LICENSE.md
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.cfg
setup.py
./LICENSE.md
./README.md
docs/average_cell_shapes.rst
docs/average_swc_shape.rst
docs/benchmarking.rst
docs/cellaligner.rst
docs/combined_slb_qgw.rst
docs/computing-gw-distances.rst
docs/computing-intracell-distance-matrices.rst
docs/conf.py
docs/fused_gw.rst
docs/gw_variants.rst
docs/index.rst
docs/laplacian_score.rst
docs/qgw.rst
docs/run_gw.rst
docs/sample_mesh.rst
docs/sample_seg.rst
docs/sample_swc.rst
docs/subcellular.rst
docs/subcellular_dl.rst
docs/swc.rst
docs/ternary_plot.rst
docs/unbalanced_gw.rst
docs/utilities.rst
docs/what-is-cajal.rst
docs/wnn.rst
docs/notebooks/Example_1.ipynb
docs/notebooks/Example_2.ipynb
docs/notebooks/Example_3.ipynb
docs/notebooks/Example_4.ipynb
docs/notebooks/Example_5.ipynb
docs/notebooks/Example_6.ipynb
docs/notebooks/Example_7.ipynb
src/cajal/EMD.h
src/cajal/EMD_wrapper.cpp
src/cajal/__init__.py
src/cajal/cajal_types.py
src/cajal/combined_slb_qgw.py
src/cajal/core.h
src/cajal/deformation_vis.py
src/cajal/full_bipartitegraph.h
src/cajal/full_bipartitegraph_omp.h
src/cajal/fused_gw_swc.py
src/cajal/gw_cython.cpp
src/cajal/gw_cython.pyx
src/cajal/laplacian_score.py
src/cajal/network_simplex_simple.h
src/cajal/network_simplex_simple_omp.h
src/cajal/partial.py
src/cajal/qgw.py
src/cajal/run_gw.py
src/cajal/sample_mesh.py
src/cajal/sample_seg.py
src/cajal/sample_swc.py
src/cajal/slb.cpp
src/cajal/slb.pyx
src/cajal/subcellular.py
src/cajal/subcellular_dl.py
src/cajal/swc.py
src/cajal/ternary.py
src/cajal/utilities.py
src/cajal/weighted_tree.py
src/cajal/wnn.py
src/cajal.egg-info/PKG-INFO
src/cajal.egg-info/SOURCES.txt
src/cajal.egg-info/dependency_links.txt
src/cajal.egg-info/requires.txt
src/cajal.egg-info/top_level.txt
src/cajal/ugw/Makefile
src/cajal/ugw/README.org
src/cajal/ugw/__init__.py
src/cajal/ugw/build_backends.py
src/cajal/ugw/common.fut
src/cajal/ugw/dune
src/cajal/ugw/dune-project
src/cajal/ugw/entropic_gw.fut
src/cajal/ugw/fused_gromov_wasserstein.fut
src/cajal/ugw/futhark.pkg
src/cajal/ugw/futhark_gw.ml
src/cajal/ugw/futhark_gw.mli
src/cajal/ugw/futhark_gw.opam
src/cajal/ugw/gw.fut
src/cajal/ugw/linear_ot.fut
src/cajal/ugw/list.fut
src/cajal/ugw/network_simplex.fut
src/cajal/ugw/scaling_generic.fut
src/cajal/ugw/scaling_unbalanced.fut
src/cajal/ugw/temp.fut
src/cajal/ugw/tree.fut
src/cajal/ugw/tree2.fut
src/cajal/ugw/unbalanced_gw.fut
src/cajal/ugw/unbalanced_gw_core.fut
src/cajal/ugw/c/unbalanced_gw_c.c
src/cajal/ugw/c/unbalanced_gw_c.h
src/cajal/ugw/c/unbalanced_gw_c.json
src/cajal/ugw/c/unbalanced_gw_c.ml
src/cajal/ugw/c/unbalanced_gw_c.mli
src/cajal/ugw/cuda/unbalanced_gw_cuda.c
src/cajal/ugw/cuda/unbalanced_gw_cuda.h
src/cajal/ugw/cuda/unbalanced_gw_cuda.json
src/cajal/ugw/cuda/unbalanced_gw_cuda.ml
src/cajal/ugw/cuda/unbalanced_gw_cuda.mli
src/cajal/ugw/lib/dune
src/cajal/ugw/lib/github.com/diku-dk/containers/.gitignore
src/cajal/ugw/lib/github.com/diku-dk/containers/array.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/array_test.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/bitset.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/bitset_test.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/list.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/list_test.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/opt.fut
src/cajal/ugw/lib/github.com/diku-dk/containers/opt_test.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/random.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/random_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/romu.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/romu_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/shuffle.fut
src/cajal/ugw/lib/github.com/diku-dk/cpprandom/shuffle_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/segmented/segmented.fut
src/cajal/ugw/lib/github.com/diku-dk/segmented/segmented_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/.gitignore
src/cajal/ugw/lib/github.com/diku-dk/sorts/bitonic_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/bitonic_sort_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/bubble_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/bubble_sort_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/insertion_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/insertion_sort_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/merge_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/merge_sort_tests.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/quick_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/quick_sort_test.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/radix_sort.fut
src/cajal/ugw/lib/github.com/diku-dk/sorts/radix_sort_tests.fut
src/cajal/ugw/multicore/unbalanced_gw_multicore.c
src/cajal/ugw/multicore/unbalanced_gw_multicore.h
src/cajal/ugw/multicore/unbalanced_gw_multicore.json
src/cajal/ugw/multicore/unbalanced_gw_multicore.ml
src/cajal/ugw/multicore/unbalanced_gw_multicore.mli
src/cajal/ugw/opencl/unbalanced_gw_opencl.c
src/cajal/ugw/opencl/unbalanced_gw_opencl.h
src/cajal/ugw/opencl/unbalanced_gw_opencl.json
src/cajal/ugw/opencl/unbalanced_gw_opencl.ml
src/cajal/ugw/opencl/unbalanced_gw_opencl.mli
tests/test_fused_gw_swc.py
tests/test_laplacian_score.py
tests/test_qgw.py
tests/test_run_gw.py
tests/test_sample_mesh.py
tests/test_sample_seg.py
tests/test_sample_swc.py
tests/test_swc.py
tests/test_ternary.py
tests/test_utilities.py