Samplers + Rcpp Interface (Milestone II and III) #124
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…in InnerBall tests.
… on sphere function
Reduce if statements in Rvolume to one and fix a bug in generate points on sphere function
…lgo to origin, improve ball membership and boundary oracles.
…. Add modules for H,V-polytopes and zonotopes. All the exported classes have a field int 'type' in order to declare the representation of the polytope.
…implex. Modify R functions for rounding, and random rotate.
…as well. Delete temp folder.
…oth R and rcpp internal functions of rounding and rotating. Change the roxygen comments accordingly.
… and fix bugs in sample_points and exact_vol functions. Make adjustments in the test functions.
…ble basis from the first LP for the second one in each HnR step.
…ix bugs from devtools::check().
…Use break inside case:
…ough modules. Fix bugs in arbitrary simplex sampler. Fix bugs in examples, and in the SOB function in volume.h in cran header.
* Use actions with -fsanitize=memory * Use actions with -fsanitize=memory * Use actions with -fsanitize=memory
GitHub actions for R interface
* 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
* fix review comments on R package * update R interface in volume and sample_points * update Rcpp modules and S4 classes * replace modules with R classes * update R documentation * fix R tests * fix R bugs * add hpoly new generator, fix bugs in rounding with biw * update the Rd files * fix c++ tests and a bug in volume.coo * fix c++ test * update polytope random generators in R, update rd files * fix bugs in R interface * seperate sdp functions
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This reverts commit 1bd54f2.
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* 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 * Delete test1.py git rm test1.py * Delete test2.py git rm test2.py * Update bindings.h new class for the preprocessing and the get_full_dimensional_polytope() function in the bindings.h * Update bindings.cpp new class for the preprocessing and the get_full_dimensional_polytope() function in the bindings.cpp * Update volestipy.pyx new class for the preprocessing and the get_full_dimensional_polytope() function in the volestipy.pyx * Update bindings.h working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version * Update bindings.cpp working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version * Update volestipy.pyx working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version * Update bindings.h set member variables for lowDimHPolytopeCPP class * Update bindings.cpp remove unessecary vars * Update volestipy.pyx remove unecessary vars in self.full_dim_polytope * Update bindings.h build the instructor for the full_dimensional_polytope() function * Update bindings.cpp 1st draft for the get_full_dimensional_polytope() function * Update volestipy.pyx 1st draft for the python interface of the get_full_dimensional_polytope() function * Update bindings.h using transpose matrices for N and A_full removing the "extra" from the shift and b_full vectors as it is not needed * Update bindings.cpp 2nd draft for the lowDimHPolytopeCPP class. we changed the N and A_full matrices to transpose to feed them in the cpp file like this. we removed the _extra from the vectors * Update volestipy.pyx 2nd draft for the lowDimHPolytopeCPP class. changed "_extra" vectors when needed. first draft that actually compiles * Create test_get_full_dim_polytope.py test file for the get_full_dimensional_polytope function not ready yet * Update test_get_full_dim_polytope.py changed the Aeq * Update test_get_full_dim_polytope.py final test for the get_full_dimensional_polytope() function * Update bindings.cpp print the N transpose and the full A transpose matrices from the C++ code * Update volestipy.pyx Attention! What C++ returns is the transpose matrix. Thus, the [i,j] element of the full A is the [j,i] of what C++ returns. That is what we fixed here * Update test_get_full_dim_polytope.py print all the outputs of the get_full_dimensional_polytope() function * Update bindings.cpp remove test prints * Update volestipy.pyx remove test printing statements add all the output in the return statement on the get_full_dim_polytope() improved comments * Delete metabolic_net_pipeline.ipynb remove the jupyter notebook * Delete metabolic_net_pipeline-checkpoint.ipynb remove the hidden directory for the jupyter notebook * Update volestipy.pyx Exceptions for the low_dim_polytope_cpp constructor added. Deletion of the A_full and the b_full variables after the initialization of the object. * Update bindings.h CheBall was removed from the case of the lowDimHPolytopeCPP * Update volestipy.pyx just some functions of gurobipy * Update volestipy.pyx first draft for the pre_process() python function * Create test_preprocess.py a test file for the pre_process() function * Update volestipy.pyx correct obj function. Aeq line was replaced by a such from A. * Update volestipy.pyx make dependencies more readable * Update volestipy.pyx test sparse function * Update test_preprocess.py change dimensions * Update volestipy.pyx loop for all the lines of A and models for each of those and its minus * Update test_preprocess.py