The version controlled source code lacks the source files that we have not written or are automatically built. These automatically generated files are included in the distributed tar ball for each distribution (for example gnuastro-X.X.tar.gz, see Version numbering) and make it easy to immediately configure, build, and install Gnuastro. However from the perspective of version control, they are just bloatware and sources of confusion (since they are not changed by Gnuastro developers).
The process of automatically building and importing necessary files into the cloned directory is known as bootstrapping. All the instructions for an automatic bootstrapping are available in bootstrap and configured using bootstrap.conf. bootstrap is the only file not written by Gnuastro developers but is under version control to enable simple bootstrapping immediately after cloning. It is maintained by the GNU Portability Library (Gnulib) and this file is an identical copy, so do not make any changes in this file since it will be replaced when Gnulib releases an update. Make all your changes in bootstrap.conf.
The bootstrapping process has its own separate set of dependencies, the full list is given in Bootstrapping dependencies. They are generally very low-level and used by a very large set of commonly used programs, so they are probably already installed on your system. The simplest way to bootstrap Gnuastro is to simply run the bootstrap script within your cloned Gnuastro directory as shown below. However, please read the next paragraph before doing so (see Version controlled source for TOPGNUASTRO).
$ cd TOPGNUASTRO/gnuastro $ ./bootstrap # Requires internet connection
Without any options, bootstrap will clone Gnulib within your cloned Gnuastro directory (TOPGNUASTRO/gnuastro/gnulib) and download the necessary Autoconf archives macros. So if you run bootstrap like this, you will need an internet connection every time you decide to bootstrap. Also, Gnulib is a large package and cloning it can be slow. It will also keep the full Gnulib repository within your Gnuastro repository, so if another one of your projects also needs Gnulib, and you insist on running bootstrap like this, you will have two copies. In case you regularly backup your important files, Gnulib will also slow down the backup process. Therefore while the simple invocation above can be used with no problem, it is not recommended. To do better, see the next paragraph.
The recommended way to get these two packages is thoroughly discussed in Bootstrapping dependencies (in short: clone them in the separate DEVDIR/ directory). The following commands will take you into the cloned Gnuastro directory and run the bootstrap script, while telling it to copy some files (instead of making symbolic links, with the --copy option, this is not mandatory33) and where to look for Gnulib (with the --gnulib-srcdir option).
$ cd $TOPGNUASTRO/gnuastro $ ./bootstrap --copy --gnulib-srcdir=$DEVDIR/gnulib
Since Gnulib and Autoconf archives are now available in your local directories, you don’t need an internet connection every time you decide to remove all untracked files and redo the bootstrap (see box below). You can also use the same command on any other project that uses Gnulib. All the necessary GNU C library functions, Autoconf macros and Automake inputs are now available along with the book figures. The standard GNU build system (Quick start) will do the rest of the job.
Undoing the bootstrap: During the development, it might happen
that you want to remove all the automatically generated and imported
files. In other words, you might want to reverse the bootstrap
process. Fortunately Git has a good program for this job:
git clean -fxd
It is best to commit any recent change before running this
command. You might have created new files since the last commit and if
they haven’t been committed, they will all be gone forever (using
Besides the bootstrap and bootstrap.conf, the bootstrapped/ directory and README-hacking file are also related to the bootstrapping process. The former hosts all the imported (bootstrapped) directories. Thus, in the version controlled source, it only contains a REAME file, but in the distributed tar-ball it also contains sub-directories filled with all bootstrapped files. README-hacking contains a summary of the bootstrapping process discussed in this section. It is a necessary reference when you haven’t built this book yet. It is thus not distributed in the Gnuastro tarball.
The --copy option is recommended because some backup systems might do strange things with symbolic links.