Tools for open geospatial science

Publishing research

The Particulars. Of Those Observations of the Planet Mars, Formerly Intimated to Have Been Made at London in the Months of February and March A. 1665/6. (1665). Philosophical Transactions (1665-1678), 1, 239-242. Retrieved from JSTOR

Publishing goals

registration so that scientists get credit
archiving so that we preserve knowledge for the future
dissemination so that people can use this knowledge
peer review so that we know it's worth it

Open Science

[Buckheit and Donoho 1995, Peng 2011, Rodríguez-Sánchez et al. 2016, Marwick 2016]

Image credit: CC BY-SA Comtebenoit, Wikimedia

Text

If the paper source format is LaTeX or other markup, the figures, tables, or even bigger parts can be generated using scripts and automatically included.

If the paper source format is Jupyter Notebook or other notebook-like format, everything including text, figures, and code is at one place included in the final document.

Collaborative writing

Overleaf, Authorea, ...
combined with Git

Scripting the process

Bash and GRASS GIS

r.in.lidar input=points.las output=elevation -e

Python and GRASS GIS

from grass.script import run_command
run_command("r.in.lidar", input="points.las", output="elevation", flags="e")

R and GRASS GIS

library(rgrass7)
execGRASS("r.in.lidar", input="points.las", output="elevation", flags="e")

Computational notebooks

interactive document with text, code, and figures
languages: Python, R, Bash, C, C++, Octave, ...
Jupyter Notebook, R Markdown (Notebook), Emacs Org-mode, ...

Publishing code

Published computational research

FUTURES - urban-rural landscape patterns simulation

model implemented as a set of GRASS GIS addon modules

r.futures.pga, r.futures.demand, r.futures.parallelpga, ...

FUTURES: Text

FUTURES: Source code

FUTURES: Source code history

FUTURES: Documentation

FUTURES: Graphical user interface

Integration into a larger project

Preprocessing, visualization, and user interface (GUI, CLI, API)
Integration with existing analytical tools
Inputs, outputs, memory management and other common features
Long-term maintenance
Options: GRASS GIS module, R package, Python package, QGIS plugin, ...

Environment to run the code

dependencies
environmental settings
file structure
Solutions: Docker, Vagrant, virtual machines ...

FROM ubuntu:16.04
RUN apt-get update
RUN apt-get install -y \
        g++ \
        python \
        python-numpy \
        netcdf-bin \
        sqlite3 \
        ...
WORKDIR /data

File versions

Revision control

Git (git), Subversion (svn), Mercurial (hg), ...

git commit script.py -m "replaced part of the main equation"

Research publication

Text	background, methods, results, discussion	PDF, HTML
Data	methods as GRASS GIS modules	open formats, *
Reusable code	generally and reusably implemented methods	Python, R, C
Specific code	scripts to generate results	Bash, Python, R, *
Environment	details about all dependencies and the code	Docker, Vagrant
Versions	repository with current and previous versions	Git, Mercurial

* Potentially included in computational notebooks such as Jupyter Notebook