Date: Sat, 28 Aug 2021 05:46:44 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 19d3a5b61140 - main - math/stan: New port: C++ package for Bayesian inference, maximum likelihood estimation, etc Message-ID: <202108280546.17S5kiWQ023584@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=19d3a5b611407b4b7f99479c80c0d28b78a83440 commit 19d3a5b611407b4b7f99479c80c0d28b78a83440 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-08-28 05:45:23 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-08-28 05:46:41 +0000 math/stan: New port: C++ package for Bayesian inference, maximum likelihood estimation, etc --- math/Makefile | 1 + math/stan/Makefile | 31 +++++++ math/stan/distinfo | 3 + math/stan/files/patch-runTests.py | 11 +++ math/stan/pkg-descr | 12 +++ math/stan/pkg-plist | 180 ++++++++++++++++++++++++++++++++++++++ 6 files changed, 238 insertions(+) diff --git a/math/Makefile b/math/Makefile index 2aaeadaa7c07..8ce08adedae1 100644 --- a/math/Makefile +++ b/math/Makefile @@ -987,6 +987,7 @@ SUBDIR += spooles-mpich SUBDIR += spot SUBDIR += sprng + SUBDIR += stan SUBDIR += stanmath SUBDIR += stp SUBDIR += suitesparse diff --git a/math/stan/Makefile b/math/stan/Makefile new file mode 100644 index 000000000000..314cfc2595f0 --- /dev/null +++ b/math/stan/Makefile @@ -0,0 +1,31 @@ +PORTNAME= stan +DISTVERSIONPREFIX= v +DISTVERSION= 2.27.0 +CATEGORIES= math + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ package for Bayesian inference, maximum likelihood estimation, etc + +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 + +SHEBANG_FILES= runTests.py + +NO_BUILD= yes +NO_ARCH= yes + +do-install: + @cd ${WRKSRC}/src && ${COPYTREE_SHARE} stan ${STAGEDIR}${PREFIX}/include + +do-test: # fails to compile: https://github.com/stan-dev/stan/issues/3058 + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ./runTests.py src/test/unit + +.include <bsd.port.mk> diff --git a/math/stan/distinfo b/math/stan/distinfo new file mode 100644 index 000000000000..741875a84019 --- /dev/null +++ b/math/stan/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1630127900 +SHA256 (stan-dev-stan-v2.27.0_GH0.tar.gz) = f6c61baccd13bd088748767646d90d9a1427b3cd88d86f9d8d6bcbdab85f023a +SIZE (stan-dev-stan-v2.27.0_GH0.tar.gz) = 4863278 diff --git a/math/stan/files/patch-runTests.py b/math/stan/files/patch-runTests.py new file mode 100644 index 000000000000..0a7caa93efe5 --- /dev/null +++ b/math/stan/files/patch-runTests.py @@ -0,0 +1,11 @@ +--- runTests.py.orig 2021-08-28 05:32:24 UTC ++++ runTests.py +@@ -107,7 +107,7 @@ def modelDependencies(tests): + + def makeTest(name, j): + """Run the make command for a given single test.""" +- doCommand("make -j%d %s" % (j or 1, name)) ++ doCommand("gmake -j%d %s" % (j or 1, name)) + + + def runTest(name): diff --git a/math/stan/pkg-descr b/math/stan/pkg-descr new file mode 100644 index 000000000000..ea9e1b75767f --- /dev/null +++ b/math/stan/pkg-descr @@ -0,0 +1,12 @@ +Stan is a state-of-the-art platform for statistical modeling and +high-performance statistical computation. Thousands of users rely on Stan for +statistical modeling, data analysis, and prediction in the social, biological, +and physical sciences, engineering, and business. + +Users specify log density functions in Stan's probabilistic programming language +and get: +* full Bayesian statistical inference with MCMC sampling (NUTS, HMC) +* approximate Bayesian inference with variational inference (ADVI) +* penalized maximum likelihood estimation with optimization (L-BFGS) + +WWW: https://mc-stan.org/ diff --git a/math/stan/pkg-plist b/math/stan/pkg-plist new file mode 100644 index 000000000000..6666cc24c551 --- /dev/null +++ b/math/stan/pkg-plist @@ -0,0 +1,180 @@ +include/stan/analyze/mcmc/autocovariance.hpp +include/stan/analyze/mcmc/compute_effective_sample_size.hpp +include/stan/analyze/mcmc/compute_potential_scale_reduction.hpp +include/stan/analyze/mcmc/split_chains.hpp +include/stan/callbacks/interrupt.hpp +include/stan/callbacks/logger.hpp +include/stan/callbacks/stream_logger.hpp +include/stan/callbacks/stream_writer.hpp +include/stan/callbacks/tee_writer.hpp +include/stan/callbacks/writer.hpp +include/stan/io/array_var_context.hpp +include/stan/io/chained_var_context.hpp +include/stan/io/cmd_line.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/is_whitespace.hpp +include/stan/io/program_reader.hpp +include/stan/io/random_var_context.hpp +include/stan/io/read_line.hpp +include/stan/io/reader.hpp +include/stan/io/serializer.hpp +include/stan/io/stan_csv_reader.hpp +include/stan/io/starts_with.hpp +include/stan/io/trim_spaces.hpp +include/stan/io/util.hpp +include/stan/io/validate_dims.hpp +include/stan/io/validate_zero_buf.hpp +include/stan/io/var_context.hpp +include/stan/io/writer.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/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_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_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/lbfgs.hpp +include/stan/services/optimize/newton.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/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
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