change the dimensions * Update volestipy.pyx draft to check whether it works fine! * Update volestipy.pyx change name in model.addConstr from "c2" to "c" in all the constraints described, fixed the solutions remove unecessary print statements * Update test_preprocess.py add print statement for the results of the pre_process() function * Update test_preprocess.py build Aeq in a way to be more like to a stoichiometric matrix * Update volestipy.pyx add model.update() and model.display() function every time we add constraints or change the objective function * Update volestipy.pyx correct typo in comment * Update volestipy.pyx add model.update() after the obj function for the minus A[i,] * Update volestipy.pyx add print statements * Update volestipy.pyx attempt to solve the issue with the solutions * Update volestipy.pyx addMConstrs * Update volestipy.pyx setMObjective() * Update volestipy.pyx correct objectives() * Update volestipy.pyx make minus obj function as it should be * Update volestipy.pyx remove print not needed statements make code more readable * Update test_preprocess.py change permission in test * Update test_preprocess.py add import volestipy in test_preprocess.py * Update volestipy.pyx remove solutions and their corresponding print statements add new line in the end of the file * Update volestipy.pyx correct comment * add bigg file of e.coli in .mat format * add a BIGG file in .json format * add function to read bigg files in .json format; keep the Aeq * develop the read json format bigg file function * add test file for reading json bigg files * add function for reading json bigg files * new directory for the bigg example files * improved function for reading json bigg files; Aeq is now m*n * print metabolites and reaction in the test for json * add function to read .mat bigg files * one test file for reading both json and mat bigg files * remove unecessary print statements * comment in the head of the file describing its purpose * update documentation on how to install volestipy * improved documentation for the dependencies * remember to explain how to get lpsolve * remember to explain how to get lpsolve * remember to explain how to get lpsolve * remember to explain how to get lpsolve * test with RECON1 for the pre-processing step were performed successfully * export .npy files with the outcome of the pre_process function so the user can load them any time * change the input file to e_coli_core * print files with the output of get_full_dim() and rounding() ; start function for inner ball * small changes to check data types * convertions to numpy arrays * complete read-preprocess-get_full_dim steps * add data types in .gitignore file * add a test with all the steps of the pipeline * draft for max ball * test for computing max ball * include get_max_ball() function * remove last empty lines * add emppty last line * lp_solve replaced by lpsolve * rounding step included in the full pipeline test * add comput_max_ball in the pipeline * fixed type for the r variable; sre_parse related issue * remove unecessary library * clean up a bit * Update volestipy.pyx empty last line * Update bindings.cpp add empty last line * improve rounding * fix svd rounding * add max_ball arguments in the rounding function * add max_ball if statement in rounding funcion * fix cheball in rounding * change variable name * add max ball in rounding function * add semicolomn * add extra variable inner_point_for_c to feed the .cpp with the inner point * change test file to include the max ball output as parameter to the rounding function * replace integer zero values in the bydefault inner point list, with fload zeros; this way we fixed bug according to which the inner_point_for_c was waiting for double but got long * replace if statement for max ball in rounding * add arguments in generate_samples() for the case that max_ball has been included * add cases for running generate_samples depending max ball input * feed sampling with max_ball params * add part for generate samples * change sampling function to support max ball and L params * change the way set_L and max_ball bool vars are set * python interface initialization * add accelerated_billiard variable * remove wrong '=' sign * remove const from end of void set_InnerBall functions * include sampling on rounded polytope using max ball function * max ball on rounded polytope * change by default number_of_points_to_burn * complete test pipeline * function for mapping sampled points to the initial polytope added * remove blank lines * remove blank line * clean code; split long lines * add blank last line * add features till get full dimensional polytope * before plotiing * plol it * histogram added * reaction 35 for plotting * add print statement for dimension * testing recon1 * testing for recon1 * notebook checkpoints * add returning min and max fluxes vectors in pre-processing * ignore png files * return float numpy types from read function * add tests for e coli and plot samples * e coli full example * further chechpoints Co-authored-by: Tolis <tolis.chal@gmail.com>
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Feb 26, 2021
* fix example errors and logical checks in sample_points(). Fix errors in InnerBall tests.
