From fe780ef1996f27a5bdf6be2be722d48b13ad0cc3 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 00:00:24 -0700 Subject: [PATCH 1/9] renaming to selectinf --- {selection => selectinf}/__init__.py | 0 {selection => selectinf}/_version.py | 0 .../algorithms/__init__.py | 0 {selection => selectinf}/algorithms/api.py | 0 .../algorithms/change_point.py | 0 .../algorithms/covtest.py | 0 {selection => selectinf}/algorithms/cv.py | 0 .../algorithms/cv_glmnet.py | 0 .../algorithms/debiased_lasso.py | 0 .../algorithms/debiased_lasso_utils.pyx | 0 .../algorithms/forward_step.py | 0 {selection => selectinf}/algorithms/lasso.py | 0 {selection => selectinf}/algorithms/pca.py | 0 .../algorithms/screening.py | 0 .../algorithms/softmax.py | 0 .../algorithms/sqrt_lasso.py | 0 .../algorithms/stopping_rules.py | 0 .../algorithms/tests/__init__.py | 0 .../algorithms/tests/test_IC.py | 0 .../algorithms/tests/test_ROSI.py | 0 .../algorithms/tests/test_change_point.py | 0 .../algorithms/tests/test_compareR.py | 0 .../algorithms/tests/test_covtest.py | 0 .../algorithms/tests/test_data_carving.py | 0 .../algorithms/tests/test_debiased_lasso.py | 0 .../algorithms/tests/test_forward_step.py | 0 .../algorithms/tests/test_lasso.py | 0 .../algorithms/tests/test_screening.py | 0 .../algorithms/tests/test_softmax.py | 0 .../algorithms/tests/test_sqrt_lasso.py | 0 {selection => selectinf}/api.py | 0 {selection => selectinf}/base.py | 0 .../constraints/__init__.py | 0 .../constraints/affine.py | 0 {selection => selectinf}/constraints/api.py | 0 {selection => selectinf}/constraints/base.py | 0 .../constraints/estimation.py | 0 .../constraints/intervals.py | 0 .../constraints/quadratic.py | 0 .../constraints/quasi_affine.py | 0 .../constraints/tests/__init__.py | 0 .../constraints/tests/test_affine.py | 0 .../constraints/tests/test_estimation.py | 0 .../constraints/tests/test_quadratic_tests.py | 0 .../constraints/tests/test_quasi.py | 0 .../constraints/tests/test_unknown_sigma.py | 0 .../distributions/__init__.py | 0 {selection => selectinf}/distributions/api.py | 0 .../distributions/chain.py | 0 .../distributions/chisq.py | 0 .../distributions/discrete_family.py | 0 .../distributions/discrete_multiparameter.py | 0 .../distributions/intervals.py | 0 .../distributions/pvalue.py | 0 .../distributions/tests/__init__.py | 0 .../distributions/tests/test_chains.py | 0 .../distributions/tests/test_discreteExFam.py | 0 .../tests/test_multiparameter.py | 0 {selection => selectinf}/glm.py | 0 {selection => selectinf}/info.py | 10 ++-- {selection => selectinf}/learning/Rfitters.py | 0 {selection => selectinf}/learning/Rutils.py | 0 {selection => selectinf}/learning/__init__.py | 0 {selection => selectinf}/learning/core.py | 0 {selection => selectinf}/learning/fitters.py | 0 .../learning/keras_fit.py | 0 {selection => selectinf}/learning/learners.py | 0 {selection => selectinf}/learning/samplers.py | 0 {selection => selectinf}/learning/utils.py | 0 .../randomized/__init__.py | 0 {selection => selectinf}/randomized/api.py | 0 .../randomized/cv_view.py | 0 .../randomized/group_lasso.py | 0 {selection => selectinf}/randomized/lasso.py | 0 {selection => selectinf}/randomized/modelQ.py | 0 {selection => selectinf}/randomized/query.py | 0 .../randomized/randomization.py | 0 .../sandbox/M_estimator_group_lasso.py | 0 .../sandbox/M_estimator_nonrandom.py | 0 .../randomized/sandbox/convenience.py | 0 .../randomized/sandbox/general_lasso.py | 0 .../randomized/sandbox/greedy_step.py | 0 .../randomized/sandbox/group_lasso.py | 0 .../randomized/sandbox/lasso_iv.py | 0 .../randomized/screening.py | 0 .../randomized/selective_MLE_utils.pyx | 0 {selection => selectinf}/randomized/slope.py | 0 .../randomized/tests/__init__.py | 0 .../randomized/tests/sandbox/test_Mest.py | 0 .../tests/sandbox/test_convenience.py | 0 .../randomized/tests/sandbox/test_cv.py | 0 .../test_cv_corrected_nonrandomized_lasso.py | 0 .../tests/sandbox/test_cv_glmnet.py | 0 .../tests/sandbox/test_cv_lee_et_al.py | 0 .../tests/sandbox/test_decompose_subgrad.py | 0 .../randomized/tests/sandbox/test_fixedX.py | 0 .../tests/sandbox/test_full_lasso.py | 0 .../tests/sandbox/test_general_lasso.py | 0 .../tests/sandbox/test_general_lasso_pval.py | 0 .../tests/sandbox/test_intervals.py | 0 .../randomized/tests/sandbox/test_lasso_iv.py | 0 .../tests/sandbox/test_multiple_splits.py | 0 .../sandbox/test_opt_weighted_intervals.py | 0 .../sandbox/test_optimization_sampler.py | 0 .../randomized/tests/sandbox/test_sampling.py | 0 .../randomized/tests/sandbox/test_split.py | 0 .../tests/sandbox/test_split_compare.py | 0 .../tests/sandbox/test_sqrt_lasso.py | 0 .../randomized/tests/test_BH.py | 0 .../randomized/tests/test_group_lasso.py | 0 .../randomized/tests/test_lasso.py | 0 .../tests/test_marginal_screening.py | 0 .../randomized/tests/test_modelQ.py | 0 .../randomized/tests/test_multiple_queries.py | 0 .../randomized/tests/test_naive.py | 0 .../randomized/tests/test_randomization.py | 0 .../randomized/tests/test_selective_MLE.py | 0 .../tests/test_selective_MLE_high.py | 0 .../tests/test_selective_MLE_onedim.py | 0 .../randomized/tests/test_slope.py | 0 .../randomized/tests/test_slope_subgrad.py | 0 .../randomized/tests/test_split_lasso.py | 0 .../randomized/tests/test_topK.py | 0 .../reduced_optimization/tests/__init__.py | 0 {selection => selectinf}/sampling/__init__.py | 0 {selection => selectinf}/sampling/api.py | 0 {selection => selectinf}/sampling/langevin.py | 0 .../sampling/sequential.py | 0 .../sampling/sqrt_lasso.pyx | 0 .../sampling/tests/__init__.py | 0 .../sampling/tests/plots_fs.py | 0 .../sampling/tests/test_fstep_langevin.py | 0 .../sampling/tests/test_kfstep.py | 0 .../sampling/tests/test_pca_langevin.py | 0 .../sampling/tests/test_sample_sphere.py | 0 .../sampling/tests/test_sequential.py | 0 .../sampling/truncnorm.pyx | 0 .../sampling/truncnorm_quadratic.pyx | 0 .../sandbox/approx_ci/__init__.py | 0 .../sandbox/approx_ci/ci_approx_density.py | 0 .../approx_ci/ci_approx_greedy_step.py | 0 .../sandbox/approx_ci/selection_map.py | 0 .../sandbox/approx_ci/tests/__init__.py | 0 .../sandbox/approx_ci/tests/test_glm.py | 0 .../approx_ci/tests/test_greedy_step.py | 0 .../approx_ci/tests/test_threshold_score.py | 0 .../sandbox/bayesian/__init__.py | 0 .../sandbox/bayesian/barrier.py | 0 .../sandbox/bayesian/credible_intervals.py | 0 .../sandbox/bayesian/dual_lasso.py | 0 .../sandbox/bayesian/estimator.py | 0 .../bayesian/forward_stepwise_reduced.py | 0 .../sandbox/bayesian/initial_soln.py | 0 .../sandbox/bayesian/lasso_reduced.py | 0 .../bayesian/marginal_screening_reduced.py | 0 .../bayesian/ms_lasso_2stage_reduced.py | 0 .../sandbox/bayesian/par_carved_reduced.py | 0 .../bayesian/par_random_lasso_reduced.py | 0 .../sandbox/bayesian/random_lasso_reduced.py | 0 .../sandbox/bayesian/tests/__init__.py | 0 .../bayesian/tests/test_carved_lasso.py | 0 .../sandbox/bayesian/tests/test_dual_lasso.py | 0 .../sandbox/bayesian/tests/test_fs.py | 0 .../sandbox/bayesian/tests/test_lasso.py | 0 .../bayesian/tests/test_ms_lasso_2stage.py | 0 .../src_C/#sample_preparation.pyx# | 0 {selection => selectinf}/src_C/HmcSampler.cpp | 0 {selection => selectinf}/src_C/HmcSampler.h | 0 {selection => selectinf}/src_C/logfile.txt | 0 .../src_C/preparation_Eig_Vect.cpp | 0 .../src_C/preparation_Eig_Vect.h | 0 .../src_C/sample_preparation.cpp | 0 .../src_C/sample_preparation.pyx | 0 {selection => selectinf}/src_C/setup.py | 0 {selection => selectinf}/tests/__init__.py | 0 {selection => selectinf}/tests/decorators.py | 0 {selection => selectinf}/tests/flags.py | 0 {selection => selectinf}/tests/instance.py | 0 .../tests/test_instance.py | 0 {selection => selectinf}/tests/tests.py | 0 {selection => selectinf}/truncated/F.py | 0 {selection => selectinf}/truncated/T.py | 0 .../truncated/__init__.py | 0 {selection => selectinf}/truncated/api.py | 0 {selection => selectinf}/truncated/base.py | 0 {selection => selectinf}/truncated/chi.py | 0 .../truncated/gaussian.py | 0 .../truncated/tests/__init__.py | 0 .../truncated/tests/test_truncated.py | 0 .../truncated/tests/test_truncatedFT.py | 0 {selection => selectinf}/utils/__init__.py | 0 {selection => selectinf}/utils/tools.py | 0 setup.py | 51 ++++++++++--------- 193 files changed, 31 insertions(+), 30 deletions(-) rename {selection => selectinf}/__init__.py (100%) rename {selection => selectinf}/_version.py (100%) rename {selection => selectinf}/algorithms/__init__.py (100%) rename {selection => selectinf}/algorithms/api.py (100%) rename {selection => selectinf}/algorithms/change_point.py (100%) rename {selection => selectinf}/algorithms/covtest.py (100%) rename {selection => selectinf}/algorithms/cv.py (100%) rename {selection => selectinf}/algorithms/cv_glmnet.py (100%) rename {selection => selectinf}/algorithms/debiased_lasso.py (100%) rename {selection => selectinf}/algorithms/debiased_lasso_utils.pyx (100%) rename {selection => selectinf}/algorithms/forward_step.py (100%) rename {selection => selectinf}/algorithms/lasso.py (100%) rename {selection => selectinf}/algorithms/pca.py (100%) rename {selection => selectinf}/algorithms/screening.py (100%) rename {selection => selectinf}/algorithms/softmax.py (100%) rename {selection => selectinf}/algorithms/sqrt_lasso.py (100%) rename {selection => selectinf}/algorithms/stopping_rules.py (100%) rename {selection => selectinf}/algorithms/tests/__init__.py (100%) rename {selection => selectinf}/algorithms/tests/test_IC.py (100%) rename {selection => selectinf}/algorithms/tests/test_ROSI.py (100%) rename {selection => selectinf}/algorithms/tests/test_change_point.py (100%) rename {selection => selectinf}/algorithms/tests/test_compareR.py (100%) rename {selection => selectinf}/algorithms/tests/test_covtest.py (100%) rename {selection => selectinf}/algorithms/tests/test_data_carving.py (100%) rename {selection => selectinf}/algorithms/tests/test_debiased_lasso.py (100%) rename {selection => selectinf}/algorithms/tests/test_forward_step.py (100%) rename {selection => selectinf}/algorithms/tests/test_lasso.py (100%) rename {selection => selectinf}/algorithms/tests/test_screening.py (100%) rename {selection => selectinf}/algorithms/tests/test_softmax.py (100%) rename {selection => selectinf}/algorithms/tests/test_sqrt_lasso.py (100%) rename {selection => selectinf}/api.py (100%) rename {selection => selectinf}/base.py (100%) rename {selection => selectinf}/constraints/__init__.py (100%) rename {selection => selectinf}/constraints/affine.py (100%) rename {selection => selectinf}/constraints/api.py (100%) rename {selection => selectinf}/constraints/base.py (100%) rename {selection => selectinf}/constraints/estimation.py (100%) rename {selection => selectinf}/constraints/intervals.py (100%) rename {selection => selectinf}/constraints/quadratic.py (100%) rename {selection => selectinf}/constraints/quasi_affine.py (100%) rename {selection => selectinf}/constraints/tests/__init__.py (100%) rename {selection => selectinf}/constraints/tests/test_affine.py (100%) rename {selection => selectinf}/constraints/tests/test_estimation.py (100%) rename {selection => selectinf}/constraints/tests/test_quadratic_tests.py (100%) rename {selection => selectinf}/constraints/tests/test_quasi.py (100%) rename {selection => selectinf}/constraints/tests/test_unknown_sigma.py (100%) rename {selection => selectinf}/distributions/__init__.py (100%) rename {selection => selectinf}/distributions/api.py (100%) rename {selection => selectinf}/distributions/chain.py (100%) rename {selection => selectinf}/distributions/chisq.py (100%) rename {selection => selectinf}/distributions/discrete_family.py (100%) rename {selection => selectinf}/distributions/discrete_multiparameter.py (100%) rename {selection => selectinf}/distributions/intervals.py (100%) rename {selection => selectinf}/distributions/pvalue.py (100%) rename {selection => selectinf}/distributions/tests/__init__.py (100%) rename {selection => selectinf}/distributions/tests/test_chains.py (100%) rename {selection => selectinf}/distributions/tests/test_discreteExFam.py (100%) rename {selection => selectinf}/distributions/tests/test_multiparameter.py (100%) rename {selection => selectinf}/glm.py (100%) rename {selection => selectinf}/info.py (93%) rename {selection => selectinf}/learning/Rfitters.py (100%) rename {selection => selectinf}/learning/Rutils.py (100%) rename {selection => selectinf}/learning/__init__.py (100%) rename {selection => selectinf}/learning/core.py (100%) rename {selection => selectinf}/learning/fitters.py (100%) rename {selection => selectinf}/learning/keras_fit.py (100%) rename {selection => selectinf}/learning/learners.py (100%) rename {selection => selectinf}/learning/samplers.py (100%) rename {selection => selectinf}/learning/utils.py (100%) rename {selection => selectinf}/randomized/__init__.py (100%) rename {selection => selectinf}/randomized/api.py (100%) rename {selection => selectinf}/randomized/cv_view.py (100%) rename {selection => selectinf}/randomized/group_lasso.py (100%) rename {selection => selectinf}/randomized/lasso.py (100%) rename {selection => selectinf}/randomized/modelQ.py (100%) rename {selection => selectinf}/randomized/query.py (100%) rename {selection => selectinf}/randomized/randomization.py (100%) rename {selection => selectinf}/randomized/sandbox/M_estimator_group_lasso.py (100%) rename {selection => selectinf}/randomized/sandbox/M_estimator_nonrandom.py (100%) rename {selection => selectinf}/randomized/sandbox/convenience.py (100%) rename {selection => selectinf}/randomized/sandbox/general_lasso.py (100%) rename {selection => selectinf}/randomized/sandbox/greedy_step.py (100%) rename {selection => selectinf}/randomized/sandbox/group_lasso.py (100%) rename {selection => selectinf}/randomized/sandbox/lasso_iv.py (100%) rename {selection => selectinf}/randomized/screening.py (100%) rename {selection => selectinf}/randomized/selective_MLE_utils.pyx (100%) rename {selection => selectinf}/randomized/slope.py (100%) rename {selection => selectinf}/randomized/tests/__init__.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_Mest.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_convenience.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_cv.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_cv_corrected_nonrandomized_lasso.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_cv_glmnet.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_cv_lee_et_al.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_decompose_subgrad.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_fixedX.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_full_lasso.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_general_lasso.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_general_lasso_pval.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_intervals.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_lasso_iv.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_multiple_splits.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_opt_weighted_intervals.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_optimization_sampler.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_sampling.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_split.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_split_compare.py (100%) rename {selection => selectinf}/randomized/tests/sandbox/test_sqrt_lasso.py (100%) rename {selection => selectinf}/randomized/tests/test_BH.py (100%) rename {selection => selectinf}/randomized/tests/test_group_lasso.py (100%) rename {selection => selectinf}/randomized/tests/test_lasso.py (100%) rename {selection => selectinf}/randomized/tests/test_marginal_screening.py (100%) rename {selection => selectinf}/randomized/tests/test_modelQ.py (100%) rename {selection => selectinf}/randomized/tests/test_multiple_queries.py (100%) rename {selection => selectinf}/randomized/tests/test_naive.py (100%) rename {selection => selectinf}/randomized/tests/test_randomization.py (100%) rename {selection => selectinf}/randomized/tests/test_selective_MLE.py (100%) rename {selection => selectinf}/randomized/tests/test_selective_MLE_high.py (100%) rename {selection => selectinf}/randomized/tests/test_selective_MLE_onedim.py (100%) rename {selection => selectinf}/randomized/tests/test_slope.py (100%) rename {selection => selectinf}/randomized/tests/test_slope_subgrad.py (100%) rename {selection => selectinf}/randomized/tests/test_split_lasso.py (100%) rename {selection => selectinf}/randomized/tests/test_topK.py (100%) rename {selection => selectinf}/reduced_optimization/tests/__init__.py (100%) rename {selection => selectinf}/sampling/__init__.py (100%) rename {selection => selectinf}/sampling/api.py (100%) rename {selection => selectinf}/sampling/langevin.py (100%) rename {selection => selectinf}/sampling/sequential.py (100%) rename {selection => selectinf}/sampling/sqrt_lasso.pyx (100%) rename {selection => selectinf}/sampling/tests/__init__.py (100%) rename {selection => selectinf}/sampling/tests/plots_fs.py (100%) rename {selection => selectinf}/sampling/tests/test_fstep_langevin.py (100%) rename {selection => selectinf}/sampling/tests/test_kfstep.py (100%) rename {selection => selectinf}/sampling/tests/test_pca_langevin.py (100%) rename {selection => selectinf}/sampling/tests/test_sample_sphere.py (100%) rename {selection => selectinf}/sampling/tests/test_sequential.py (100%) rename {selection => selectinf}/sampling/truncnorm.pyx (100%) rename {selection => selectinf}/sampling/truncnorm_quadratic.pyx (100%) rename {selection => selectinf}/sandbox/approx_ci/__init__.py (100%) rename {selection => selectinf}/sandbox/approx_ci/ci_approx_density.py (100%) rename {selection => selectinf}/sandbox/approx_ci/ci_approx_greedy_step.py (100%) rename {selection => selectinf}/sandbox/approx_ci/selection_map.py (100%) rename {selection => selectinf}/sandbox/approx_ci/tests/__init__.py (100%) rename {selection => selectinf}/sandbox/approx_ci/tests/test_glm.py (100%) rename {selection => selectinf}/sandbox/approx_ci/tests/test_greedy_step.py (100%) rename {selection => selectinf}/sandbox/approx_ci/tests/test_threshold_score.py (100%) rename {selection => selectinf}/sandbox/bayesian/__init__.py (100%) rename {selection => selectinf}/sandbox/bayesian/barrier.py (100%) rename {selection => selectinf}/sandbox/bayesian/credible_intervals.py (100%) rename {selection => selectinf}/sandbox/bayesian/dual_lasso.py (100%) rename {selection => selectinf}/sandbox/bayesian/estimator.py (100%) rename {selection => selectinf}/sandbox/bayesian/forward_stepwise_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/initial_soln.py (100%) rename {selection => selectinf}/sandbox/bayesian/lasso_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/marginal_screening_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/ms_lasso_2stage_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/par_carved_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/par_random_lasso_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/random_lasso_reduced.