* Create setup_hz.py

* Create bindings_hz.cpp

* Create volestipy_hz.pyx

* Create bindings_hz.h

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* Update bindings_hz.cpp

* Create volestipy_old.pyx

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* 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

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* Update test1.py

* Create test1_old.py

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* 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

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* Update bindings.cpp

* Create test_rounding.py

* Create test1.py

* Create test2.py

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* 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 bindings.cpp

add empty last line

* add empty lines in the end of test files

* Update test_compute_max_ball.py

add space  in last line

* Update test_compute_max_ball.py

* Update test_compute_volume.py

* Update test_get_full_dim_polytope.py

* Update test_random_sampling.py

* Update test_read_bigg_files.py

* Update test_rounding.py

* Update bindings.h