Metadata-Version: 2.1
Name: pub.tools
Version: 4.0
Summary: Package of tools for formatting publication data and accessing data from PubMed's Entrez tool
Home-page: http://git.imsweb.com/wohnlice/pub.tools
Author: Eric Wohnlich
Author-email: wohnlice@imsweb.com
License: GPL
Description: # Introduction
        To use this tool you will need to set your Entrez API key in the following environment variables:
        * ENTREZ_EMAIL
        * ENTREZ_API_KEY
        
        Tools available:
        
        * entrez - streamlines BioPython
        * citations - creates citations for 6 different types using IMS standards
        * date - formats dates into our desired format
        * sanitizer - mostly useful for forcing unicode compliance in python2
        
        ## Citations
        
        Citations are based on a standard defined by PubMed https://www.ncbi.nlm.nih.gov/books/NBK7256/.
        For some publication types, passing the italicize parameter with a True value will return
        HTML with italic tagged journals or conference names.
        
        ## Journals
        
        The journals module uses the PMC source file https://www.ncbi.nlm.nih.gov/pmc/journals/?format=csv
        to construct a library of journals keyed by abbreviation or full title.
        # Changelog
        
        ## [3.0.1] - 22 Aug 2019
        - journals module reconfigured to not write to disk on startup
        
        ## [3.0] - 12 Aug 2019
        - Exlusively supports python 3
        
        ## [2.1] - unreleased
        - Redesign of citation with abstract behavior.
        - "italicize" option has been replaced with an "html" option and does not do any safe escape
        - add docstrings to citation functions
        
        ## [2.0.2] - 25 Jan 2019
        - Revert safe_unicode use but have it be only applicable for python 2. Not an issue in python 3
        - Unescape all fields except title and abstract if using the "escape" parameter. Those two fields are treated as HTML 
        if escape is false all other fields are plain text 
        
        ## [2.0] - 17 October 2018
        - Six implementation with support for python 2 and 3 [hoskins]
        
        ## [1.7] - 10 May 2018
        - Refactor some entrez functions to make it more obvious what the API endpoints are
        - Convert docstring of all intended end point functions to reST
        - Add ability to find publication by PMC ID. This is done by querying the PMC database
        - Refactor generate_search_query slightly
        
        ## [1.6] - 1 March 2018
        - Fixed the book REST API calls to allow for failure
        - book REST API calls now use requests module
        - the isbndb.com database is now a paid service only. It *should* work but I don't have a service to verify this
        
        ## [1.5]
        - Citations can now be generated as plain text without <i> tags on journals, etc. It defaults to true
        here but will default to false in a future release.
        - Removed some unused parameters from citation functions
        - Cleaned up unit tests
        - Fixed issue with eCollection dates in citations
        
        ## [1.4]
        - Refactor and reformat for pep8
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