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/__init__.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/test_carved_lasso.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/test_dual_lasso.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/test_fs.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/test_lasso.py (100%) rename {selection => selectinf}/sandbox/bayesian/tests/test_ms_lasso_2stage.py (100%) rename {selection => selectinf}/src_C/#sample_preparation.pyx# (100%) rename {selection => selectinf}/src_C/HmcSampler.cpp (100%) rename {selection => selectinf}/src_C/HmcSampler.h (100%) rename {selection => selectinf}/src_C/logfile.txt (100%) rename {selection => selectinf}/src_C/preparation_Eig_Vect.cpp (100%) rename {selection => selectinf}/src_C/preparation_Eig_Vect.h (100%) rename {selection => selectinf}/src_C/sample_preparation.cpp (100%) rename {selection => selectinf}/src_C/sample_preparation.pyx (100%) rename {selection => selectinf}/src_C/setup.py (100%) rename {selection => selectinf}/tests/__init__.py (100%) rename {selection => selectinf}/tests/decorators.py (100%) rename {selection => selectinf}/tests/flags.py (100%) rename {selection => selectinf}/tests/instance.py (100%) rename {selection => selectinf}/tests/test_instance.py (100%) rename {selection => selectinf}/tests/tests.py (100%) rename {selection => selectinf}/truncated/F.py (100%) rename {selection => selectinf}/truncated/T.py (100%) rename {selection => selectinf}/truncated/__init__.py (100%) rename {selection => selectinf}/truncated/api.py (100%) rename {selection => selectinf}/truncated/base.py (100%) rename {selection => selectinf}/truncated/chi.py (100%) rename {selection => selectinf}/truncated/gaussian.py (100%) rename {selection => selectinf}/truncated/tests/__init__.py (100%) rename {selection => selectinf}/truncated/tests/test_truncated.py (100%) rename {selection => selectinf}/truncated/tests/test_truncatedFT.py (100%) rename {selection => selectinf}/utils/__init__.py (100%) rename {selection => selectinf}/utils/tools.py (100%) diff --git a/selection/__init__.py b/selectinf/__init__.py similarity index 100% rename from selection/__init__.py rename to selectinf/__init__.py diff --git a/selection/_version.py b/selectinf/_version.py similarity index 100% rename from selection/_version.py rename to selectinf/_version.py diff --git a/selection/algorithms/__init__.py b/selectinf/algorithms/__init__.py similarity index 100% rename from selection/algorithms/__init__.py rename to selectinf/algorithms/__init__.py diff --git a/selection/algorithms/api.py b/selectinf/algorithms/api.py similarity index 100% rename from selection/algorithms/api.py rename to selectinf/algorithms/api.py diff --git a/selection/algorithms/change_point.py b/selectinf/algorithms/change_point.py similarity index 100% rename from selection/algorithms/change_point.py rename to selectinf/algorithms/change_point.py diff --git a/selection/algorithms/covtest.py b/selectinf/algorithms/covtest.py similarity index 100% rename from selection/algorithms/covtest.py rename to selectinf/algorithms/covtest.py diff --git a/selection/algorithms/cv.py b/selectinf/algorithms/cv.py similarity index 100% rename from selection/algorithms/cv.py rename to selectinf/algorithms/cv.py diff --git a/selection/algorithms/cv_glmnet.py b/selectinf/algorithms/cv_glmnet.py similarity index 100% rename from selection/algorithms/cv_glmnet.py rename to selectinf/algorithms/cv_glmnet.py diff --git a/selection/algorithms/debiased_lasso.py b/selectinf/algorithms/debiased_lasso.py similarity index 100% rename from selection/algorithms/debiased_lasso.py rename to selectinf/algorithms/debiased_lasso.py diff --git a/selection/algorithms/debiased_lasso_utils.pyx b/selectinf/algorithms/debiased_lasso_utils.pyx similarity index 100% rename from selection/algorithms/debiased_lasso_utils.pyx rename to selectinf/algorithms/debiased_lasso_utils.pyx diff --git a/selection/algorithms/forward_step.py b/selectinf/algorithms/forward_step.py similarity index 100% rename from selection/algorithms/forward_step.py rename to selectinf/algorithms/forward_step.py diff --git a/selection/algorithms/lasso.py b/selectinf/algorithms/lasso.py similarity index 100% rename from selection/algorithms/lasso.py rename to selectinf/algorithms/lasso.py diff --git a/selection/algorithms/pca.py b/selectinf/algorithms/pca.py similarity index 100% rename from selection/algorithms/pca.py rename to selectinf/algorithms/pca.py diff --git a/selection/algorithms/screening.py b/selectinf/algorithms/screening.py similarity index 100% rename from selection/algorithms/screening.py rename to selectinf/algorithms/screening.py diff --git a/selection/algorithms/softmax.py b/selectinf/algorithms/softmax.py similarity index 100% rename from selection/algorithms/softmax.py rename to selectinf/algorithms/softmax.py diff --git a/selection/algorithms/sqrt_lasso.py b/selectinf/algorithms/sqrt_lasso.py similarity index 100% rename from selection/algorithms/sqrt_lasso.py rename to selectinf/algorithms/sqrt_lasso.py diff --git a/selection/algorithms/stopping_rules.py b/selectinf/algorithms/stopping_rules.py similarity index 100% rename from selection/algorithms/stopping_rules.py rename to selectinf/algorithms/stopping_rules.py diff --git a/selection/algorithms/tests/__init__.py b/selectinf/algorithms/tests/__init__.py similarity index 100% rename from selection/algorithms/tests/__init__.py rename to selectinf/algorithms/tests/__init__.py diff --git a/selection/algorithms/tests/test_IC.py b/selectinf/algorithms/tests/test_IC.py similarity index 100% rename from selection/algorithms/tests/test_IC.py rename to selectinf/algorithms/tests/test_IC.py diff --git a/selection/algorithms/tests/test_ROSI.py b/selectinf/algorithms/tests/test_ROSI.py similarity index 100% rename from selection/algorithms/tests/test_ROSI.py rename to selectinf/algorithms/tests/test_ROSI.py diff --git a/selection/algorithms/tests/test_change_point.py b/selectinf/algorithms/tests/test_change_point.py similarity index 100% rename from selection/algorithms/tests/test_change_point.py rename to selectinf/algorithms/tests/test_change_point.py diff --git a/selection/algorithms/tests/test_compareR.py b/selectinf/algorithms/tests/test_compareR.py similarity index 100% rename from selection/algorithms/tests/test_compareR.py rename to selectinf/algorithms/tests/test_compareR.py diff --git a/selection/algorithms/tests/test_covtest.py b/selectinf/algorithms/tests/test_covtest.py similarity index 100% rename from selection/algorithms/tests/test_covtest.py rename to selectinf/algorithms/tests/test_covtest.py diff --git a/selection/algorithms/tests/test_data_carving.py b/selectinf/algorithms/tests/test_data_carving.py similarity index 100% rename from selection/algorithms/tests/test_data_carving.py rename to selectinf/algorithms/tests/test_data_carving.py diff --git a/selection/algorithms/tests/test_debiased_lasso.py b/selectinf/algorithms/tests/test_debiased_lasso.py similarity index 100% rename from selection/algorithms/tests/test_debiased_lasso.py rename to selectinf/algorithms/tests/test_debiased_lasso.py diff --git a/selection/algorithms/tests/test_forward_step.py b/selectinf/algorithms/tests/test_forward_step.py similarity index 100% rename from selection/algorithms/tests/test_forward_step.py rename to selectinf/algorithms/tests/test_forward_step.py diff --git a/selection/algorithms/tests/test_lasso.py b/selectinf/algorithms/tests/test_lasso.py similarity index 100% rename from selection/algorithms/tests/test_lasso.py rename to selectinf/algorithms/tests/test_lasso.py diff --git a/selection/algorithms/tests/test_screening.py b/selectinf/algorithms/tests/test_screening.py similarity index 100% rename from selection/algorithms/tests/test_screening.py rename to selectinf/algorithms/tests/test_screening.py diff --git a/selection/algorithms/tests/test_softmax.py b/selectinf/algorithms/tests/test_softmax.py similarity index 100% rename from selection/algorithms/tests/test_softmax.py rename to selectinf/algorithms/tests/test_softmax.py diff --git a/selection/algorithms/tests/test_sqrt_lasso.py b/selectinf/algorithms/tests/test_sqrt_lasso.py similarity index 100% rename from selection/algorithms/tests/test_sqrt_lasso.py rename to selectinf/algorithms/tests/test_sqrt_lasso.py diff --git a/selection/api.py b/selectinf/api.py similarity index 100% rename from selection/api.py rename to selectinf/api.py diff --git a/selection/base.py b/selectinf/base.py similarity index 100% rename from selection/base.py rename to selectinf/base.py diff --git a/selection/constraints/__init__.py b/selectinf/constraints/__init__.py similarity index 100% rename from selection/constraints/__init__.py rename to selectinf/constraints/__init__.py diff --git a/selection/constraints/affine.py b/selectinf/constraints/affine.py similarity index 100% rename from selection/constraints/affine.py rename to selectinf/constraints/affine.py diff --git a/selection/constraints/api.py b/selectinf/constraints/api.py similarity index 100% rename from selection/constraints/api.py rename to selectinf/constraints/api.py diff --git a/selection/constraints/base.py b/selectinf/constraints/base.py similarity index 100% rename from