├── .github └── workflows │ ├── ci.yml │ ├── publich_mkdocs.yml │ └── publish_to_pypi.yml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── docs ├── api-docs │ └── treeviz.md ├── cli-docs │ └── phytreeviz.md ├── getting_started.ipynb ├── images │ ├── api_example01.png │ ├── api_example02.png │ ├── api_example03.png │ ├── api_example04.png │ ├── cli_example01.png │ ├── cli_example02.png │ └── cli_example03.png ├── index.md └── plot_api_example.ipynb ├── example ├── example.zip ├── large_example.nwk ├── medium_example.nwk └── small_example.nwk ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml ├── src └── phytreeviz │ ├── __init__.py │ ├── scripts │ ├── __init__.py │ └── cli.py │ ├── treeviz.py │ └── utils │ ├── __init__.py │ └── example_data │ ├── large_example.nwk │ ├── medium_example.nwk │ └── small_example.nwk └── tests ├── __init__.py ├── scripts └── test_cli.py └── test_treeviz.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/publich_mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/.github/workflows/publich_mkdocs.yml -------------------------------------------------------------------------------- /.github/workflows/publish_to_pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/.github/workflows/publish_to_pypi.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/.gitignore -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/README.md -------------------------------------------------------------------------------- /docs/api-docs/treeviz.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/api-docs/treeviz.md -------------------------------------------------------------------------------- /docs/cli-docs/phytreeviz.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/cli-docs/phytreeviz.md -------------------------------------------------------------------------------- /docs/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/getting_started.ipynb -------------------------------------------------------------------------------- /docs/images/api_example01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/api_example01.png -------------------------------------------------------------------------------- /docs/images/api_example02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/api_example02.png -------------------------------------------------------------------------------- /docs/images/api_example03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/api_example03.png -------------------------------------------------------------------------------- /docs/images/api_example04.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/api_example04.png -------------------------------------------------------------------------------- /docs/images/cli_example01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/cli_example01.png -------------------------------------------------------------------------------- /docs/images/cli_example02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/cli_example02.png -------------------------------------------------------------------------------- /docs/images/cli_example03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/images/cli_example03.png -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/plot_api_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/docs/plot_api_example.ipynb -------------------------------------------------------------------------------- /example/example.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/example/example.zip -------------------------------------------------------------------------------- /example/large_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/example/large_example.nwk -------------------------------------------------------------------------------- /example/medium_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/example/medium_example.nwk -------------------------------------------------------------------------------- /example/small_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/example/small_example.nwk -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/poetry.lock -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/pyproject.toml -------------------------------------------------------------------------------- /src/phytreeviz/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/__init__.py -------------------------------------------------------------------------------- /src/phytreeviz/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/phytreeviz/scripts/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/scripts/cli.py -------------------------------------------------------------------------------- /src/phytreeviz/treeviz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/treeviz.py -------------------------------------------------------------------------------- /src/phytreeviz/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/utils/__init__.py -------------------------------------------------------------------------------- /src/phytreeviz/utils/example_data/large_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/utils/example_data/large_example.nwk -------------------------------------------------------------------------------- /src/phytreeviz/utils/example_data/medium_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/utils/example_data/medium_example.nwk -------------------------------------------------------------------------------- /src/phytreeviz/utils/example_data/small_example.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/src/phytreeviz/utils/example_data/small_example.nwk -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/scripts/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/tests/scripts/test_cli.py -------------------------------------------------------------------------------- /tests/test_treeviz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moshi4/phyTreeViz/HEAD/tests/test_treeviz.py --------------------------------------------------------------------------------