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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2022-04-15 04:57:54 +0200
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2022-04-15 05:22:19 +0200
commit91799fe4b6d62230e99a1520a23a0d30c3eb963e (patch)
tree7b04b6e7ec5901b2d7d3f4096ec8dac2b78da001 /tex/delete-me.tex
parentc5d7f2adbea2038d240868e0192fb306256e3b92 (diff)
IMPORTANT: more generic, robust and secure INPUTS.conf and download.mk
SUMMARY: it is necessary to update your 'INPUTS.conf' and 'download.mk'. Until now, adding an input file involved several steps that needed manual (and inconvenient!) intervention: for every file, you needed to define four variables in 'INPUTS.conf', and in 'reproduce/analysis/make/download.mk' you had to use a (complex for large number of files) shell 'if/elif/else' condition to link the names of the input files to those variables. Besides inconvenience, this could cause bugs (typos!). Furthermore, a basic MD5 checksum was used for verifying the files. With this commit, a new structure has been defined for 'INPUTS.conf' that (thanks to some pretty useful GNU Make features), removes the need for users to manually edit 'reproduce/analysis/make/download.mk', and reduces the number of variables necessary for each file to three (from four). Furthermore, we now use the SHA256 checksum for input data validation. Regarding the trick used in 'INPUTS.conf' (form the newly added description in 'download.mk'): In GNU Make, '.VARIABLES' "... expands to a list of the names of all global variables defined so far" (from the "Other Special Variables" section of the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only used for input files, we find all the variables that contain the input file names (the '%' is the filename). Finally, using the pattern-substitution function ('patsubst'), we remove the fixed string at the start and end of the variable name. Steps you need to take: - INPUTS.conf: translate your old format to the new format (after carefully reading the description in the comments at the start of the file). After applying the new standards, you don't need to use the variables of 'INPUTS.conf' directly in your Makefiles! For example if one of your input datasets is called 'abc.fits', the checksum variable will be 'INPUT-abc.fits-sha256' and in your high-level Makefiles, you can simply set '$(indir)/abc.fits' as a prerequisite (like you probably did already). - reproduce/analysis/make/download.mk: for the definition and rule of 'inputdatasets', simply use the Maneage branch, and remove anything you had added in your project. In the process, I also noticed that 'README-hacking.md' still referred to 'master' as the main project branch, while we have used 'main' in the paper (and is the common convention with Git).
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