├── .coveragerc ├── .eslintignore ├── .eslintrc.js ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── documentation.md │ ├── enhancement.md │ └── question.md └── workflows │ ├── binder-on-pr.yml │ ├── lint.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── .npmignore ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc ├── LICENSE ├── MANIFEST.in ├── README.md ├── appveyor.yml ├── codecov.yml ├── css └── widget.css ├── docs ├── Makefile ├── environment.yml ├── make.bat └── source │ ├── _static │ └── helper.js │ ├── conf.py │ ├── contributing.rst │ ├── develop-install.rst │ ├── examples │ ├── DAGData.json │ ├── colaData.json │ ├── concentricData.json │ ├── geneData.json │ ├── geneStyle.json │ ├── graph-init.nblink │ ├── gridData.json │ ├── index.rst │ ├── interaction.nblink │ ├── json.nblink │ ├── labels.nblink │ ├── networkx.nblink │ ├── node-text.nblink │ └── pandas.nblink │ ├── index.rst │ └── installing.rst ├── dodo.py ├── environment.yml ├── examples ├── Concentric example.ipynb ├── DAG example.ipynb ├── DAGData.json ├── Graph Initialization.ipynb ├── Grid example.ipynb ├── HTML interaction with graph.ipynb ├── Ipycytoscape from Scratch.ipynb ├── Ipycytoscape-overview.ipynb ├── Labels.ipynb ├── Neo4j_Example.ipynb ├── NetworkX Example.ipynb ├── Test NetworkX methods.ipynb ├── Text on node.ipynb ├── Tip gene example.ipynb ├── Tooltips example.ipynb ├── colaData.json ├── concentricData.json ├── geneData.json ├── geneStyle.json ├── graph-from-json.ipynb ├── gridData.json ├── interaction-example.ipynb └── pandas.ipynb ├── ipycytoscape ├── __init__.py ├── _frontend.py ├── _version.py ├── cytoscape.py ├── nbextension │ ├── __init__.py │ └── static │ │ └── extension.js ├── style.json └── tests │ ├── __init__.py │ ├── _util.py │ ├── conftest.py │ ├── test_graph_creation.py │ ├── test_graph_deletion.py │ ├── test_graph_methods.py │ └── test_nbextension_path.py ├── jupyter-cytoscape.json ├── package.json ├── pyproject.toml ├── pytest.ini ├── readthedocs.yml ├── setup.cfg ├── setup.py ├── src ├── extension.ts ├── graph.ts ├── index.ts ├── plugin.ts ├── version.ts └── widget.ts ├── tsconfig.json └── webpack.config.js /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | omit = ipycytoscape/tests/* 3 | -------------------------------------------------------------------------------- /.eslintignore: -------------------------------------------------------------------------------- 1 | node_modules 2 | dist 3 | coverage 4 | **/*.d.ts 5 | tests 6 | -------------------------------------------------------------------------------- /.eslintrc.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.eslintrc.js -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/documentation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/ISSUE_TEMPLATE/documentation.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/enhancement.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/ISSUE_TEMPLATE/enhancement.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/ISSUE_TEMPLATE/question.md -------------------------------------------------------------------------------- /.github/workflows/binder-on-pr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/workflows/binder-on-pr.yml -------------------------------------------------------------------------------- /.github/workflows/lint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/workflows/lint.yml -------------------------------------------------------------------------------- /.github/workflows/release.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/workflows/release.yml -------------------------------------------------------------------------------- /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.gitignore -------------------------------------------------------------------------------- /.npmignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.npmignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.prettierignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/.prettierignore -------------------------------------------------------------------------------- /.prettierrc: -------------------------------------------------------------------------------- 1 | { 2 | "singleQuote": true 3 | } 4 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/README.md -------------------------------------------------------------------------------- /appveyor.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/appveyor.yml -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/codecov.yml -------------------------------------------------------------------------------- /css/widget.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/css/widget.css -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/environment.yml -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/source/_static/helper.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/_static/helper.js -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/contributing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/contributing.rst -------------------------------------------------------------------------------- /docs/source/develop-install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/develop-install.rst -------------------------------------------------------------------------------- /docs/source/examples/DAGData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/DAGData.json -------------------------------------------------------------------------------- /docs/source/examples/colaData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/colaData.json -------------------------------------------------------------------------------- /docs/source/examples/concentricData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/concentricData.json -------------------------------------------------------------------------------- /docs/source/examples/geneData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/geneData.json -------------------------------------------------------------------------------- /docs/source/examples/geneStyle.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/geneStyle.json -------------------------------------------------------------------------------- /docs/source/examples/graph-init.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/graph-init.nblink -------------------------------------------------------------------------------- /docs/source/examples/gridData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/gridData.json -------------------------------------------------------------------------------- /docs/source/examples/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/index.rst -------------------------------------------------------------------------------- /docs/source/examples/interaction.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/interaction.nblink -------------------------------------------------------------------------------- /docs/source/examples/json.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/json.nblink -------------------------------------------------------------------------------- /docs/source/examples/labels.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/labels.nblink -------------------------------------------------------------------------------- /docs/source/examples/networkx.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/networkx.nblink -------------------------------------------------------------------------------- /docs/source/examples/node-text.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/node-text.nblink -------------------------------------------------------------------------------- /docs/source/examples/pandas.nblink: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/examples/pandas.nblink -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/installing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/docs/source/installing.rst -------------------------------------------------------------------------------- /dodo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/dodo.