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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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All occurances of "pipeline" have been chanaged to "project" or "template"
withint the text (comments, READMEs, and comments) of the template. The
main template branch is now also named `template'.
This was all because `pipeline' is too generic and couldn't be
distinguished from the base, and customized project.
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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, 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').
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If the `./for-group' script is not used properly, it can lead to the whole
pipeline being re-run. Therefore it is important to do a sanity check
immediately at the start of Make's processing and inform the user if there
is a problem.
With this commit, `./for-group' exports the `reproducible_paper_for_group'
variable which is used by both the initial `./configure' script, and later
in each call to Make. The `./configure' script will use it to write a value
in `reproduce/config/pipeline/LOCAL.mk' and Make will use it to compare
with the value in `reproduce/config/pipeline/LOCAL.mk'.
If there is an inconsistency, Make will not even attempt to build anything
and will just print a message and abort.
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Since the current implementation of this pipeline officially started in
2018, all the files only had 2018 in their copyright years. This has now
been corrected to 2018-2019.
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To avoid redundant steps in the the top-level Makefile and make it simpler
and easier to follow, we now define the base names of all the Makefiles in
the `makesrc' variable of the top-level Makefile. `makesrc' is then used to
define the Makefiles to include and the necessary TeX macros at the same
time. This is much more clear and obvious than the previous case were we
had to list the Makefiles and TeX macro files separately in the top level
Makefile.
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