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A few small conflicts showed up here and there. They are fixed with this
merge.
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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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A few minor conflicts occurred and were fixed.
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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The unnecessary parts were removed and the project now runs.
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The checklist descriptions were slightly edited to be more clear. Also,
while following them, I noticed that while removing the "delete-me" parts
on `verify.mk', would cause an error: the `if [ $$m == delete-me ];'
statement we were saying to delete cause an error because `elif' was the
first statement Bash would see. So with this commit, the `download'
conditional (which isn't instructed to be deleted) was set to be the top
(with an `if') and the `delete-me' conditional now has an `elif'.
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Until now, if the file to be verified didn't exist, a different checksum
would be generated, and it would stop, but it wasn't immediately clear if
the differing checksum is because the file doesn't exist at all!
With this commit, before calculating the checksum, we first make sure if
the file exists. If it doesn't exist an explicit error is printed and thus
will help the project editor to find the cause of the problem.
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Until now, the only verification that the template provided was the
published PDF. Users had to manually compare the published and generated
PDFs (numbers, plots, tables) and see if they obtained the same
result. However, this type of manual verification is not good and is prone
to frustration and missing important differences.
With this commit, a new Makefile has been added in the analysis steps:
`verify.mk'. It provides facilities to easily verify the results that go
into the paper. For example tables that go into making the paper's plots,
or the LaTeX macros that blend into the text. See the updated parts in
`README-hacking.md` for a more complete explanation.
This completes task #15497.
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