[gnuastro-commits] master f2d563a 2/2: New Dependencies from package managers section in doc

[Mohammad Akhlaghi]

branch: master
commit f2d563afc9190af83197592e5e0c6bec2ccaa91e
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>

    New Dependencies from package managers section in doc
    
    The start of the "Dependencies" section was getting too long. Also, it
    would help to have "package managers" as a section title (to be included in
    the contents). Therefore the discussion on package managers and the example
    commands have been moved to a new subsection under "Dependencies", that is
    called "Dependencies from package managers".
    
    Some minor corrections were also made in the description of this
    section. In particular, since Arch Linux is less common than Homebrew, its
    description was moved below Homebrew. Also, the description of Homebrew was
    broken up into two paragraphs for easier reading along with some small
    edits.
---
 doc/gnuastro.texi | 252 ++++++++++++++++++++++++++++--------------------------
 1 file changed, 133 insertions(+), 119 deletions(-)

diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index d912ab3..a1ef5c1 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -254,6 +254,7 @@ Dependencies
 * Mandatory dependencies::      Gnuastro will not install without these.
 * Optional dependencies::       Adding more functionality.
 * Bootstrapping dependencies::  If you have the version controlled source.
+* Dependencies from package managers::  Installing from OS package managers.
 
 Mandatory dependencies
 
@@ -4472,134 +4473,31 @@ Gnuastro but might be useful in conjunction with it is 
discussed.
 @node Dependencies, Downloading the source, Installation, Installation
 @section Dependencies
 
-The dependencies needed to build and install Gnuastro are defined by the
-features you want and how you would like to obtain the source code (see
address@hidden the source}). A minimal set of dependencies are mandatory,
-if they are not present you cannot get passed the configuration step. Such
-mandatory dependencies are therefore very basic (low-level) tools which are
-easy to obtain, build and install, see @ref{Mandatory dependencies} for a
-full discussion.
+A minimal set of dependencies are mandatory for building Gnuastro from the
+standard tarball release. If they are not present you cannot pass
+Gnuastro's configuration step. The mandatory dependencies are therefore
+very basic (low-level) tools which are easy to obtain, build and install,
+see @ref{Mandatory dependencies} for a full discussion.
 
