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Until now, I was writing the paper without the template. But we will soon
be adding a tutorial to the template, and I thought it will be good to have
an example demonstration here too. So I just brought the hole project into
the template structure, allowing us to add the template analysis later when
its ready, and also allowing us to easily reproduce this paper ofcourse
(without having to worry about the host's TeXLive installation.
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The unnecessary parts were removed and the project now runs.
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Newer versions of Astropy package has been released. With this commit,
it has been updated. It has been increased from v3.2.1 to v4.0
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Now that its 2020, its necessary to include this year in the copyright
statements.
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With this commit, we now have the core R interpretter within the
template. We should later include instructions to install R packages
(possibly in a separate top-level Makefile like Python).
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Recent builds of the template need these three packages to build the PDF.
This was reported by Hamed Altafi.
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Until now we weren't including this package, but Alberto Madrigal recently
reported that his build of the template failed because it needed it.
With this commit, it is now being installed with the template.
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Newer versions of these packages have recently come out with major
improvements, so they have been updated in the template.
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These two packages are necessary to build the GNU C Library.
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Perl is necessary to build Texinfo and later to build LaTeX. Until now we
were just using the host operating system's installation of Perl, but in
some instances that Perl can be too old and not suppor the features
necessary. With this commit, Perl is now built from source during the basic
installation step of the template.
This was reported by Idafen Santana Pérez, after trying the pipeline on an
Amazon AWS EC2 system (a Linux distro by Amazon for its cloud services).
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When building the log4cxx tarball from its Git history, I noticed that
files with very long names are not packaged by tar (because by default
Automake uses the ancient v7 tar format that only supports file names less
than 99 characters).
So I build the tarball with the `tar-ustar' option to Automake (by
modifying the log4cxx source) and the resulting tarball was able to compile
and run successfully. This has been described above the rule to build
log4cxx and I also sent an email to their developing mailing list to inform
them of this problem. If they address it, I will remove the note on the
necessary corrections.
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Some minor corrections were made in the template:
- When making the distribution, `.swp' files (created by Vim) are also
removed.
- Autoconf is set as a prerequisite of Automake
I was also trying to add the Apache log4cxx, but its default 0.10.0 tarball
needs some patches, so I have just left it half done until someone actually
needs it and we apply the patch.
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Until now, the tarballs were the first normal prerequisite of the
software. As a result if their date changed, the whole software would be
re-built. However, for tarballs specifically, we actually check their
contents with a checksum, so their date is irrelevant (if its newer than
the built program, but has the same checksum, there is no need to re-build
the software).
Also, calling the tarball name as an argument to the building process (for
example `gbuild') was redundant. It is now automatically found from the
list of order-only prerequisites within `gbuild' and `cbuild' (similar to
how it was previously found in the `pybuild' for Python building).
A `README.md' file has also been placed in `reproduce/software/make' to
help describe the shared properties of the software building
Makefiles. This will hopefully grow much larger in the future.
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Python's `lmfit' module and all its major dependencies (`asteval',
`corner', `emcee' and `uncertainties') have been included in the template.
While doing this I noticed that if the tarballs are the last prerequisite
of each software building rule, then when building in parallel, the
template will immediately start building packages as soon as the first one
is downloaded. Not like the current way that it will attempt to download
several, then start building. For now, this has been implemented in the
Python build rules for all the modules and we'll later do the same for the
other programs and libraries. This also motivated a simplification of the
`pybuild' function: it now internally looks into the prerequisites and
selects the tarball from the prerequisite that is in the tarballs
directory.
This isn't a problem for the build, but I just don't understand why Python
can't recognize the version of `emcee', Python reads the version of `emcee'
as `0.0.0'! But it doesn't cause any crash in the build, so for now its
fine.
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The tarball of HEALPix includes multiple languages and doesn't include the
ready-to-run GNU Build System by default, we actually have to build the
`./configure' script for the C/C++ libraries. So it was necessary to also
include GNU Autoconf and GNU Automake as prerequisites of HEALPix.
