pigmy

NOTE 2021-10-08: This repository is no longer maintained. I recommend you look into the markmeld package, which can do everything pigmy did and more. I will leave this code here for reference purposes.

Are you annoyed by having to maintain your list of active and pending grants in 5 different formats? You have the NIH Research Support format, which excludes amounts, the NIH Other Support format, which includes amounts, NSF formats, internal formats for P&T committees, and your own personal list to keep track of deadlines and applications... and the list goes on.

What a pain to keep all these things updated, requiring hours of time. Now, pigmy can help! pigmy (pronounced 'pygmy') is a python application that makes formatting grant metadata easy. It's the PI grant metadata yeoman, here to take care of your grant metadata management needs.

Just maintain your list of grants once, in a human- and computer-readable yaml format, and pigmy will use pandoc to output whatever you want in a template-based, customizable output. We have built-in templates for common output formats (like those specified above), but you can also make whatever output format you want.

Getting started

Examples

The grant metadata file example_grants.yaml can create the output file example_research_support.pdf. This example is based on the nih_other_support.txt format and the research_support_template.md document template.

Further example grants.yaml files are in grant_metadata, and example output is in output.

Run on the command line:

python pigmy.py -g grants.yaml -f output_format.txt

python pigmy.py --help

How it works

pigmy is quite simple. It will read your grants.yaml file, which is just a list of grants in yaml format, and then uses a user-provided template to output those grants in the format you want. The built-in templates are in markdown format, so pigmy will output markdown text, which you can then pipe through pandoc to get a PDF or docx.

There are two user-customizable files that determine how pigmy will format the output: the format files and document templates.

Format files, found in /formats, provide a way for you specify how text from a single grant will be organized. An example is:

{namePlusPI} &nbsp; &nbsp; &nbsp; {dates} &nbsp; &nbsp; &nbsp; {effort}  
{funder}  
Title: {title}  
Role: {role}

The bracketed values (like {title}) will be populated with information from the grant. These formats specify how each individual grant will be formatted.

Document files, found in /document_templates, show how the grants will be organized in a file. An example is the NIH research support template, which looks like this:

# D. Research support

## Active

{active}

Here, you use bracketed status codes. In this example, all the active grants, formatted according to the format file and appended in a list, will replace the {active} tag. You can use this to insert your grants list into any document format you like.

Recipes

Generate an NIH-style 'research support' that can be appended to the end of a NIH-format Biosketch:

python pigmy.py -e -g grant_metadata/example_grants.yaml \
	-d document_templates/research_support_template.md \
	-f formats/nih_other_support.txt \
	| pandoc --reference-doc pandoc_templates/template.docx \
	-o output/example_research_support.docx

Use LibreOffice to generate a PDF of said output

python pigmy.py -e -g grant_metadata/example_grants.yaml \
	-d document_templates/research_support_template.md \
	-f formats/nih_other_support.txt \
	| pandoc --reference-doc pandoc_templates/template.docx \
	-o output/example_research_support.docx

soffice --convert-to pdf output/example_research_support.docx --outdir output

Run a web-server

pigmy uses the lightweight flask microframework to give you a web interface, making it even easier to get the format you need, if you like pointy-clicky.

Run like:

FLASK_APP=flask_pigmy.py flask run

Then point browser to: http://127.0.0.1:5000

databio / pigmy