| b574878 | hariszaf | 06 August 2020, 12:41:15 UTC | Rounding (#107) * Create setup_hz.py * Create bindings_hz.cpp * Create volestipy_hz.pyx * Create bindings_hz.h * Update bindings_hz.h * Update bindings_hz.cpp * Create volestipy_old.pyx * Delete volestipy_hz.pyx * Create bindings_old.cpp * Delete bindings_hz.cpp * Update bindings.cpp * Create bindings_old.h * Delete bindings_hz.h * Create setup_old.py * Delete setup_hz.py * Update setup.py * Update volestipy.pyx * Update bindings.h * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update setup.py * Update bindings.h * Update setup.py * Update setup_old.py * Update bindings.cpp * Update setup.py * Update setup.py * Update volestipy.pyx * Update test1.py * Create test1_old.py * Update test1.py * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.h * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.h * Update bindings.cpp * Update bindings.h * Update setup.py * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volume_cb_hpolytope.cpp * Update test1.py * Update bindings.cpp * Update test1.py * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Create .gitignore * Delete test1_old.py * Delete setup_old.py * Delete bindings_old.h * Delete bindings_old.cpp * Delete volestipy_old.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update .gitignore * Update volume_cb_hpolytope.cpp * Update test1.py * Update test2.py * Update bindings.h * Update setup.py * Update credits.md * on .gitignore: files on test/Testing/Temporary/ were removed from the .gitignore file * first attempt - not working - for rounding * rounding function: does not work; trying to figure it out * round_val now works; still new_A and new_b need to be included * Create metabolic_net_pipeline.ipynb * Update metabolic_net_pipeline.ipynb * Update metabolic_net_pipeline.ipynb * Update metabolic_net_pipeline.ipynb * Update metabolic_net_pipeline.ipynb * Update metabolic_net_pipeline.ipynb * Update volestipy.pyx * Update bindings.cpp * Create test_rounding.py * Create test1.py * Create test2.py * Delete test2.py * Update test1.py * Create metabolic_net_pipeline-checkpoint.ipynb * Update setup.py * Update .gitignore * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.h * Update bindings.cpp * Update bindings.cpp * Update test1.py * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update test_rounding.py * Create test_rounding.py * Delete test1.py * Update test_rounding.py * Update test1.py * Update bindings.cpp * Update volestipy.pyx * Update test_rounding.py * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update test_rounding.py * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update test_rounding.py * Update bindings.cpp print all dimensions of the variables included in cpp * Update volestipy.pyx print all dimensions of the variables included in cython * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update test_rounding.py * Update bindings.cpp * Update bindings.cpp * Update volestipy.pyx * Update volestipy.pyx * Update bindings.cpp correct the dimensions of the shift and the T_matrix; that was the cause of the strange memory errors we used to get (e.g free(): invalid pointer , Fatal Python error: GC object already tracked etc) * Delete test_rounding.py * Update test_rounding.py * Update setup.py * Update bindings.h * Update bindings.cpp remove print lines for checking dimensions * Update volestipy.pyx remove print lines for checking dimensions * Update bindings.h * Update bindings.cpp better variable names * Update volestipy.pyx better variable names * Update .gitignore * Update test_rounding.py * Update .gitignore add .ipynb to the .gitignore of the branch * Update .gitignore * Update .gitignore * Update .gitignore * Delete metabolic_net_pipeline.ipynb * Update bindings.cpp change variables names * Update bindings.cpp change variable names - correct * Delete metabolic_net_pipeline-checkpoint.ipynb remove jupyter hidden directory * Delete test1.py * Delete test2.py * Create test_compute_volume.py test script for the compute_volume() function * Create test_random_sampling.py test script for the random_sampling() function * Update test_rounding.py test script for the rounding() function | 06 August 2020, 12:41:15 UTC |
| dae7b62 | AlexManochis | 05 August 2020, 14:55:05 UTC | MCMC diagnostics (#106) * implement multivariate psrf * implement multivariate gweke diagnostics * use matrices as input variable and implement R wrapper * request export in R * improve mc diagnostics * initial implmentation of raftery diagnostics * implement empquant subroutine for raftery diagnostic * implement thin subroutine for raftery diagnostic * implement mctest subroutine for raftery diagnostic * implement mctest subroutine for raftery diagnostic * implement indtest subroutine for raftery diagnostic * implement ppnd subroutine for raftery diagnostic * export to R function raftery and fix compiler errors * complete raftery implmentation * remove unused samples and add roxygen comments * update mcmc diagnostics code and comments * remove unused comments and update roxygen comments * fix bugs in billiard and mcmc diagnostics * improve comments and raftery marginal diagnostic * add mcmc diagnostics test * improve raftery implmenation. Add comments to describe mcmc diagnostics * update roxygen comments and variable names in mcmc diagnostics * improve raftery diagnostic * optimizations in prsf and geweke diagnostics, fix params warning in geweke Rcpp function * fix c++ tests and improve raftery diagnostic Co-authored-by: Tolis <tolis.chal@gmail.com> | 05 August 2020, 14:55:05 UTC |
