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2018-02-15Choice to build final PDF removed from LOCAL settingsMohammad Akhlaghi-19/+14
The previous change where we had set the building of the PDF as a local (and thus not version controlled) setting was not good, because different commits might be made without the high-level preparations for the final PDF (especially during the initial/testing phases of a research). Therefore, if the runner of the pipeline is ignorant to this, they may hit some errors in LaTeX which can be frustrating. To have a clean reproduction, it is thus necessary to have the choice of pdf-building under version control along with the rest of the pipeline.
2018-02-14Sanity checks added, local settings now in LOCAL.mk.inMohammad Akhlaghi-18/+23
The choice of whether or not to make a PDF is now also a local system issue, not a general pipeline issue. So it has been put in the new `LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local settings (things that when changed should not be version-controlled) should be defined in this file. A sanity check was added to find if `./configure' has been run before `make' or not (using the `LOCAL.mk' file which is an output of the configuration step). If `LOCAL.mk' doesn't exist, an error will be printed informing the user that `./configure' needs to be run first. The configure script also provides more clear and hopefully better information on its purpose and what must be done. Since `make clean', it is executed even when `./configure' hasn't been run, it will only delete the build directory and its contents when local configuration has been done. A `distclean' target was also added which will first "clean" the pipeline, then delete the `LOCAL.mk.in' file. To allow rules like `make' to be run even if `BDIR' isn't defined (`./configure' hasn't been run yet), a fake `BDIR' is defined in such cases.
2018-02-07First commit to the reproduction pipeline templateMohammad Akhlaghi-0/+131
Let's start working on this pipeline independently with this first commit. It is based on my previous experiences, but I had never made a skeleton of a pipeline before, it was always within a working analysis. But now that the pipeline has a separate repository for its self, we will be able to work on it and use it as a base for future work and modify it to make it even better. Hopefully in time (and with the help of others), it will grow and become much more robust and useful.