CMakeLists.txt
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
lib/IntervalTree.h
lib/pybind11/CMakeLists.txt
lib/pybind11/include/pybind11/attr.h
lib/pybind11/include/pybind11/buffer_info.h
lib/pybind11/include/pybind11/cast.h
lib/pybind11/include/pybind11/chrono.h
lib/pybind11/include/pybind11/common.h
lib/pybind11/include/pybind11/complex.h
lib/pybind11/include/pybind11/eigen.h
lib/pybind11/include/pybind11/embed.h
lib/pybind11/include/pybind11/eval.h
lib/pybind11/include/pybind11/functional.h
lib/pybind11/include/pybind11/iostream.h
lib/pybind11/include/pybind11/numpy.h
lib/pybind11/include/pybind11/operators.h
lib/pybind11/include/pybind11/options.h
lib/pybind11/include/pybind11/pybind11.h
lib/pybind11/include/pybind11/pytypes.h
lib/pybind11/include/pybind11/stl.h
lib/pybind11/include/pybind11/stl_bind.h
lib/pybind11/include/pybind11/detail/class.h
lib/pybind11/include/pybind11/detail/common.h
lib/pybind11/include/pybind11/detail/descr.h
lib/pybind11/include/pybind11/detail/init.h
lib/pybind11/include/pybind11/detail/internals.h
lib/pybind11/include/pybind11/detail/typeid.h
lib/pybind11/tests/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/installed_embed/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/installed_function/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/installed_target/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/subdirectory_embed/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/subdirectory_function/CMakeLists.txt
lib/pybind11/tests/test_cmake_build/subdirectory_target/CMakeLists.txt
lib/pybind11/tests/test_embed/CMakeLists.txt
lib/pybind11/tools/FindCatch.cmake
lib/pybind11/tools/FindEigen3.cmake
lib/pybind11/tools/FindPythonLibsNew.cmake
lib/pybind11/tools/pybind11Tools.cmake
src/pinetree/__init__.py
src/pinetree/__init__.pyc
src/pinetree/averager.py
src/pinetree/batch.py
src/pinetree/choices.cpp
src/pinetree/choices.hpp
src/pinetree/core.cpython-36m-darwin.so
src/pinetree/event_signal.hpp
src/pinetree/feature.cpp
src/pinetree/feature.hpp
src/pinetree/gillespie.cpp
src/pinetree/gillespie.hpp
src/pinetree/model.cpp
src/pinetree/model.hpp
src/pinetree/polymer.cpp
src/pinetree/polymer.hpp
src/pinetree/python_bindings.cpp
src/pinetree/reaction.cpp
src/pinetree/reaction.hpp
src/pinetree/tracker.cpp
src/pinetree/tracker.hpp
src/pinetree.egg-info/PKG-INFO
src/pinetree.egg-info/SOURCES.txt
src/pinetree.egg-info/dependency_links.txt
src/pinetree.egg-info/not-zip-safe
src/pinetree.egg-info/requires.txt
src/pinetree.egg-info/top_level.txt
src/pinetree/__pycache__/__init__.cpython-36.pyc
tests/__init__.py
tests/__init__.pyc
tests/cpp_test.pyc
tests/feature_test.py
tests/integration_test.py
tests/integration_test.pyc
tests/polymer_test.py
tests/reaction_test.py
tests/__pycache__/__init__.cpython-36.pyc
tests/__pycache__/cpp_test.cpython-36.pyc
tests/__pycache__/degrade_test.cpython-36.pyc
tests/__pycache__/feature_test.cpython-36.pyc
tests/__pycache__/integration_test.cpython-36.pyc
tests/__pycache__/polymer_test.cpython-36.pyc
tests/__pycache__/reaction_test.cpython-36.pyc
tests/__pycache__/test_cpp.cpython-36.pyc
tests/__pycache__/test_run_simulation.cpython-36.pyc
tests/bin/pinetree_test
tests/models/__init__.py
tests/models/__init__.pyc
tests/models/consecutive_promoters.yml
tests/models/consecutive_promoters_test.yml
tests/models/degrade_test.py
tests/models/dual_polymerases.yml
tests/models/dual_promoter.yml
tests/models/genome_entry.yml
tests/models/lotka_voltera.yml
tests/models/overlapping_genes.yml
tests/models/promoter_gene_overlap.yml
tests/models/readthrough.yml
tests/models/single_gene.py
tests/models/single_gene.pyc
tests/models/single_gene.yml
tests/models/single_gene_x.pyc
tests/models/three_genes.yml
tests/models/three_genes_recoded.yml
tests/models/three_genes_runoff.yml
tests/models/__pycache__/__init__.cpython-36.pyc
tests/models/__pycache__/single_gene.cpython-36.pyc
tests/models/__pycache__/single_gene_x.cpython-36.pyc
tests/output/consecutive_promoters_counts.tsv
tests/output/dual_polymerases_counts.tsv
tests/output/dual_promoter_counts.tsv
tests/output/genome_entry_counts.tsv
tests/output/lotka_voltera_counts.tsv
tests/output/overlapping_genes_counts.tsv
tests/output/promoter_gene_overlap_counts.tsv
tests/output/readthrough_counts.tsv
tests/output/single_gene_counts.tsv
tests/output/single_gene_counts_old.tsv
tests/output/three_genes_counts.tsv
tests/output/three_genes_no_deg_counts.tsv
tests/output/three_genes_prom_counts.tsv
tests/output/three_genes_prom_deg_counts.tsv
tests/output/three_genes_rnase_prom_counts.tsv
tests/output/three_genes_rnase_site_counts.tsv
tests/output/three_genes_runoff_counts.tsv
tests/output/three_genes_w_deg_counts.tsv