hamishgibbs / bubble

Automate your makefile automation.

Hi there 👋

I'm a PhD Student at University College London. I study large-scale mobility datasets to improve their use in emergencies. You can see more about my research interests here.

• Since 2021, I've been a PhD student in the UCL Department of Geography.
• From 2018 to 2021, I was a Research Assistant at the London School of Hygiene and Tropical Medicine (LSHTM).
• At LSHTM, I studied behavioral responses to COVID-19 travel restrictions. This led to publications in Nature Communications and PLOS Computational Biology. I also helped create the WHO Public Health and Social Measures dataset.
• In 2018, I recieved my MSc in Geoinformation Technology and Cartography at the University of Glasgow. In my thesis, I used multi-sensor remote sensing data to measure vegetation growth.
• In 2017, I graduated from Syracuse University with a BA in Geography and minors in Spanish and Applied Statistics.

bubble's Issues

Add dockerfile and makefile templates

Add readme in project structure

Add dockerfile templates

Individual dockerfile templates for R and Python

Possibly specify language=None in scaffold.

Adopt container name from project folder name.

Add make build and make bash and custom R studio up make targets to Makefile

This will require a new function scaffold_dockerfile which will depend on scaffold

Structure:

• Define dockerfile language from args (py or r)

  -d py or -d r

• scaffold dockerfile template

• add dockerfile make targets

Tests

Need some tests of various command args

simplest tests:

• check that files are created as needed.

Once these tests succeed:

• create r/py file
• test that file exists
• update r make target
• test that r make target exists
• update py make target
• test that r and py make target exists

create project directory structure

Discover Makefile targets

Automatically discover and update files and update their makefile targets.

This should be done in the root directory with bubble -m.

Should try to make the target for each file and pass it if this fails.

Insert Makefile target in place

Would be nice if an existing makefile target is found, it is inserted in place

Makefile updates

add backslash in makefile new lines \.

remove working directory string from file paths and replace with ${PWD}.
Doing this automatically will mean the project is portable between users.

i.e.:

• wd = os.getcwd() at project root
• input_string.replace(wd, '')
• input_string = ${PWD} + '/' + input_string

Warn about single quotes

Currently only supporting double quotes in input/output paths.

Add an exception if single quotes are found.

Overhaul Project

Propose overhauling project to automate portions of data processing, data ingestion, and processing - leaving space for custom logic inside a single responsibility input - output workflow.

Important components:

• System agnostic - should rely on Docker to transport easily between systems.
• File type agnostic - should be easily extensible for new file types.
• Future - could be coupled with graph visualisation GUI for overview of project and manual updating.
• Should be automatically integrated with Make. - make file_name should produce any target in a project directory.

Add emojis and colors in console interface.

Would be nice to have console interface return colors and emojis for different actions.