However, the official GNU Autoconf tarball (dating from 2012) doesn't build
on modern systems, so I just cloned it from its source and bootstrapped it
and built its modern tarball which we are using here.
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The following software are added with this commit: eigency, esutil, flake8,
future, galsim, lsstdesccoord, pybind11 and pyflakes.
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As part of an effort to bring in all the dependencies of the LSST Science
pipeline (which includes the last commit), these software are now available
in the template.
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With this commit these three software packages are now installable with
this template.
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Carlos Morales Socorro reported that his LaTeX build was missing the
`trimspaces' package, so it is now included in the pipeline.
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It was some time since these three software were not updated! With this
commit the template now uses the most recent stable release of these
packages.
Also, the hosting server for ImageMagick was moved to my own webpage
because unfortunately ImageMagick removes its tarballs from its own
version.
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New versions of astropy, bash, cmake, curl, findutils, gawk, gcc,
ghostscript, git, make, gsl had recently come so they are updated with this
commit.
About GNU Findutils and GNU Make: I was bootstrapping (building the tarball
of) these two separately separately because their standard tarball release
had problems on some systems. Both have been updated now so I am no longer
using my own webpage as their main URL.
A special note about GNU Make. I just noticed that during bootstrapping,
GNU Make would use the fixed version string of `4.2.90' for any commit!!!
But fortunately they have officially released their 4.2.90 version, so we
are safely using their own webpage. The only difference is the compression
format. My old bootstrapped build was `tar.lz', but the standard release is
`tar.gz'.
Also, all the basic programs (installed in `.local/bin') in `basic.mk' are
now existance-only dependencies (after a `|'). Because later programs just
use them at a very basic level, so there is no need to rebuild everything
when Bash gets updated for example.
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Until this commit, the name of the variable for `beautifulsoup4'
checksum was wrong, and because of that, it was not able to install it.
With this commit, `beautifulsoup-checksum' has been replaced for
`beautifulsoup4-checksum' in the `reproduce/software/make/python.mk'
Makefile, and the problem has been fixed. This was not noticed
previously because this Python package is only installed when some high
level programs are requested to be installed.
With this commit the version of `imagemagick' program has been also
updated because the previous version is not available in the official
website anymore.
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This was a bug in WCSLIB 6.3 that has been fixed in WCSLIB 6.4. From
WCSLIB's changelog: "The rule change to the Fortran makefile in v6.3 to add
getwcstab_f.o to the sharable library causes it to depend on CFITSIO to
resolve fits_get_wcstab(). Hence backed out of that change.".
The actual error was like this:
Undefined symbols for architecture x86_64:
"_fits_read_wcstab", referenced from:
_ftwcst_ in getwcstab_f.o
"_gFitsFiles", referenced from:
_ftwcst_ in getwcstab_f.o
ld: symbol(s) not found for architecture x86_64
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These three libraries are dependencies of Biber, so we will need them
later, but since we don't build biber from source now, we can't control
what library it links with. With this commit, we have just added their
versions, checksum, download URL and build rule incase they are useful in
other software.
Later, when we build Biber (and Texlive in general) from source, we'll be
able to use these.
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Until now, OpenMPI was being installed without any dependency. This was
fine because it would indeed build. But the moment you tried loading
something that depends on it (for example `mpi4py' through `astropy'), you
would get an error complaining that SSH isn't present.
With this commit, the pipeline now also installs OpenSSH to solve this
problem.
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A new version of Gnuastro was recently released with many improvments and
bug fixes, so it is updated here too.
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Until now, in version 3.0.1, mpi4py couldn't be built with the most recent
version of OpenMPI. However, after trying the next version (3.0.2), I
noticed that it builds successfully without a problem.
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Until now, there was no check on the integrity of the contents of the
downloaded/copied software tarballs, we only relied on the tarball
name. This could be bad for reproducibility and security, for example on
one server the name of a tarball may be the same but with different
content.
With this commit, the SHA512 checksums of all the software are stored in
the newly created `checksums.mk' (similar to how the versions are stored in
the `versions.mk'). The resulting variable is then defined for each
software and after downloading/copying the file we check to see if the new
tarball has the same checksum as the stored value. If it doesn't the script
will crash with an error, informing the user of the problem.
