refactoring of the code to match package tree

README.md

deconvolution/d2graph/__init__.py

deconvolution/d2graph/d2_algorithms.py

deconvolution/d2graph/d2_graph.py

deconvolution/d2graph/d2_reduction.py

deconvolution/d2graph/path_algorithms.py

deconvolution/d2graph/path_optimization.py

deconvolution/dgraph/FixedDGIndex.py

deconvolution/dgraph/VariableDGIndex.py

deconvolution/dgraph/d_graph.py

deconvolution/main/__init__.py

deconvolution/main/d2_to_path.py

deconvolution/main/generate_fake_barcode_graph.py

deconvolution/main/generate_fake_molecule_graph.py

deconvolution/main/to_d2_graph.py

setup.py

tests/Index_test.py

tests/d2_graph_test.py

tests/d_graph_test.py

tests/graph_manipulation_test.py