selection/constraints/base.py rename to selectinf/constraints/base.py diff --git a/selection/constraints/estimation.py b/selectinf/constraints/estimation.py similarity index 100% rename from selection/constraints/estimation.py rename to selectinf/constraints/estimation.py diff --git a/selection/constraints/intervals.py b/selectinf/constraints/intervals.py similarity index 100% rename from selection/constraints/intervals.py rename to selectinf/constraints/intervals.py diff --git a/selection/constraints/quadratic.py b/selectinf/constraints/quadratic.py similarity index 100% rename from selection/constraints/quadratic.py rename to selectinf/constraints/quadratic.py diff --git a/selection/constraints/quasi_affine.py b/selectinf/constraints/quasi_affine.py similarity index 100% rename from selection/constraints/quasi_affine.py rename to selectinf/constraints/quasi_affine.py diff --git a/selection/constraints/tests/__init__.py b/selectinf/constraints/tests/__init__.py similarity index 100% rename from selection/constraints/tests/__init__.py rename to selectinf/constraints/tests/__init__.py diff --git a/selection/constraints/tests/test_affine.py b/selectinf/constraints/tests/test_affine.py similarity index 100% rename from selection/constraints/tests/test_affine.py rename to selectinf/constraints/tests/test_affine.py diff --git a/selection/constraints/tests/test_estimation.py b/selectinf/constraints/tests/test_estimation.py similarity index 100% rename from selection/constraints/tests/test_estimation.py rename to selectinf/constraints/tests/test_estimation.py diff --git a/selection/constraints/tests/test_quadratic_tests.py b/selectinf/constraints/tests/test_quadratic_tests.py similarity index 100% rename from selection/constraints/tests/test_quadratic_tests.py rename to selectinf/constraints/tests/test_quadratic_tests.py diff --git a/selection/constraints/tests/test_quasi.py b/selectinf/constraints/tests/test_quasi.py similarity index 100% rename from selection/constraints/tests/test_quasi.py rename to selectinf/constraints/tests/test_quasi.py diff --git a/selection/constraints/tests/test_unknown_sigma.py b/selectinf/constraints/tests/test_unknown_sigma.py similarity index 100% rename from selection/constraints/tests/test_unknown_sigma.py rename to selectinf/constraints/tests/test_unknown_sigma.py diff --git a/selection/distributions/__init__.py b/selectinf/distributions/__init__.py similarity index 100% rename from selection/distributions/__init__.py rename to selectinf/distributions/__init__.py diff --git a/selection/distributions/api.py b/selectinf/distributions/api.py similarity index 100% rename from selection/distributions/api.py rename to selectinf/distributions/api.py diff --git a/selection/distributions/chain.py b/selectinf/distributions/chain.py similarity index 100% rename from selection/distributions/chain.py rename to selectinf/distributions/chain.py diff --git a/selection/distributions/chisq.py b/selectinf/distributions/chisq.py similarity index 100% rename from selection/distributions/chisq.py rename to selectinf/distributions/chisq.py diff --git a/selection/distributions/discrete_family.py b/selectinf/distributions/discrete_family.py similarity index 100% rename from selection/distributions/discrete_family.py rename to selectinf/distributions/discrete_family.py diff --git a/selection/distributions/discrete_multiparameter.py b/selectinf/distributions/discrete_multiparameter.py similarity index 100% rename from selection/distributions/discrete_multiparameter.py rename to selectinf/distributions/discrete_multiparameter.py diff --git a/selection/distributions/intervals.py b/selectinf/distributions/intervals.py similarity index 100% rename from selection/distributions/intervals.py rename to selectinf/distributions/intervals.py diff --git a/selection/distributions/pvalue.py b/selectinf/distributions/pvalue.py similarity index 100% rename from selection/distributions/pvalue.py rename to selectinf/distributions/pvalue.py diff --git a/selection/distributions/tests/__init__.py b/selectinf/distributions/tests/__init__.py similarity index 100% rename from selection/distributions/tests/__init__.py rename to selectinf/distributions/tests/__init__.py diff --git a/selection/distributions/tests/test_chains.py b/selectinf/distributions/tests/test_chains.py similarity index 100% rename from selection/distributions/tests/test_chains.py rename to selectinf/distributions/tests/test_chains.py diff --git a/selection/distributions/tests/test_discreteExFam.py b/selectinf/distributions/tests/test_discreteExFam.py similarity index 100% rename from selection/distributions/tests/test_discreteExFam.py rename to selectinf/distributions/tests/test_discreteExFam.py diff --git a/selection/distributions/tests/test_multiparameter.py b/selectinf/distributions/tests/test_multiparameter.py similarity index 100% rename from selection/distributions/tests/test_multiparameter.py rename to selectinf/distributions/tests/test_multiparameter.py diff --git a/selection/glm.py b/selectinf/glm.py similarity index 100% rename from selection/glm.py rename to selectinf/glm.py diff --git a/selection/info.py b/selectinf/info.py similarity index 93% rename from selection/info.py rename to selectinf/info.py index c3e1bdd9d..b228f8e56 100644 --- a/selection/info.py +++ b/selectinf/info.py @@ -7,9 +7,9 @@ # full release. '.dev' as a _version_extra string means this is a development # version _version_major = 0 -_version_minor = 0 -_version_micro = 1 -_version_extra = '.dev' +_version_minor = 1 +_version_micro = 0 +_version_extra = '' # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z" __version__ = "%s.%s.%s%s" % (_version_major, @@ -48,12 +48,12 @@ PYINTER_MIN_VERSION = "0.1.6" SKLEARN_MIN_VERSION = '0.19' -NAME = 'selection' +NAME = 'selectinf' MAINTAINER = "Jonathan Taylor" MAINTAINER_EMAIL = "" DESCRIPTION = description LONG_DESCRIPTION = long_description -URL = "http://github.org/jonathan.taylor/fixed_lambda" +URL = "http://github.org/jonathan.taylor/selective-inference" DOWNLOAD_URL = "" LICENSE = "BSD license" CLASSIFIERS = CLASSIFIERS diff --git a/selection/learning/Rfitters.py b/selectinf/learning/Rfitters.py similarity index 100% rename from selection/learning/Rfitters.py rename to selectinf/learning/Rfitters.py diff --git a/selection/learning/Rutils.py b/selectinf/learning/Rutils.py similarity index 100% rename from selection/learning/Rutils.py rename to selectinf/learning/Rutils.py diff --git a/selection/learning/__init__.py b/selectinf/learning/__init__.py similarity index 100% rename from selection/learning/__init__.py rename to selectinf/learning/__init__.py diff --git a/selection/learning/core.py b/selectinf/learning/core.py similarity index 100% rename from selection/learning/core.py rename to selectinf/learning/core.py diff --git a/selection/learning/fitters.py b/selectinf/learning/fitters.py similarity index 100% rename from selection/learning/fitters.py rename to selectinf/learning/fitters.py diff --git a/selection/learning/keras_fit.py b/selectinf/learning/keras_fit.py similarity index 100% rename from selection/learning/keras_fit.py rename to selectinf/learning/keras_fit.py diff --git a/selection/learning/learners.py b/selectinf/learning/learners.py similarity index 100% rename from selection/learning/learners.py rename to selectinf/learning/learners.py diff --git a/selection/learning/samplers.py b/selectinf/learning/samplers.py similarity index 100% rename from selection/learning/samplers.py rename to selectinf/learning/samplers.py diff --git a/selection/learning/utils.py b/selectinf/learning/utils.py similarity index 100% rename from selection/learning/utils.py rename to selectinf/learning/utils.py diff --git a/selection/randomized/__init__.py b/selectinf/randomized/__init__.py similarity index 100% rename from selection/randomized/__init__.py rename to selectinf/randomized/__init__.py diff --git a/selection/randomized/api.py b/selectinf/randomized/api.py similarity index 100% rename from selection/randomized/api.py rename to selectinf/randomized/api.py diff --git a/selection/randomized/cv_view.py b/selectinf/randomized/cv_view.py similarity index 100% rename from selection/randomized/cv_view.py rename to selectinf/randomized/cv_view.py diff --git a/selection/randomized/group_lasso.py b/selectinf/randomized/group_lasso.py similarity index 100% rename from selection/randomized/group_lasso.py rename to selectinf/randomized/group_lasso.py diff --git a/selection/randomized/lasso.py b/selectinf/randomized/lasso.py similarity index 100% rename from selection/randomized/lasso.py rename to selectinf/randomized/lasso.py diff --git a/selection/randomized/modelQ.py b/selectinf/randomized/modelQ.py similarity index 100% rename from selection/randomized/modelQ.py rename to selectinf/randomized/modelQ.py diff --git a/selection/randomized/query.py b/selectinf/randomized/query.py similarity index 100% rename from selection/randomized/query.py rename to selectinf/randomized/query.py diff --git a/selection/randomized/randomization.py b/selectinf/randomized/randomization.py similarity index 100% rename from selection/randomized/randomization.py rename to selectinf/randomized/randomization.py diff --git a/selection/randomized/sandbox/M_estimator_group_lasso.py b/selectinf/randomized/sandbox/M_estimator_group_lasso.py similarity index 100% rename from selection/randomized/sandbox/M_estimator_group_lasso.py rename to