Minor documentation changes and added citation file.

Author: ptth222

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.0.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Thompson"
+  given-names: "Travis"
+  orcid: "https://orcid.org/0000-0002-8198-1327"
+- family-names: "Powell"
+  given-names: "Christian"
+  orcid: "https://orcid.org/0000-0002-4242-080X"
+- family-names: "Moseley"
+  given-names: "Hunter"
+  orcid: "https://orcid.org/0000-0003-3995-5368"
+title: "academic_tracker"
+version: 1.0.3
+date-released: 2022-03-28
+url: "https://github.com/MoseleyBioinformaticsLab/academic_tracker"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Thompson"
+    given-names: "Travis"
+    orcid: "https://orcid.org/0000-0002-8198-1327"
+  - family-names: "Moseley"
+    given-names: "Hunter"
+    orcid: "https://orcid.org/0000-0003-3995-5368"
+  doi: "10.1371/journal.pone.0277834"
+  journal: "Plos one"
+  month: 11
+  title: "Academic Tracker: Software for tracking and reporting publications associated with authors and grants"
+  number: 11
+  volume: 17
+  year: 2022

README.rst

@@ -17,8 +17,8 @@ Academic Tracker
    :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
+.. image:: https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0277834-blue.svg
+   :target: https://doi.org/10.1371/journal.pone.0277834
    :alt: Citation link
 
 .. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/academic_tracker.svg?style=social&label=Star

docs/conf.py

@@ -70,7 +70,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -200,3 +200,20 @@
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
+
+
+
+# def process_main_docstring(app, what, name, obj, options, lines):
+#     if what == 'module' and "__main__" in name:
+#         for i in range(len(lines)):
+#             lines[i] = "   " + lines[i]
+#         lines.insert(0, "")
+#         lines.insert(0, ".. code-block:: console")
+
+# def setup(app):
+#     app.connect('autodoc-process-docstring', process_main_docstring)
+
+
+rinoh_documents = [
+    dict(doc='index', target='AcademicTracker', template='article')
+]

docs/guide.rst

@@ -223,35 +223,10 @@ by the publication references given in the reference file or URL. Details about
 the JSON files are in the :doc:`jsonschema` section, and more information about 
 the use cases with examples are in the :doc:`tutorial` section.
 
-.. code-block:: console
-
-    Usage:
-        academic_tracker author_search <config_json_file> [--test --prev_pub=<file-path> --no_GoogleScholar --no_ORCID --no_Crossref --verbose --silent]
-        academic_tracker reference_search <config_json_file> <references_file_or_URL> [--test --prev_pub=<file-path> --PMID_reference --MEDLINE_reference --no_Crossref --verbose --silent]
-        academic_tracker find_ORCID <config_json_file> [--verbose --silent]
-        academic_tracker find_Google_Scholar <config_json_file> [--verbose --silent]
-        academic_tracker add_authors <config_json_file> <authors_file> [--verbose --silent]
-        academic_tracker tokenize_reference <references_file_or_URL> [--MEDLINE_reference --verbose --silent]
-        academic_tracker gen_reports_and_emails_auth <config_json_file> <publication_json_file> [--test --verbose --silent]
-        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]
-        
-    Options:
-        -h --help                         Show this screen.
-        --version                         Show version.
-        --verbose                         Print hidden error messages.
-        --silent                          Do not print anything to the screen.
-        --test                            Generate pubs and email texts, but do not send emails.
-        --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.
-        
-    Reference Type Options:    
-        --PMID_reference                  Indicates that the reference_file is a PMID file and only PubMed info will be returned.
-        --MEDLINE_reference               Indicates that the reference_file is a MEDLINE file.
-    
-    Search Options:
-        --no_GoogleScholar                Don't search Google Scholar.
-        --no_ORCID                        Don't search ORCID.
-        --no_Crossref                     Don't search Crossref.
-
+.. literalinclude:: ../src/academic_tracker/__main__.py
+    :start-at: Usage:
+    :end-before: """
+    :language: none
 
 
 

src/academic_tracker/__main__.py

@@ -1,4 +1,4 @@
-"""   
+"""
 Usage:
     academic_tracker author_search <config_json_file> [--test --prev_pub=<file-path> --no_GoogleScholar --no_ORCID --no_Crossref --verbose --silent]
     academic_tracker reference_search <config_json_file> <references_file_or_URL> [--test --prev_pub=<file-path> --PMID_reference --MEDLINE_reference --no_Crossref --verbose --silent]
@@ -11,7 +11,7 @@
     
 Options:
     -h --help                         Show this screen.
-    --version                         Show version.
+    -v --version                      Show version.
     --verbose                         Print hidden error messages.
     --silent                          Do not print anything to the screen.
     --test                            Generate pubs and email texts, but do not send emails.

src/academic_tracker/fileio.py

@@ -9,9 +9,9 @@
 import re
 import os
 import sys
+import json
 
 import docx
-import json
 import pandas
 
 from . import helper_functions

src/academic_tracker/tracker_schema.py

@@ -12,7 +12,7 @@
 cli_schema = {
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "Command Line Inputs",
- "description": "Input file that contains information for how the program should run.",
+ "description": "Schema to check that program arguments are valid.",
 
  "type": "object",
  "properties": {