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2019-04-04Better option-reading in configure, using .build to access BDIRMohammad Akhlaghi-76/+70
Until now, the steps to manage the command-line options of the configure script were limited (couldn't accept an equal sign or space between the option name and value). With this commit, it can now also accept optional equal signs between the option name and value. Thus not causing many confusions. Also, it is more logically consistent for the link to the build-directory to be placed in the top directory (as a hidden file like `.local' until now), and not as a visible directory like `reproduce/build' (which we used until now). Therefore, with this commit, the link to easily access the build-directory is `.build' in the top source directory. Finally, because `minmapsize' is too specific to Gnuastro and has now been given its default value at the start of the configure script, the description for `minmapsize' has been removed (to not confuse users who don't use Gnuastro). If anyone is familiar enough with Gnuastro to change it, they already know it from its book.
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-0/+25
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-03-01Elaboration in README-hacking.mk's future improvements sectionMohammad Akhlaghi-30/+43
This section was a little outdated and since then, a more clear/exact image of using the Nix experience for the reproducible paper template has been added.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-17/+10
In order to collaborate effectively in the project, even project members that don't necessarily want (or have the capacity) to do the whole analysis must be able to contribute to the project. Until now, the users of the distributed tarball could only modify the text and not the figures (built with PGFPlots) of the paper. With this commit, the management of TeX source files in the pipeline was slightly modified to allow this as cleanly as I could think of now! In short, the hand-written TeX files are now kept in `tex/src' and for the pipeline's generated TeX files (in particular the old `tex/pipeline.tex'), we now have a `tex/pipeline' symbolic-link/directory that points to the `tex' directory under the build directory. When packaging the project, `tex/pipeline' will be a full directory with a copy of all the necessary files. Therefore as far as LaTeX is concerned, having a build-directory is no longer relevant. Many other small changes were made to do this job cleanly which will just make this commit message too long! Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as in the standard GNU Build system).
2019-02-01Group name is now part of the local configurationMohammad Akhlaghi-21/+13
Until now, the group name to build the project actually went into the Git source of the project! This doesn't allow exact reproducibility on different machines (where the group name may be different). With this commit, the `for-group' script has been modified to accept the group name as its first argument and pass that onto `configure' and Make. This is much better now, because not only the existance of a group installation is checked, but also the name of the group. It also made things simpler (in particular in `LOCAL.mk.in').
2019-01-23New note to checklist for including pipeline-origin in new cloneMohammad Akhlaghi-0/+16
I needed to take these steps in a few occasions on a project I am building over this pipeline. This will commonly happen when a team starts using this pipeline, so it was added to make things easier.
2019-01-23README-pipeline.md is now called README-hacking.mdMohammad Akhlaghi-0/+999
To be more generic and recognizable, the `README-pipeline.md' script was renamed to `README-hacking.md'. In essence, it is just that: to hack the existing pipeline for your own project. We follow a similar naming convention in many GNU software.