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Open Bases python helpers for https://openbases.github.io

Home Page: https://openbases.github.io/openbases-python/

License: Other

Python 79.70% Dockerfile 0.52% Makefile 0.52% CSS 0.86% Shell 1.37% TeX 17.03%

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[core] paper markdown parsing

The first easy function of whedon-python should be to parse the paper.md and prepare the pandoc command to make it easily to generate the pdf (or other). This will be used in whedon-docker.

to the extent possible, whedon-python should serve as a wrapper for whedon! And of course check for installation, report version, etc. This will also make it easier for Python preferring folk to use whedon from their python applications.

allow user to specify custom color

If the user specifies a custom color, it should override the default assignment per base names. This is to ensure that the tool has broader use.

Add testing suite for paper markdown

should be able to define a recipe of criteria, and then run it against a paper.

add badge for specification type

We are adding a "specification" template type (e.g., for openschemas and don't have a well fitting type.

[core] badge generator

I would want to be able to easily generate a badge, see openbases/openbases.github.io#3

Something like:

Could be generated via

ob-badge experiment lab-js

In the format

ob-badge <base-type> <base-name>

paper references minimum fields

hey @arfon ! What would you consider the minimum required fields for references (meaning present and defined?) so far I have a type (e.g., article) and title, month, and year. But we might want some additional checks, like giving a warning if missing a doi, or requiring a journal OR url? Let me know your thoughts! Just for perusing, here are the listing of fields for the current references I'm testing with. I'm not saying this is right / wrong, but rather a "real world" example:

['title', 'abstract', 'publisher', 'month', 'year']
['title', 'affiliation', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year', 'language']
['title', 'booktitle', 'abstract', 'month', 'year', 'howpublished', 'note']
['title', 'abstract', 'institution']
['title', 'abstract', 'journal', 'publisher', 'volume', 'month', 'year', 'keywords']
['title', 'abstract', 'howpublished', 'note']
['title', 'abstract', 'journal']
['title', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year']
['title', 'month', 'year', 'note', 'doi', 'url']
['title', 'year']
['title', 'affiliation', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year']
['title', 'publisher', 'series', 'year']
['title', 'journal', 'publisher', 'volume', 'number', 'month', 'year', 'address']
['title', 'abstract', 'journal', 'publisher', 'pages', 'doi', 'month', 'year', 'language']
['title', 'affiliation', 'abstract', 'journal', 'publisher', 'volume', 'pages', 'month', 'year', 'keywords', 'language', 'doi']
['title', 'affiliation', 'abstract', 'journal', 'publisher', 'volume', 'pages', 'month', 'year', 'doi', 'keywords', 'language']
['title', 'abstract', 'month', 'year', 'archivePrefix', 'primaryClass', 'doi', 'eprint']
['title', 'abstract', 'journal', 'publisher', 'volume', 'month', 'year', 'doi']
['title', 'abstract', 'month', 'year', 'archivePrefix', 'primaryClass', 'eprint']

And given my validation, the simple test passes for all of the above:

Testing bibliography entry Stodden2010-cu
  type: article
  title: The Scientific Method in Practice: Reproducibility in the Computational Sciences
Testing bibliography entry Ram2013-km
  type: article
  title: Git can facilitate greater reproducibility and increased transparency in science
Testing bibliography entry noauthor_2015-ig
  type: misc
  title: Docker-based solutions to reproducibility in science - Seven Bridges
Testing bibliography entry noauthor_undated-pi
  type: misc
  title: expfactory-docker
Testing bibliography entry Sochat2016-pu
  type: article
  title: The Experiment Factory: Standardizing Behavioral Experiments
Testing bibliography entry noauthor_undated-sn
  type: misc
  title: Science is in a reproducibility crisis: How do we resolve it?
Testing bibliography entry Baker_undated-bx
  type: article
  title: Over half of psychology studies fail reproducibility test
Testing bibliography entry Open_Science_Collaboration2015-hb
  type: article
  title: {PSYCHOLOGY}. Estimating the reproducibility of psychological science
Testing bibliography entry vanessa_sochat_2017_1059119
  type: misc
  title: {expfactory/expfactory: The Experiment Factory (v3.0) Release}
Testing bibliography entry McDonnell2012-ns
  type: misc
  title: psiTurk (Version 1.02)[Software]. New York, {NY}: New York University
Testing bibliography entry De_Leeuw2015-zw
  type: article
  title: jsPsych: a {JavaScript} library for creating behavioral experiments in a Web browser
Testing bibliography entry Smith2005-kg
  type: book
  title: Virtual Machines: Versatile Platforms for Systems and Processes
Testing bibliography entry Merkel2014-da
  type: misc
  title: Docker: Lightweight Linux Containers for Consistent Development and Deployment
Testing bibliography entry Ali2016-rh
  type: article
  title: The Case for Docker in Multicloud Enabled Bioinformatics Applications
Testing bibliography entry Moreews2015-dy
  type: article
  title: {BioShaDock}: a community driven bioinformatics shared Docker-based tools registry
Testing bibliography entry Belmann2015-eb
  type: article
  title: Bioboxes: standardised containers for interchangeable bioinformatics software
Testing bibliography entry Boettiger2014-cz
  type: article
  title: An introduction to Docker for reproducible research, with examples from the {R} environment
Testing bibliography entry Santana-Perez2015-wo
  type: article
  title: Towards Reproducibility in Scientific Workflows: An {Infrastructure-Based} Approach
Testing bibliography entry Wandell2015-yt
  type: article
  title: Data management to support reproducible research

Add parser for getting icons

Akin to ob-paper, we need an ob-icon (or similar) entry point where the user can do things like get an icon https://github.com/openbases/openbases-icons. It also maybe should be more general (e.g., ob-resource) ?

bug: dash needs to be underscore in name

input name "builder-pdf" would generate:

https://img.shields.io/badge/paper-builder-pdf-%231ab170.svg

and instead needs to be

https://img.shields.io/badge/paper-builder_pdf-%231ab170.svg

adding testing for paper validation

need to have tests before merging #15

[bug] github pages isn't honoring ".nojekyll"

The Github Pages rendered in "docs" should honor the ".nojekyll" file and include static files. It currently does not. https://openbases.github.io/whedon-python/html/

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