The only limitation now is a bootstrapping problem: if the host system
doesn't already an `sha512sum' executable, we will not do any checksum
verification until we install our `sha512sum' (as part of GNU
Coreutils). All the tarballs downloaded after GNU Coreutils are built will
have their checksums validated. By default almost all GNU/Linux systems
will have a usable `sha512sum' (its part of GNU Coreutils after all for a
long time: from the Coreutils Changelog file atleast since 2013).
This completes task #15347.
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Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.
This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).
With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:
$ ./project configure
$ ./project make
To work on the project with other users in a group these commands can be
used:
$ ./project configure --group=GROUPNAME
$ ./project make --group=GROUPNAME
The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:
$ ./project configure -e --host-cc
$ ./project make -j8
The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.
On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).
This fixes bug #56682.
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Until now, like all other software, PatchELF would install with dynamic
linking. However, PatchELF links with `libstdc++' so on one system, I
noticed that PatchELF gives a segmentation fault and corrupts `libstdc++'
while correcting its RPATH (after installing GCC). The solution is to build
PatchELF statically.
With this commit, we force PatchELF to be built statically (it only
installs on GNU/Linux systems anyway, so there is no problem with static
linking on macOS). This solved the problem on that system.
While looking at its documentation, I also noticed that a new version of
PatchELF has been released after almost three years, so it has been updated
in the template also.
This fixes bug #56673.
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Some bugs have been fixed in the new version of WCSLIB, so it has been
updated in the template.
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More than two releases and bug fixes have been made to libgit2. So we are
now using a more recent version in the template.
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While testing on a system with no Texinfo, we noticed that M4 depends on
Texinfo. To fix this problem, with this commit, it is now included in the
pipeline.
While doing a clean build, a few minor issues were also found and corrected
in the other rules.
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While reviewing Prasenjit's commits, I noticed that we had forgot to add
the citation for TIDES, also to make things clear, the program/library
build rules are now sorted alphabetically.
Finally, I noticed that after building the TiKZ PDF figures, it is crashing
(like on Prasenjit's computer). After looking around, I noticed its because
we were setting the of the `TEXINPUTS' environment variable to be the
installed TeX Live directory (which was ultimately redundant because by
default TeX will look into where it was installed). The important thing is
just that we remove any possible value the host system has, not to set new
directories.
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TIDES is an ODE integrator with multiple-precision arithmetic.
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Several corrections were necessary in the basic build: 1) the
version of GCC on some systems includes an `_' which would cause
a crash when building the PDF. 2) libcharset had to be manually
added to the Git build.
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Prasenjit Saha reported that while building on a macOS, Git complained
about not finding `libiconv' functions. Therefore with this commit,
`libiconv' is also built as a dependency of Git.
Also, since the build of Binutils (and the subsequent GCC) doesn't depend
on the exact versions of the other basic software, they are set as
existance-only prerequsites (ignoring their timestamps). This is done to
avoid re-building when it is not needed.
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The recent work by Raul to import Imfit is now merged into the master
branch. Only a few minor conflicts came up due to the update with CFITSIO
(that Raul also done in parallel on this branch).
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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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`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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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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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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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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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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In the warnings output by LaTeX during the building of a project, I noticed
that `csquotes' is recommended for some features of BibLaTeX (a warning was
printed) so it is added with this commit.
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Until now the software names and versions in
`reproduce/software/config/installation/versions.mk' were placed such that
all the versions were placed under each other. This had a visual effect,
but since many of the software have shorter names, it could sometimes cause
visual confusion on which number belongs to which software.
Since we recently removed a similar situation with the backslashes, with
this commit, there is only a single space between the variable name, `='
and the version number.
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GCC 9.1 was just released and includes many new optimization features that
can benefit projects in this template also.
Also, the build directory of GCC has been moved inside the unpacked
directory (similar to all the other programs). As a result, while GCC is
being built, the `.build/software/build-tmp' directory will only have one
directory for GCC. Until now, there was one `gcc-build' directory and one
unpacked tarball.
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