| 35ca94f | AlexManochis | 30 July 2020, 09:53:26 UTC | Adding two rounding methods (#96) * initial implementation of billiard walk * improved billiard completed for H-polytopes * modify v-polytopes and zonotopes to be used by improved billiard walk * update polytope intersection ball to be used by new billiard walk * update point and volume rcpp function * expose improved billiard to sample_points R function * fix bugs including header in rcpp interface * fix compile bugs in compute_reflection of ball.h * update contribution comments in new header file * update contribution comments in new header files * implement svd rounding and create new folder for preproccessing methods * update rounding interface in R to use the new method * remove unused comments and improve R interface * update roxygen comments * implement interior point method to compute the chebychev ball * implement maximum volume enclosed ellipsoid method * implement rounding based on mve method * fix errors in mve rounding * fix default random walk in volume computation, remove unused comments * update Rcpp function volume * implement extraction of low dimensional polytope * improve full dimensional polytope extraction * create Aeq in Rcpp module of Hpolytope and import it in Rcpp rounding function * improve computation of null space * fix c++ tests * add return variables-matrices for low dimensional polytopes * expose in R get_full_dimensional_polytope * fix compile errors * improve stability on qr decomposition and fix bugs in rounding a low dimensional polytope * improve stopping criterion in maxx_inner_ball computation * improve full dimensional computation * minor improvements and update roxygen comments in volume.cpp * improve R interface in volume.cpp * remove unused comments * improve r interface in sample_points.cpp * improve mve rounding * fix compiler errors * improve computation of AA in billiard * improve eigenvalue computation and fix compiler errors * improve code comments * fix compiler error and update roxygen comments * update copyright comments * fix R tests and update documentation * remove unused comments and update roxygen comments and Rd files * add polishing comments and improve function names * improve rounding options in R-proj/volume.cpp * update rd files * fix c++ tests and update rd files * fix R tests * fix R tests * PR comments: improve names, variable names and declaration. * change number of varialble inputs in rounding * use std::tuple on rounding algorithms | 30 July 2020, 09:53:26 UTC |
| 2b2a598 | Tolis Chalkis | 27 July 2020, 09:24:07 UTC | Fix sampling issue #72 (#101) * set default walk length equal to 1, fix sample_points bug from given starting point * improve Rd files | 27 July 2020, 09:24:07 UTC |
| b8a5b65 | Vissarion Fisikopoulos | 23 July 2020, 09:45:34 UTC | Adding R vignette (#99) | 23 July 2020, 09:45:34 UTC |
| 3d526f3 | Vissarion Fisikopoulos | 23 July 2020, 09:07:38 UTC | Logo and README update (#98) | 23 July 2020, 09:07:38 UTC |
| 29266fb | Marios Papachristou | 20 July 2020, 06:44:53 UTC | Fix R-CMD-ubuntu test (#97) * Initialize report * Add solvers file * WIP: Add Euler ODE Solver * WIP: Add Euler Method * Add boundary reflections to Euler * Fix boundary reflections * Add test for ODE dx/dt = -x for Euler Method * Add test for dx/dt = x in [0, 1] * Add is_in for multiple reflections * Add normalize flag to get_direction * Minor modifications * WIP: Add HMC for log-concave densities * Add tests for HMC * Add details to README * Add tests for leapfrog method * Add leapfrog method * Add HMC and HMC tests * Separate Euler and Leapfrog * Remove ode_solvers.h * Refactor solver implementations 1. Move solvers to separate file 2. Fix includes. The ode_solvers.h base file includes the rest of the solvers and is respon- sible for doing the correct includes. * Add RK methods header file * WIP: Add generic RK methods * Implement RK methods with testing * Add collocation method header files * Fix bug in RK methods * WIP: Collocation method constructors * WIP: Implement collocation method * Add root_finders header file * Add CHECK() statements and fix minor bugs * Bug fix for boundary oracle * Add CHEK() for constrained leapfrog * Add Newton-Raphson method for root finding * Add return statement * Add notice * Add regularization (smoothing) and max_iters * Add const where needed * Add BS method * Add Bulirsch-Stoer implementation * Add Bulirsch-Stoer implementation * Add constrained BS method * WIP: Debug collocation method * WIP: Debug collocation method * Add rational fcn and grad of rational fcn functors * WIP: Add testcase for collocation methods * Fix BS method * Minor changes * Add resources to ODE solvers * Initialize curve_intersect for Hpoly * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Add isinf for well-posedness of denominator in NR * Move func template one level above (for ULD to work later) * Initialize boundary oracles test * Add boundary oracle test CMake targets * Initialize boundary oracles tests * Working boundary oracle for H-polytope 1. Uses Newton-Raphson for solving transcendental equations 2. Can find multiple/one root 3. Tests are implemented for the curves (t, t) and (t, 2t^2) * Initialize NLP oracles (general curve w/ polytope) * Finish boundary oracle tests for H-polytope * Add ifopt and ipopt to CMakeLists.txt * Add wrapper function for nlp oracles * Working nlp H-polyoracle * Rename nlp polyoracles to avoid confusion with lp oracles * Remove old polyoracles file * Document NLP hpolyoracles * Minor refactoring * Add wrapper function * WIP: Initialize NLP oracle for V-polytope * Update readme with GSoC information * Add benchmarks with random polynomials * Modify membership condition * Restrain test to t only * Bug fixes * Code cleanup * Move to old commit (before merge) * Merge ode solvers * Rename testcases * Merge root finders test * Move hmc to sampling/ directory * Partial fix for V polyoracles with ipopt * Fix linear