selectinf/randomized/sandbox/M_estimator_group_lasso.py diff --git a/selection/randomized/sandbox/M_estimator_nonrandom.py b/selectinf/randomized/sandbox/M_estimator_nonrandom.py similarity index 100% rename from selection/randomized/sandbox/M_estimator_nonrandom.py rename to selectinf/randomized/sandbox/M_estimator_nonrandom.py diff --git a/selection/randomized/sandbox/convenience.py b/selectinf/randomized/sandbox/convenience.py similarity index 100% rename from selection/randomized/sandbox/convenience.py rename to selectinf/randomized/sandbox/convenience.py diff --git a/selection/randomized/sandbox/general_lasso.py b/selectinf/randomized/sandbox/general_lasso.py similarity index 100% rename from selection/randomized/sandbox/general_lasso.py rename to selectinf/randomized/sandbox/general_lasso.py diff --git a/selection/randomized/sandbox/greedy_step.py b/selectinf/randomized/sandbox/greedy_step.py similarity index 100% rename from selection/randomized/sandbox/greedy_step.py rename to selectinf/randomized/sandbox/greedy_step.py diff --git a/selection/randomized/sandbox/group_lasso.py b/selectinf/randomized/sandbox/group_lasso.py similarity index 100% rename from selection/randomized/sandbox/group_lasso.py rename to selectinf/randomized/sandbox/group_lasso.py diff --git a/selection/randomized/sandbox/lasso_iv.py b/selectinf/randomized/sandbox/lasso_iv.py similarity index 100% rename from selection/randomized/sandbox/lasso_iv.py rename to selectinf/randomized/sandbox/lasso_iv.py diff --git a/selection/randomized/screening.py b/selectinf/randomized/screening.py similarity index 100% rename from selection/randomized/screening.py rename to selectinf/randomized/screening.py diff --git a/selection/randomized/selective_MLE_utils.pyx b/selectinf/randomized/selective_MLE_utils.pyx similarity index 100% rename from selection/randomized/selective_MLE_utils.pyx rename to selectinf/randomized/selective_MLE_utils.pyx diff --git a/selection/randomized/slope.py b/selectinf/randomized/slope.py similarity index 100% rename from selection/randomized/slope.py rename to selectinf/randomized/slope.py diff --git a/selection/randomized/tests/__init__.py b/selectinf/randomized/tests/__init__.py similarity index 100% rename from selection/randomized/tests/__init__.py rename to selectinf/randomized/tests/__init__.py diff --git a/selection/randomized/tests/sandbox/test_Mest.py b/selectinf/randomized/tests/sandbox/test_Mest.py similarity index 100% rename from selection/randomized/tests/sandbox/test_Mest.py rename to selectinf/randomized/tests/sandbox/test_Mest.py diff --git a/selection/randomized/tests/sandbox/test_convenience.py b/selectinf/randomized/tests/sandbox/test_convenience.py similarity index 100% rename from selection/randomized/tests/sandbox/test_convenience.py rename to selectinf/randomized/tests/sandbox/test_convenience.py diff --git a/selection/randomized/tests/sandbox/test_cv.py b/selectinf/randomized/tests/sandbox/test_cv.py similarity index 100% rename from selection/randomized/tests/sandbox/test_cv.py rename to selectinf/randomized/tests/sandbox/test_cv.py diff --git a/selection/randomized/tests/sandbox/test_cv_corrected_nonrandomized_lasso.py b/selectinf/randomized/tests/sandbox/test_cv_corrected_nonrandomized_lasso.py similarity index 100% rename from selection/randomized/tests/sandbox/test_cv_corrected_nonrandomized_lasso.py rename to selectinf/randomized/tests/sandbox/test_cv_corrected_nonrandomized_lasso.py diff --git a/selection/randomized/tests/sandbox/test_cv_glmnet.py b/selectinf/randomized/tests/sandbox/test_cv_glmnet.py similarity index 100% rename from selection/randomized/tests/sandbox/test_cv_glmnet.py rename to selectinf/randomized/tests/sandbox/test_cv_glmnet.py diff --git a/selection/randomized/tests/sandbox/test_cv_lee_et_al.py b/selectinf/randomized/tests/sandbox/test_cv_lee_et_al.py similarity index 100% rename from selection/randomized/tests/sandbox/test_cv_lee_et_al.py rename to selectinf/randomized/tests/sandbox/test_cv_lee_et_al.py diff --git a/selection/randomized/tests/sandbox/test_decompose_subgrad.py b/selectinf/randomized/tests/sandbox/test_decompose_subgrad.py similarity index 100% rename from selection/randomized/tests/sandbox/test_decompose_subgrad.py rename to selectinf/randomized/tests/sandbox/test_decompose_subgrad.py diff --git a/selection/randomized/tests/sandbox/test_fixedX.py b/selectinf/randomized/tests/sandbox/test_fixedX.py similarity index 100% rename from selection/randomized/tests/sandbox/test_fixedX.py rename to selectinf/randomized/tests/sandbox/test_fixedX.py diff --git a/selection/randomized/tests/sandbox/test_full_lasso.py b/selectinf/randomized/tests/sandbox/test_full_lasso.py similarity index 100% rename from selection/randomized/tests/sandbox/test_full_lasso.py rename to selectinf/randomized/tests/sandbox/test_full_lasso.py diff --git a/selection/randomized/tests/sandbox/test_general_lasso.py b/selectinf/randomized/tests/sandbox/test_general_lasso.py similarity index 100% rename from selection/randomized/tests/sandbox/test_general_lasso.py rename to selectinf/randomized/tests/sandbox/test_general_lasso.py diff --git a/selection/randomized/tests/sandbox/test_general_lasso_pval.py b/selectinf/randomized/tests/sandbox/test_general_lasso_pval.py similarity index 100% rename from selection/randomized/tests/sandbox/test_general_lasso_pval.py rename to selectinf/randomized/tests/sandbox/test_general_lasso_pval.py diff --git a/selection/randomized/tests/sandbox/test_intervals.py b/selectinf/randomized/tests/sandbox/test_intervals.py similarity index 100% rename from selection/randomized/tests/sandbox/test_intervals.py rename to selectinf/randomized/tests/sandbox/test_intervals.py diff --git a/selection/randomized/tests/sandbox/test_lasso_iv.py b/selectinf/randomized/tests/sandbox/test_lasso_iv.py similarity index 100% rename from selection/randomized/tests/sandbox/test_lasso_iv.py rename to selectinf/randomized/tests/sandbox/test_lasso_iv.py diff --git a/selection/randomized/tests/sandbox/test_multiple_splits.py b/selectinf/randomized/tests/sandbox/test_multiple_splits.py similarity index 100% rename from selection/randomized/tests/sandbox/test_multiple_splits.py rename to selectinf/randomized/tests/sandbox/test_multiple_splits.py diff --git a/selection/randomized/tests/sandbox/test_opt_weighted_intervals.py b/selectinf/randomized/tests/sandbox/test_opt_weighted_intervals.py similarity index 100% rename from selection/randomized/tests/sandbox/test_opt_weighted_intervals.py rename to selectinf/randomized/tests/sandbox/test_opt_weighted_intervals.py diff --git a/selection/randomized/tests/sandbox/test_optimization_sampler.py b/selectinf/randomized/tests/sandbox/test_optimization_sampler.py similarity index 100% rename from selection/randomized/tests/sandbox/test_optimization_sampler.py rename to selectinf/randomized/tests/sandbox/test_optimization_sampler.py diff --git a/selection/randomized/tests/sandbox/test_sampling.py b/selectinf/randomized/tests/sandbox/test_sampling.py similarity index 100% rename from selection/randomized/tests/sandbox/test_sampling.py rename to selectinf/randomized/tests/sandbox/test_sampling.py diff --git a/selection/randomized/tests/sandbox/test_split.py b/selectinf/randomized/tests/sandbox/test_split.py similarity index 100% rename from selection/randomized/tests/sandbox/test_split.py rename to selectinf/randomized/tests/sandbox/test_split.py diff --git a/selection/randomized/tests/sandbox/test_split_compare.py b/selectinf/randomized/tests/sandbox/test_split_compare.py similarity index 100% rename from selection/randomized/tests/sandbox/test_split_compare.py rename to selectinf/randomized/tests/sandbox/test_split_compare.py diff --git a/selection/randomized/tests/sandbox/test_sqrt_lasso.py b/selectinf/randomized/tests/sandbox/test_sqrt_lasso.py similarity index 100% rename from selection/randomized/tests/sandbox/test_sqrt_lasso.py rename to selectinf/randomized/tests/sandbox/test_sqrt_lasso.py diff --git a/selection/randomized/tests/test_BH.py b/selectinf/randomized/tests/test_BH.py similarity index 100% rename from selection/randomized/tests/test_BH.py rename to selectinf/randomized/tests/test_BH.py diff --git a/selection/randomized/tests/test_group_lasso.py b/selectinf/randomized/tests/test_group_lasso.py similarity index 100% rename from selection/randomized/tests/test_group_lasso.py rename to selectinf/randomized/tests/test_group_lasso.py diff --git a/selection/randomized/tests/test_lasso.py b/selectinf/randomized/tests/test_lasso.py similarity index 100% rename from selection/randomized/tests/test_lasso.py rename to selectinf/randomized/tests/test_lasso.py diff --git a/selection/randomized/tests/test_marginal_screening.py b/selectinf/randomized/tests/test_marginal_screening.py similarity index 100% rename from selection/randomized/tests/test_marginal_screening.py rename to selectinf/randomized/tests/test_marginal_screening.py diff --git a/selection/randomized/tests/test_modelQ.py b/selectinf/randomized/tests/test_modelQ.py similarity index 100% rename from selection/randomized/tests/test_modelQ.py rename to selectinf/randomized/tests/test_modelQ.py diff --git a/selection/randomized/tests/test_multiple_queries.py b/selectinf/randomized/tests/test_multiple_queries.py similarity index 100% rename from selection/randomized/tests/test_multiple_queries.py rename to selectinf/randomized/tests/test_multiple_queries.py diff --git