diff --git a/math/stan/Makefile b/math/stan/Makefile index 4871d131208d..5dc26a36ada8 100644 --- a/math/stan/Makefile +++ b/math/stan/Makefile @@ -1,36 +1,36 @@ PORTNAME= stan DISTVERSIONPREFIX= v -DISTVERSION= 2.34.1 +DISTVERSION= 2.39.0 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= C++ package for Bayesian inference, maximum likelihood estimation, etc WWW= https://mc-stan.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md RUN_DEPENDS= stanmath>0:math/stanmath TEST_DEPENDS= gmake:devel/gmake USES= eigen:3,run gmake python:test shebangfix USE_GITHUB= yes GH_ACCOUNT= stan-dev GH_TUPLE= stan-dev:math:c26bd83:stan_math/lib/stan_math SHEBANG_FILES= runTests.py MAKE_ENV= CXX_TYPE=clang NO_BUILD= yes NO_ARCH= yes do-install: @cd ${WRKSRC}/src && ${COPYTREE_SHARE} stan ${STAGEDIR}${PREFIX}/include # tests attempt to download some executable #do-test: # @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ./runTests.py src/test/unit .include diff --git a/math/stan/distinfo b/math/stan/distinfo index 36878853a4b9..2e886e8c52af 100644 --- a/math/stan/distinfo +++ b/math/stan/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1706078819 -SHA256 (stan-dev-stan-v2.34.1_GH0.tar.gz) = c38864706bbeb1ee1ad92d97cd0d8db24844bb01c4a431bd7f9d6e87fd0f0bd0 -SIZE (stan-dev-stan-v2.34.1_GH0.tar.gz) = 4377341 +TIMESTAMP = 1779256418 +SHA256 (stan-dev-stan-v2.39.0_GH0.tar.gz) = 8cbbf43f917977574b21fc4256161302419ab78be33404d74e7bbb8f8fafb7a8 +SIZE (stan-dev-stan-v2.39.0_GH0.tar.gz) = 4682704 SHA256 (stan-dev-math-c26bd83_GH0.tar.gz) = 4b02d9dcdd4f7d176f7fa12e60b0a9929b17158fc9e24858912c44f7eed566b1 SIZE (stan-dev-math-c26bd83_GH0.tar.gz) = 30100879 diff --git a/math/stan/pkg-plist b/math/stan/pkg-plist index f465812e7905..5c636206d4aa 100644 --- a/math/stan/pkg-plist +++ b/math/stan/pkg-plist @@ -1,186 +1,195 @@ include/stan/analyze/mcmc/autocovariance.hpp +include/stan/analyze/mcmc/check_chains.hpp include/stan/analyze/mcmc/compute_effective_sample_size.hpp include/stan/analyze/mcmc/compute_potential_scale_reduction.hpp +include/stan/analyze/mcmc/ess.hpp +include/stan/analyze/mcmc/mcse.hpp +include/stan/analyze/mcmc/rank_normalization.hpp +include/stan/analyze/mcmc/rhat.hpp include/stan/analyze/mcmc/split_chains.hpp +include/stan/analyze/mcmc/split_rank_normalized_ess.hpp +include/stan/analyze/mcmc/split_rank_normalized_rhat.hpp +include/stan/callbacks/concurrent_writer.hpp include/stan/callbacks/interrupt.hpp include/stan/callbacks/json_writer.hpp include/stan/callbacks/logger.hpp include/stan/callbacks/stream_logger.hpp include/stan/callbacks/stream_writer.hpp include/stan/callbacks/structured_writer.hpp include/stan/callbacks/tee_writer.hpp include/stan/callbacks/unique_stream_writer.hpp include/stan/callbacks/writer.hpp include/stan/io/array_var_context.hpp include/stan/io/chained_var_context.hpp include/stan/io/deserializer.hpp include/stan/io/dump.hpp include/stan/io/empty_var_context.hpp include/stan/io/ends_with.hpp include/stan/io/json/json_data.hpp include/stan/io/json/json_data_handler.hpp include/stan/io/json/json_error.hpp include/stan/io/json/json_handler.hpp include/stan/io/json/rapidjson_parser.hpp include/stan/io/random_var_context.hpp include/stan/io/serializer.hpp include/stan/io/stan_csv_reader.hpp include/stan/io/validate_dims.hpp include/stan/io/validate_zero_buf.hpp include/stan/io/var_context.hpp include/stan/lang/rethrow_located.hpp include/stan/mcmc/base_adaptation.hpp include/stan/mcmc/base_adapter.hpp include/stan/mcmc/base_mcmc.hpp include/stan/mcmc/chains.hpp +include/stan/mcmc/chainset.hpp include/stan/mcmc/covar_adaptation.hpp