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Until now, TeXlive would only attempt to download/update LaTeX packages,
but after some time, it will be necessary for it to update itself. When
this happens, it complains about running it with `update --self'.
To fix this problem, before installing/updating the LaTeX packages, we will
first update tlmgr in any case.
Also, we weren't removing the TeXlive package version file before appending
the values to it. So it was just repeating the packages every time it was
updated. With this commit, it is being removed on every new build.
Finally, the version of Git was updated to its most recent version.
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Until this commit, 'imfit' was installed using proper flags in order to
use our own libraries. However, it looks first of all to the default
system. As a consecuence, `imfit' program was linked to the host system
libraries, even when we told to use our own libraries!!
With this commit, the installation of `imfit' has been modified in order
to remove the default paths already set in the `SConstruct' script. By
doing this, only our paths are take into account for compiling the
program. It has been tested on Mac OS laptop and it works fine. Test on
GNU/Linux systems remain before merge into the main project branch.
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Until this commit, `fftw' was building single precission float library
because `scamp' had problem on using the default double precission
library. However,`imfit' and maybe other programs will use double
precission float libraries.
With this commit, `fftw' installation is done twice in order to build
single and double precission float libraries. It does not complain and
goes up to the end without crashing. However, more tests are needed in
order to ensure that there is not problem on having both libraries
because in principle, they share the same header file and that could
cause problems.
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`cfitsio' was recently updated and it cames up with a problem when
trying to build shared libraries (on Mac OS system laptop). This is
because the `configure' script for building `cfitsio' include by default
`rpath'.
With this commit, this issue is fixed by modifying the installation of
`cfitsio'. Using `sed', each ocurrence of `@rpath' in `configure' is
replaced by `$(ildir)'. Once it has been done, the installation of
`cfitsio' goes as normal.
In this commit, the version of the `cfitsio' has been also updated to
the most recent one.
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With this commit, I have corrected a typo in the installation of
`imfit'. In principle it is working on Mac OS system but when I tried to
install it in GNU/Linux system it crashed. It complains about a problem
with the `cfitsio' library:
/pathto/libcfitsio.a: error adding symbols: File format not recognized
As in the last commits done by Mohammad in the project, `cfitsio'
installation has been upgraded and also the installation has been
modified, I am going to try this new version. I will also check if it is
a problem about dynamic/static library.
It also seems that the installation is taking libraries and variables
from the host system, so I will check that everything used is from our
own programs/libraries.
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Until now, CFITSIO had several peculiar features which needed special
attention: 1) Its tarball didn't have a `.' in the version name and would
sometimes have extra `0's. 2) When unpacked it was just `cfitsio'. 3) It
hard coded the directory to search for cURL library. All of these forced us
to do a lot of extra steps for CFITSIO.
So I got in touch with them and fortunately they were very open to
correcting these issues and with version 3.47 all such issues have been
addressed in the tarball. Thanks to these changes, with this commit,
CFITSIO's build rule is now very similar to many other programs.
I also noticed that it has an optional `--with-bz2' feature to enable
unpacking `.fits.bz2' files. So this feature is also added.
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Until this commit, `imfit' paper was not included into the
acknowledgements.
With this commit, a bib tex file for `imfit' has been added. So, now it
is properly cited into the final paper.
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With this commit, `imfit' has been included into the project. As described
in the official webpage (http://www.mpe.mpg.de/~erwin/code/imfit/):
Imfit is a program for fitting astronomical images -- especially images
of galaxies, though it can in principle be used for fitting other
sources.
This program uses the `scons' program to build itself (not the traditional
GNU `configure' and `make' system). I have tested it by using an example
that can be found in the `examples' directory of the decompressed
tarball. It works fine without any error on my Mac OS system.
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With this commit, SCons has been included into the project. As in the
official webpage of this program says:
SCons is an Open Source software construction tool—that is, a
next-generation build tool. Think of SCons as an improved,
cross-platform substitute for the classic Make utility with integrated
functionality similar to autoconf/automake and compiler caches such as
ccache. In short, SCons is an easier, more reliable and faster way to
build software.
The motivation for including this software into the project is because
there are some software that use this system for the installation. In
particular, the necessity of installing it comes from Imfit. This is an
astronomical software that uses this system so that is why it has been
included into the project. In principle it is simple, and I have tested
it on Mac OS sytem without any problem.
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Until this commit, the name of the decompressed tarball directory of
PyYAML Python package was wrong. It has to be `PyYAML-version' instead
of `pyyaml-version'. When I run the installation on Mac OS system it
went up to the end of the installation with no error. However, when I
tried to install it on a GNU/Linux system, it complained about no
finding the `pyyaml-version' directory, which is the expected because
the name was wrong!
With this commit, I have fixed this issue by writting correctly the name
of the decompressed tarball directory.
