To enable easy/proper reproduction of results, all the high-level dependencies are now built within the pipeline and installed in a fixed directory that is added to the PATH of the Makefile. This includes GNU Bash and GNU Make, which are then used to run the pipeline. The `./configure' script will first build Bash and Make within itself, then it will build All the dependencies are also built to be static. So after they are built, changing of the system's low-level libraries (like C library) won't change the tarballs. Currently the C library and C compiler aren't built within the pipeline, but we'll hopefully add them to the build process also. With this change, we now have full control of the shell and Make that will be used in the pipeline, so we can safely remove some of the generalities we had before.
On some systems, the default shell `/bin/sh' doesn't point to Bash and this can cause problems and failures when the designer uses its features. Bash (and its extra features) make things very easy and it is very ubiquitous, so it is safe to assume users will have it. This problem was reported by Alejandro Serrano Borlaff.
Making plots and including references are integral parts of a scientific paper. Therefore to demonstrate how cleanly they can be used within the pipeline, they are now used to produce the final PDF. To use PGFPlots a random dataset is made (using AWK's random function) and is plotted using PGFPlots. The minimum and maximum values of the dataset are also included in the text to further show how such calculations can go into the macros and text. For the references, the NoiseChisel paper was added as a reference to cite when using this pipeline along with the MUSE UDF paper I, which uses this pipeline for two sections. Following this discussion, citation is also discussed in `README.md` and the NoiseChisel paper is also added as a published work with a reproduction pipeline.
Until now, the copyright statement was left empty for the users of the pipeline to fill. However, the files have already been created and have an author (or contributing authors) before the user starts using the pipeline. So the original authors of the files are added along with the year. The user can add their own name to the existing files under the "Contributing author" when they start and they will be the "Original author" of the new files they create. Several changes were also made to the TeX management: - LaTeX is run within a `reproduce/build/tex/build' directory now. Not in the top reproduction pipeline directory. This helps keep all the auxiliary TeX files and directories in that directory and keep the top reproduction pipeline directory clean. After the final PDF is built, a copy is put in the top reproduction pipeline directory for easy viewing. - The PGFPlots preamble was also made more useful, allowing the name of the `.tex' file to also be the name of the final plot that is produced. This is a GREAT feature, because without it, the TiKZ externalization would be based on order of the plots within the paper. But now, order is irrelevant and we can even delete the TiKZ files within the processing workhorse-Makefiles so the plots are definitly rebuilt on the next run. - The paper is now in a two-column format to be more similar to published papers. A tip on debugging Make was added to `README.md'.
`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.
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.
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).
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'.
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.
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.