Package: pycax-client
pycaxpycax is a Python client for the Coordinated AssessmentsREST API. Make sure to review theStreamNet Terms of Usefor these data, theStreamNet Data Policyand thecitation informationfor database queries. pycax was developed by the Northwest Fisheries Science Center Math Bio Program by Elizabeth Holmes and Mari Williams.NWFSC Math Bio CAX REST API clients:Python client:pycax on GitHub at nwfsc-math-bio/pycaxR client:rCAX on GitHub at nwfsc-math-bio/rCAXInstallationFrom pypipipinstallpycax-clientFrom GitHub (development version)pipinstallgit+git://github.com/nwfsc-math-bio/pycax.git#egg=pycax-clientDocumentationThe official documentation is hosted on GitHub Pageshttps://nwfsc-math-bio.github.io/pycax.Library APIpycaxis split up into modules for each of the groups of API methods.hli- Get HLI tables.datasets- Get metadata of tablestables- The workhorse modules for querying tablesSample analysisSome Jupyter notebooks are in thenotebooksdirectory.ContributingFork and put in a pull request!To install editable dev version from github for local development. System prerequisites: python3, conda. Note replacepython3withpythonif your Python installation points to 3+.requirements-dev.txtincludes all the requirements needed for local development, testing and documentation building.# fetch codegitclonegit@github.com:nwfsc-math-bio/pycax.gitcdpycax# install the requirementspython3-mpipinstall-rrequirements.txt
python3-mpipinstall-rrequirements-dev.txt# After making changes, reinstall usingpython3-mpipinstall-e.# test your installationpython3-mpytest# test and generate a coverage reportpython3-mpytest-rxs--cov=pycax--cov-reportterm-missing./pycax# make the documentation in docs/_build/htmlcddocs# pycax/docsmakecleanhtmlcodecov# linkcheck # linkcheck not workingCitationHolmes, 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.Make 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/SeeCITATIONfile for bibtex version.CreditsThanks to the developers ofpyobispackage 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. Thepygbifpackage 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.DisclaimerThis 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.LicenseThis 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.