 If you have the packages of @ref{Optional dependencies}, Gnuastro will have
 additional functionality (for example converting FITS images to JPEG or
 PDF). If you are installing from a tarball as explained in @ref{Quick
-start}, you can stop reading after this section. However, if you decided to
-use the version controlled source instead of the tarball (see @ref{Version
-controlled source}), an additional bootstrapping step is required before
-configuration and its dependencies are explained in @ref{Bootstrapping
-dependencies}.
-
address@hidden Package managers
address@hidden Source code building
address@hidden Building from source
address@hidden Compiling from source
address@hidden Source code compilation
address@hidden Distributions, GNU/Linux
-The most basic way to install a package on your system is to build the
-packages from source yourself. Alternatively, you can use your operating
-system's package manager to download pre-compiled files and install
-them. The latter choice is easier and faster. However, we recommend that
-you build the @ref{Mandatory dependencies} yourself from source (all
-necessary commands and links are given in the respective section). Here are
-some basic reasons behind this recommendation.
-
address@hidden
-
address@hidden
-Your distribution's pre-built package might not be the most recent
-release.
-
address@hidden
-For each package, Gnuastro might preform better (or require) certain
-configuration options that your distribution's package managers didn't add
-for you. If present, these configuration options are explained during the
-installation of each in the sections below (for example in
address@hidden). When the proper configuration has not been set, the
-programs should complain and inform you.
-
address@hidden
-For the libraries, they might separate the binary file from the header
-files which can cause confusion, see @ref{Known issues}.
-
address@hidden
-Like any other tool, the science you derive from Gnuastro's tools highly
-depend on these lower level dependencies, so generally it is much better to
-have a close connection with them. By reading their manuals, installing
-them and staying up to date with changes/bugs in them, your scientific
-results and understanding (of what is going on, and thus how you interpret
-your scientific results) will also correspondingly improve.
address@hidden enumerate
-
-Based on your operating system's package manager, you can use any of the
-following commands to install the mandatory and optional dependencies. If
-your operating system is not included, please send us the respective
-command, so we add it here. Gnuastro itself if also already packaged in
-some package managers (for example Debian).
-
-As discussed above, we recommend installing the @emph{mandatory}
-dependencies manually from source. Therefore, in each command below, first
-the optional dependencies are given. The mandatory dependencies are
-included after an empty line. If you would like to install the mandatory
-dependencies with your package manager, just ignore the empty line.
-
address@hidden @asis
address@hidden Debian-based (@command{apt-get})
address@hidden Debian
address@hidden Ubuntu
-Debian-based GNU/Linux
address@hidden@url{https://en.wikipedia.org/wiki/List_of_Linux_distributions#Debian-based}}
-(for example Ubuntu or its derivatives) are arguably the largest, and most
-used, class of GNU/Linux distributions. All such GNU/Linux distributions
-use Debian's Advanced Packaging Tool (APT, for example @command{apt-get})
-for managing packages.
address@hidden
-$ sudo apt-get install ghostscript libtool-bin  libjpeg-dev \
-                       libtiff-dev libgit2-dev              \
-                                                            \
-                       libgsl0-dev libcfitsio-dev wcslib-dev
address@hidden example
-
address@hidden Arch Linux (@command{pacman})
address@hidden Arch Linux
-Arch Linux is a smaller GNU/Linux distribution. As discussed in
address@hidden://en.wikipedia.org/wiki/Arch_Linux, Wikipedia}, it follows ``the
-KISS principle ("keep it simple, stupid") as the general guideline, and
-focuses on elegance, code correctness, minimalism and simplicity, and
-expects the user to be willing to make some effort to understand the
-system's operation''. Arch Linux uses ``Package manager'' (Pacman) to
-manage its packages.
address@hidden
-$ sudo pacman -S ghostscript libtool libjpeg libtiff libgit2 \
-                                                             \
-                 gsl cfitsio wcslib
address@hidden example
-
address@hidden macOS (@command{brew})
address@hidden macOS
-macOS is the operating system used on Apple devices
-(@url{https://en.wikipedia.org/wiki/MacOS}). macOS does not come with a
-package manager pre-installed, but several widely used, third-party package
-managers exist, such as Homebrew or MacPorts.  Installation with Homebrew
-is tested and therefore recommended by the Gnuastro developers.  If not
-already installed, first obtain Homebrew by following the instructions at
address@hidden://brew.sh}.  Homebrew manages packages in different `taps'.  If
-you plan to install @command{wcslib} via Homebrew you will need to
address@hidden into @command{brewsci/science} first (the tap may change in
-the future, but can be found by calling @command{brew search wcslib}).
address@hidden
-$ brew install ghostscript libtool libjpeg libtiff libgit2 \
-                                                           \
-               gsl cfitsio
-$ brew tap brewsci/science
-$ brew install wcslib
address@hidden example
address@hidden table
+start}, you can stop reading after this section. If you are cloning the
+version controlled source (see @ref{Version controlled source}), an
+additional bootstrapping step is required before configuration and its
+dependencies are explained in @ref{Bootstrapping dependencies}.
 
+Your operating system's package manager is an easy and convenient way to
+download and install the dependencies that are already pre-built for your
+operating system. In @ref{Dependencies from package managers}, we'll list
+some common operating system package manager commands to install the
+optional and mandatory dependencies.
 
 @menu
 * Mandatory dependencies::      Gnuastro will not install without these.
 * Optional dependencies::       Adding more functionality.
 * Bootstrapping dependencies::  If you have the version controlled source.
+* Dependencies from package managers::  Installing from OS package managers.
 @end menu
 
 @node Mandatory dependencies, Optional dependencies, Dependencies, Dependencies
@@ -4874,7 +4772,7 @@ package managers for this.
 
 
 
address@hidden Bootstrapping dependencies,  , Optional dependencies, 
Dependencies
address@hidden Bootstrapping dependencies, Dependencies from package managers, 
Optional dependencies, Dependencies
 @subsection Bootstrapping dependencies
 
 Bootstrapping is only necessary if you have decided to obtain the full
@@ -5027,6 +4925,122 @@ formats necessary for the various book formats.
 