collocation method * Fix collocation with approximate computation * Improve README file * Add precomputation flag * Improve NR solver * Add central method for curve_intersect * Change return type of nlp vpolyoracle to return dummy facet * WIP: Integrate boundary oracles to collocation * Fix collocation method boundary oracles (w/ tests) * Bug fixes * Add mpsolve and gmp to CMakeLists.txt * Implement mpsolve wrapper * WIP: Integrate mpsolve * Fix preprocessor directives * Add boundary oracle with mpsolve * Fix minor issues * Fix existing working tests * Add min_pos optimization problem * WIP: Minor changes in way of reflection * Remove hmc sampler temporarily (move it to temp branch) * Fix reflections * Add dependencies(mpsolve, ipopt/ifopt) to CircleCI * Fix config * Fix config * Fix config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add root finders test * Minor fixes in boundary oracles * Fix bounded collocation * Typo fix * Add missing test to cmakelists * Add #undef where it is needed * Remove extraneous dynamic linking * Fix erroneous flag * Remove hmc tests (moved to other branch) * Update clang and g++ workflows * Fix failing R tests * Fix failing R tests * Split checking for ubuntu/macOS * Remove misplaced if statement * Add CMAKE_CXX_COMPILER flag to ifopt * Correct test name * Remove sudo in front of brew cmd * Add automake dependency * Change error_on from "warning" to "error" * Add preprocessor directive to disable NLP oracles * Add flag for disabling oracles * Add macro definitions for disabling oracles * Add windows workflow * Modify windows workflow * Change Makevars.win * Change Makevars.win * Change Makevars.win * Disable NLP oracles to all tests * Modify circleci build * Modify circleci build * Add preprocessor directive * Remove report * Remove GSoC details * Move macro * Remove unused typedefs * Modify copyright notices * Fix typo * Rename rk.h to runge_kutta.hpp * Minor correction * Rename .h to .hpp in ODE solvers * Rename nlp oracles from .h to .hpp * Rename root finders * Remove duplicate include * Reorder #include directives * Refactoring * Rename file * Add velocity reflections * Remove extraneous constructors * Add general docs for solvers * Temp refactoring * Fix minor bugs * Remove flag from richardson implementation * Add facet ignore * Finish oracles refactoring * Consistent copyright notices * Add accidentally removed templates * Consistent copyright notices * Add nlp_oracles.hpp main header file * Minor modifications * Change variable name from oracle to intersection_oracle * Remove unused file * Add higher-order reflections * Add missing ignore_facet * Wrap long lines * Remove print statement * Impose sticky boundary conditions for collocation * Impose sticky boundary conditions for collocation * WIP: Add integral collocation method class prototype * Delete integral_collocation.hpp * Modifications to collocation method * Iteratively solve non-linear equations * Fix bugs * Minor modifications to test routines * Optimize function oracles * Comment for future work * Minor changes * Remove comments from yaml * Restore README * Restore README * Remove unecessary comments * Remove comments * Add 3 badges | 20 July 2020, 06:44:53 UTC |
| b2470c5 | AlexManochis | 17 July 2020, 09:08:47 UTC | Accelerated billiard walk (#92) * initial implementation of billiard walk * improved billiard completed for H-polytopes * modify v-polytopes and zonotopes to be used by improved billiard walk * update polytope intersection ball to be used by new billiard walk * update point and volume rcpp function * expose improved billiard to sample_points R function * fix bugs including header in rcpp interface * fix compile bugs in compute_reflection of ball.h * update contribution comments in new header file * update contribution comments in new header files * fix default random walk in volume computation, remove unused comments * update Rcpp function volume * fix c++ tests * minor improvements and update roxygen comments in volume.cpp * improve R interface in volume.cpp * improve r interface in sample_points.cpp * fix compiler errors * improve computation of AA in billiard * remove useless comments | 17 July 2020, 09:08:47 UTC |
| c0cc48c | Marios Papachristou | 17 July 2020, 07:44:29 UTC | ODE Solvers (Milestone I) (#90) * Initialize report * Add solvers file * WIP: Add Euler ODE Solver * WIP: Add Euler Method * Add boundary reflections to Euler * Fix boundary reflections * Add test for ODE dx/dt = -x for Euler Method * Add test for dx/dt = x in [0, 1] * Add is_in for multiple reflections * Add normalize flag to get_direction * Minor modifications * WIP: Add HMC for log-concave densities * Add tests for HMC * Add details to README * Add tests for leapfrog method * Add leapfrog method * Add HMC and HMC tests * Separate Euler and Leapfrog * Remove ode_solvers.h * Refactor solver implementations 1. Move solvers to separate file 2. Fix includes. The ode_solvers.h base file includes the rest of the solvers and is respon- sible for doing the correct includes. * Add RK methods header file * WIP: Add generic RK methods * Implement RK methods with testing * Add collocation method header files * Fix bug in RK methods * WIP: Collocation method constructors * WIP: Implement collocation method * Add root_finders header file * Add CHECK() statements and fix minor bugs * Bug fix for boundary oracle * Add CHEK() for constrained leapfrog * Add Newton-Raphson method for root finding * Add return statement * Add notice * Add regularization (smoothing) and max_iters * Add const where needed * Add BS method * Add Bulirsch-Stoer implementation * Add Bulirsch-Stoer implementation * Add constrained BS method * WIP: Debug collocation method * WIP: Debug collocation method * Add rational fcn and