a/selection/randomized/tests/test_naive.py b/selectinf/randomized/tests/test_naive.py similarity index 100% rename from selection/randomized/tests/test_naive.py rename to selectinf/randomized/tests/test_naive.py diff --git a/selection/randomized/tests/test_randomization.py b/selectinf/randomized/tests/test_randomization.py similarity index 100% rename from selection/randomized/tests/test_randomization.py rename to selectinf/randomized/tests/test_randomization.py diff --git a/selection/randomized/tests/test_selective_MLE.py b/selectinf/randomized/tests/test_selective_MLE.py similarity index 100% rename from selection/randomized/tests/test_selective_MLE.py rename to selectinf/randomized/tests/test_selective_MLE.py diff --git a/selection/randomized/tests/test_selective_MLE_high.py b/selectinf/randomized/tests/test_selective_MLE_high.py similarity index 100% rename from selection/randomized/tests/test_selective_MLE_high.py rename to selectinf/randomized/tests/test_selective_MLE_high.py diff --git a/selection/randomized/tests/test_selective_MLE_onedim.py b/selectinf/randomized/tests/test_selective_MLE_onedim.py similarity index 100% rename from selection/randomized/tests/test_selective_MLE_onedim.py rename to selectinf/randomized/tests/test_selective_MLE_onedim.py diff --git a/selection/randomized/tests/test_slope.py b/selectinf/randomized/tests/test_slope.py similarity index 100% rename from selection/randomized/tests/test_slope.py rename to selectinf/randomized/tests/test_slope.py diff --git a/selection/randomized/tests/test_slope_subgrad.py b/selectinf/randomized/tests/test_slope_subgrad.py similarity index 100% rename from selection/randomized/tests/test_slope_subgrad.py rename to selectinf/randomized/tests/test_slope_subgrad.py diff --git a/selection/randomized/tests/test_split_lasso.py b/selectinf/randomized/tests/test_split_lasso.py similarity index 100% rename from selection/randomized/tests/test_split_lasso.py rename to selectinf/randomized/tests/test_split_lasso.py diff --git a/selection/randomized/tests/test_topK.py b/selectinf/randomized/tests/test_topK.py similarity index 100% rename from selection/randomized/tests/test_topK.py rename to selectinf/randomized/tests/test_topK.py diff --git a/selection/reduced_optimization/tests/__init__.py b/selectinf/reduced_optimization/tests/__init__.py similarity index 100% rename from selection/reduced_optimization/tests/__init__.py rename to selectinf/reduced_optimization/tests/__init__.py diff --git a/selection/sampling/__init__.py b/selectinf/sampling/__init__.py similarity index 100% rename from selection/sampling/__init__.py rename to selectinf/sampling/__init__.py diff --git a/selection/sampling/api.py b/selectinf/sampling/api.py similarity index 100% rename from selection/sampling/api.py rename to selectinf/sampling/api.py diff --git a/selection/sampling/langevin.py b/selectinf/sampling/langevin.py similarity index 100% rename from selection/sampling/langevin.py rename to selectinf/sampling/langevin.py diff --git a/selection/sampling/sequential.py b/selectinf/sampling/sequential.py similarity index 100% rename from selection/sampling/sequential.py rename to selectinf/sampling/sequential.py diff --git a/selection/sampling/sqrt_lasso.pyx b/selectinf/sampling/sqrt_lasso.pyx similarity index 100% rename from selection/sampling/sqrt_lasso.pyx rename to selectinf/sampling/sqrt_lasso.pyx diff --git a/selection/sampling/tests/__init__.py b/selectinf/sampling/tests/__init__.py similarity index 100% rename from selection/sampling/tests/__init__.py rename to selectinf/sampling/tests/__init__.py diff --git a/selection/sampling/tests/plots_fs.py b/selectinf/sampling/tests/plots_fs.py similarity index 100% rename from selection/sampling/tests/plots_fs.py rename to selectinf/sampling/tests/plots_fs.py diff --git a/selection/sampling/tests/test_fstep_langevin.py b/selectinf/sampling/tests/test_fstep_langevin.py similarity index 100% rename from selection/sampling/tests/test_fstep_langevin.py rename to selectinf/sampling/tests/test_fstep_langevin.py diff --git a/selection/sampling/tests/test_kfstep.py b/selectinf/sampling/tests/test_kfstep.py similarity index 100% rename from selection/sampling/tests/test_kfstep.py rename to selectinf/sampling/tests/test_kfstep.py diff --git a/selection/sampling/tests/test_pca_langevin.py b/selectinf/sampling/tests/test_pca_langevin.py similarity index 100% rename from selection/sampling/tests/test_pca_langevin.py rename to selectinf/sampling/tests/test_pca_langevin.py diff --git a/selection/sampling/tests/test_sample_sphere.py b/selectinf/sampling/tests/test_sample_sphere.py similarity index 100% rename from selection/sampling/tests/test_sample_sphere.py rename to selectinf/sampling/tests/test_sample_sphere.py diff --git a/selection/sampling/tests/test_sequential.py b/selectinf/sampling/tests/test_sequential.py similarity index 100% rename from selection/sampling/tests/test_sequential.py rename to selectinf/sampling/tests/test_sequential.py diff --git a/selection/sampling/truncnorm.pyx b/selectinf/sampling/truncnorm.pyx similarity index 100% rename from selection/sampling/truncnorm.pyx rename to selectinf/sampling/truncnorm.pyx diff --git a/selection/sampling/truncnorm_quadratic.pyx b/selectinf/sampling/truncnorm_quadratic.pyx similarity index 100% rename from selection/sampling/truncnorm_quadratic.pyx rename to selectinf/sampling/truncnorm_quadratic.pyx diff --git a/selection/sandbox/approx_ci/__init__.py b/selectinf/sandbox/approx_ci/__init__.py similarity index 100% rename from selection/sandbox/approx_ci/__init__.py rename to selectinf/sandbox/approx_ci/__init__.py diff --git a/selection/sandbox/approx_ci/ci_approx_density.py b/selectinf/sandbox/approx_ci/ci_approx_density.py similarity index 100% rename from selection/sandbox/approx_ci/ci_approx_density.py rename to selectinf/sandbox/approx_ci/ci_approx_density.py diff --git a/selection/sandbox/approx_ci/ci_approx_greedy_step.py b/selectinf/sandbox/approx_ci/ci_approx_greedy_step.py similarity index 100% rename from selection/sandbox/approx_ci/ci_approx_greedy_step.py rename to selectinf/sandbox/approx_ci/ci_approx_greedy_step.py diff --git a/selection/sandbox/approx_ci/selection_map.py b/selectinf/sandbox/approx_ci/selection_map.py similarity index 100% rename from selection/sandbox/approx_ci/selection_map.py rename to selectinf/sandbox/approx_ci/selection_map.py diff --git a/selection/sandbox/approx_ci/tests/__init__.py b/selectinf/sandbox/approx_ci/tests/__init__.py similarity index 100% rename from selection/sandbox/approx_ci/tests/__init__.py rename to selectinf/sandbox/approx_ci/tests/__init__.py diff --git a/selection/sandbox/approx_ci/tests/test_glm.py b/selectinf/sandbox/approx_ci/tests/test_glm.py similarity index 100% rename from selection/sandbox/approx_ci/tests/test_glm.py rename to selectinf/sandbox/approx_ci/tests/test_glm.py diff --git a/selection/sandbox/approx_ci/tests/test_greedy_step.py b/selectinf/sandbox/approx_ci/tests/test_greedy_step.py similarity index 100% rename from selection/sandbox/approx_ci/tests/test_greedy_step.py rename to selectinf/sandbox/approx_ci/tests/test_greedy_step.py diff --git a/selection/sandbox/approx_ci/tests/test_threshold_score.py b/selectinf/sandbox/approx_ci/tests/test_threshold_score.py similarity index 100% rename from selection/sandbox/approx_ci/tests/test_threshold_score.py rename to selectinf/sandbox/approx_ci/tests/test_threshold_score.py diff --git a/selection/sandbox/bayesian/__init__.py b/selectinf/sandbox/bayesian/__init__.py similarity index 100% rename from selection/sandbox/bayesian/__init__.py rename to selectinf/sandbox/bayesian/__init__.py diff --git a/selection/sandbox/bayesian/barrier.py b/selectinf/sandbox/bayesian/barrier.py similarity index 100% rename from selection/sandbox/bayesian/barrier.py rename to selectinf/sandbox/bayesian/barrier.py diff --git a/selection/sandbox/bayesian/credible_intervals.py b/selectinf/sandbox/bayesian/credible_intervals.py similarity index 100% rename from selection/sandbox/bayesian/credible_intervals.py rename to selectinf/sandbox/bayesian/credible_intervals.py diff --git a/selection/sandbox/bayesian/dual_lasso.py b/selectinf/sandbox/bayesian/dual_lasso.py similarity index 100% rename from selection/sandbox/bayesian/dual_lasso.py rename to selectinf/sandbox/bayesian/dual_lasso.py diff --git a/selection/sandbox/bayesian/estimator.py b/selectinf/sandbox/bayesian/estimator.py similarity index 100% rename from selection/sandbox/bayesian/estimator.py rename to selectinf/sandbox/bayesian/estimator.py diff --git a/selection/sandbox/bayesian/forward_stepwise_reduced.py b/selectinf/sandbox/bayesian/forward_stepwise_reduced.py similarity index 100% rename from selection/sandbox/bayesian/forward_stepwise_reduced.py rename to selectinf/sandbox/bayesian/forward_stepwise_reduced.py diff --git a/selection/sandbox/bayesian/initial_soln.py b/selectinf/sandbox/bayesian/initial_soln.py similarity index 100% rename from selection/sandbox/bayesian/initial_soln.py rename to selectinf/sandbox/bayesian/initial_soln.py diff --git a/selection/sandbox/bayesian/lasso_reduced.py b/selectinf/sandbox/bayesian/lasso_reduced.py similarity index 100% rename from selection/sandbox/bayesian/lasso_reduced.py rename to selectinf/sandbox/bayesian/lasso_reduced.py diff --git a/selection/sandbox/bayesian/marginal_screening_reduced.py b/selectinf/sandbox/bayesian/marginal_screening_reduced.py similarity index 