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/environment.yml -------------------------------------------------------------------------------- /examples/Concentric example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Concentric example.ipynb -------------------------------------------------------------------------------- /examples/DAG example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/DAG example.ipynb -------------------------------------------------------------------------------- /examples/DAGData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/DAGData.json -------------------------------------------------------------------------------- /examples/Graph Initialization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Graph Initialization.ipynb -------------------------------------------------------------------------------- /examples/Grid example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Grid example.ipynb -------------------------------------------------------------------------------- /examples/HTML interaction with graph.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/HTML interaction with graph.ipynb -------------------------------------------------------------------------------- /examples/Ipycytoscape from Scratch.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Ipycytoscape from Scratch.ipynb -------------------------------------------------------------------------------- /examples/Ipycytoscape-overview.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Ipycytoscape-overview.ipynb -------------------------------------------------------------------------------- /examples/Labels.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Labels.ipynb -------------------------------------------------------------------------------- /examples/Neo4j_Example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Neo4j_Example.ipynb -------------------------------------------------------------------------------- /examples/NetworkX Example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/NetworkX Example.ipynb -------------------------------------------------------------------------------- /examples/Test NetworkX methods.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Test NetworkX methods.ipynb -------------------------------------------------------------------------------- /examples/Text on node.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Text on node.ipynb -------------------------------------------------------------------------------- /examples/Tip gene example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Tip gene example.ipynb -------------------------------------------------------------------------------- /examples/Tooltips example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/Tooltips example.ipynb -------------------------------------------------------------------------------- /examples/colaData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/colaData.json -------------------------------------------------------------------------------- /examples/concentricData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/concentricData.json -------------------------------------------------------------------------------- /examples/geneData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/geneData.json -------------------------------------------------------------------------------- /examples/geneStyle.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/geneStyle.json -------------------------------------------------------------------------------- /examples/graph-from-json.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/graph-from-json.ipynb -------------------------------------------------------------------------------- /examples/gridData.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/gridData.json -------------------------------------------------------------------------------- /examples/interaction-example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/interaction-example.ipynb -------------------------------------------------------------------------------- /examples/pandas.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/examples/pandas.ipynb -------------------------------------------------------------------------------- /ipycytoscape/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/__init__.py -------------------------------------------------------------------------------- /ipycytoscape/_frontend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/_frontend.py -------------------------------------------------------------------------------- /ipycytoscape/_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/_version.py -------------------------------------------------------------------------------- /ipycytoscape/cytoscape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/cytoscape.py -------------------------------------------------------------------------------- /ipycytoscape/nbextension/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/nbextension/__init__.py -------------------------------------------------------------------------------- /ipycytoscape/nbextension/static/extension.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/nbextension/static/extension.js -------------------------------------------------------------------------------- /ipycytoscape/style.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/style.json -------------------------------------------------------------------------------- /ipycytoscape/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /ipycytoscape/tests/_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/_util.py -------------------------------------------------------------------------------- /ipycytoscape/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/conftest.py -------------------------------------------------------------------------------- /ipycytoscape/tests/test_graph_creation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/test_graph_creation.py -------------------------------------------------------------------------------- /ipycytoscape/tests/test_graph_deletion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/test_graph_deletion.py -------------------------------------------------------------------------------- /ipycytoscape/tests/test_graph_methods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/test_graph_methods.py -------------------------------------------------------------------------------- /ipycytoscape/tests/test_nbextension_path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/ipycytoscape/tests/test_nbextension_path.py -------------------------------------------------------------------------------- /jupyter-cytoscape.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/jupyter-cytoscape.json -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/package.json -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/pyproject.toml -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/pytest.ini -------------------------------------------------------------------------------- /readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/readthedocs.yml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/setup.py -------------------------------------------------------------------------------- /src/extension.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/extension.ts -------------------------------------------------------------------------------- /src/graph.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/graph.ts -------------------------------------------------------------------------------- /src/index.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/index.ts -------------------------------------------------------------------------------- /src/plugin.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/plugin.ts -------------------------------------------------------------------------------- /src/version.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/version.ts -------------------------------------------------------------------------------- /src/widget.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/src/widget.ts -------------------------------------------------------------------------------- /tsconfig.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/tsconfig.json -------------------------------------------------------------------------------- /webpack.config.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cytoscape/ipycytoscape/HEAD/webpack.config.js --------------------------------------------------------------------------------