Restructure estimagic.

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,

src/estimagic/inference/bootstrap.py → 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

src/estimagic/inference/bootstrap_ci.py → 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(

src/estimagic/inference/bootstrap_outcomes.py → 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(

src/estimagic/estimation/estimate_ml.py → 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,

src/estimagic/estimation/estimate_msm.py → 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,

src/estimagic/inference/ml_covs.py → 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
 
 

src/estimagic/inference/msm_covs.py → 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
 
 

src/estimagic/sensitivity/msm_sensitivity.py → 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
 
 

src/estimagic/estimation/msm_weighting.py → 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

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

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,

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

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,

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
 

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,
 )

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,

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,

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

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,

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,

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
 

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,

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():