 
 
address@hidden Dependencies from package managers,  , Bootstrapping 
dependencies, Dependencies
address@hidden Dependencies from package managers
+
address@hidden Package managers
address@hidden Source code building
address@hidden Building from source
address@hidden Compiling from source
address@hidden Source code compilation
address@hidden Distributions, GNU/Linux
+The most basic way to install a package on your system is to build the
+packages from source yourself. Alternatively, you can use your operating
+system's package manager to download pre-compiled files and install
+them. The latter choice is easier and faster. However, we recommend that
+you build the @ref{Mandatory dependencies} yourself from source (all
+necessary commands and links are given in the respective section). Here are
+some basic reasons behind this recommendation.
+
address@hidden
+
address@hidden
+Your distribution's pre-built package might not be the most recent
+release.
+
address@hidden
+For each package, Gnuastro might preform better (or require) certain
+configuration options that your distribution's package managers didn't add
+for you. If present, these configuration options are explained during the
+installation of each in the sections below (for example in
address@hidden). When the proper configuration has not been set, the
+programs should complain and inform you.
+
address@hidden
+For the libraries, they might separate the binary file from the header
+files which can cause confusion, see @ref{Known issues}.
+
address@hidden
+Like any other tool, the science you derive from Gnuastro's tools highly
+depend on these lower level dependencies, so generally it is much better to
+have a close connection with them. By reading their manuals, installing
+them and staying up to date with changes/bugs in them, your scientific
+results and understanding (of what is going on, and thus how you interpret
+your scientific results) will also correspondingly improve.
address@hidden enumerate
+
+Based on your operating system and its package manager, you can use any of
+the following commands to install the mandatory and optional
+dependencies. If your operating system or package manager are not included,
+please send us the respective command, so we add it here. Gnuastro itself
+if also already packaged in some package managers (for example Debian or
+Homebrew).
+
+As discussed above, we recommend installing the @emph{mandatory}
+dependencies manually from source. Therefore, in each command below, first
+the optional dependencies are given. The mandatory dependencies are
+included after an empty line. If you would also like to install the
+mandatory dependencies with your package manager, just ignore the empty
+line.
+
address@hidden @asis
address@hidden Debian-based OSs (@command{apt-get})
address@hidden Debian
address@hidden Ubuntu
+Debian-based GNU/Linux
address@hidden@url{https://en.wikipedia.org/wiki/List_of_Linux_distributions#Debian-based}}
+(for example Ubuntu or its derivatives) are arguably the largest, and most
+used, class of GNU/Linux distributions. All such GNU/Linux distributions
+use Debian's Advanced Packaging Tool (APT, for example @command{apt-get})
+for managing packages.
address@hidden
+$ sudo apt-get install ghostscript libtool-bin  libjpeg-dev \
+                       libtiff-dev libgit2-dev              \
+                                                            \
+                       libgsl0-dev libcfitsio-dev wcslib-dev
address@hidden example
+
address@hidden macOS (@command{brew})
address@hidden macOS
+macOS is the operating system used on Apple devices
+(@url{https://en.wikipedia.org/wiki/MacOS}). macOS does not come with a
+package manager pre-installed, but several widely used, third-party package
+managers exist, such as Homebrew or MacPorts. Both are free
+software. Currently we have only tested Gnuastro's installation with
+Homebrew and described below.
+
+If not already installed, first obtain Homebrew by following the
+instructions at @url{https://brew.sh}. Homebrew manages packages in
+different `taps'. To install WCSLIB (discussed in @ref{Mandatory
+dependencies}) via Homebrew you will need to @command{tap} into
address@hidden/science} first (the tap may change in the future, but can
+be found by calling @command{brew search wcslib}).
address@hidden
+$ brew install ghostscript libtool libjpeg libtiff libgit2 \
+                                                           \
+               gsl cfitsio
+$ brew tap brewsci/science
+$ brew install wcslib
address@hidden example
+
address@hidden Arch Linux (@command{pacman})
address@hidden Arch Linux
+Arch Linux is a smaller GNU/Linux distribution. As discussed in
address@hidden://en.wikipedia.org/wiki/Arch_Linux, Wikipedia}, it follows ``the
+KISS principle ("keep it simple, stupid") as the general guideline, and
+focuses on elegance, code correctness, minimalism and simplicity, and
+expects the user to be willing to make some effort to understand the
+system's operation''. Arch Linux uses ``Package manager'' (Pacman) to
+manage its packages.
address@hidden
+$ sudo pacman -S ghostscript libtool libjpeg libtiff libgit2 \
+                                                             \
+                 gsl cfitsio wcslib
address@hidden example
address@hidden table
+
+
+