grad of rational fcn functors * WIP: Add testcase for collocation methods * Fix BS method * Minor changes * Add resources to ODE solvers * Initialize curve_intersect for Hpoly * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Boundary oracles * WIP: Add isinf for well-posedness of denominator in NR * Move func template one level above (for ULD to work later) * Initialize boundary oracles test * Add boundary oracle test CMake targets * Initialize boundary oracles tests * Working boundary oracle for H-polytope 1. Uses Newton-Raphson for solving transcendental equations 2. Can find multiple/one root 3. Tests are implemented for the curves (t, t) and (t, 2t^2) * Initialize NLP oracles (general curve w/ polytope) * Finish boundary oracle tests for H-polytope * Add ifopt and ipopt to CMakeLists.txt * Add wrapper function for nlp oracles * Working nlp H-polyoracle * Rename nlp polyoracles to avoid confusion with lp oracles * Remove old polyoracles file * Document NLP hpolyoracles * Minor refactoring * Add wrapper function * WIP: Initialize NLP oracle for V-polytope * Update readme with GSoC information * Add benchmarks with random polynomials * Modify membership condition * Restrain test to t only * Bug fixes * Code cleanup * Move to old commit (before merge) * Merge ode solvers * Rename testcases * Merge root finders test * Move hmc to sampling/ directory * Partial fix for V polyoracles with ipopt * Fix linear collocation method * Fix collocation with approximate computation * Improve README file * Add precomputation flag * Improve NR solver * Add central method for curve_intersect * Change return type of nlp vpolyoracle to return dummy facet * WIP: Integrate boundary oracles to collocation * Fix collocation method boundary oracles (w/ tests) * Bug fixes * Add mpsolve and gmp to CMakeLists.txt * Implement mpsolve wrapper * WIP: Integrate mpsolve * Fix preprocessor directives * Add boundary oracle with mpsolve * Fix minor issues * Fix existing working tests * Add min_pos optimization problem * WIP: Minor changes in way of reflection * Remove hmc sampler temporarily (move it to temp branch) * Fix reflections * Add dependencies(mpsolve, ipopt/ifopt) to CircleCI * Fix config * Fix config * Fix config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add dependency at circleci config * Add root finders test * Minor fixes in boundary oracles * Fix bounded collocation * Typo fix * Add missing test to cmakelists * Add #undef where it is needed * Remove extraneous dynamic linking * Fix erroneous flag * Remove hmc tests (moved to other branch) * Update clang and g++ workflows * Fix failing R tests * Fix failing R tests * Split checking for ubuntu/macOS * Remove misplaced if statement * Add CMAKE_CXX_COMPILER flag to ifopt * Correct test name * Remove sudo in front of brew cmd * Add automake dependency * Change error_on from "warning" to "error" * Add preprocessor directive to disable NLP oracles * Add flag for disabling oracles * Add macro definitions for disabling oracles * Add windows workflow * Modify windows workflow * Change Makevars.win * Change Makevars.win * Change Makevars.win * Disable NLP oracles to all tests * Modify circleci build * Modify circleci build * Add preprocessor directive * Remove report * Remove GSoC details * Move macro * Remove unused typedefs * Modify copyright notices * Fix typo * Rename rk.h to runge_kutta.hpp * Minor correction * Rename .h to .hpp in ODE solvers * Rename nlp oracles from .h to .hpp * Rename root finders * Remove duplicate include * Reorder #include directives * Refactoring * Rename file * Add velocity reflections * Remove extraneous constructors * Add general docs for solvers * Temp refactoring * Fix minor bugs * Remove flag from richardson implementation * Add facet ignore * Finish oracles refactoring * Consistent copyright notices * Add accidentally removed templates * Consistent copyright notices * Add nlp_oracles.hpp main header file * Minor modifications * Change variable name from oracle to intersection_oracle * Remove unused file * Add higher-order reflections * Add missing ignore_facet * Wrap long lines * Remove print statement * Impose sticky boundary conditions for collocation * Impose sticky boundary conditions for collocation * WIP: Add integral collocation method class prototype * Delete integral_collocation.hpp * Modifications to collocation method * Iteratively solve non-linear equations * Fix bugs * Minor modifications to test routines * Optimize function oracles * Comment for future work * Minor changes * Remove comments from yaml * Restore README * Restore README | 17 July 2020, 07:44:29 UTC |
| 21c6bf5 | Vissarion Fisikopoulos | 15 July 2020, 08:21:21 UTC | Update README.md | 15 July 2020, 08:21:21 UTC |
| ac15c1c | hariszaf | 10 July 2020, 10:06:15 UTC | Update python interface (#94) * Create setup_hz.py * Create bindings_hz.cpp * Create volestipy_hz.pyx * Create bindings_hz.h * Update bindings_hz.h * Update bindings_hz.cpp * Create volestipy_old.pyx * Delete volestipy_hz.pyx * Create bindings_old.cpp * Delete bindings_hz.cpp * Update bindings.cpp * Create bindings_old.h * Delete bindings_hz.h * Create setup_old.py * Delete setup_hz.py * Update setup.py * Update volestipy.pyx * Update bindings.h * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update setup.py * Update bindings.h * Update setup.py * Update setup_old.py * Update bindings.cpp * Update setup.py * Update setup.py * Update volestipy.pyx * Update test1.py * Create test1_old.py * Update test1.py * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.h * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.h * Update bindings.cpp * Update bindings.h * Update setup.py * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volume_cb_hpolytope.cpp * Update test1.py * Update bindings.cpp * Update test1.py * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update bindings.cpp * Update volestipy.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Create .gitignore * Delete test1_old.py * Delete setup_old.py * Delete bindings_old.h * Delete bindings_old.cpp * Delete volestipy_old.pyx * Update volestipy.pyx * Update bindings.cpp * Update bindings.h * Update .gitignore * Update volume_cb_hpolytope.cpp * Update test1.py * Update test2.py * Update bindings.h * Update setup.py * Update credits.md * on .gitignore: files on test/Testing/Temporary/ were removed from the .gitignore file | 10 July 2020, 10:06:15 UTC |