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With this commit, PyYAML Python package has been added into the project.
It is widely used in the Python community and the goal is to have human
readable configuration files. As in the web page
(https://pypi.org/project/PyYAML/) says:
YAML is a data serialization format designed for human readability and
interaction with scripting languages. PyYAML is a YAML parser and
emitter for Python.
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With this commit, LibYAML library has been added. This library is a
prerequisite of the Python package PyYAML, which is widely used in the
Python community when configuration scripts are needed.
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By default (when you run `make' within CFITSIO), it only builds a static
library. So until now, the template would only install a static version of
this library.
To be more clear about which libraries are used during the linking of
programs that use CFITSIO, it would be helpful to have shared library
versions also. Also, if the system has problems with static libraries (like
macOS systems), then it won't go looking outside the template to link with
them (these paths are hardcoded in the linker, which we don't build on
macOS and just use the system's tools).
With this commit, we are explicity running `make shared' in the CFITSIO
installation to have shared CFITSIO also. I also removed the old `static'
element (which we don't use anymore in any of the programs and have to
remove some time later!).
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With this commit, extra spaces in the definition of two variables in the
`configure' script have been removed. Since they are defined in a
`shell' context (not in `make'), variable assignation is not allow to
have any space at both sides of the `=' character. I detected these
typos when trying to run `./configure' in a particular project.
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Matplotlib can optionally use LaTeX and Ghostscript as dependencies to
render text with LaTeX.
Since we already have their build rules, with this commit, they have been
added as its prerequisites.
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There weren't any conflicts in this merge.
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A title in the checklist was mistakenly using "project" (customized
template) instead of "template".
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With this commit, ImageMagick program has been set as prerequisite of
Matplotlib Python package. Since some submodules of Matplotlib rely on
ImageMagick programs (for example, those to make image animations), and
now we have ImageMagick into the project, it is good to install
ImageMagick when Matplotlib is requested to be installed.
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With this commit, ImageMagick software has been added into the project.
This software is useful to deal and treat images from the command line.
Since it is widely used and a lot of other programs rely on it, it is
worth to have it into the project.
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Until now, the `tex/build' symbolic link was put in the clone/source tree
when the build-directory's `tex' directory was being built. Thanks to
Roberto Baena, we just found a bug because of this behavior: when a second
group member is trying to build the pipeline, since the build directory's
`tex' directory already exists, no `tex/build' will be put in their
clone/source directory. As a result, the PDF building will crash.
To fix this (and keep things organized), the two `tex/build' and `tex/tikz'
links (to the build directory) are now built in the configure step while it
is building all the top-level directories. They are no longer built within
the Makefiles.
Also, a comment was added on top of every directory built during the
configuration phase to be clear.
This fixes bug #56362.
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Until now, the `for-group' script was using the system's `chmod' at the end
of its operation. But when `for-group' reaches this level, we already have
our own custom `chmod'.
With this commit, for a consistent operation, we are now using our custom
`chmod' program for this final step.
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In the previous commits where Metastore's recipe was updated, all the
`TAB's in the recipe were saved as spaces just before the commit (due to a
copying and pasting from the terminal, not the text editor). With this
commit, I am correcting this.
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Until this commit, we were installing `netpbm' without disabling the X
Windows System in GNU/Linux. That is the default option in the configure
step of `netpbm'. However, we are not installing the necessary libraries
(X11) and headers for that. As a consecuence, when testing in a system
where we don't have these libraries/headers (Ubuntu 14.04), it crashes.
With this commit, we disable the X Windows System option in `netpbm' by
giving the answer `none' to one of the last answers to that question in
the configure step.
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Until this commit, we were installing `cairo' without disabling the X
Windows System. That is the default option in the configure step of
`cairo'. However, we are not installing the necessaries libraries (X11)
and headers for that. As a consecuence, when testing in a system where
we don't have these libraries/headers (Ubuntu 14.04), it crashes.
With this commit, we disable the X Windows System option in `cairo'
configure step by setting the option `--with-x=no'.
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In the last imported work about fixing all backslashes, the extension of
`netpbm' tarball was not the correct one. Now we are using `.tar.gz'
instead of `.tgz'.
With this commit, we fix this typo by replacing the `.tgz' by `.tar.gz'
in the rule of `netpbm'.
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Until this commit, `m4' was not a prerequisite of `gmp'. However, during
a test in Ubuntu 14.04 using one single core in the configure step, it
crashed complaining about not having `m4' installed.
With this commit, we set `m4' as a prerequisite of `gmp'.
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In some rules there were some spaces when we should use TAB, and
also the other way around. We were using TAB instead using spaces.
With this commit, we fix that spaces/TAB in the necessary rules.
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Until now, we were missing `numpy' and `six' as prerequisites of `h5py'.