* add Hpolytope converter from Rcpp::Reference.
* comment out te converter in Rvolume.cpp
* Reduce if statements in Rvolume to one and fix bug in generate points on sphere function
* Add an example of volume computation
* Update README.md
* Update README.md
* Update README.md
* return 2d facets for inner ball in zonotopes. Shift polytope in SOB algo to origin, improve ball membership and boundary oracles.
* Rvolume: define the input variables, add wrappers to Rvolume function. Add modules for H,V-polytopes and zonotopes. All the exported classes have a field int 'type' in order to declare the representation of the polytope.
* modify the generators R functions. Create rcpp function sample_points.
* modify sample_points.
* add innerball.cpp, sample_points.cpp
* create rcpp funtions for exact volume computations, copulas, sliceofsimplex. Modify R functions for rounding, and random rotate.
* create rd files for all the rcpp functions and the polytopes modules as well. Delete temp folder.
* write the roxygen comments for the documentation. Change inputs for both R and rcpp internal functions of rounding and rotating. Change the roxygen comments accordingly.
* create the updated .Rd files and the pdf of the documentation
* add generators for H and V random polytopes. Update the documentation and fix bugs in sample_points and exact_vol functions. Make adjustments in the test functions.
* add boundary oracles for V-polytopes and zonotopes that use the feasible basis from the first LP for the second one in each HnR step.
* fix bug in rounding.cpp. Add Rd files by hand for polytope classes. Fix bugs from devtools::check().
* use switch instead of if-else if. Enable the c++ tests.
* use std::numeric_limits::max() and lowest().
* create Rd files for the exposed c++ classes. Use switch in poly_gen. Use break inside case:
* update the Rd files of the C++ classes and of the exposed classes through modules. Fix bugs in arbitrary simplex sampler. Fix bugs in examples, and in the SOB function in volume.h in cran header.
* update the roxygen comments for the documentation.
* use walk_step instead of walk_length.Update the documentation.
* use var.cdhr_walk and var.rdhr_walk for the type of HnR.
* include volume.h
* solve a Note from the devtools::build_win(). Update the cran-comments.md in cran_gen folder.
* disable skinny_cube_20 for rounding test
* fix rounding test
* fix rounding test
* change the cran-comments.md file and add the correct date to description file.
* update the cran version readme and add the cran-comments.md file into inst folder in cran package. Update fileToMatrix documentation.
* update the cran version readme.
* modify description and update documentation
* fix urls in cran readme.md and remove cran-comments from the inst folder.
* fix c++ tests for cg algo.
* fix c++ tests
* update the documentation and the description file.
* fix tests for CG algo in H-rep.
* fix c++ tests
* Add pararellism to CI
* relax V-poly tests
* Update config.yml to execute tests in parallel
* Fix problem with parallel build
* fix cg test for zonotopes
* replace Eigen::Random() in rotating.cpp. Modify the return value of rotating and rand_rotate() in order to return the matrix of the linear map as well. Use wrappers in ExtractMatPoly.h and modigy poly_gen.cpp and R generator functions accordingly. Update the documentation and add ' in mis-spells in description file to avoid the cran Notes.
* fix namespace and add innerball implementation for the intersection of two V-polytopes and modify InnerBall.cpp, sample_points.cpp and volume.cpp accordingly. Add operater == to point.h.
* remove single quotes from description and change the varsion to 1.0.0
* change description.
* edit description file to declare contributors. Change \dontrun{} with \donttest{} in Rd files and modify polytope_modules.cpp to declare copyrights.
