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Some problems with using the number of threads in dependency building were
fixed.
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The version of Git was updated to the most recent version (2.20.0).
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Some host Make systems may not allow automatic passing of the number of
threads to sub-Makes. So while building the basic dependencies, we'll need
to explicity add the `-j' option to the Make files that can benefit most
from it: those that are dependencies of many others (Tar & Make), or are
the last to build (Coreutils).
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Gnuastro's BuildProgram is a little special: it is actually built during
the building of Gnuastro to keep important include and lib directory
information and if someone wants to use BuildProgram, this information is
necessary. So a special configuration is added for it in
`reproduce/config/gnuastro'. This configuration file will allow users to
set their own special configuration if they like, then it will load the
installed BuildProgram configuration file.
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On Mac OS systems, CFITSIO doesn't use path to find the `curl-config'
program (used by to give the library header and linking options), but uses
an absolute path. Therefore the only way we can ask CFITSIO to look into
our build of cURL is to manually change that absolute address.
Also, since all the libraries are now linked dynamically, we don't need the
extra linking flags when building WCSLIB (so it finds CFITSIO).
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Mac OS's `install_name_tool' program's command is broken up into two lines,
but I had forgotten to add a line-break so the command would fail. I didn't
notice it myself because this error only shows up on Mac OS systems that
actually need to parse it.
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The build systems of Libgit2 and WCSLIB on Mac OS does not account for
installation in non-standard addresses: `Libgit2' keeps the absolute
address of its build directory (not the installation directory) and WCSLIB
doesn't write any absolute address at all (so the system uses the first one
it finds).
To address these issues, we are now using Mac OS's `install_name_tool'
program to fix the absolute path within the installed shared library.
Since the version of the library is actually present in its shared library
name, in `dependency-versions.mk' we have also separated these two
libraries so later when their version is changed, we are careful in
correcting the shared library name also.
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`ln' will complain about a link already existing. So to avoid having to
rely on the `-f' option (which may not be portable across systems), when we
are making symbolic links to the OS tools that we won't be building, we now
remove the file if it exists, then make a new symbolic link.
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Until now the low-level links that we put in our internal installation from
the operating system were a prerequisite of essentially all the basic
dependencies. So a change in them would mean a full re-build of all the
basic dependencies. But in building the basic dependencies, we already have
the operating system's PATH and other environment variables. So unlike the
higher-level dependencies, they don't need these links at all!
With this commit, the `low-level-links' file is placed in `installed/bin'
and is a top-level target of the basic dependencies build. In this way, if
it is necessary to update/change to use something from the host operating
system, we can simply delete it and run `./configure' again wihout having
to re-build all the basic dependencies.
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On Mac OS systems, the `sw_vers' executable prints information about the
operating system. It is used by TeX Live to determine the necessary builds
to download and install. We are thus importing it as a low-level tool in
`dependency-basics.mk'.
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Until now, we were checking the existance of the `configure' file and if it
wasn't present, we would check for `config' (for OpenSSL which also has a
lower-level "Configure" script that is called by the `config' script). But
after two tests on Mac machines by Raul Infante Sainz and Cristina Martínez
Lombilla, we found out that Mac Os's file names aren't case sensitive and
thus the build wouldn't use `config', but `Configure'.
Now, the exact configuration script can be specified as the 7th argument to
the `gbuild' script. If it isn't given, the standard `configure' name will
be used, but when it is, the given name will be used.
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OpenSSL can't automatically detect the architecture of Mac OS systems, so
as it suggests on its Wiki, it needs some help for doing that. With this
commit, we are checking the build on Mac OS with the presence of `otool'
(Mac OS's linker). If it's there, we'll add the OpenSSL configuration
options suggested by OpenSSL's Wiki.
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Until now, we weren't including the `rpath' linking options to the basic
dependencies. They are now added. Also, when the download of an input file
fails for any reason, an empty file won't be replaced there any more.
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In the previous commit, I forgot to actually add some changes to the
staging area before committing an pushing. So some of the changes discussed
in the previous commit and now commited.
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Make builds the dependencies of each package based on the order in the
prerequisites list. So when building in parallel, it can greatly help the
over-all build speed if larger packages are built first. Therefore the
three larger Gnuastro dependencies are now placed at earlier places of the
prerequisites.
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We were missing a `\' at the end of the `$(call' function of Coreutils to
connect the two lines. It has been fixed now.
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To enable easy downloading of HTTPS links with Wget (this pipeline's defaut
downloader), we need a set of trusted CA certificates. Until the time that
we can generate one ourselves, one generic set of trusted CA certificates
is now downloaded like a tarball and placed in the OpenSSL configuration
directory.
With these CA certificates, within the pipeline we can now safely use the
pipeline's own installed Wget.
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Some high-level programs like Wget and cURL need to be built in shared mode
because they also include dynamic loading of libraries. Therefore, if we
only build the lower-level libraries in static mode, our own build will be
ignored and they will go and find the system's shared libraries to link
with. Because of this, for now, we have manually set the `static_build'
variable in the configure script to `no'.
Also, if the downloader fails, we'll delete the output (an empty file in
the case of Wget) because it interefers with a target definition.
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The TeX Live installer needs Wget to operate smoothly, especially on recent
Mac OS systems that don't have Wget pre-installed. Also, it would be good
for the pipeline to have its own downloader. So with this commit, the
pipeline also installs Wget and OpenSSL which is a dependency.
Many other small changes/fixes were done in this process.
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Thanks to the check by Cristina Martínez, some corrections were made when
we attempt to download and install TeXLive. Further checks and corrections
will be in due time.
