels.api as sm from estimagic.config import EXAMPLE_DIR -from estimagic.visualization.estimation_table import ( +from estimagic.estimation_table import ( _apply_number_format, _check_order_of_model_names, _convert_frame_to_string_series, diff --git a/tests/estimagic/visualization/test_lollipop_plot.py b/tests/estimagic/visualization/test_lollipop_plot.py index fe0a801ae..06a4552b3 100644 --- a/tests/estimagic/visualization/test_lollipop_plot.py +++ b/tests/estimagic/visualization/test_lollipop_plot.py @@ -1,6 +1,6 @@ import numpy as np import pandas as pd -from estimagic.visualization.lollipop_plot import lollipop_plot +from estimagic.lollipop_plot import lollipop_plot def test_lollipop_plot_runs():