* add COPYRIGHTS file, add copyright and modification declarations in external/minimum_ellipsoid header files.
* move lp_solve to externals and modify makevars and lpsolve makefile accordingly, as well as the R script grcran.R
* Fixing references in description file
* generate new documentation.
* add AUTHORS file in inst folder and a reference in description files. This file contains the contributors of other packages. We update the documentation
* improve AUTHORS file, update documentation pdf, fix a bug in lp_solve.h for the membership of zonotope
* new header file for rotating and fix bugs of solaris building in minimum_ellipsoid in external.
* fix non-external bugs from solaris
* remove .Rhistory file
* Change \` with \' in COPYRIGHTS
* commit the version 1.0.2 with ficed bugs and cran violations.
* update NEWS file for version 1.0.2
* Update NEWS.md
* Delete R documentation pdf
* fix bug foe ine files, when the coefficients are seperated by tab.
* fix point == operator.
* remove unused flags from makevars, fix error in lp_MPS.c, set version 1.0.3
* fix cran warning in lpkit.h
* modify NEWS.md file
* change date in description file
* fix cg algo's c++ tests
* add new computation of V-polytope inscribed ball, by coomputing an inscribed cube first.
* implement functions is_feasible() and ComputeInnerBall() in intersection of VP class. Use them in Rcpp functions.
* remove unused comments and add a reference in point.h
* python wrapper for volesti (volestipy)
* added short readme
* use liblpsolve55.so (somwhere on machine) + clean setup.py
* nothing really
* updated readme
* updated readme
* updated readme
* some small cleanup, nothing substantial.
* removed dead code
* Update README.md
* Fix some pass by value parameters and useless imports and README in python interface
* Passing volume constants by reference (GeomScale#50)
Passing volume constants by reference
* removed some typos form readme, added sequence of balls volume, bumped minor release (GeomScale#52)
* Create CONTRIBUTING.md
* Create CODE_OF_CONDUCT.md (GeomScale#53)
* Update issue templates
* split polytope classes and lp oracles functions in differetnt header files. Use pre-malloc in lp oracles.
* add new algo
* change the names of functions and inputs
* remove printing and fix includes of header files in cran version
* add boost header files for the new algo and fix the c++ interface
* improve the R documentation
* fix the R tests and improve R documentation
* fix R tests and bugs in examples of R functions. Fix a bug in c++ tests.
* update description, README.md, NEWS.md files for the new version and input variables' names in round_polytope R function.
* fix c++ tests
* change version and improve c++ code in new volume functions.
* implement the PR comments: declare const, improve names of functions and geeral coding
* define constants and add max number of iterations to check if the annealing fails. Update sample_points rd file. Fix bug in c++ generator.
* update description file and fix windows bug in ball_annealing.h
* fix template declarations and minor improvements in ratio_estimation.h
* minor improvments in exact_vol.h
* implment acceleration of rdhr for both volume and sampling.
* resolve PR in ball anealing and increase cdhr sliding window
* add billiard walk for volume
* add billiard to sample_points interface and fix documentation of R function of volume.
* improve rounding in R interface and documentation for sample_points and volume R functions.
* fix c++ interface and c++ tests
* update descriion file in R-proj
* update rd files
* fix bugs in Rd files and update the NEWS.md file
* improve the initialization of delta (ball_walk) and diameter. fix errors in doxumentation and update Rd files
* improve initialization of diameter for billiard walk. Fix C++ tests' bugs.
* remove volume.h file from cran version.
* use const variables and remove useless comments.
* reduce c++ cg volume test
* improve c++ interface and fix c++ tests
* Merge copula functions and new compute indicators R function (GeomScale#56)
* merge two copulas functions into one.
* add compute_indicators R function.
* develop compute_indicator R function and copula.cpp in R-proj
* improve roxygen comments in compute_indicator R function and copula.cpp in R-proj
* fix bugs in copulas.cpp
* fix bugs in compute_indicators.R
* fix R tests for copulas and set to lowercase the inputvariables in the new functions
* improve compute_indicators.R
* Exact volume (GeomScale#57)
* merge two copulas functions into one.
