├── .claude ├── agents │ ├── scientific-ux-reviewer.md │ └── spectral-code-reviewer.md └── commands │ └── freshstart.md ├── .github └── workflows │ └── release.yml ├── .gitignore ├── .mailmap ├── .readthedocs.yaml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATION.cff ├── CLAUDE.md ├── CODE_OF_CONDUCT.md ├── CODE_REVIEW.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── TASKS.md ├── UX_REVIEW.md ├── conda-recipe ├── README.md ├── build.sh └── meta.yaml ├── coverage.lcov ├── docs ├── CONNECTIVITY_METRIC_RANGES.md ├── Makefile ├── NOTEBOOK_SNAPSHOT_TESTS.md ├── STYLE.md ├── _templates │ ├── custom-class-template.rst │ └── custom-module-template.rst ├── api.rst ├── conf.py ├── contributing.md ├── examples │ └── README.md ├── index.md ├── make.bat └── requirements-docs.txt ├── environment.yml ├── examples ├── Intro_tutorial.ipynb ├── Intro_tutorial.py ├── Tutorial_On_Simulated_Examples.ipynb ├── Tutorial_On_Simulated_Examples.py ├── Tutorial_Using_Paper_Examples.ipynb └── Tutorial_Using_Paper_Examples.py ├── paper.bib ├── paper.md ├── postBuild ├── pyproject.toml ├── spectral_connectivity ├── __init__.py ├── connectivity.py ├── minimum_phase_decomposition.py ├── py.typed ├── simulate.py ├── statistics.py ├── transforms.py ├── utils.py └── wrapper.py └── tests ├── __init__.py ├── __snapshots__ ├── test_notebook_snapshots.ambr └── test_notebooks.ambr ├── conftest.py ├── test_advanced_connectivity.py ├── test_coherence_bounds.py ├── test_connectivity.py ├── test_error_messages.py ├── test_expectation_validation.py ├── test_gpu.py ├── test_gpu_request.py ├── test_metric_ranges.py ├── test_minimum_phase_decomposition.py ├── test_notebooks.py ├── test_parameter_helpers.py ├── test_simulate.py ├── test_statistics.py ├── test_transforms.py ├── test_wrapper.py └── test_wrapper_errors.py /.claude/agents/scientific-ux-reviewer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.claude/agents/scientific-ux-reviewer.md -------------------------------------------------------------------------------- /.claude/agents/spectral-code-reviewer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.claude/agents/spectral-code-reviewer.md -------------------------------------------------------------------------------- /.claude/commands/freshstart.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.claude/commands/freshstart.md -------------------------------------------------------------------------------- /.github/workflows/release.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.github/workflows/release.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.gitignore -------------------------------------------------------------------------------- /.mailmap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.mailmap -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/.vscode/settings.json -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CITATION.cff -------------------------------------------------------------------------------- /CLAUDE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CLAUDE.md -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CODE_REVIEW.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CODE_REVIEW.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/README.md -------------------------------------------------------------------------------- /TASKS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/TASKS.md -------------------------------------------------------------------------------- /UX_REVIEW.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/UX_REVIEW.md -------------------------------------------------------------------------------- /conda-recipe/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/conda-recipe/README.md -------------------------------------------------------------------------------- /conda-recipe/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/conda-recipe/build.sh -------------------------------------------------------------------------------- /conda-recipe/meta.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/conda-recipe/meta.yaml -------------------------------------------------------------------------------- /coverage.lcov: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/coverage.lcov -------------------------------------------------------------------------------- /docs/CONNECTIVITY_METRIC_RANGES.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/CONNECTIVITY_METRIC_RANGES.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/NOTEBOOK_SNAPSHOT_TESTS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/NOTEBOOK_SNAPSHOT_TESTS.md -------------------------------------------------------------------------------- /docs/STYLE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/STYLE.md -------------------------------------------------------------------------------- /docs/_templates/custom-class-template.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/_templates/custom-class-template.rst -------------------------------------------------------------------------------- /docs/_templates/custom-module-template.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/_templates/custom-module-template.rst -------------------------------------------------------------------------------- /docs/api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/api.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/contributing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/contributing.md -------------------------------------------------------------------------------- /docs/examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/examples/README.md -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/requirements-docs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/docs/requirements-docs.txt -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/environment.yml -------------------------------------------------------------------------------- /examples/Intro_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Intro_tutorial.ipynb -------------------------------------------------------------------------------- /examples/Intro_tutorial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Intro_tutorial.py -------------------------------------------------------------------------------- /examples/Tutorial_On_Simulated_Examples.