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2018-02-20Pipeline architecture described in README.mdMohammad Akhlaghi-2/+7
`README.md' didn't contain a general description of the pipeline's design architecture. So a few paragraphs have been added to help someone new to it to understand it better.
2018-02-15Choice to build final PDF removed from LOCAL settingsMohammad Akhlaghi-6/+6
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.
2018-02-14Some extra space in alert when no PDF is createdMohammad Akhlaghi-0/+2
To help view that everything is OK and that there were no errors, an extra blank line followed by one with `----' is added to the notice when we won't be making a PDF. These two lines help the eye more clearly see everything is fine (given that above it, there are MANY commands and outputs).
2018-02-14Symbolic link to build directory now permanently addedMohammad Akhlaghi-22/+11
Managing this symbolic link as a prerequisite that may or maynot be defined just made the code too dirty. It is almost always needed, so it is now a super-high-level prerequisite (first dependency of the `all' target, even before the final PDF). In this way, we can be sure it is always built and that nothing else depends on it. If the user doesn't want it, they can simply remove it from the top `Makefile'.
2018-02-14Sanity checks added, local settings now in LOCAL.mk.inMohammad Akhlaghi-4/+5
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/+110
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.