* add compute_indicators R function.
* develop compute_indicator R function and copula.cpp in R-proj
* improve roxygen comments in compute_indicator R function and copula.cpp in R-proj
* fix bugs in copulas.cpp
* fix bugs in compute_indicators.R
* fix R tests for copulas and set to lowercase the inputvariables in the new functions
* improve compute_indicators.R
* add volume field in R module polytope classes
* add volume declaration for known polytopes in R interface
* modify exact_vol.cpp in R interface
* set NaN the volume initialization in Rcpp modules of polytopes, update NEWS.md file
* modify namespace
* Improve interfaces, generators and bug fixes (GeomScale#58)
* use cdhr in rounding, improve t-test iterations, change diameter of H-polytopes, minor modifications in both interfaces.
* improve c++ interface, add c++ test for cooling bodies with billiard walk
* improve new c++ test
* add random generators
* update R random generators
* update Rd files
* update R volume interface
* fix generators in both c++ and R interfaces, improve exact_volume check in c++ interface
* fix bug in hpoly zonotope volume approximation
* improve c++ documentation (help command)
* fix c++ tests
* fix c++ tests
* improve cpp generator interface
* improve cpp generator interface
* Zonotope approximation (GeomScale#59)
* use cdhr in rounding, improve t-test iterations, change diameter of H-polytopes, minor mpdifications in both interfaces.
* improve c++ interface, add c++ test for cooling bodies with billiard walk
* improve new c++ test
* add random generators
* update R random generators
* update Rd files
* update R volume interface
* fix generators in both c++ and R interfaces, improve exact_volume check in c++ interface
* fix bug in hpoly zonotope volume approximation
* improve c++ documentation (help command)
* add zonotope_approximation in R interface. improve R volume and sample_points documentation
* fix c++ tests
* fix bug in zonotope approximation
Co-authored-by: Vissarion Fisikopoulos <fisikop@gmail.com>
* Fix tests and issue GeomScale#8 (GeomScale#60)
* modify c++ tests
* improve input variable names in R functions
* check for negative error parameter in both interfaces
* update Rd files
* Update README.md
* Various improvements (tests, documentation, names) (GeomScale#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
* README: folder name changed from R-prog to R-proj (GeomScale#63)
* Folder name changed from R-prog to R-proj
* Delete .Rhistory
* Delete .Rhistory
* Delete RcppExports.cpp
* Readme correction and -help error in generator (GeomScale#64)
* add mode and starting point as inputs in samlpe_points()
* fix GeomScale#65
* add direct_sampling R function
* improve comp_diam() function in polytopes
* Update README.md
Closes GeomScale#67
* Update README.md
* Fix bug in hpolytope print function (GeomScale#68)
* Update readme, add `doc` directory and tutorials (GeomScale#70)
* Use eigen types as internal structures (GeomScale#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
* Fix non const parameters in rand_exp_range (GeomScale#71)
Remove const from function parameter
* 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 gen_rand_hpoly (GeomScale#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
* new volume structure SoB plus random walks
* Use billiard walk in SOB algorithm (GeomScale#75)
* fix seed in rand_hpoly_generator
* enable SOB algorithm with billiard walk
* enable SOB algorithm with billiard walk in c++ interface
* correct input list algo in Rcpp volume.cpp
* Update readme, add `doc` directory and tutorials (GeomScale#70)
* Cleanup SoB volume algorithm
* New volume function example
* Optimization: move random generators creation outside of random walk helpers
* Expose rnd seed in highest level
* Random number generator struct
* RNG interface with fixed seed
* Design simpler Walk interface
* Ball walk for GC algorithm
* RDHR walk for GC algorithm
* CDHR walk for GC algorithm
* Update delta for ball walk and removing unused paremeter passing in gaussing cooling algorithm
* Fixing the scope of several variables in gaussian cooling
* Fixing the scope of variables and using const where possible in gausian annealing
* New design for cooling balls algorithm
* Improvements in rounding and rotating R functions (GeomScale#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
* Fix line_intersect function
* Add const refs, missing includes, const vars for tolerance, fix some code styling
* Remove unnecessary constructors in random walks, put const refs
* Fix non const parameters in rand_exp_range (GeomScale#71)
Remove const from function parameter
* 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 gen_rand_hpoly (GeomScale#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
