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A few minor conflicts came up that were easily fixed.
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Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.
With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.
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Until now we would simply return the version numbers as they were written
into the separate files and situations can happen where the version numbers
contain an underscore (`_'). However, this character is a methematical
character in LaTeX, causing LaTeX to complain and abort.
With this commit, a step has been added at the end of the configure script
to convert any possible `_' to `\_'. Once it is commented (a backslash is
put behind it), the underscore will be printed as it is in the final PDF.
This commit was originally written by Mohammad Akhlaghi
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Until now we would simply return the version numbers as they were written
into the separate files and situations can happen where the version numbers
contain an underscore (`_'). However, this character is a methematical
character in LaTeX, causing LaTeX to complain and abort.
With this commit, a step has been added at the end of the configure script
to convert any possible `_' to `\_'. Once it is commented (a backslash is
put behind it), the underscore will be printed as it is in the final PDF.
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A few minor conflicts occurred and were fixed.
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MissFITS is package for manipulating FITS files.
I added it as my first commit to the project for educational
purposes.
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Until now, we defined `LIBRARY_PATH' to fix the problem of the `ld' linker
of Binutils needing several `*crt*.o' files to run. However, some software
(for example ImageMagick) over-write `LIBRARY_PATH', therefore there is no
other way than to put a link to these necessary files in our local build
directory.
With this commit, we fixed the problem by putting a link to the system's
relevant files in the local library directory. This fixed the problem with
ImageMagick. Later, when we build the GNU C Library in the project, we
should remove this step.
This bug reported by Raul Castellanos Sanchez.
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Until now, when a Fortran compiler didn't exist on the host operating
system, the configure script would crash with a warning. But some projects
may not need Fortran, so this is just an extra/annoying crash!
With this commit, it will still print the warning, but instead of a crash,
it will just sleep for some seconds, then continue. Later, when if a
software needs Fortran, it's building will crash, but atleast the user was
warned.
In the future, we should add a step to check on the necessary software and
see if Fortran is necessary for the project or not. The project
configuration should indeed crash if Fortran is necessary, but we should
tell the user that software XXXX needs Fortran so we can't continue without
a Fortran compiler.
Also, a small sentence ("Project's configuration will continue in XXXX
seconds.") was added after all the warnings that won't cause a crash, so
user's don't think its a crash.
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Until now, Make was just run ordinarily on the two Makefiles of the
software building phase. Therefore when there was a problem with one
software while building in parallel, Make would only complete the running
rules and stop afterwards. But when other rules don't depened on the
crashed rule, its a waste of time to stop the whole thing.
With this commit, both calls to Make in the `configure.sh' script are done
with the `-k' option (or `--keep-going' in GNU Make). With this option, if
a rule crashes, the other rules that don't depend on it will also be
run. Generally, anything that doesn't depend on the crashed rule will be
done. The `-k' option is a POSIX definition in Make, so it is present in
most implemenetations (for the call to `basic.mk').
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Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.
With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.
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