| a74ae6a | Tolis Chalkis | 22 June 2020, 07:13:58 UTC | Fix bug in boundary cdhr random walk (#91) | 22 June 2020, 07:13:58 UTC |
| d8748d8 | Vissarion Fisikopoulos | 18 June 2020, 14:18:31 UTC | Fix deprecated ftime in lpsolve and update README (#89) | 18 June 2020, 14:18:31 UTC |
| a91a312 | Panagiotis Repouskos | 16 June 2020, 11:45:27 UTC | fix clang++ segmentation fault (#87) * fix clang++ segmentation fault There was a problem with clang when accessing elements of vector spectrahedron.getLMI().getMatrices() - getMatrices() returns std::vector const &. The fix was to make Spectrahedron class method getLMI() return LMI const & - also make LMI constructor take parameter const &, not just & * fix #include paths | 16 June 2020, 11:45:27 UTC |
| dc3bade | Vissarion Fisikopoulos | 04 June 2020, 14:21:42 UTC | Merge pull request #86 from vissarion/github-actions-cran GitHub actions for R interface | 04 June 2020, 14:21:42 UTC |
| 800886c | Vissarion Fisikopoulos | 31 May 2020, 19:19:19 UTC | actions for R | 04 June 2020, 13:53:22 UTC |
| d10b749 | Vissarion Fisikopoulos | 03 June 2020, 10:41:50 UTC | Activate tests in github actions (and clang sanitizer) (#85) * Use actions with -fsanitize=memory * Use actions with -fsanitize=memory * Use actions with -fsanitize=memory | 03 June 2020, 10:41:50 UTC |
| b354f40 | Panagiotis Repouskos | 03 June 2020, 07:27:56 UTC | Sdpa format (#36) * expose Spectrahedron interface to R - create class spectrahedron - expose function to write sdpa format files in R * expose read_sdpa function to R and documentation * R documentation and examples - fix examples - add data for example - add roxygen comments * tests for sdpa format manager - add copyrights headers - add test that writes and reads a sdpa format file - add the test in test/CMakeLists.txt * add example code for sdpa files - create folder examples in root - add an example main to read / write sdpa format files * fix file format * fix file encoding * use soft wrap with lines * create folder spectrahedra - move in new folder spectrahedron.h, LMI.h - update CMakeLists.txt in folder examples, tests - update Makevars in R-prog/src and in cran_gen - add documentation for sdpa file example * examples/spectrahedra documentation * examples/spectrahedra documentation fix headers * rename R modules - rename module in polytopes_modules.cpp to "polytopes" - rename module in spectrahedron_module.cpp to "spectrahedron" - fix dates in copyrights headers in files - add a newline in end of file spectrahedron.h * make LMI::getMatrices() return std::vector const & Also fix parameters documentation in R for functions - readSDPAFormatFile - loadSDPAFormatFile - writeSDPAFormatFile * rename typedefs in spectrahedron.cpp - rename SPECTRAHEDRON typedef to Spectrahedron - remove unneeded class _Spectrahedron in spectrahedron.cpp | 03 June 2020, 07:27:56 UTC |
| 01a99a2 | Vissarion Fisikopoulos | 01 June 2020, 08:40:23 UTC | Update/restructure Readme (#84) * Update README * Update README | 01 June 2020, 08:40:23 UTC |
| de42d90 | Tolis Chalkis | 01 June 2020, 06:58:11 UTC | Improvements on cran tests and R interface (#83) * fix windows errors in cran checks * update Rd files, fix bugs in direct_sampling and boundary sampling * improve R tests, update description file and fix seeding in cooling hpoly * re order template classes in volume functions * remove skiping for 32-bit in R tests * fix declaration of random walks for uniform sampling * fix the default value of the ball walk radius, fix zonotope c++ test * fix c++ tests * fix c++ tests * fix memory leak in cg algorithm. update R examples and tests * remove unused comments * update dicumentation and Rd files * fix error in lpsolve, seeding in vpolytopeintersection and c++ tests * fix vpolytope-intersection c++ test | 01 June 2020, 06:58:11 UTC |
| 294b6a2 | Vissarion Fisikopoulos | 31 May 2020, 19:19:19 UTC | cran actions | 31 May 2020, 19:19:19 UTC |
| 200c02b | Tolis Chalkis | 25 May 2020, 07:47:16 UTC | Fix CRAN interface (#81) * pass cran check * fix billiard initialization, rounding shifting and seeding * add seed to copula computations | 25 May 2020, 07:47:16 UTC |
| 95d18a8 | Vissarion Fisikopoulos | 22 May 2020, 12:30:18 UTC | Add simple github actions CI for gcc and clang (#80) | 22 May 2020, 12:30:18 UTC |
| 58a079f | Tolis Chalkis | 21 May 2020, 19:35:33 UTC | Merge pull request #79 from vissarion/random_walk_strategies_try Refactoring volume algorithms and random walks | 21 May 2020, 19:35:33 UTC |
| f50bbcb | Vissarion Fisikopoulos | 17 May 2020, 19:30:19 UTC | Remove unnecessary constructors in random walks, put const refs | 17 May 2020, 19:30:19 UTC |
| a429037 | Vissarion Fisikopoulos | 17 May 2020, 19:24:19 UTC | Add const refs, missing includes, const vars for tolerance, fix some code styling | 17 May 2020, 19:24:19 UTC |
| a40a3d1 | Vissarion Fisikopoulos | 17 May 2020, 19:19:19 UTC | Removing unused variables, setting const refs where needed | 17 May 2020, 19:19:19 UTC |
| e398712 | Vissarion Fisikopoulos | 18 May 2020, 11:03:06 UTC | Enable tests for CB algorithm with V-cubes | 18 May 2020, 11:03:06 UTC |
