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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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Until now, the files where the people were meant to change didn't have a
proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was
wrong because the license does not convey copyright ownership. So the name
of the file's original author must always be included and when people
modify it (and add their own copyright-able modifications).
With this commit, the file's original author (and email) are added to the
copyright notice and when more than one person modified a file, both names
have their individual copyright notice.
Based on this, the description for adding a copyright notice in
`README-hacking.md' has also been modified.
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Until now, for short files, we only had a license notice, not an actual
copyright notice. With this commit, a copyright notice has also been
added. We use this new command to find these files, suggested by
`ineiev@gnu.org'.
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A short, all-permisive copyright notice was added to the configuration
files that were missing one.
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Gnuastro's BuildProgram is a little special: it is actually built during
the building of Gnuastro to keep important include and lib directory
information and if someone wants to use BuildProgram, this information is
necessary. So a special configuration is added for it in
`reproduce/config/gnuastro'. This configuration file will allow users to
set their own special configuration if they like, then it will load the
installed BuildProgram configuration file.
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