100% rename from selection/sandbox/bayesian/marginal_screening_reduced.py rename to selectinf/sandbox/bayesian/marginal_screening_reduced.py diff --git a/selection/sandbox/bayesian/ms_lasso_2stage_reduced.py b/selectinf/sandbox/bayesian/ms_lasso_2stage_reduced.py similarity index 100% rename from selection/sandbox/bayesian/ms_lasso_2stage_reduced.py rename to selectinf/sandbox/bayesian/ms_lasso_2stage_reduced.py diff --git a/selection/sandbox/bayesian/par_carved_reduced.py b/selectinf/sandbox/bayesian/par_carved_reduced.py similarity index 100% rename from selection/sandbox/bayesian/par_carved_reduced.py rename to selectinf/sandbox/bayesian/par_carved_reduced.py diff --git a/selection/sandbox/bayesian/par_random_lasso_reduced.py b/selectinf/sandbox/bayesian/par_random_lasso_reduced.py similarity index 100% rename from selection/sandbox/bayesian/par_random_lasso_reduced.py rename to selectinf/sandbox/bayesian/par_random_lasso_reduced.py diff --git a/selection/sandbox/bayesian/random_lasso_reduced.py b/selectinf/sandbox/bayesian/random_lasso_reduced.py similarity index 100% rename from selection/sandbox/bayesian/random_lasso_reduced.py rename to selectinf/sandbox/bayesian/random_lasso_reduced.py diff --git a/selection/sandbox/bayesian/tests/__init__.py b/selectinf/sandbox/bayesian/tests/__init__.py similarity index 100% rename from selection/sandbox/bayesian/tests/__init__.py rename to selectinf/sandbox/bayesian/tests/__init__.py diff --git a/selection/sandbox/bayesian/tests/test_carved_lasso.py b/selectinf/sandbox/bayesian/tests/test_carved_lasso.py similarity index 100% rename from selection/sandbox/bayesian/tests/test_carved_lasso.py rename to selectinf/sandbox/bayesian/tests/test_carved_lasso.py diff --git a/selection/sandbox/bayesian/tests/test_dual_lasso.py b/selectinf/sandbox/bayesian/tests/test_dual_lasso.py similarity index 100% rename from selection/sandbox/bayesian/tests/test_dual_lasso.py rename to selectinf/sandbox/bayesian/tests/test_dual_lasso.py diff --git a/selection/sandbox/bayesian/tests/test_fs.py b/selectinf/sandbox/bayesian/tests/test_fs.py similarity index 100% rename from selection/sandbox/bayesian/tests/test_fs.py rename to selectinf/sandbox/bayesian/tests/test_fs.py diff --git a/selection/sandbox/bayesian/tests/test_lasso.py b/selectinf/sandbox/bayesian/tests/test_lasso.py similarity index 100% rename from selection/sandbox/bayesian/tests/test_lasso.py rename to selectinf/sandbox/bayesian/tests/test_lasso.py diff --git a/selection/sandbox/bayesian/tests/test_ms_lasso_2stage.py b/selectinf/sandbox/bayesian/tests/test_ms_lasso_2stage.py similarity index 100% rename from selection/sandbox/bayesian/tests/test_ms_lasso_2stage.py rename to selectinf/sandbox/bayesian/tests/test_ms_lasso_2stage.py diff --git a/selection/src_C/#sample_preparation.pyx# b/selectinf/src_C/#sample_preparation.pyx# similarity index 100% rename from selection/src_C/#sample_preparation.pyx# rename to selectinf/src_C/#sample_preparation.pyx# diff --git a/selection/src_C/HmcSampler.cpp b/selectinf/src_C/HmcSampler.cpp similarity index 100% rename from selection/src_C/HmcSampler.cpp rename to selectinf/src_C/HmcSampler.cpp diff --git a/selection/src_C/HmcSampler.h b/selectinf/src_C/HmcSampler.h similarity index 100% rename from selection/src_C/HmcSampler.h rename to selectinf/src_C/HmcSampler.h diff --git a/selection/src_C/logfile.txt b/selectinf/src_C/logfile.txt similarity index 100% rename from selection/src_C/logfile.txt rename to selectinf/src_C/logfile.txt diff --git a/selection/src_C/preparation_Eig_Vect.cpp b/selectinf/src_C/preparation_Eig_Vect.cpp similarity index 100% rename from selection/src_C/preparation_Eig_Vect.cpp rename to selectinf/src_C/preparation_Eig_Vect.cpp diff --git a/selection/src_C/preparation_Eig_Vect.h b/selectinf/src_C/preparation_Eig_Vect.h similarity index 100% rename from selection/src_C/preparation_Eig_Vect.h rename to selectinf/src_C/preparation_Eig_Vect.h diff --git a/selection/src_C/sample_preparation.cpp b/selectinf/src_C/sample_preparation.cpp similarity index 100% rename from selection/src_C/sample_preparation.cpp rename to selectinf/src_C/sample_preparation.cpp diff --git a/selection/src_C/sample_preparation.pyx b/selectinf/src_C/sample_preparation.pyx similarity index 100% rename from selection/src_C/sample_preparation.pyx rename to selectinf/src_C/sample_preparation.pyx diff --git a/selection/src_C/setup.py b/selectinf/src_C/setup.py similarity index 100% rename from selection/src_C/setup.py rename to selectinf/src_C/setup.py diff --git a/selection/tests/__init__.py b/selectinf/tests/__init__.py similarity index 100% rename from selection/tests/__init__.py rename to selectinf/tests/__init__.py diff --git a/selection/tests/decorators.py b/selectinf/tests/decorators.py similarity index 100% rename from selection/tests/decorators.py rename to selectinf/tests/decorators.py diff --git a/selection/tests/flags.py b/selectinf/tests/flags.py similarity index 100% rename from selection/tests/flags.py rename to selectinf/tests/flags.py diff --git a/selection/tests/instance.py b/selectinf/tests/instance.py similarity index 100% rename from selection/tests/instance.py rename to selectinf/tests/instance.py diff --git a/selection/tests/test_instance.py b/selectinf/tests/test_instance.py similarity index 100% rename from selection/tests/test_instance.py rename to selectinf/tests/test_instance.py diff --git a/selection/tests/tests.py b/selectinf/tests/tests.py similarity index 100% rename from selection/tests/tests.py rename to selectinf/tests/tests.py diff --git a/selection/truncated/F.py b/selectinf/truncated/F.py similarity index 100% rename from selection/truncated/F.py rename to selectinf/truncated/F.py diff --git a/selection/truncated/T.py b/selectinf/truncated/T.py similarity index 100% rename from selection/truncated/T.py rename to selectinf/truncated/T.py diff --git a/selection/truncated/__init__.py b/selectinf/truncated/__init__.py similarity index 100% rename from selection/truncated/__init__.py rename to selectinf/truncated/__init__.py diff --git a/selection/truncated/api.py b/selectinf/truncated/api.py similarity index 100% rename from selection/truncated/api.py rename to selectinf/truncated/api.py diff --git a/selection/truncated/base.py b/selectinf/truncated/base.py similarity index 100% rename from selection/truncated/base.py rename to selectinf/truncated/base.py diff --git a/selection/truncated/chi.py b/selectinf/truncated/chi.py similarity index 100% rename from selection/truncated/chi.py rename to selectinf/truncated/chi.py diff --git a/selection/truncated/gaussian.py b/selectinf/truncated/gaussian.py similarity index 100% rename from selection/truncated/gaussian.py rename to selectinf/truncated/gaussian.py diff --git a/selection/truncated/tests/__init__.py b/selectinf/truncated/tests/__init__.py similarity index 100% rename from selection/truncated/tests/__init__.py rename to selectinf/truncated/tests/__init__.py diff --git a/selection/truncated/tests/test_truncated.py b/selectinf/truncated/tests/test_truncated.py similarity index 100% rename from selection/truncated/tests/test_truncated.py rename to selectinf/truncated/tests/test_truncated.py diff --git a/selection/truncated/tests/test_truncatedFT.py b/selectinf/truncated/tests/test_truncatedFT.py similarity index 100% rename from selection/truncated/tests/test_truncatedFT.py rename to selectinf/truncated/tests/test_truncatedFT.py diff --git a/selection/utils/__init__.py b/selectinf/utils/__init__.py similarity index 100% rename from selection/utils/__init__.py rename to selectinf/utils/__init__.py diff --git a/selection/utils/tools.py b/selectinf/utils/tools.py similarity index 100% rename from selection/utils/tools.py rename to selectinf/utils/tools.py diff --git a/setup.py b/setup.py index c8fc1e0ec..22836d4a6 100755 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -''' Installation script for selection package ''' +''' Installation script for selectinf package ''' import os import sys @@ -24,8 +24,8 @@ from setup_helpers import (SetupDependency, read_vars_from, make_np_ext_builder) -# Get various parameters for this version, stored in selection/info.py -info = read_vars_from(pjoin('selection', 'info.py')) +# Get various parameters for this version, stored in selectinf/info.py +info = read_vars_from(pjoin('selectinf', 'info.py')) # Try to preempt setuptools monkeypatching of Extension handling when Pyrex # is missing. Otherwise the monkeypatched Extension will change .pyx @@ -43,23 +43,23 @@ # Define extensions EXTS = [] for modulename, other_sources in ( - ('selection.sampling.truncnorm', []), - ('selection.sampling.truncnorm_quadratic', []), - ('selection.sampling.sqrt_lasso', []), + ('selectinf.sampling.truncnorm', []), + ('selectinf.sampling.truncnorm_quadratic', []), + ('selectinf.sampling.sqrt_lasso', []), ): pyx_src = pjoin(*modulename.split('.')) + '.pyx' EXTS.append(Extension(modulename,[pyx_src] + other_sources, libraries=['m']), ) -EXTS.append(Extension('selection.algorithms.debiased_lasso_utils', - ['selection/algorithms/debiased_lasso_utils.pyx', +EXTS.append(Extension('selectinf.algorithms.debiased_lasso_utils', + ['selectinf/algorithms/debiased_lasso_utils.pyx', 'C-software/src/quadratic_program_wide.c'], libraries=['m'], include_dirs=['C-software/src'])) -EXTS.append(Extension('selection.randomized.selective_MLE_utils', - ['selection/randomized/selective_MLE_utils.pyx', +EXTS.append(Extension('selectinf.randomized.selective_MLE_utils', + ['selectinf/randomized/selective_MLE_utils.pyx', 'C-software/src/selective_mle.c'], libraries=['m'], include_dirs=['C-software/src'])) @@ -107,21 +107,22 @@ def main(**extra_args): version=versioneer.get_version(), requires=info.REQUIRES, provides=info.PROVIDES, - packages = ['selection', - 'selection.utils', - 'selection.truncated', - 'selection.truncated.tests', - 'selection.constraints', - 'selection.constraints.tests', - 'selection.distributions', - 'selection.distributions.tests', - 'selection.algorithms', - 'selection.algorithms.tests', - 'selection.sampling', - 'selection.sampling.tests', - 'selection.randomized', - 'selection.randomized.tests', - 'selection.tests' + packages = ['selectinf', + 'selectinf.utils', + 'selectinf.truncated', + 'selectinf.truncated.tests', + 'selectinf.constraints', + 'selectinf.constraints.tests', + 'selectinf.distributions', + 'selectinf.distributions.tests', + 'selectinf.algorithms', + 'selectinf.algorithms.tests', + 'selectinf.sampling', + 'selectinf.sampling.tests', + 'selectinf.randomized', + 'selectinf.randomized.tests', + 'selectinf.tests', + 'selectinf.learning' ], ext_modules = EXTS, package_data = {}, From 214ae8d7c9fe2098dc4baed9b4b1e9ff1e239f00 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 00:05:29 -0700 Subject: [PATCH 2/9] fix package name in travis.yml --- .travis.