{ "info": { "author": "Albert Wang", "author_email": "git@albertyw.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "iTOL Python API\n===============\n\n|PyPI|\n|Python Version|\n|License|\n\n|Codeship|\n|CodeCov|\n|Code Climate|\n|Dependency Status|\n\n\nPython API for the Interactive Tree of Life (iTOL)\n\nCreated by Albert Wang (git at albertyw.com)\n\nWith Complements to: `iTOL (Interactive Tree of Life)`_, `Python requests package`.\n\nThis iTOL API allows local software to upload trees to iTOL using ``itol.py``\nand export uploaded trees using ``itolexport.py`` using direct Python\ncalls or through shell. An active internet connection to the\n`iTOL website`_ is required.\n\nInstallation\n------------\n\n``pip install itolapi``\n\nUploading Trees To iTOL (itol.py)\n---------------------------------\n\nFrom Command Line\n~~~~~~~~~~~~~~~~~\n\n(If you need to do anything more than displaying basic tree structures,\nyou must call the Python iTOL API from within a Python program)\n\n::\n\n $ itol.py /path/to/example.tree\n http://itol.embl.de/external.cgi?tree=1234567890&restore_saved=1\n\nFrom Python\n~~~~~~~~~~~\n\nRunning from a python program is much more flexible than running from\ncommand line and allows access to all `iTOL options`_\n\n::\n\n from itolapi import Itol\n itol_uploader = Itol()\n itol_uploader.add_file('/path/to/example.tree')\n itol_uploader.params['treeName'] = 'apple'\n status = itol_uploader.upload()\n assert status != False\n itol_uploader.comm.upload_output\n # SUCCESS: 1234567890\n itol_uploader.comm.tree_id\n # 1234567890\n itol_uploader.get_webpage()\n # http://itol.embl.de/external.cgi?tree=1234567890&restore_saved=1\n itol_uploader.get_itol_export()\n # \n\nAn example for using the Python iTOL API can found in\n``examples/example.py``.\n\nDownloading Trees From iTOL (itolexport.py)\n-------------------------------------------\n\nFrom Command Line\n~~~~~~~~~~~~~~~~~\n\n(If you would like to set any parameters other than the tree id,\nlocation to save the file, file format, and whether to display datasets,\nyou must use ItolExport from a Python program)\n\n::\n\n $ itolexport.py TREEID FILELOCATION FORMAT [OPTIONS]\n\nOptions include:\n * ``-d``: show datasets\n * ``-v``: verbose output\n * ``-h``: help\n\nFrom Python\n~~~~~~~~~~~\n\nRunning itolexport.py from a Python program allows you to use all the\noptions that iTOL has available.\n\n::\n\n from itolapi import ItolExport\n itol_exporter = ItolExport()\n itol_exporter.add_export_param_value('tree', tree_id)\n assert format in ['png', 'svg', 'eps', 'ps', 'pdf', 'nexus', 'newick']\n itol_exporter.add_export_param_value('format', format)\n itol_exporter.add_export_param_value(param_key, param_value)\n itol_exporter.export(file_location)\n\nValid ``param_key`` and ``param_value`` values can be found on `the iTOL API page`_.\n\nBugs/Comments\n-------------\nSend bugs and comments as issues on the `Github`_ repository.\n\nDevelopment\n-----------\nTo run tests:\n\n::\n\n python setup.py install\n pip install -r requirements-test.txt\n pip install -r requirements-test-python3.txt\n mypy itolapi\n coverage run setup.py test\n coverage report -m\n\nTo update PyPI:\n\n::\n\n pip install twine\n python setup.py sdist bdist_wheel\n twine upload dist/*\n\n.. _iTOL (Interactive Tree of Life): http://itol.embl.de/\n.. _iTOL website: http://itol.embl.de/\n.. _iTOL options: http://itol.embl.de/help.cgi#batch\n.. _the iTOL API page: http://itol.embl.de/help.cgi#batch\n.. _Github: https://github.com/albertyw/itolapi/\n\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/itolapi.svg\n :target: https://pypi.python.org/pypi/itolapi/\n :alt: Latest Version\n\n.. |Python Version| image:: https://img.shields.io/pypi/pyversions/itolapi.svg\n\n.. |License| image:: https://img.shields.io/pypi/l/itolapi.svg\n :target: https://pypi.python.org/pypi/itolapi/\n :alt: License\n\n\n.. |Codeship| image:: https://codeship.com/projects/d6470c00-c832-0132-4536-627bbcd2f5ed/status?branch=master\n :target: https://codeship.com/projects/75058\n :alt: Codeship\n\n.. |CodeCov| image:: https://codecov.io/github/albertyw/itolapi/coverage.svg?branch=master\n :target: https://codecov.io/github/albertyw/itolapi?branch=master\n\n.. |Code Climate| image:: https://codeclimate.com/github/albertyw/itolapi/badges/gpa.svg\n :target: https://codeclimate.com/github/albertyw/itolapi\n :alt: CodeClimate\n\n.. |Dependency Status| image:: https://pyup.io/repos/github/albertyw/itolapi/shield.svg\n :target: https://pyup.io/repos/github/albertyw/itolapi/\n\n\n", 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