| 154e500 | Vissarion Fisikopoulos | 18 May 2020, 09:44:01 UTC | Resolving conflicts after merging with develop | 18 May 2020, 09:44:01 UTC |
| 6f24233 | Vissarion Fisikopoulos | 17 May 2020, 06:51:07 UTC | Fix line_intersect function | 17 May 2020, 06:51:07 UTC |
| 3527a44 | Vissarion Fisikopoulos | 17 May 2020, 06:51:07 UTC | Remove duplicate seed from rcpp | 17 May 2020, 06:51:07 UTC |
| 79cf540 | Tolis Chalkis | 02 May 2020, 06:51:07 UTC | Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly | 18 May 2020, 08:43:38 UTC |
| ad2fbf2 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Removing old implementation files and renaming | 18 May 2020, 08:43:38 UTC |
| a00946e | Tolis Chalkis | 02 May 2020, 06:51:07 UTC | Improvements and corrections in Rcpp functions (#4) * correct input list algo in Rcpp volume.cpp * Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly * overloading rotating() function and remove unused comments * implement zonotope volume computation with cb algorithm and hpoly in MMC * fix all bugs in new cooling_hpoly algorithm and improve test function * all tests for zonotopes with c algortihm passed successfully * implmentation of diameter computation of all convex bodies except Vpoly-intersection * add Vpolyintersection diameter computation and volume approximation * new implmentation of rounding * add rounding in zonotope volume approximation with Hpoly in MMC * dispatching in ratio estimation * update ratio estimation functions * implmemrnt dispatching for diameter computation * improve ratio estimation code structure * update declaration of parameters in random walks * update parameter declaretion for both ball and billiard walks * modify Rcpp expose for volume and sampling C++ functions * modify Rcpp rounding function * update rounding, sampling, volume rcpp dunctions: typedefs and includes * modify zonotope approximation Rcpp function. minor changes to Rcpp volume and sampling functions * fix compiler errors * update d files * fix compiler errors in c++ tests * add seed in rounding and direct_sampling Rcpp functions * add a second volume function to use fixed seed in Rcpp interface * fix rcpp interface | 18 May 2020, 08:43:38 UTC |
| 28da0e8 | Vissarion Fisikopoulos | 14 May 2020, 16:39:12 UTC | Restructuring volume algorithms and random walks | 18 May 2020, 08:43:38 UTC |
| ede4c5b | Tolis Chalkis | 14 May 2020, 08:07:06 UTC | Rcpp functions with the new structure (#3) * correct input list algo in Rcpp volume.cpp * Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly * overloading rotating() function and remove unused comments * implement zonotope volume computation with cb algorithm and hpoly in MMC * fix all bugs in new cooling_hpoly algorithm and improve test function * all tests for zonotopes with c algortihm passed successfully * implmentation of diameter computation of all convex bodies except Vpoly-intersection * add Vpolyintersection diameter computation and volume approximation * new implmentation of rounding * add rounding in zonotope volume approximation with Hpoly in MMC * dispatching in ratio estimation * update ratio estimation functions * implmemrnt dispatching for diameter computation * improve ratio estimation code structure * update declaration of parameters in random walks * update parameter declaretion for both ball and billiard walks * modify Rcpp expose for volume and sampling C++ functions * modify Rcpp rounding function * update rounding, sampling, volume rcpp dunctions: typedefs and includes * modify zonotope approximation Rcpp function. minor changes to Rcpp volume and sampling functions * fix compiler errors * update d files * fix compiler errors in c++ tests * add seed in rounding and direct_sampling Rcpp functions * add a second volume function to use fixed seed in Rcpp interface | 18 May 2020, 08:43:38 UTC |
| 8021daf | Tolis Chalkis | 26 April 2020, 15:55:04 UTC | New rounding implementation ans volume approximation for V-poytopes intersection (#2) * correct input list algo in Rcpp volume.cpp * Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly * overloading rotating() function and remove unused comments * implement zonotope volume computation with cb algorithm and hpoly in MMC * fix all bugs in new cooling_hpoly algorithm and improve test function * all tests for zonotopes with c algortihm passed successfully * implmentation of diameter computation of all convex bodies except Vpoly-intersection * add Vpolyintersection diameter computation and volume approximation * new implmentation of rounding * add rounding in zonotope volume approximation with Hpoly in MMC * dispatching in ratio estimation * update ratio estimation functions * implmemrnt dispatching for diameter computation * improve ratio estimation code structure | 18 May 2020, 08:43:38 UTC |
| 70114b2 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Passing walks as objects to volume with runtime arguments | 18 May 2020, 08:43:38 UTC |
| b48b411 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Fixing tests | 18 May 2020, 08:43:38 UTC |
| f922c71 | Tolis Chalkis | 21 April 2020, 07:25:52 UTC | Implementation of cb algorithm with H-polytopes in MMC for zonotopes (#1) * correct input list algo in Rcpp volume.cpp * Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly * overloading rotating() function and remove unused comments * implement zonotope volume computation with cb algorithm and hpoly in MMC * fix all bugs in new cooling_hpoly algorithm and improve test function * all tests for zonotopes with c algortihm passed successfully | 18 May 2020, 08:43:38 UTC |
| ade5951 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Tests for CG/vpolytopes | 18 May 2020, 08:43:38 UTC |
| c92df0c | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Update delta after walk construction | 18 May 2020, 08:43:38 UTC |