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Tutorial_On_Simulated_Examples.ipynb -------------------------------------------------------------------------------- /examples/Tutorial_On_Simulated_Examples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Tutorial_On_Simulated_Examples.py -------------------------------------------------------------------------------- /examples/Tutorial_Using_Paper_Examples.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Tutorial_Using_Paper_Examples.ipynb -------------------------------------------------------------------------------- /examples/Tutorial_Using_Paper_Examples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/examples/Tutorial_Using_Paper_Examples.py -------------------------------------------------------------------------------- /paper.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/paper.bib -------------------------------------------------------------------------------- /paper.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/paper.md -------------------------------------------------------------------------------- /postBuild: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | pip install -e . 4 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/pyproject.toml -------------------------------------------------------------------------------- /spectral_connectivity/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/__init__.py -------------------------------------------------------------------------------- /spectral_connectivity/connectivity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/connectivity.py -------------------------------------------------------------------------------- /spectral_connectivity/minimum_phase_decomposition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/minimum_phase_decomposition.py -------------------------------------------------------------------------------- /spectral_connectivity/py.typed: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /spectral_connectivity/simulate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/simulate.py -------------------------------------------------------------------------------- /spectral_connectivity/statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/statistics.py -------------------------------------------------------------------------------- /spectral_connectivity/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/transforms.py -------------------------------------------------------------------------------- /spectral_connectivity/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/utils.py -------------------------------------------------------------------------------- /spectral_connectivity/wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/spectral_connectivity/wrapper.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/__snapshots__/test_notebook_snapshots.ambr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/__snapshots__/test_notebook_snapshots.ambr -------------------------------------------------------------------------------- /tests/__snapshots__/test_notebooks.ambr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/__snapshots__/test_notebooks.ambr -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/test_advanced_connectivity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_advanced_connectivity.py -------------------------------------------------------------------------------- /tests/test_coherence_bounds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_coherence_bounds.py -------------------------------------------------------------------------------- /tests/test_connectivity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_connectivity.py -------------------------------------------------------------------------------- /tests/test_error_messages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_error_messages.py -------------------------------------------------------------------------------- /tests/test_expectation_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_expectation_validation.py -------------------------------------------------------------------------------- /tests/test_gpu.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_gpu.py -------------------------------------------------------------------------------- /tests/test_gpu_request.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_gpu_request.py -------------------------------------------------------------------------------- /tests/test_metric_ranges.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_metric_ranges.py -------------------------------------------------------------------------------- /tests/test_minimum_phase_decomposition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_minimum_phase_decomposition.py -------------------------------------------------------------------------------- /tests/test_notebooks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_notebooks.py -------------------------------------------------------------------------------- /tests/test_parameter_helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_parameter_helpers.py -------------------------------------------------------------------------------- /tests/test_simulate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_simulate.py -------------------------------------------------------------------------------- /tests/test_statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_statistics.py -------------------------------------------------------------------------------- /tests/test_transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_transforms.py -------------------------------------------------------------------------------- /tests/test_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_wrapper.py -------------------------------------------------------------------------------- /tests/test_wrapper_errors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Eden-Kramer-Lab/spectral_connectivity/HEAD/tests/test_wrapper_errors.py --------------------------------------------------------------------------------