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Even though the Coreutils configure script says that it adds `rpath' to its
executables, its executables don't have it. As a result, it goes to use the
host operating system libraries, causing failures when they don't match
with the template.
Unfortunately after some tests with the configure script, I couldn't find
any way to include `rpath'! Even though `-rpath-link' is present in all
linking commands during Coreutils' build, the installed files still don't
have it!
So I was forced to use PatchELF. However, one problem is that Coreutils
installs many programs, not just one like Bash or AWK.
As a brute-force solution, with this commit, we are running PatchELF on all
the installed programs. It won't hurt those that already have it, but it
will fix all those that don't.
With this commit, I am also making the following non-related small changes:
- In `build-rules.mk', the `&&' characters were placed at the start of the
line for better readability.
- Bash, Readline and NCURSES are now built in parallel on systems that
support it (during `basic.mk').
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The BibTeX data for `sip_tpv' didn't have a copyright notice, so one was
added for it.
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There wasn't any conflict in this merge.
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Until now, we were not citing the paper of `sip_tpv' package.
With this commit, we have been fix this issue.
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With this commit, we let the Python package `sip_tpv' to be optional in
order to not install it by default. It is a very specific package and I
forgot to remove it from `TARGETS.mk' in the previous commit.
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With this commit, we add `sip_tpv' Python package into the template.
This is a small package to convert SIP distorsion coefficients into PV
distorsion coefficients, and the other way around.
This package is useful in a astronomical context, specially when `swarp'
is going to be used in order to resample images. The reason is that
`swarp' only can understand PV distorsion coefficients.
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With this commit, we add `sympy' Python package into the template. This
is a package to do symbolic mathematics.
The motivation is that it is a prerequisite of `sip_tpv' Python package,
which is useful to convert SIP distorsion coefficients into PV
coefficients (in the context of astronomical images). However, the
availability of `sympy' in the template will be useful for anyone
interested in this package.
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With this commit, we add `mpmath' Python package into the template. This
package is a prerequisite of `sympy', a package to do symbolic
mathematics.
The motivation of adding this package is because it is a dependency of
`sympy', which is more widely used into the Python science community.
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Until now we were using the official tarball of GNU Bash. However, Bash is
distributed using patches, not a public version controlled history. So to
implement newer features of Bash, its necessary to apply those patches and
make the tarball ourselves.
With this commit, we have done just that: we used the 7 patches that have
been released since version 5.0.0 and made a tarball to use for this
template. The instructions on how to make the patched tarball are also
given above the Bash build rule.
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Until now, `metastore' did not depend on the necessaries programs that
we use to install it (`awk', `coreutils' and `sed'). They are not
official dependencies of `metastore', but we need them to install it.
With this commit, we put these programs as prerequisites of `metastore'
in order to be able to install it without any problem.
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Until now, to specify which high-level software you want the project to
contain, it was necessary to go into the `high-level.mk' Makefile that is
complicated and can create bugs.
With this commit, a new `reproduce/software/config/installation/TARGETS.mk'
file has been created that is easily/cleanly in charge of documenting the
final high-level software that must be built for the project.
Also, until now, FFTW was set as a dependency of Numpy while we couldn't
actually get Numpy to use it! It was just there for future reference and to
justify its build rule. But now that many software won't be built and there
is no problem with having rules even though a project might not use them,
it has been removed.
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Git and Metastore are very basic and fundamental tools for the template, so
to keep things clean (let the `high-level.mk' software only represent
optional software in the template), these two software (and their
dependencies: `cURL' and `Libbsd') will now be built in `basic.mk'.
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Until this commit, ATLAS was a prerequisite of Scamp. The documentation
says that. However, we have been able to install Scamp without having
ATLAS installed. As a consecuence, ATLAS does not have to be a
prerequisite of Scamp anymore.
With this commit, we remove ATLAS as prerequisite of Scamp. We also put
available software in the template as optional because not all people
are going to use these software.
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With this commit, we add SCAMP into the project. This program is part of
the Astromatic software and the main purpose is to make the fine
astrometry and the distorsion correction astronomical images.
In principle, SCAMP needs ATLAS library to be able to work (that is what
the documentation says). However, we had some problems with ATLAS
libraries on Mac OS system, and due to that, we set the option
`--enable-openblas' in the configure step. By doing that, we are be able
to install SCAMP with no problems.
One dependency of SCAMP is `cdsclient', it has been also added with this
commit. The `cdsclient' package is a set of C and shell routines which can
be built on Unix stations or PCs running Linux, which once compiled
allow to query some databases located at CDS or on mirrors over the
network.
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With this commit, we add SExtractor to be installed into the project. It
is a widely used program to detect object and build catalogues from
astronomical images.
We had some problems when installing it because it could not link with
some ATLAS libraries. But, since we have OpenBLAS installed, we can use
it to override the problem with ATLAS.
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Until now, there were erros in the citation of Astrometry-net and Scamp
papers.
With this commit, we fix these problems. The Swarp bibtex has also been
modify to follow the stetic of the citation style we have right now in
the project.
We also added the `dependency-bib.tex' as a prerequisite of `paper.bbl'.
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SWarp resamples and co-adds together FITS images using any arbitrary
astrometric projection defined in the WCS standard. It is a very useful
program for astronomy and that is why we added it to the pipeline.
With this commit, we also cite the paper for Astrometry-net that until
now was missing.
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Until this commit, we didn't install Binutils. However, we need `strip'
for installing Netpbm, and `strip' is part of the Binutil software.
With this commit, we include Binutils as a dependency of GCC for
GNU/Linux systems. For Mac OS systems we create a symbolic link to
`strip' just after the generation of the symbolic link to `gcc'.
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Due to the copy/paste of rules from other files, in some rules there
were some spaces insteand of tab. There were also a lack of semicolon in
the building of CC, and bad extensions in various tarballs.
With this commit, all of these typos have been fixed.
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With this commit, we include Astrometry-net software and one remaining
dependency of it (Swig). In principle it should work as far as we tested
all of this software in GNU/Linux, but we need to test also in Mac OS.
As a result, this commit is just for setting all the rules and
dependencies, but more tests are necessaries to ensure it works
properly, specially in Mac OS systems.
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With this commit, the installation of `netpbm' has been included. This
software has a crazy dialogue installation that we override by giving to
it the answers (they differs on GNU/Linux and Mac OS systems). `libxml2'
also has been built (a remaining dependency of `netpbm').
In this commit, `libpng' version has been downgraded because it is
required by `netpbm'.
The motivation of installing `netpbm' is that it is a dependency of
Astrometry-net software.
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Until now, we did not have CC. This is an obsolete way of calling C
Compiler, nowadays it is GCC. However, there could be some software
that is still using this convention (for example, `netpbm').
With this commit, we make the symbolic link `cc' pointing to the
installed `gcc'.
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In this commit we add Cairo library. The motivation of including this
library is because it is a dependency of Astrometry-net (which is a
common software used in astronomy projects). In principle it will not
be build by default by de pipeline, but we will keep the rule just in
case it is needed.
Pixman is another library which is a prerequisite of Cairo, it is also
built with this commit.
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Until this commit, we were using `python3' when calling Python (because
we were using Python version 3.6.8). This will force us to change the
name in the future. For example, when `python4' were available and into
the pipeline.
With this commit, at the end of the Python installation it creates a
symbolic link to the Python bin executable with the new name `python'.
As a consecuence, whatever version of Python was installed, into the
project we will use allways `python' to invoke it.
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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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