| 38b2f82 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Fix accuracy of CDHR in CG | 18 May 2020, 08:43:38 UTC |
| 597b37a | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Fixes in cooling gaussian algorithm and tests | 18 May 2020, 08:43:38 UTC |
| f880d8d | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Fix tests for CB algorithm and hpolytopes | 18 May 2020, 08:43:38 UTC |
| c138a05 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Fix walk initialization for CB algorithm | 18 May 2020, 08:43:38 UTC |
| e15b560 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Tests for CB algorithms and various walks (expect to fail at this stage) | 18 May 2020, 08:43:38 UTC |
| 2feee11 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Benchmarks and tests (sob and gc algorithms) | 18 May 2020, 08:43:38 UTC |
| 770feee | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Tests for sob algo using hpoly | 18 May 2020, 08:43:38 UTC |
| 00032c3 | Vissarion Fisikopoulos | 02 May 2020, 06:51:07 UTC | Const references and styling for cooling balls algorithm | 18 May 2020, 08:43:38 UTC |
| 25d9824 | Tolis | 10 April 2020, 13:56:59 UTC | overloading rotating() function and remove unused comments | 10 April 2020, 13:56:59 UTC |
| ef5da16 | Tolis Chalkis | 10 April 2020, 13:35:17 UTC | Improvements in rounding and rotating R functions (#76) * add seed in rotate_polytope and update Rd files * update R rounding function to return the linear map * fix rounding in V-poly | 10 April 2020, 13:35:17 UTC |
| 1dbcd6e | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | New design for cooling balls algorithm | 04 April 2020, 06:51:07 UTC |
| c660509 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Fixing the scope of variables and using const where possible in gausian annealing | 04 April 2020, 06:51:07 UTC |
| cd56f60 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Fixing the scope of several variables in gaussian cooling | 04 April 2020, 06:51:07 UTC |
| 2bdf48f | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Update delta for ball walk and removing unused paremeter passing in gaussing cooling algorithm | 04 April 2020, 06:51:07 UTC |
| ea889a9 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | CDHR walk for GC algorithm | 04 April 2020, 06:51:07 UTC |
| c3d40df | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | RDHR walk for GC algorithm | 04 April 2020, 06:51:07 UTC |
| 63ec811 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Ball walk for GC algorithm | 04 April 2020, 06:51:07 UTC |
| 2c7024a | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Design simpler Walk interface | 04 April 2020, 06:51:07 UTC |
| 4a4357a | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | RNG interface with fixed seed | 04 April 2020, 06:51:07 UTC |
| 9d700f5 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Random number generator struct | 04 April 2020, 06:51:07 UTC |
| d507165 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Expose rnd seed in highest level | 04 April 2020, 06:51:07 UTC |
| 3ac7cdb | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Optimization: move random generators creation outside of random walk helpers | 04 April 2020, 06:51:07 UTC |
| e173645 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | New volume function example | 04 April 2020, 06:51:07 UTC |
| 209c13a | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Cleanup SoB volume algorithm | 04 April 2020, 06:51:07 UTC |
| 69664de | Tolis Chalkis | 04 April 2020, 06:51:07 UTC | Use billiard walk in SOB algorithm (#75) * fix seed in rand_hpoly_generator * enable SOB algorithm with billiard walk * enable SOB algorithm with billiard walk in c++ interface | 04 April 2020, 06:51:07 UTC |
| fa05bcf | Tolis Chalkis | 28 March 2020, 18:54:51 UTC | Fix seed in gen_rand_hpoly (#74) * update input variable names in sample_points(), direct_sampling() and vpolytope-intersection R class * change 'algo' to 'settings' in volume function. remove unused methods in c++ polytope classes * update R tests and NEWS.md file * update zonotope_approximation input variables * delete cran package files * fix seed in rand_hpoly_generator | 18 May 2020, 08:36:29 UTC |
| e78733f | Tolis | 24 March 2020, 23:38:32 UTC | delete cran package files | 18 May 2020, 08:36:29 UTC |
| 0a82201 | Tolis | 24 March 2020, 20:11:48 UTC | update zonotope_approximation input variables | 18 May 2020, 08:36:29 UTC |
| 5235766 | Tolis | 24 March 2020, 18:49:58 UTC | update R tests and NEWS.md file | 18 May 2020, 08:36:29 UTC |
| d55ff2b | Tolis | 24 March 2020, 18:11:06 UTC | change 'algo' to 'settings' in volume function. remove unused methods in c++ polytope classes | 18 May 2020, 08:36:29 UTC |
| 44c9b7c | Tolis | 24 March 2020, 16:42:05 UTC | update input variable names in sample_points(), direct_sampling() and vpolytope-intersection R class | 18 May 2020, 08:36:29 UTC |
| 96f9576 | Panagiotis Repouskos | 23 March 2020, 13:51:21 UTC | Fix non const parameters in rand_exp_range (#71) Remove const from function parameter | 18 May 2020, 08:36:29 UTC |
| 3ec8e41 | Vissarion Fisikopoulos | 04 April 2020, 06:51:07 UTC | Update readme, add `doc` directory and tutorials (#70) | 04 April 2020, 06:51:07 UTC |
| 64e7a39 | Tolis | 01 April 2020, 15:05:30 UTC | correct input list algo in Rcpp volume.cpp | 01 April 2020, 15:05:30 UTC |
| d3bda40 | Tolis Chalkis | 28 March 2020, 18:57:32 UTC | Use billiard walk in SOB algorithm (#75) * fix seed in rand_hpoly_generator * enable SOB algorithm with billiard walk * enable SOB algorithm with billiard walk in c++ interface | 28 March 2020, 18:57:32 UTC |
| ddcbfeb | Vissarion Fisikopoulos | 28 March 2020, 18:55:03 UTC | new volume structure SoB plus random walks | 28 March 2020, 18:55:03 UTC |
