Refactor

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
 .ipynb_checkpoints/*
+env/*

README.md

@@ -59,6 +59,7 @@ And editorials and research highlights of this work:
 * Z. Budrikis (2020). Growing citation gender gap. *Nature Reviews Physics*. [doi: https://doi.org/10.1038/s42254-020-0207-3](https://doi.org/10.1038/s42254-020-0207-3)
 * D. J. Sweet (2021). New at cell press: the inclusion and diversity statement. *Cell*, 184(1), 1-2. [doi: https://doi.org/10.1016/j.cell.2020.12.019](https://www.sciencedirect.com/science/article/pii/S0092867420316895?via%3Dihub)
 * B. Rowson, S.M. Duma, M.R. King, I. Efimov, A. Saterbak, and N.C. Chesler (2021). Citation diversity statement in BMES journals. *Annals of Biomedical Engineering*, 1-3. [doi: https://doi.org/10.1007/s10439-021-02739-6](https://link.springer.com/article/10.1007/s10439-021-02739-6)
+* D. Kwon (2022). The rise of citational justice: how scholars are making references fairer. *Nature*, 603(7902), 568-571. [doi: https://doi.org/10.1038/d41586-022-00793-1](https://www.nature.com/articles/d41586-022-00793-1)
 
 For `.pdf` and `.tex` templates of the statement, see the `/diversityStatement` directory in this repository.
 
@@ -118,7 +119,7 @@ ___
 
 2. Launch the coding environment. Please refresh the page if the Binder does not load after 5-10 mins.
 
-    [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dalejn/cleanBib/34b3a896b6fe0961b2dfc3ad22214cf45da48cca?urlpath=/tree/)
+    [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dalejn/cleanBib/refactor?urlpath=/tree/)
 
 3. Open the notebook `cleanBib.ipynb`. Follow the instructions above each code block. It can take 10 minutes to 1 hour complete all of the instructions, depending on the state and size of your `.bib` file. We expect that the most time-consuming step will be manually modifying the `.bib` file to find missing author names, fill incomplete entries, and fix formatting errors. These problems arise because automated methods of reference mangagers and Google Scholar sometimes can not retrieve full information, for example if some journals only provide an author's first initial instead of their full first name.
 
@@ -333,6 +334,7 @@ ___
 * Christopher Camp
 * Eli Cornblath
 * Jordan Dworkin
+* Kieran Murphy
 * Jordan Matelsky
 * Cleanthis Michael
 * Kendra Oudyk
@@ -344,6 +346,15 @@ ___
 * Dale Zhou
 
 # Changelog
+* __11/28/2022__
+  * major refactor (thanks, Jeni!)
+  * removed SOS notebook
+  * upgraded all packages and libraries
+  * all R code now in Python
+  * majority of code now call functions located in utils/
+  * automate removal of identified duplicates and self-citations
+  * query how many credits left and save some by only querying unique names (thanks, Kieran!)
+  * fixes issue introduced by [protobuf upgrade](https://github.com/protocolbuffers/protobuf/issues/10051)
 
 * __9/14/2021__
   * force Binder to load with [classic theme](https://discourse.jupyter.org/t/mybinder-org-using-jupyterlab-by-default/10715) because new default breaks SOS notebook R code

requirements.txt

@@ -0,0 +1,120 @@
+absl-py
+appnope
+argon2-cffi
+argon2-cffi-bindings
+asttokens
+astunparse
+attrs
+backcall
+beautifulsoup4
+bibtexparser==1.3.0
+bleach
+cachetools
+certifi
+cffi
+charset-normalizer
+cycler
+debugpy
+decorator
+defusedxml
+entrypoints
+ethnicolr==0.9.1
+executing
+fastjsonschema
+flatbuffers
+fonttools
+folium
+future
+gast
+google-auth
+google-auth-oauthlib
+google-pasta
+grpcio
+h5py
+habanero==1.2.2
+idna
+imgaug
+importlib-metadata
+ipykernel
+ipython
+jedi
+Jinja2
+jsonschema
+jupyter
+jupyter-client
+jupyter-console
+jupyter-core
+jupyterlab-pygments
+jupyterlab-widgets
+keras==2.8.0
+keras-preprocessing==1.1.2
+kiwisolver
+latexcodec==2.0.1
+Markdown
+MarkupSafe
+matplotlib
+matplotlib-inline
+mistune
+nbclient
+nbconvert
+nbformat
+nest-asyncio
+notebook
+numpy==1.22.3
+oauthlib
+opt-einsum
+packaging
+pandas==1.4.3
+pandocfilters
+parso
+pexpect
+pickleshare
+Pillow
+prometheus-client
+prompt-toolkit
+protobuf==3.20.1
+psutil
+ptyprocess
+pure-eval
+pyasn1
+pyasn1-modules
+pybtex==0.24.0
+pycparser
+Pygments
+pylatexenc==2.10
+pyparsing
+pyrsistent
+python-dateutil
+pytz
+PyYAML
+pyzmq
+qtconsole
+QtPy
+requests
+requests-oauthlib
+rsa
+scipy==1.7.3
+seaborn==0.11.2
+Send2Trash
+six
+soupsieve
+stack-data
+tensorboard==2.8.0
+tensorboard-data-server==0.6.0
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.8.1
+tensorflow-estimator
+termcolor
+terminado
+tinycss2
+tornado
+tqdm
+traitlets
+typing-extensions
+urllib3
+wcwidth
+webencodings
+Werkzeug
+widgetsnbextension
+wrapt
+zipp

runtime.txt

@@ -1 +1 @@
-r-3.6-2019-04-12
+python-3.10.5