CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
docs/benchmark_schema.md
docs/release_checklist.md
docs/reproducibility.md
docs/assets/3ff22687bd403a67cd66caeacc95baee.png
installer/windows/README.md
installer/windows/TopoPPI.iss
installer/windows/install_topoppi.ps1
installer/windows/uninstall_topoppi.ps1
src/topoppi/__init__.py
src/topoppi/_version.py
src/topoppi/cli.py
src/topoppi/config.py
src/topoppi/errors.py
src/topoppi/gui.py
src/topoppi/install_optcuts.py
src/topoppi/logging_utils.py
src/topoppi/pipeline.py
src/topoppi.egg-info/PKG-INFO
src/topoppi.egg-info/SOURCES.txt
src/topoppi.egg-info/dependency_links.txt
src/topoppi.egg-info/entry_points.txt
src/topoppi.egg-info/requires.txt
src/topoppi.egg-info/top_level.txt
src/topoppi/assets/__init__.py
src/topoppi/assets/topoppi.ico
src/topoppi/assets/topoppi.png
src/topoppi/atlas/__init__.py
src/topoppi/atlas/metrics.py
src/topoppi/benchmarking/__init__.py
src/topoppi/benchmarking/metrics_utils.py
src/topoppi/benchmarking/reporting.py
src/topoppi/benchmarking/runner.py
src/topoppi/gui_app/__init__.py
src/topoppi/gui_app/app.py
src/topoppi/gui_app/constants.py
src/topoppi/gui_app/forms.py
src/topoppi/gui_app/plot_mixin.py
src/topoppi/gui_app/ui_mixin.py
src/topoppi/gui_app/workflow_mixin.py
src/topoppi/interactions/__init__.py
src/topoppi/interactions/interaction_engine.py
src/topoppi/interactions/metadata.py
src/topoppi/io/__init__.py
src/topoppi/io/io_loader.py
src/topoppi/mesh/__init__.py
src/topoppi/mesh/parameterization.py
src/topoppi/mesh/surface.py
src/topoppi/mesh/topology.py
src/topoppi/optimization/__init__.py
src/topoppi/optimization/optcuts/__init__.py
src/topoppi/optimization/optcuts/joint_optimizer.py
src/topoppi/visualization/__init__.py
src/topoppi/visualization/visualizer.py
tests/test_atlas_metrics.py
tests/test_benchmark_reporting.py
tests/test_benchmark_runner_preprocess.py
tests/test_cli.py
tests/test_config.py
tests/test_gui_forms.py
tests/test_imports.py
tests/test_install_optcuts.py
tests/test_interaction_engine.py
tests/test_io_loader.py
tests/test_optcuts_optimizer.py
tests/test_topology.py
tests/fixtures/1bvk.pdb
tests/fixtures/prolif_interactions.json
tests/fixtures/tiny_complex.pdb
tools/OptCuts/LICENSE.txt
tools/OptCuts/NOTICE.md
tools/OptCuts/build_windows_optcuts.ps1
tools/OptCuts/install_optcuts.sh