include/stan/mcmc/fixed_param_sampler.hpp include/stan/mcmc/hmc/base_hmc.hpp include/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp include/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp include/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp include/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp include/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp include/stan/mcmc/hmc/hamiltonians/ps_point.hpp include/stan/mcmc/hmc/hamiltonians/softabs_metric.hpp include/stan/mcmc/hmc/hamiltonians/softabs_point.hpp include/stan/mcmc/hmc/hamiltonians/unit_e_metric.hpp include/stan/mcmc/hmc/hamiltonians/unit_e_point.hpp include/stan/mcmc/hmc/integrators/base_integrator.hpp include/stan/mcmc/hmc/integrators/base_leapfrog.hpp include/stan/mcmc/hmc/integrators/expl_leapfrog.hpp include/stan/mcmc/hmc/integrators/impl_leapfrog.hpp include/stan/mcmc/hmc/nuts/adapt_dense_e_nuts.hpp include/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp include/stan/mcmc/hmc/nuts/adapt_softabs_nuts.hpp include/stan/mcmc/hmc/nuts/adapt_unit_e_nuts.hpp include/stan/mcmc/hmc/nuts/base_nuts.hpp include/stan/mcmc/hmc/nuts/dense_e_nuts.hpp include/stan/mcmc/hmc/nuts/diag_e_nuts.hpp include/stan/mcmc/hmc/nuts/softabs_nuts.hpp include/stan/mcmc/hmc/nuts/unit_e_nuts.hpp include/stan/mcmc/hmc/nuts_classic/adapt_dense_e_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/adapt_diag_e_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/adapt_unit_e_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/base_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/dense_e_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/diag_e_nuts_classic.hpp include/stan/mcmc/hmc/nuts_classic/unit_e_nuts_classic.hpp include/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp include/stan/mcmc/hmc/static/adapt_diag_e_static_hmc.hpp include/stan/mcmc/hmc/static/adapt_softabs_static_hmc.hpp include/stan/mcmc/hmc/static/adapt_unit_e_static_hmc.hpp include/stan/mcmc/hmc/static/base_static_hmc.hpp include/stan/mcmc/hmc/static/dense_e_static_hmc.hpp include/stan/mcmc/hmc/static/diag_e_static_hmc.hpp include/stan/mcmc/hmc/static/softabs_static_hmc.hpp include/stan/mcmc/hmc/static/unit_e_static_hmc.hpp include/stan/mcmc/hmc/static_uniform/adapt_dense_e_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/adapt_diag_e_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/adapt_softabs_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/adapt_unit_e_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/base_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/dense_e_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/diag_e_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/softabs_static_uniform.hpp include/stan/mcmc/hmc/static_uniform/unit_e_static_uniform.hpp include/stan/mcmc/hmc/xhmc/adapt_dense_e_xhmc.hpp include/stan/mcmc/hmc/xhmc/adapt_diag_e_xhmc.hpp include/stan/mcmc/hmc/xhmc/adapt_softabs_xhmc.hpp include/stan/mcmc/hmc/xhmc/adapt_unit_e_xhmc.hpp include/stan/mcmc/hmc/xhmc/base_xhmc.hpp include/stan/mcmc/hmc/xhmc/dense_e_xhmc.hpp include/stan/mcmc/hmc/xhmc/diag_e_xhmc.hpp include/stan/mcmc/hmc/xhmc/softabs_xhmc.hpp include/stan/mcmc/hmc/xhmc/unit_e_xhmc.hpp include/stan/mcmc/sample.hpp include/stan/mcmc/stepsize_adaptation.hpp include/stan/mcmc/stepsize_adapter.hpp include/stan/mcmc/stepsize_covar_adapter.hpp include/stan/mcmc/stepsize_var_adapter.hpp include/stan/mcmc/var_adaptation.hpp include/stan/mcmc/windowed_adaptation.hpp include/stan/model/finite_diff_grad.hpp include/stan/model/grad_hess_log_prob.hpp include/stan/model/grad_tr_mat_times_hessian.hpp include/stan/model/gradient.hpp