* Use billiard walk in SOB algorithm (GeomScale#75)
* fix seed in rand_hpoly_generator
* enable SOB algorithm with billiard walk
* enable SOB algorithm with billiard walk in c++ interface
* Const references and styling for cooling balls algorithm
* Tests for sob algo using hpoly
* Benchmarks and tests (sob and gc algorithms)
* Tests for CB algorithms and various walks (expect to fail at this stage)
* Fix walk initialization for CB algorithm
* Fix tests for CB algorithm and hpolytopes
* Fixes in cooling gaussian algorithm and tests
* Fix accuracy of CDHR in CG
* Update delta after walk construction
* Tests for CG/vpolytopes
* 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 (GeomScale#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
* Fixing tests
* Passing walks as objects to volume with runtime arguments
* 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 (GeomScale#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
* Rcpp functions with the new structure (#3)
* correct input list algo in Rcpp volume.cpp
* Improvements in rounding and rotating R functions (GeomScale#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
* Restructuring volume algorithms and random walks
* Improvements and corrections in Rcpp functions (#4)
* correct input list algo in Rcpp volume.cpp
* Improvements in rounding and rotating R functions (GeomScale#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
* Removing old implementation files and renaming
* Improvements in rounding and rotating R functions (GeomScale#76)
* add seed in rotate_polytope and update Rd files
* update R rounding function to return the linear map
* fix rounding in V-poly
* Remove duplicate seed from rcpp
* Enable tests for CB algorithm with V-cubes
* Removing unused variables, setting const refs where needed
* Add simple github actions CI for gcc and clang (GeomScale#80)
* Fix CRAN interface (GeomScale#81)
* pass cran check
* fix billiard initialization, rounding shifting and seeding
* add seed to copula computations
* cran actions
* Improvements on cran tests and R interface (GeomScale#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
* Update/restructure Readme (GeomScale#84)
* Update README
* Update README
* Sdpa format (GeomScale#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
* Activate tests in github actions (and clang sanitizer) (GeomScale#85)
* Use actions with -fsanitize=memory
* Use actions with -fsanitize=memory
* Use actions with -fsanitize=memory
* actions for R
* fix clang++ segmentation fault (GeomScale#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
* Fix deprecated ftime in lpsolve and update README (GeomScale#89)
* CRAN version 1.1.2 (GeomScale#118)
* fix review comments on R package
* update R interface in volume and sample_points
* update Rcpp modules and S4 classes
* replace modules with R classes
* update R documentation
* fix R tests
* fix R bugs
* add hpoly new generator, fix bugs in rounding with biw
* update the Rd files
* fix c++ tests and a bug in volume.coo
* fix c++ test
* update polytope random generators in R, update rd files
* fix bugs in R interface
* seperate sdp functions
* Squash commits into one
* Revert "Max ball param in generate_samples and rounding (GeomScale#115)"
This reverts commit 1bd54f2.
* Remove std::cout
* Max ball param in generate_samples and rounding (GeomScale#115)
* 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
* Delete test1.py
git rm test1.py
* Delete test2.py
git rm test2.py
* Update bindings.h
new class for the preprocessing and the get_full_dimensional_polytope() function in the bindings.h
* Update bindings.cpp
new class for the preprocessing and the get_full_dimensional_polytope() function in the bindings.cpp
* Update volestipy.pyx
new class for the preprocessing and the get_full_dimensional_polytope() function in the volestipy.pyx
* Update bindings.h
working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version
* Update bindings.cpp
working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version
* Update volestipy.pyx
working on the lowDimHPolytopeCPP class - just a draft with the main ideas, not a stable version
* Update bindings.h
set member variables for lowDimHPolytopeCPP class
* Update bindings.cpp
remove unessecary vars
* Update volestipy.pyx
remove unecessary vars in self.full_dim_polytope
* Update bindings.h
build the instructor for the full_dimensional_polytope() function
* Update bindings.cpp
1st draft for the get_full_dimensional_polytope() function
* Update volestipy.pyx
1st draft for the python interface of the get_full_dimensional_polytope() function
* Update bindings.h
using transpose matrices for N and A_full
removing the "extra" from the shift and b_full vectors as it is not needed
* Update bindings.cpp
2nd draft for the lowDimHPolytopeCPP class.
