Example files for http://blog.byronjsmith.com/makefile-shortcuts.html, a default makefile for computational research projects

.gitattributes

*.ipynb	filter=dropoutput_jupyter
*.[tc]sv	diff=daff-csv
*.[tc]sv	merge=daff-csv

drop_jupyter_output.sh

#!/usr/bin/env bash
# run `chmod +x drop_jupyter_output.sh` to make it executable.

file=$(mktemp)
cat <&0 >$file
jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True \
    $file --stdout 2>/dev/null

Makefile

define PROJECT_HELP_MSG

Usage:
    make help                   show this message
    make clean                  remove intermediate files (see CLEANUP)

    make ${VENV}                make a virtualenv in the base directory (see VENV)
    make python-reqs            install python packages in requirements.pip
    make git-config             set local git configuration
    make setup                  git init; make python-reqs git-config

    make start-jupyter          launch a jupyter server from the local virtualenv

endef
export PROJECT_HELP_MSG

help:
	echo $$PROJECT_HELP_MSG | less

.git:
	git init

git-config: | .git 
	git config --local filter.dropoutput_jupyter.clean \
        drop_jupyter_output.sh
	git config --local filter.dropoutput_jupyter.smudge cat
	git config --local core.page 'less -x4'
	git config --local diff.daff-csv.command "daff.py diff --git"
	git config --local merge.daff-csv.name "daff.py tabular merge"
	git config --local merge.daff-csv.driver "daff.py merge --output %A %O %A %B"

VENV = .venv
export VIRTUAL_ENV := $(abspath ${VENV})
export PATH := ${VIRTUAL_ENV}/bin:${PATH}

${VENV}:
	python3 -m venv $@

python-reqs: requirements.pip | ${VENV}
	pip install --upgrade -r requirements.pip

setup: python-reqs git-config | .git ${VENV}

start-jupyter:
	jupyter notebook --config=jupyter_notebook_config.py

CLEANUP = *.pyc

clean:
	rm -rf ${CLEANUP}

.PHONY: help git-config start-jupter python-reqs setup clean

requirements.pip

jupyter
daff

Huh. Hadn't thought about the risks yet of that particular cleanup recipe. I'll take a look at your stuff.

In general, I wouldn't use this makefile outside of a single, well defined, project directory, so I wasn't as concerned about broader fs structure.