Revision f3da2bd424e61627ce943892037737ce6e1f827d authored by hariszaf on 13 August 2020, 16:11:28 UTC, committed by GitHub on 13 August 2020, 16:11:28 UTC
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* Create bindings_hz.cpp

* Create volestipy_hz.pyx

* Create bindings_hz.h

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* Create volestipy_old.pyx

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* Create bindings_old.cpp

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* Update bindings.cpp

* Create bindings_old.h

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* Create setup_old.py

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* Update setup.py

* Update volestipy.pyx

* Update bindings.h

* Update volestipy.pyx

* Update bindings.cpp

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* Update setup.py

* Update bindings.h

* Update setup.py

* Update setup_old.py

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* Update setup.py

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* Update test1.py

* Create test1_old.py

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* 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

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* 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

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* Update volestipy.pyx

* 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
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