we changed the N and A_full matrices to transpose to feed them in the cpp file like this.
we removed the _extra from the vectors
* Update volestipy.pyx
2nd draft for the lowDimHPolytopeCPP class.
changed "_extra" vectors when needed.
first draft that actually compiles
* Create test_get_full_dim_polytope.py
test file for the get_full_dimensional_polytope function
not ready yet
* Update test_get_full_dim_polytope.py
changed the Aeq
* Update test_get_full_dim_polytope.py
final test for the get_full_dimensional_polytope() function
* Update bindings.cpp
print the N transpose and the full A transpose matrices from the C++ code
* Update volestipy.pyx
Attention! What C++ returns is the transpose matrix.
Thus, the [i,j] element of the full A is the [j,i] of what C++ returns. That is what we fixed here
* Update test_get_full_dim_polytope.py
print all the outputs of the get_full_dimensional_polytope() function
* Update bindings.cpp
remove test prints
* Update volestipy.pyx
remove test printing statements
add all the output in the return statement on the get_full_dim_polytope()
improved comments
* Delete metabolic_net_pipeline.ipynb
remove the jupyter notebook
* Delete metabolic_net_pipeline-checkpoint.ipynb
remove the hidden directory for the jupyter notebook
* Update volestipy.pyx
Exceptions for the low_dim_polytope_cpp constructor added.
Deletion of the A_full and the b_full variables after the initialization of the object.
* Update bindings.h
CheBall was removed from the case of the lowDimHPolytopeCPP
* Update volestipy.pyx
just some functions of gurobipy
* Update volestipy.pyx
first draft for the pre_process() python function
* Create test_preprocess.py
a test file for the pre_process() function
* Update volestipy.pyx
correct obj function. Aeq line was replaced by a such from A.
* Update volestipy.pyx
make dependencies more readable
* Update volestipy.pyx
test sparse function
* Update test_preprocess.py
change dimensions
* Update volestipy.pyx
loop for all the lines of A and models for each of those and its minus
* Update test_preprocess.py
change the dimensions
* Update volestipy.pyx
draft to check whether it works fine!
* Update volestipy.pyx
change name in model.addConstr from "c2" to "c" in all the constraints described, fixed the solutions
remove unecessary print statements
* Update test_preprocess.py
add print statement for the results of the pre_process() function
* Update test_preprocess.py
build Aeq in a way to be more like to a stoichiometric matrix
* Update volestipy.pyx
add model.update() and model.display() function every time we add constraints or change the objective function
* Update volestipy.pyx
correct typo in comment
* Update volestipy.pyx
add model.update() after the obj function for the minus A[i,]
* Update volestipy.pyx
add print statements
* Update volestipy.pyx
attempt to solve the issue with the solutions
* Update volestipy.pyx
addMConstrs
* Update volestipy.pyx
setMObjective()
* Update volestipy.pyx
correct objectives()
* Update volestipy.pyx
make minus obj function as it should be
* Update volestipy.pyx
remove print not needed statements
make code more readable
* Update test_preprocess.py
change permission in test
* Update test_preprocess.py
add import volestipy in test_preprocess.py
* Update volestipy.pyx
remove solutions and their corresponding print statements
add new line in the end of the file
* Update volestipy.pyx
correct comment
* add bigg file of e.coli in .mat format
* add a BIGG file in .json format
* add function to read bigg files in .json format; keep the Aeq
* develop the read json format bigg file function
* add test file for reading json bigg files
* add function for reading json bigg files
* new directory for the bigg example files
* improved function for reading json bigg files; Aeq is now m*n
* print metabolites and reaction in the test for json
* add function to read .mat bigg files
* one test file for reading both json and mat bigg files
* remove unecessary print statements
* comment in the head of the file describing its purpose
* update documentation on how to install volestipy
