====== make ======
''make'' (specifically [[https://www.gnu.org/software/make/|GNU make]]) only updates upstream dependencies of files that have changed based on modification time of the "source" and "destination" file. source and destination are defined by rules in the file named ''Makefile'' in the current working directory. Other build tools include google's [[https://bazel.build/|bazel]], [[https://gittup.org/tup/|tup]] (( and [[https://www.scons.org/|scons]], [[https://www.gnu.org/software/cons/stable/cons.html|cons]], [[https://waf.io/book/|waf]] cf. language specific like ant, gradle, lein, rake, cargo, dune, ...))

===== Why =====

[[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735413/|[2016 Frontiers Neuroinform]
Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance]]

If you see a ''Makefile'' (especially in a top level script directory), viewing it will likely outline how important files are made and what the dependencies of each step are. It is documentation.

''make'' is available nearly everywhere and it is still a foundation tool in many software projects. It's useful to know and less niche than e.g. ''tup''
===== Usage =====

<code=make>
# output: dependencies
# 	command-to-generate-output 
# 	# MUST BE TAB INDENTED. spaces will result in error

ages.txt: dob_visit.txt
	./visit_age.bash dob_visit.txt > ages.txt
</code>

a file named ''Makefile'' contains the recipes/rules to create outputs from inputs. In the above example, the rule to make ''age.txt'' depends a ''dob_visit.txt'' file. When ''dob_visit.txt'' file has been modified more recently than ''ages.txt'', the ''visit_age.bash'' will be run. nothing will run if ''ages.txt'' is newer than ''dob_visit.txt''. Make will only regenerate ages when there are new DOBs+visits
 
===== LNCD Tools tweaks =====
[[tools:lncdtools]] provides some functions to create "sentinel" files that can be useful to know if a pipeline with lots of file outputs should be rerun. ((This is a poor approximation of hashing and cache-ing a la bazel or ninja))

<code=make>
all_BIDS.txt: $(wildcard MRData/*/DICOM/)
	./00_dcm2bids                       # makes may files like bids/*/*.nii.gz
	mkls all_BIDS.txt "bids/*/*.nii.gz" # list of all files into all_BIDS.txt

</code>

''mkls'' will only update ''all_BIDS.txt'' if there is a new file. as long as ''all_BIDS.txt'' is newer than any ''DICOM/'' dir, the rule will not need to run.


''mkstat'' and ''mkmissing -1 $step1_glob -2 $step2_glob'' are variations on this idea.