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The main problems with this dataset was the names of the journals (which
sometimes have single quotes or apostrophes in them that is really annoying
for SED)! But ultimately, for the simple study we want to do here, the
journal names are irrelevant, so in the end I just ignored the names. Later
we can set an identifier for the journals if necessary.
But now we have the basic information in a way that is usable in a plot to
show in this paper.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until now, when an input dataset already exists in `INDIR', the template
would just make a symbolic link to it in the build directory. However, in
many cases, the files in INDIR will actually be links to other locations on
the filesystem and some programs have problems following too many links.
With this commit, the template is now using the `readlink' program (part of
GNU Coreutils) to follow a possible link and point the link in the build
directory directly to an actual non-link file.
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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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