* improved documentation for the dependencies
* remember to explain how to get lpsolve
* remember to explain how to get lpsolve
* remember to explain how to get lpsolve
* remember to explain how to get lpsolve
* test with RECON1 for the pre-processing step were performed successfully
* export .npy files with the outcome of the pre_process function so the user can load them any time
* change the input file to e_coli_core
* print files with the output of get_full_dim() and rounding() ; start function for inner ball
* small changes to check data types
* convertions to numpy arrays
* complete read-preprocess-get_full_dim steps
* add data types in .gitignore file
* add a test with all the steps of the pipeline
* draft for max ball
* test for computing max ball
* include get_max_ball() function
* remove last empty lines
* add emppty last line
* lp_solve replaced by lpsolve
* rounding step included in the full pipeline test
* add comput_max_ball in the pipeline
* fixed type for the r variable; sre_parse related issue
* remove unecessary library
* clean up a bit
* Update volestipy.pyx
empty last line
* Update bindings.cpp
add empty last line
* improve rounding
* fix svd rounding
* add max_ball arguments in the rounding function
* add max_ball if statement in rounding funcion
* fix cheball in rounding
* change variable name
* add max ball in rounding function
* add semicolomn
* add extra variable inner_point_for_c to feed the .cpp with the inner point
* change test file to include the max ball output as parameter to the rounding function
* replace integer zero values in the bydefault inner point list, with fload zeros; this way we fixed bug according to which the inner_point_for_c was waiting for double but got long
* replace if statement for max ball in rounding
* add arguments in generate_samples() for the case that max_ball has been included
* add cases for running generate_samples depending max ball input
* feed sampling with max_ball params
* add part for generate samples
* change sampling function to support max ball and L params
* change the way set_L and max_ball bool vars are set
* python interface initialization
* add accelerated_billiard variable
* remove wrong '=' sign
* remove const from end of void set_InnerBall functions
* include sampling on rounded polytope using max ball function
* max ball on rounded polytope
* change by default number_of_points_to_burn
* complete test pipeline
* function for mapping sampled points to the initial polytope added
* remove blank lines
* remove blank line
* clean code; split long lines
* add blank last line
* add features till get full dimensional polytope
* before plotiing
* plol it
* histogram added
* reaction 35 for plotting
* add print statement for dimension
* testing recon1
* testing for recon1
* notebook checkpoints
* add returning min and max fluxes vectors in pre-processing
* ignore png files
* return float numpy types from read function
* add tests for e coli and plot samples
* e coli full example
* further chechpoints
Co-authored-by: Tolis <tolis.chal@gmail.com>
* Regenerate R docs
* Update date field and add redirection to examples
* Reorder initializations
* Correct example
* Add high dimensional test
* Add high-dimensional example
* Add example for random H-polytope with Gaussian centered at the Chebyshev center
Co-authored-by: tolischal <tolis.chal@gmail.com>
Co-authored-by: Vissarion Fysikopoulos <vissarion.fysikopoulos@oracle.com>
Co-authored-by: Vissarion Fisikopoulos <fisikop@gmail.com>
Co-authored-by: pedrozudo <pedrozuidbergdosmartires@gmail.com>
Co-authored-by: Sharat-Bhat <45495724+Sharat-Bhat@users.noreply.github.com>
Co-authored-by: KunalKatiyar <katiyarkunal2011@gmail.com>
Co-authored-by: Vaibhav Thakkar <vaibhav.thakkar.22.12.99@gmail.com>
Co-authored-by: Panagiotis Repouskos <panagiotisrep@gmail.com>
Co-authored-by: hariszaf <haris-zaf@hcmr.gr>
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This pull request contains the following contributions
std::functionsample_pointsode_solveA tutorial is currently being drafted.
References
UPDATE Re-opened #100