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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2020-01-23 18:54:29 +0000
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2020-01-23 19:16:16 +0000
commit2264c0fea5668cd8f827cdbd89004fd390b0b14f (patch)
tree99af64b55557bfb69ea630a653bb8bf07586c63a /reproduce/software/shell/configure.sh
parentcf0427009decbcad33a269898a428341e9c0ceff (diff)
IMPORTANT: Project preparation is now also done with project make
Until now, the main commands to run the project were these: `./project configure' (to build the software), `./project prepare' (to possibly arrange input datasets and build special configuration Makefiles) and finally `./project make' to run the project. The main logic behind the "prepare" phase `top-prepare.mk' is to build configuration files that can be fed into the "make" step and optimize its operation. For example when the total number of necessary inputs for the majority of the analysis is not as large as the total number of inputs. With "prepare" (when necessary), you go through the raw inputs, select the ones that are necessary for the rest of the project. The output of `top-prepare.mk' is a configuration file (a Make variable) that keeps the IDs (numbers, names, etc). That configuration file would then be used in the `top-make.mk' to identify the lower level targets and allow optimal project organization and management. But the last two are both part of the analysis, and while they indeed need different calls to Make to be executed, many projects don't actually need a preparation phase: ultimately, its an implementation choice by the project developers and doesn't concern the project users (or the developers when they are running it). To avoid confusing the users, or simply annoying them when a projet doesn't need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk' Makefiles are called with the single `./project make' command and `./project prepare' has been dropped. I noticed this while writing the paper on this system.
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