include/stan/model/gradient_dot_vector.hpp include/stan/model/hessian.hpp include/stan/model/hessian_times_vector.hpp include/stan/model/indexing.hpp include/stan/model/indexing/access_helpers.hpp include/stan/model/indexing/assign.hpp include/stan/model/indexing/assign_cl.hpp include/stan/model/indexing/assign_varmat.hpp include/stan/model/indexing/deep_copy.hpp include/stan/model/indexing/index.hpp include/stan/model/indexing/rvalue.hpp include/stan/model/indexing/rvalue_at.hpp include/stan/model/indexing/rvalue_cl.hpp include/stan/model/indexing/rvalue_index_size.hpp include/stan/model/indexing/rvalue_varmat.hpp include/stan/model/log_prob_grad.hpp include/stan/model/log_prob_propto.hpp include/stan/model/model_base.hpp include/stan/model/model_base_crtp.hpp include/stan/model/model_functional.hpp include/stan/model/model_header.hpp include/stan/model/prob_grad.hpp include/stan/model/rethrow_located.hpp include/stan/model/test_gradients.hpp include/stan/optimization/bfgs.hpp include/stan/optimization/bfgs_linesearch.hpp include/stan/optimization/bfgs_update.hpp include/stan/optimization/lbfgs_update.hpp include/stan/optimization/newton.hpp include/stan/services/diagnose/defaults.hpp include/stan/services/diagnose/diagnose.hpp include/stan/services/error_codes.hpp include/stan/services/experimental/advi/defaults.hpp include/stan/services/experimental/advi/fullrank.hpp include/stan/services/experimental/advi/meanfield.hpp include/stan/services/optimize/bfgs.hpp include/stan/services/optimize/defaults.hpp include/stan/services/optimize/laplace_sample.hpp include/stan/services/optimize/lbfgs.hpp include/stan/services/optimize/newton.hpp include/stan/services/pathfinder/multi.hpp include/stan/services/pathfinder/psis.hpp include/stan/services/pathfinder/single.hpp include/stan/services/sample/defaults.hpp include/stan/services/sample/fixed_param.hpp include/stan/services/sample/hmc_nuts_dense_e.hpp include/stan/services/sample/hmc_nuts_dense_e_adapt.hpp include/stan/services/sample/hmc_nuts_diag_e.hpp include/stan/services/sample/hmc_nuts_diag_e_adapt.hpp include/stan/services/sample/hmc_nuts_unit_e.hpp include/stan/services/sample/hmc_nuts_unit_e_adapt.hpp include/stan/services/sample/hmc_static_dense_e.hpp include/stan/services/sample/hmc_static_dense_e_adapt.hpp include/stan/services/sample/hmc_static_diag_e.hpp include/stan/services/sample/hmc_static_diag_e_adapt.hpp include/stan/services/sample/hmc_static_unit_e.hpp include/stan/services/sample/hmc_static_unit_e_adapt.hpp include/stan/services/sample/standalone_gqs.hpp include/stan/services/util/create_rng.hpp include/stan/services/util/create_unit_e_dense_inv_metric.hpp include/stan/services/util/create_unit_e_diag_inv_metric.hpp include/stan/services/util/duration_diff.hpp include/stan/services/util/experimental_message.hpp include/stan/services/util/generate_transitions.hpp include/stan/services/util/gq_writer.hpp include/stan/services/util/initialize.hpp include/stan/services/util/inv_metric.hpp include/stan/services/util/mcmc_writer.hpp include/stan/services/util/read_dense_inv_metric.hpp include/stan/services/util/read_diag_inv_metric.hpp include/stan/services/util/run_adaptive_sampler.hpp include/stan/services/util/run_sampler.hpp include/stan/services/util/validate_dense_inv_metric.hpp include/stan/services/util/validate_diag_inv_metric.hpp include/stan/variational/advi.hpp include/stan/variational/base_family.hpp include/stan/variational/families/normal_fullrank.hpp include/stan/variational/families/normal_meanfield.hpp include/stan/variational/print_progress.hpp include/stan/version.hpp