Managing papers and bibliography databases at the command line

My approach to managing papers and references is to have single folder containing all my pdf reprints and a BibTeX format bibliography database file. I use a python script called papers to manage my database and create BibTeX entries with cross referencing to the pdf files. The papers program can extract the doi information from a pdf file, gather information online to create a BibTeX entry and store a renamed copy of the associated pdf in a folder; the new file name and location is included as a ‘file’ field of the new bibtex item added to the database file. Papers can even do this recursively for a folder full of pdf reprints. Very cool. Installation is easy. First clone the git project:

git clone

then use the pip python installer to install python dependencies

pip install unidecode crossrefapi bibtexparser scholarly fuzzywuzzy six

and install the poppler pdf rendering library. On mac OSX this is done using brew

brew install poppler

Then run the python installer in the cloned papers project directory

python install

To test whether the program is installed successfully type

papers -h

which should produce the output

Bruces-MBP-2:~ bruce$ papers -h
usage: papers [-h]

library management tool

positional arguments:

optional arguments:
  -h, --help            show this help message and exit

Using ebib to manage citations within emacs

I wanted a reference manager that I could use to embed citations in org projects that would link out to the bibtex entry, a pdf reprint, etc. Of course, I needed to embed citation in latex documents as well. The emacs ebib-mode does all this and more. Install ebib mode from the melpa archive using list-packages for example. The only hitch was that some hooks for org were not installed properly. I found the lisp file org-ebib.el at the authors github site and installed it manually.

;; added directory for org-ebib.el loading
(add-to-list 'load-path "~/.emacs.d/lisp/")
(load "org-ebib")

Everything now worked. I set some options using M-x customize-group ebib including the directory for my bib database. Also set it up to open my main bibliography file by default when ebib is started. The next issue was to get ebib to automatically open my local pdfs of entries that had been archived using the papers script. By default ebib looks for a file entry to specify the location of a reprint file. The problem is that papers adds ‘:’ at the start of the file path and appends ‘:pdf’ on the end. This confused ebib. The solution was to again use customize to remove file as the default field for a file search and leave the field blank which triggers a search in a default directory using the bibtex entry key (+ .pdf). That is fine as papers also names the pdfs it creates using the bibtex key. The next problem was that papers automatically creates subfolders for years when organizing the reprints but ebib does not search subdirectories so each directory has to be explicitly specified. Ugh, no way I was going to do that. Instead, I created a subfolder in my home directory and wrote a bash script to create hard links to all the pdf reprints in that single folder which then becomes the search target for ebib. The bash script is

rm -Rf ~/allreprints/*
for dir in $(ls -1FA | grep / | tr -d /); do ln $dir/* ~/allreprints; done

and is run after I add new entries to my database using papers. Works like a charm so far. Ebib has some promising features like linking an org note to an entry and creating reading lists (as org files). Also nice search tools using regex are available in the main window.

Preparing exams in latex I recently discovered a great package called ‘‘exam’’ that is part of the standard packages in texlive. The package has commands for adding multiple choice questions and so on, and automatically tracks the total points.

Pedigrees in latex I often include pedigree questions on exams for my EVE 131 course (requiring calculation of kinship coefficients etc). Another exciting discovery I made recently was that a good latex package exists for drawing pedigrees. Just include the following packages \usepackage{pst-pdgr,pstricks,pst-pdf} and compile the file using xelatex. Information on the pst-pdgr package is here.