* 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 (#50)

Passing volume constants by reference

* removed some typos form readme, added sequence of balls volume, bumped minor release (#52)

* Create CONTRIBUTING.md

* Create CODE_OF_CONDUCT.md (#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 (#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 (#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 (#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 (#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 #8 (#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) (#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 (#63)

* Folder name changed from R-prog to R-proj

* Delete .Rhistory

* Delete .Rhistory

* Delete RcppExports.cpp

* Readme correction and -help error in generator (#64)

* add mode and starting point as inputs in samlpe_points()

* fix #65

* add direct_sampling R function

* improve comp_diam() function in polytopes

* Update README.md

Closes #67

* Update README.md

* Fix bug in hpolytope print function (#68)

* Update readme, add `doc` directory and tutorials (#70)

* 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

* Fix non const parameters in rand_exp_range (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#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 (#80)

* Fix CRAN interface (#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 (#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 (#84)



* Update README

* Update README

* 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

* Activate tests in github actions (and clang sanitizer) (#85)

* Use actions with -fsanitize=memory

* Use actions with -fsanitize=memory

* Use actions with -fsanitize=memory

* actions for R

* 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

* Fix deprecated ftime in lpsolve and update README (#89)

* CRAN version 1.1.2 (#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 (#115)"

This reverts commit 1bd54f22a81c869b2054ac91ad45c3fef42bd539.

* Remove std::cout

* Max ball param in generate_samples and rounding (#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>