| f10edad | Tolis Chalkis | 28 March 2020, 18:54:51 UTC | Fix seed in gen_rand_hpoly (#74) * update input variable names in sample_points(), direct_sampling() and vpolytope-intersection R class * change 'algo' to 'settings' in volume function. remove unused methods in c++ polytope classes * update R tests and NEWS.md file * update zonotope_approximation input variables * delete cran package files * fix seed in rand_hpoly_generator | 28 March 2020, 18:54:51 UTC |
| 02b9afa | Tolis Chalkis | 28 March 2020, 18:46:16 UTC | Merge pull request #73 from TolisChal/improve_interface Improvements in R interface | 28 March 2020, 18:46:16 UTC |
| 4b6b1ec | Tolis | 24 March 2020, 23:38:32 UTC | delete cran package files | 24 March 2020, 23:38:32 UTC |
| dabf4fd | Tolis | 24 March 2020, 20:11:48 UTC | update zonotope_approximation input variables | 24 March 2020, 20:11:48 UTC |
| aed400c | Tolis | 24 March 2020, 18:49:58 UTC | update R tests and NEWS.md file | 24 March 2020, 18:49:58 UTC |
| aed8e01 | Tolis | 24 March 2020, 18:11:06 UTC | change 'algo' to 'settings' in volume function. remove unused methods in c++ polytope classes | 24 March 2020, 18:11:06 UTC |
| 3c4b065 | Tolis | 24 March 2020, 16:42:05 UTC | update input variable names in sample_points(), direct_sampling() and vpolytope-intersection R class | 24 March 2020, 16:42:05 UTC |
| 0369391 | Panagiotis Repouskos | 23 March 2020, 13:51:21 UTC | Fix non const parameters in rand_exp_range (#71) Remove const from function parameter | 23 March 2020, 13:51:21 UTC |
| 8f36ef4 | Panagiotis Repouskos | 23 March 2020, 13:03:17 UTC | Use eigen types as internal structures (#29) * Changed class point to store coefficients to Eigen vector instead of std::vector. Made required code updates in polytopes.h, rounding.h,ballintersectconvex.h and updated CMakeLists.txt to include the directory with Eigen. * fixed bug * fix for quicker access to data When accessing the data of class Point don't copy the whole vector, but use the [] operator (changes requested during the pull request). * Eigen clean existing code, make changes in leftover files with previous implementation * Optimizations - avoid creating copies - code cleanup - more coherent coding, using Eigen and eradicating std::vector * Optimizations - Vectorize when possible the operations in line_intersect functions - Change the matrix in HPolytope to be RowMajor * Major - change uses of std::vector to Eigen vector - Change the matrix in HPolytope NOT to be RowMajor (seemed slower, needs more testing) - enabled no debug macro for Eigen in /test/CmakeList - added 2 tests, to compute volume with rdhr and with BiW * Bug Error in creating Point * bug * use cooling balls in test * edit initialization * edit /test/CMakeLists.txt * Optimizations - Use eigen function noalias() to avoid creating temporary copies when multiplying matrices - in getDirection() (samplers.h) don't use std::vector, only Eigen::Vector - fix bug in point.h, in constructor * leftovers from merge - make changes in code from last merge - delete tests I had previously added * cleanup - requested changes * update copyrights * bug * bug * requested changes * use += *= operators with points * use += *= operators with points | 23 March 2020, 13:03:17 UTC |
| 2704f59 | Vissarion Fisikopoulos | 20 March 2020, 11:28:53 UTC | Update readme, add `doc` directory and tutorials (#70) | 20 March 2020, 11:28:53 UTC |
| 8f24239 | Vaibhav Thakkar | 17 March 2020, 10:27:15 UTC | Fix bug in hpolytope print function (#68) | 17 March 2020, 10:27:15 UTC |
| 79887a4 | Vissarion Fisikopoulos | 16 March 2020, 15:16:47 UTC | Update README.md | 16 March 2020, 15:16:47 UTC |
| eb98614 | Vissarion Fisikopoulos | 16 March 2020, 13:34:07 UTC | Update README.md Closes #67 | 16 March 2020, 13:34:07 UTC |
| 9b24028 | Tolis Chalkis | 15 March 2020, 23:45:12 UTC | Merge pull request #66 from TolisChal/improve_sampling Improve sampling | 15 March 2020, 23:45:12 UTC |
| 4e0465d | Tolis | 15 March 2020, 23:19:59 UTC | improve comp_diam() function in polytopes | 15 March 2020, 23:19:59 UTC |
| abca095 | Tolis | 13 March 2020, 00:22:13 UTC | Merge branch 'develop' into improve_sampling | 13 March 2020, 00:22:13 UTC |
| 49d3777 | Tolis | 13 March 2020, 00:20:47 UTC | add direct_sampling R function | 13 March 2020, 00:20:47 UTC |
| 955c865 | Tolis | 12 March 2020, 14:16:19 UTC | fix #65 | 12 March 2020, 14:16:19 UTC |
| 4d4b49b | Tolis | 11 March 2020, 21:45:24 UTC | add mode and starting point as inputs in samlpe_points() | 11 March 2020, 21:45:24 UTC |
| b84a8a0 | KunalKatiyar | 04 March 2020, 13:59:49 UTC | Readme correction and -help error in generator (#64) | 04 March 2020, 13:59:49 UTC |
| 55e296b | Sharat-Bhat | 03 March 2020, 13:47:29 UTC | README: folder name changed from R-prog to R-proj (#63) * Folder name changed from R-prog to R-proj * Delete .Rhistory * Delete .Rhistory * Delete RcppExports.cpp | 03 March 2020, 13:47:29 UTC |
| e4ce0b6 | Tolis Chalkis | 27 February 2020, 09:46:11 UTC | Various improvements (tests, documentation, names) (#61) * modify c++ tests * improve input variable names in R functions * check for negative error parameter in both interfaces * update Rd files * update compute_indicators * update rotating R functions * update sample_points.cpp * update volume.cpp and Rd files * update zonotope_approximation functons and the Rd files * fix examples, tests, documentation errors * update rounding and fix a bug in sample_points gaussian sampling, update Rd files, fix cran errors * add the option to set seed for the random polytope generator * fix cran check errors * add boundary sampling in R interface * add references in rounding functions and fix bug in vol.cpp | 27 February 2020, 09:46:11 UTC |
