Metadata-Version: 2.1
Name: academic-tracker
Version: 1.0.0
Summary: Find publications on PubMed, Crossref, ORCID, and Google Scholar for given authors or references.
Home-page: https://github.com/MoseleyBioinformaticsLab/academic_tracker
Author: Travis Thompson
Author-email: ptth222@gmail.com
License: BSD
Description: Academic Tracker
        ================
        
        .. image:: https://img.shields.io/pypi/v/academic_tracker.svg
           :target: https://pypi.org/project/academic_tracker
           :alt: Current library version
        
        .. image:: https://img.shields.io/pypi/pyversions/academic_tracker.svg
           :target: https://pypi.org/project/academic_tracker
           :alt: Supported Python versions
        
        .. image:: https://github.com/MoseleyBioinformaticsLab/academic_tracker/actions/workflows/build.yml/badge.svg
           :target: https://github.com/MoseleyBioinformaticsLab/academic_tracker/actions/workflows/build.yml
           :alt: Build status
        
        .. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/academic_tracker/branch/main/graphs/badge.svg?branch=main
           :target: https://codecov.io/gh/MoseleyBioinformaticsLab/academic_tracker
           :alt: Code coverage information
        
        .. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg
           :target: https://doi.org/10.3390/metabo11030163
           :alt: Citation link
        
        .. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/academic_tracker.svg?style=social&label=Star
            :target: https://github.com/MoseleyBioinformaticsLab/academic_tracker
            :alt: GitHub project
        
        |
        
        Academic Tracker was created to automate the process of making sure that NIH 
        funded publications get listed on PubMed and that the grant funding source for 
        them is cited. 
        
        Academic Tracker is a command line tool to search PubMed, ORCID, Google Scholar, 
        and Crossref for publications. The program can either be given a list of authors 
        to look for publications for, or references/citations to publications themselves. 
        The program will then will look for publications on the aforementioned sources 
        and return what relevant information is available from those sources.
        
        The primary use case is to give the program a list of authors to find publications 
        for. From this list of publications it can then be determined which ones need 
        further action to be in compliance with NIH.
        
        
        
        Links
        ~~~~~
        
           * Academic Tracker @ GitHub_
           * Academic Tracker @ PyPI_
           * Documentation @ ReadTheDocs_
        
        
        Installation
        ~~~~~~~~~~~~
        The Academic Tracker package runs under Python 3.7+. Use pip_ to install.
        Starting with Python 3.4, pip_ is included by default. Be sure to use the latest 
        version of pip as older versions are known to have issues grabbing all dependencies. 
        Academic Tracker relies on sendmail to send emails, so if you need to use that 
        feature be sure sendmail is installed and in PATH.
        
        
        Install on Linux, Mac OS X
        --------------------------
        
        .. code:: bash
        
           python3 -m pip install academic_tracker
        
        
        Install on Windows
        ------------------
        
        .. code:: bash
        
           py -3 -m pip install academic_tracker
           
        
        Upgrade on Linux, Mac OS X
        --------------------------
        
        .. code:: bash
        
           python3 -m pip install academic_tracker --upgrade
           
        
        Upgrade on Windows
        ------------------
        
        .. code:: bash
        
           py -3 -m pip install academic_tracker --upgrade
        
        
        
        Quickstart
        ~~~~~~~~~~
        Academic Tracker has several commands and options. The simplest most common use 
        case is simply:
        
        .. code:: bash
            
            academic_tracker author_search config_file.json
        
        Academic Tracker's behavior can be quite complex though, so it is highly encouraged 
        to read the `guide <https://moseleybioinformaticslab.github.io/academic_tracker/guide.html>`_ 
        and `tutorial <https://moseleybioinformaticslab.github.io/academic_tracker/tutorial.html>`_.
        
        
        Creating The Configuration JSON
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        A configuration JSON file is required to run Academic Tracker, but initially creating 
        it the first time can be burdensome. Unfortunately, there is no easy solution for 
        this. It is encouraged to read the configuration JSON section in `jsonschema <https://moseleybioinformaticslab.github.io/academic_tracker/jsonschema.html>`_ 
        and use the example there to create it initially. The add_authors command can help 
        with building the Authors section if you already have a csv file with author 
        information. A good tool to help track down pesky JSON syntax errors is `here <https://csvjson.com/json_validator>`__.
        
        
        Registering With ORCID
        ~~~~~~~~~~~~~~~~~~~~~~
        In order to have this program search ORCID you must register with ORCID and obtain 
        a key and secret. Details on how to do that are `here <https://info.orcid.org/documentation/integration-guide/registering-a-public-api-client/>`__. 
        If you do not want to do that then the --no_ORCID option can be used to skip searching 
        ORCID.
        
                  
        Mac OS Note
        ~~~~~~~~~~~
        When you try to run the program on Mac OS you may get an SSL error.
        
            certificate verify failed: unable to get local issuer certificate
            
        This is due to a change in Mac OS and Python. To fix it go to to your Python 
        folder in Applications and run the Install Certificates.command shell command. 
        This should fix the issue.
        
        
        Email Sending Note
        ~~~~~~~~~~~~~~~~~~
        Academic Tracker uses sendmail to send emails, so any system it is going to be 
        used on needs to have sendmail installed and the path in PATH. If you try to 
        send emails without this the program will display a warning. This can be avoided 
        by using the --test option though. The --test option blocks email sending. Email 
        sending can also be avoided by leaving the from_email attribute out of the report 
        sections of the configuration JSON file.
        
        
        How Authors Are Identified
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        When searching by authors it is necessary to confirm that the author given to 
        Academic Tracker matches the author returned in the query. In general this matching 
        is done by matching the first and last names and at least one affiliation given 
        for the author in the configuration JSON file. Note that affiliations can change 
        over time as authors move, so they may need many affiliations to accurately match 
        them to their publications depending on how far back you want to search in time.
        
        
        How Publications Are Matched
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        When searching by publications it is necessary to confirm that the publication 
        in the given reference matches the publication returned in the query. This is done 
        by either matching the DOIs, PMIDs, or the title and at least one author. Titles 
        are fuzzy matched using fuzzywuzzy which is why at least one author must also be 
        matched. Author's are matched using last name and at least one affiliation.
        
        
        License
        ~~~~~~~
        This package is distributed under the BSD `license`.
        
        
        .. _GitHub: https://github.com/MoseleyBioinformaticsLab/academic_tracker
        .. _ReadTheDocs: http://academic_tracker.readthedocs.io
        .. _PyPI: https://pypi.org/project/academic_tracker
        .. _pip: https://pip.pypa.io
Keywords: PubMed publications citations Crossref ORCID Google Scholar
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/x-rst