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 0f0d21446..7a788d9b5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -91,7 +91,7 @@ before_install: install: - # Install selection + # Install selectinf - if [ "$RUN_R_TESTS" ]; then pip install rpy2 -c constraints.txt ; fi ; @@ -125,13 +125,13 @@ script: fi - if [ "${COVERAGE}" == "1" ]; then cp ../.coveragerc .; - COVER_ARGS="--with-coverage --cover-package selection"; + COVER_ARGS="--with-coverage --cover-package selectinf"; fi - | if [ "$RUN_R_TESTS" ]; then - nosetests -v ../selection/algorithms/tests/test_compareR.py + nosetests -v ../selectinf/algorithms/tests/test_compareR.py else - env USE_SMALL_SAMPLES=1 USE_TEST_SEED=1 nosetests $DOCTEST_ARGS --verbose $COVER_ARGS selection + env USE_SMALL_SAMPLES=1 USE_TEST_SEED=1 nosetests $DOCTEST_ARGS --verbose $COVER_ARGS selectinf fi after_success: - if [ "${COVERAGE}" == "1" ]; then coveralls; fi From d80d173d19e44df66a8070564d90389e60b7bfad Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 00:26:50 -0700 Subject: [PATCH 3/9] regreg requirement travis regreg --- .travis.yml | 6 ------ requirements.txt | 1 + 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 7a788d9b5..6a08b3944 100644 --- a/.travis.yml +++ b/.travis.yml @@ -77,12 +77,6 @@ matrix: before_install: - source travis-tools/utils.sh - travis_before_install - # Install regreg - - git clone https://github.com/jonathan-taylor/regreg.git - - cd regreg - - pip install -r requirements.txt - - pip install -e . - - cd .. - sudo apt-get install software-properties-common - sudo add-apt-repository -y ppa:marutter/c2d4u - sudo add-apt-repository -y ppa:marutter/rrutter diff --git a/requirements.txt b/requirements.txt index 414d8a70a..77eced0f0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,6 +2,7 @@ cython pandas numpy>=1.12.0 scipy +regreg mpmath pyinter statsmodels From 8db385f356aa7f18c480d2b3cfab69a98804dfb8 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 09:59:19 -0700 Subject: [PATCH 4/9] BF: doctest fixes for rename; imports in learning --- selectinf/learning/core.py | 2 +- selectinf/learning/learners.py | 2 +- selectinf/learning/utils.py | 2 +- selectinf/truncated/chi.py | 4 ++-- selectinf/truncated/gaussian.py | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/selectinf/learning/core.py b/selectinf/learning/core.py index d1261e3e1..a0b1d4c40 100644 --- a/selectinf/learning/core.py +++ b/selectinf/learning/core.py @@ -11,7 +11,7 @@ from scipy.stats import norm as ndist from scipy.stats import binom -from ...distributions.discrete_family import discrete_family +from ..distributions.discrete_family import discrete_family # local imports diff --git a/selectinf/learning/learners.py b/selectinf/learning/learners.py index 1593fe749..c34a80d5a 100644 --- a/selectinf/learning/learners.py +++ b/selectinf/learning/learners.py @@ -3,7 +3,7 @@ import numpy as np from scipy.stats import norm as ndist -from ...distributions.discrete_family import discrete_family +from ..distributions.discrete_family import discrete_family from .samplers import normal_sampler diff --git a/selectinf/learning/utils.py b/selectinf/learning/utils.py index f42d6a98b..0dbb8f19e 100644 --- a/selectinf/learning/utils.py +++ b/selectinf/learning/utils.py @@ -4,7 +4,7 @@ import pandas as pd from scipy.stats import norm as normal_dbn -from ...algorithms.lasso import ROSI, lasso +from ..algorithms.lasso import ROSI, lasso from .core import (infer_full_target, infer_general_target, diff --git a/selectinf/truncated/chi.py b/selectinf/truncated/chi.py index 7cccde525..19804de96 100644 --- a/selectinf/truncated/chi.py +++ b/selectinf/truncated/chi.py @@ -13,7 +13,7 @@ class truncated_chi(truncated): """ - >>> from selection.constraints.intervals import intervals + >>> from selectinf.constraints.intervals import intervals >>> I = intervals.intersection(intervals((-1, 6)), ... intervals(( 0, 7)), ... ~intervals((1, 4))) @@ -126,7 +126,7 @@ class truncated_chi2(truncated): """ - >>> from selection.constraints.intervals import intervals + >>> from selectinf.constraints.intervals import intervals >>> I = intervals.intersection(intervals((-1, 6)), ... intervals(( 0, 7)), ... ~intervals((1, 4))) diff --git a/selectinf/truncated/gaussian.py b/selectinf/truncated/gaussian.py index 1defbcaf2..c1b0bbbef 100644 --- a/selectinf/truncated/gaussian.py +++ b/selectinf/truncated/gaussian.py @@ -17,7 +17,7 @@ class truncated_gaussian(truncated): """ - >>> from selection.constraints.intervals import intervals + >>> from selectinf.constraints.intervals import intervals >>> I = intervals.intersection(intervals((-1, 6)), \ intervals(( 0, 7)), \ ~intervals((1, 4))) From 4417358cef231076b7c06c1b40174cce66aaf128 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 10:10:30 -0700 Subject: [PATCH 5/9] using minimum versions from regreg --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 77eced0f0..f751a8540 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ -cython +cython>=0.18 +numpy>=1.7.1 +scipy>=0.9.0 pandas -numpy>=1.12.0 -scipy regreg mpmath pyinter From 4f29eafdfe2aa07526c04d465a3a8566a2f84015 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 10:20:45 -0700 Subject: [PATCH 6/9] moving most tests to py35 --- .travis.yml | 15 ++++++--------- requirements.txt | 2 +- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/.travis.yml b/.travis.yml index 6a08b3944..969a1ecd6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,28 +23,28 @@ matrix: env: - RUN_R_TESTS=1 # Testing without matplotlib - - python: 2.7 + - python: 3.5 env: - DEPENDS="cython numpy scipy" # Documentation doctests - - python: 2.7 + - python: 3.5 env: - DOC_DOC_TEST=1 # Setup.py install - - python: 2.7 + - python: 3.5 env: - INSTALL_TYPE=setup - - python: 2.7 + - python: 3.5 env: # Sdist install should collect all dependencies - INSTALL_TYPE=sdist - DEPENDS="cython numpy scipy" - - python: 2.7 + - python: 3.5 env: # Wheel install should collect all dependencies - INSTALL_TYPE=wheel - DEPENDS="cython numpy scipy" - - python: 2.7 + - python: 3.5 env: - INSTALL_TYPE=requirements - DEPENDS= @@ -57,9 +57,6 @@ matrix: env: - DOC_DOC_TEST=1 # Setup.py install - - python: 3.5 - env: - - INSTALL_TYPE=setup - python: 3.5 env: # Sdist install should collect all dependencies diff --git a/requirements.txt b/requirements.txt index f751a8540..157777f85 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ cython>=0.18 -numpy>=1.7.1 +numpy>=1.14.5 scipy>=0.9.0 pandas regreg From 9ac92e9629f7a748e8c3b52de445a520013f676f Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 10:22:52 -0700 Subject: [PATCH 7/9] redundant entry in .travis.yml --- .travis.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 969a1ecd6..a2d17d907 100644 --- a/.travis.yml +++ b/.travis.yml @@ -26,10 +26,6 @@ matrix: - python: 3.5 env: - DEPENDS="cython numpy scipy" - # Documentation doctests - - python: 3.5 - env: - - DOC_DOC_TEST=1 # Setup.py install - python: 3.5 env: From 0287dff9587c1c5f0f7c9d089eb775ae2fa3ad4b Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 10:46:09 -0700 Subject: [PATCH 8/9] trying without minimum requirements again --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 157777f85..034a0ad22 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ -cython>=0.18 -numpy>=1.14.5 -scipy>=0.9.0 +cython +numpy +scipy pandas regreg mpmath From 8182c50d2c05a8e1eec2d8224f4480b1835a9059 Mon Sep 17 00:00:00 2001 From: Jonathan Taylor Date: Wed, 18 Sep 2019 10:55:10 -0700 Subject: [PATCH 9/9] some tests in 27 --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index a2d17d907..12cfb1f75 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,17 +30,17 @@ matrix: - python: 3.5 env: - INSTALL_TYPE=setup - - python: 3.5 + - python: 2.7 env: # Sdist install should collect all dependencies - INSTALL_TYPE=sdist - DEPENDS="cython numpy scipy" - - python: 3.5 + - python: 2.7 env: # Wheel install should collect all dependencies - INSTALL_TYPE=wheel - DEPENDS="cython numpy scipy" - - python: 3.5 + - python: 2.7 env: - INSTALL_TYPE=requirements - DEPENDS=