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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![pypi](https://img.shields.io/pypi/v/pycax-client.svg)](https://pypi.python.org/pypi-client/pycax-client)\n[![github](https://img.shields.io/github/v/release/noaa-nwfsc/pycax?color=brightgreen\u0026label=GitHub)](https://github.com/noaa-nwfsc/pycax/releases/latest)\n[![docs](https://github.com/noaa-nwfsc/pycax/actions/workflows/deploy-docs.yml/badge.svg)](https://noaa-nwfsc.github.io/pycax)\n[![tests](https://github.com/noaa-nwfsc/pycax/actions/workflows/tests.yml/badge.svg)](https://github.com/noaa-nwfsc/pycax/actions/workflows/tests.yml)\n[![coverage](https://noaa-nwfsc.github.io/pycax/coverage.svg)](https://noaa-nwfsc.github.io/pycax/_codecoverage/index.html)\n[![PyPi license](https://badgen.net/pypi/license/pycax-client/)](https://pypi.org/project/pycax-client/)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7855729.svg)](https://doi.org/10.5281/zenodo.7855729)\n\npycax \u003cimg src=\"https://raw.githubusercontent.com/nwfsc-math-bio/pycax/main/docs/pycaxlogo.png\" align=\"right\" width=\"20%\"  hspace=\"20\" vspace=\"20\"/\u003e\n========\n\n\u003c!--\n[![Conda Version](https://img.shields.io/conda/vn/conda-forge/pycax-client.svg)](https://anaconda.org/conda-forge/pycax-client)\n--\u003e\n\npycax is a Python client for the Coordinated Assessments [REST API](https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/). Make sure to review the [StreamNet Terms of Use](https://nwfsc-math-bio.github.io/rCAX/articles/terms.html) for these data, the [StreamNet Data Policy](https://www.streamnet.org/resources/exchange-tools/data-agreements/) and the [citation information](https://www.streamnet.org/resources/citing-sn/) for database queries. pycax was developed by the Northwest Fisheries Science Center Math Bio Program by Elizabeth Holmes and Mari Williams.\n\nNWFSC Math Bio CAX REST API clients:\n\n* Python client: [pycax on GitHub at noaa-nwfsc/pycax](https://github.com/noaa-nwfsc/pycax)\n* R client: [rCAX on GitHub at nwfsc-math-bio/rCAX](https://github.com/nwfsc-math-bio/rCAX)\n\n## Citation\n\nHolmes, E. E and M. Williams. 2023. pycax: a Python client for the Coordinated Assessments data exchange REST API. vX.X.X. doi:10.5281/zenodo.7855729.\n\nMake sure to include a citation for the Coordinated Assessments Partnership (CAP) data tables that you use. For details on citing CAP content see: https://www.streamnet.org/resources/citing-sn/\n\nSee [CITATION](https://github.com/noaa-nwfsc/pycax/blob/main/CITATION) file for bibtex version.\n\n## Installation\n\nFrom pypi\n\n```bash\npip install pycax-client\n```\n\nFrom GitHub (development version)\n\n```bash\npip install git+git://github.com/noaa-nwfsc/pycax.git#egg=pycax-client\n```\n\n## Documentation\n\nThe official documentation is hosted on GitHub Pages [https://noaa-nwfsc.github.io/pycax](https://noaa-nwfsc.github.io/pycax).\n\n## Library API\n\n`pycax` is split up into modules for each of the groups of API methods.\n\n+ `hli` - Get HLI tables.\n+ `datasets` - Get metadata of tables\n+ `tables` - The workhorse modules for querying tables\n\n## Sample analysis\n\nSome Jupyter notebooks are in the [notebooks](https://github.com/noaa-nwfsc/pycax/tree/main/notebooks) directory.\n\n## Contributing\n\nFork and put in a pull request!\n\nTo install editable dev version from github for local development. System prerequisites: python3, conda. Note replace `python3` with `python` if your Python installation points to 3+. `requirements-dev.txt` includes all the requirements needed for local development, testing and documentation building.\n\n```bash\n# fetch code\ngit clone git@github.com:noaa-nwfsc/pycax.git\ncd pycax\n# install the requirements\npython3 -m pip install -r requirements.txt\npython3 -m pip install -r requirements-dev.txt\n# After making changes, reinstall using\npython3 -m pip install -e .\n# test your installation\npython3 -m pytest\n# test and generate a coverage report\npython3 -m pytest -rxs --cov=pycax --cov-report term-missing ./pycax\n# make the documentation in docs/_build/html\ncd docs # pycax/docs\nmake clean html codecov # linkcheck # linkcheck not working\n```\n\n## Credits\n\nThanks to the developers of [pyobis](https://github.com/iobis/pyobis) package who created a package that was easy to use as a full template for a REST API client with tests, documentation files, and GitHub Actions and included the instructions and requirements for local development. The structure of pycax mimics pyobis structure but was adapted and changed for the CAX API. The [pygbif](https://github.com/gbif/pygbif) package is similar (and seems to have influenced pyobis). pygbif source was used for reference and study though no code directly used. Some pygbif code may appear in pycax if pyobis used pygbif functions for reference. Notably the Sphinx documentation configuration files seem to originate from pygbif.\n\n## Contributors\n\n[![Contributors](https://contrib.rocks/image?repo=noaa-nwfsc/pycax)](https://github.com/noaa-nwfsc/pycax/graphs/contributors)\n\n\u003chr\u003e\n\n### Disclaimer\n\nThis repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project content is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.\n\n### License\n\nThis content was created by U.S. Government employees as part of their official duties. This content is not subject to copyright in the United States (17 U.S.C. §105) and is in the public domain within the United States of America. Additionally, copyright is waived worldwide through the MIT License.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnoaa-nwfsc%2Fpycax","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnoaa-nwfsc%2Fpycax","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnoaa-nwfsc%2Fpycax/lists"}