Because we did the configure step with all cores, `numpy' and `six'
allways were built before `h5py' with any crash. However, in a single
thread configure run we noticed that we were missing these two
dependencies.
With this commit, we fix this issue by setting `numpy' and `six' as
prerequisites of `h5py'.
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With this commit, the copyright information of some files have been
modify in order to include the work of Raul Infante-Sainz.
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Until this commit, the prerequisites of `sip_tpv' were `mpmath' and
`sympy'. However, the real prerequisites of `sip_tpv' are `astropy',
`numpy' and `sympy'.
With this commit, we fix this issue, and now `mpmath' is only a
prerequisite of `sympy'.
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Until this commit, we had a problem in the installation of
Astrometry-net in Mac OS systems. During the runing of the Makefile, it
stopped at the reporting stage because it tried to do a couple of steps
that in Mac OS are not possible:
$ cat /proc/cpuinfo
$ free
The reason is that `/proc/cpuinfo' and `free' doesn't exist in Mac OS.
With this commit, we override these two steps. Since they are only for
reporting, they are not mandatory. So, we avoid doing them by using
`sed' before running the Makefile.
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Until this commit, we were using `libpng' version 1.4.22 (out dated).
The reason is that with `libpng` versions > 1.5, there was some
problems with `netpbm'. But we have update `netpbm' version and now
there is no conflict betweem them.
With this commit, we increase the version of `libpng' to have the most
recent one.
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Until now, we installed `netpbm' by setting the default paths to
libraries and headers. That worked fine for GNU/Linux systems, however,
in Mac OS systems we have to explicity say to `netpbm' questions what
are the paths to the libraries and headers. We found this problem
because we tried to run `solve-field' to obtain the astrometry of some
images, and then it goes to use `pnmfile', a program that failed because
it was not properly linked with `libnetpmb'.
With this commit, we fix this problem by answering properly the
questions in the configure step of `netpbm' and setting explicity where
we want to place the libraries and headers. With this commit, we also
update `netpbm' version. To do that, we have to download the last
version, for which it doesn't exist a tarball. So, we built this tarball
and put it in the Mohammad's webpage.
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Until this commit, in Mac OS we were installing `binutils' as symbolic
links of various programs (`as', `ar', `ld', `nm',` ps' and `ranlib').
However, there was a missing semicolon at the end of each line. As a
consecuence, the installation of `binutils' on Mac OS systems failed.
With this commit, we fix this problem by typing a semicolon at the end
of each makelink line.
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Until this commit, FFTW was installed by default, without the single
precission option. However, when installing `sextractor' in a new system
we found an error in the installation complaining about not having
single precission files of FFTW. More explicity the error was: "FFTW
single precision library files not found in [...]".
With this commit, we fix this problem by passing the option
`--enable-single' in the installation of FFTW.
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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, `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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In two places, I had mistakenly put a <'> instead of a <`>, causing bad
highlighting in the markdown rendering. They have been corrected.
Also, one long line in was broken up into several.
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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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Since `.file-metadata' is a binary file, we can't include a copyright
inside of it so we have to use `README.md' to mention its copyright and
license notice. However, this was not done clearly and is now corrected.
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Until now we weren't including the citation for FFTW (one of the template's
optional packages). With this commit, it is added.
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Until now, there was a single `tex/src/references.tex' file that housed the
BibTex entries for everything (software and non-software).
Since we have started to include the BibTeX entry for more software, it
will be hard to manage the large (sometime unused) BibTeX entries of the
software in the middle of the non-software related citations in the text of
the paper.
Therefore, with this commit, a `tex/dependencies' directory has been made
which has a separate BibTeX entry file for each software that needs
one. After the software is built, this file is copied to the new
`.local/version-info/cite' directory. At the end, the configure script will
concatenate all the files in this directory into one file which will later
be used with `tex/src/references.tex' by BibLaTeX.
This greatly simplifies managing of citations. Allowing us to focus on the
software-building and paper-writing citations separately/cleanly (and thus
be more efficient in both).
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Until now, we did not have `file'. It was in other project, where a
problem with `Astrometry-net' software, ends up with the necessity of
having `file' into the pipeline.
With this commit, we add `file' to the project. Since it is a low level
program, it is set in `dependencies-basic.mk' as a prerequisite of GCC.
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Until now, the Scipy citation was only one paper and not the correct one
(it was the online manual).
With this commit, Scipy is properly cited using the two papers. Also
some modifications in the `tex/src/references.tex' have been done
(remove last page number).
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Until now, name and version of all Python packages were indicated in the
final paper, but not the main paper of them (if it exists).
With this commit, some Python packages (Cython, Matplotlib, Numpy and
Scipy) are now properly acknoledged by citating the source paper.
`mpi4py' is also cited although this package is not yet included into
the pipeline.
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