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Minor documentation changes and added citation file.
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CITATION.cff

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cff-version: 1.0.0
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message: "If you use this software, please cite it as below."
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authors:
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- family-names: "Thompson"
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given-names: "Travis"
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orcid: "https://orcid.org/0000-0002-8198-1327"
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- family-names: "Powell"
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given-names: "Christian"
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orcid: "https://orcid.org/0000-0002-4242-080X"
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- family-names: "Moseley"
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given-names: "Hunter"
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orcid: "https://orcid.org/0000-0003-3995-5368"
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title: "academic_tracker"
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version: 1.0.3
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date-released: 2022-03-28
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url: "https://github.com/MoseleyBioinformaticsLab/academic_tracker"
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preferred-citation:
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type: article
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authors:
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- family-names: "Thompson"
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given-names: "Travis"
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orcid: "https://orcid.org/0000-0002-8198-1327"
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- family-names: "Moseley"
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given-names: "Hunter"
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orcid: "https://orcid.org/0000-0003-3995-5368"
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doi: "10.1371/journal.pone.0277834"
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journal: "Plos one"
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month: 11
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title: "Academic Tracker: Software for tracking and reporting publications associated with authors and grants"
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number: 11
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volume: 17
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year: 2022

README.rst

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:target: https://codecov.io/gh/MoseleyBioinformaticsLab/academic_tracker
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:alt: Code coverage information
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.. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg
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:target: https://doi.org/10.3390/metabo11030163
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.. image:: https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0277834-blue.svg
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:target: https://doi.org/10.1371/journal.pone.0277834
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:alt: Citation link
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.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/academic_tracker.svg?style=social&label=Star

docs/conf.py

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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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language = "en"
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = True
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# def process_main_docstring(app, what, name, obj, options, lines):
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# if what == 'module' and "__main__" in name:
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# for i in range(len(lines)):
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# lines[i] = " " + lines[i]
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# lines.insert(0, "")
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# lines.insert(0, ".. code-block:: console")
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# def setup(app):
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# app.connect('autodoc-process-docstring', process_main_docstring)
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rinoh_documents = [
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dict(doc='index', target='AcademicTracker', template='article')
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]

docs/guide.rst

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the JSON files are in the :doc:`jsonschema` section, and more information about
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the use cases with examples are in the :doc:`tutorial` section.
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.. code-block:: console
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Usage:
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academic_tracker author_search <config_json_file> [--test --prev_pub=<file-path> --no_GoogleScholar --no_ORCID --no_Crossref --verbose --silent]
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academic_tracker reference_search <config_json_file> <references_file_or_URL> [--test --prev_pub=<file-path> --PMID_reference --MEDLINE_reference --no_Crossref --verbose --silent]
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academic_tracker find_ORCID <config_json_file> [--verbose --silent]
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academic_tracker find_Google_Scholar <config_json_file> [--verbose --silent]
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academic_tracker add_authors <config_json_file> <authors_file> [--verbose --silent]
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academic_tracker tokenize_reference <references_file_or_URL> [--MEDLINE_reference --verbose --silent]
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academic_tracker gen_reports_and_emails_auth <config_json_file> <publication_json_file> [--test --verbose --silent]
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academic_tracker gen_reports_and_emails_ref <config_json_file> <references_file_or_URL> <publication_json_file> [--test --prev_pub=<file-path> --MEDLINE_reference --verbose --silent]
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Options:
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-h --help Show this screen.
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--version Show version.
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--verbose Print hidden error messages.
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--silent Do not print anything to the screen.
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--test Generate pubs and email texts, but do not send emails.
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--prev_pub=<file-path> Filepath to json or csv with publication ids to ignore. Enter "ignore" for the <file_path> to not look for previous publications.json files in tracker directories.
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Reference Type Options:
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--PMID_reference Indicates that the reference_file is a PMID file and only PubMed info will be returned.
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--MEDLINE_reference Indicates that the reference_file is a MEDLINE file.
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Search Options:
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--no_GoogleScholar Don't search Google Scholar.
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--no_ORCID Don't search ORCID.
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--no_Crossref Don't search Crossref.
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.. literalinclude:: ../src/academic_tracker/__main__.py
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:start-at: Usage:
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:end-before: """
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:language: none
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src/academic_tracker/__main__.py

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"""
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"""
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Usage:
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academic_tracker author_search <config_json_file> [--test --prev_pub=<file-path> --no_GoogleScholar --no_ORCID --no_Crossref --verbose --silent]
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academic_tracker reference_search <config_json_file> <references_file_or_URL> [--test --prev_pub=<file-path> --PMID_reference --MEDLINE_reference --no_Crossref --verbose --silent]
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Options:
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-h --help Show this screen.
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--version Show version.
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-v --version Show version.
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--verbose Print hidden error messages.
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--silent Do not print anything to the screen.
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--test Generate pubs and email texts, but do not send emails.

src/academic_tracker/fileio.py

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import re
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import os
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import sys
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import json
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import docx
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import json
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import pandas
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from . import helper_functions

src/academic_tracker/tracker_schema.py

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cli_schema = {
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "Command Line Inputs",
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"description": "Input file that contains information for how the program should run.",
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"description": "Schema to check that program arguments are valid.",
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"type": "object",
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"properties": {

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