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Until now, we were downloading TeX Live's tarball within the same rule that
unpacked it. But this causes problems for situations were it cannot be
downloaded within the pipeline (and manually placed in the tarball
directory). So now, the TeX Live downloader is treated like all the other
downloaders.
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The main reason I wasn't using cURL as a downloading tool was that I wasn't
familar with how to ask it to follow a re-direct. But I just found out that
its with the `-L' configure time option. So it is now added as a downloader
tool to the pipeline.
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On the Libgit2 webpage, it has recommended to build it statically on Mac
systems. By default we are doing this on Linux systems, but the `-static'
flag failed on Mac. But apparently CMake might be able to deal with the
issue in a different way.
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While testing on another computer, I noticed that to operate properly, the
file given to `flock' must be created before it is called. This is a
low-level difference (how the system treats files), so it wasn't apparent
on my system. To fix it, we have added a `touch' command before it.
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There was an extra `$(lockdir)' target in `download.mk'. This has been
corrected.
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Thanks to a test build on Raul Infante Sainz's Mac OS computer, we were
able to address some issues and will be trying them after this commit:
a) The LLVM linker on that computer didn't recognize `-rpath-link'! So at
configure time we now check for it and only include it when the linker
recognizes it.
b) CMake corrections: 1) `CMAKE_LIBRARY_PATH' is now defined so CMake can
look in our custom directory to find the necessary libraries. 2) To
build and install the CMake built programs, we now simply use `make'
and `make install'.
c) To avoid particular linking problems with WCSLIB (which has special
problems compared to other libraries), we are now deleting the shared
library version (both on GNU and Mac systems).
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GNU Binutils (which provides the GNU Linker) is not ported to Mac OS
systems. GCC also takes a very long time to build, and if we are to still
have linking problems with LLVM's linker, it would be better to just ignore
GCC also and use the system's C compiler and linker together.
So for the time being, GCC isn't a main target of the basic dependencies
and won't be installed. But we have kept the rules that were checked on a
GNU/Linux operating system.
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Previously the SHELL environment variable was only set in `./configure',
`make', and `make install' after our internal Bash was installed. This
caused problems with Lzip's configure script on older shells (tested on a
Mac OS by Raul Infante Sainz).
So now, before having our own Bash, we set it to a possibly existing Bash
on the system and if that isn't present, just the standard `/bin/sh'.
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The pipeline now installs GCC and all its necessary prerequisites.
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The linker of LLVM version 10.0.0 (clang-1000.11.45.5) doesn't recognize
the `-rpath' linker option! After some searching, apparently it does
recognize `-rpath-link' so we are testing with that now.
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Until now we weren't explicity writing the full path of the dynamic
libraries necessary for linking a program. But now with
`-Wl,-rpath=$(ildir)' we ensure that the linker keeps the address of the
dynamic libraries necessary for linking at linking time, not running
time. Also, `pkg-config' is also built when preparing the basics. Several
other minor corrections were made thanks to the great help of Raúl Infante
Sainz.
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We had forgot to add the rule to build the lock file directory for
downloading data. This has been corrected.
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The high-level dependencies are now built without having access to the
system's PATH. To do this, all the necessary software that we aren't
building ourselves are now brought into the installed `bin/' directory
using a symbolic link to the corresponding software on the host. To do
this, it was also necessary to increase the number of basic/low-level
packages that we are building, and add several more (Diffutils and
Findutils).
With this process in place, we now have a list of the exact software
packages that we are not building our selves, enabling easy building of all
such dependencies in the future.
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While working on a research project using this pipeline, I noticed that we
don't have any `sh' executable within our PATH. However, some programs
(including Gnuastro's configure script, when it is checking for shells to
use with Libtool) check and use it. So after building Bash, we also build
an `sh' symbolic link to point to the built Bash executable.
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To avoid redundant steps in the the top-level Makefile and make it simpler
and easier to follow, we now define the base names of all the Makefiles in
the `makesrc' variable of the top-level Makefile. `makesrc' is then used to
define the Makefiles to include and the necessary TeX macros at the same
time. This is much more clear and obvious than the previous case were we
had to list the Makefiles and TeX macro files separately in the top level
Makefile.
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Until now, we were keeping the input file within the reproduction
pipeline's directories using the same name as the database/server. Now, we
are using a short/summarized filename convention for the input dataset.
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In most analysis situations (except for simulations), an input dataset is
necessary, but that part of the pipeline was just left out and a general
`SURVEY' variable was set and never used. So with this commit, we actually
use a sample FITS file from the FITS standard webpage, show it (as well as
its histogram) and do some basic calculations on it.
This preparation of the input datasets is done in a generic way to enable
easy addition of more datasets if necessary.
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A new version of the ghostscript package is now available, so the used
version in the pipeline (previously 9.25) has been incremented to 9.26.
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When you point to this project, the `README.md' file is the default file
that opens on GitLab and other online git repositories. Since a
reproduction pipeline project is different from the actual pipeline, its
best for the default text that opens to describe the paper, not the
pipeline. The old `README.md' is also kept, but its now called
`REAME-pipeline.md'.
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When there is a problem in creating the final TeX Live installation, the
previous version of the pipeline would not understand and just finish! We
would later have problems in building the paper.
So the following series of steps were taken: to keep the recipes in a
shorter and easier to understand way, the steps to install TeX Live are now
one rule (that produce `.local/bin/texlive-ready-tlmgr' when its
successful), and the steps to install the necessary packages are in another
rule (that produce `.local/bin/texlive-ready' when its successful).
When control comes back inside configure, if `.local/bin/texlive-ready'
isn't there (something failed during the TeX Live installation, or building
packages), then the whole TeX Live installation directory
(`.local/texlive') will be deleted along with the two output files. This
will help ensure that future steps can check the availablility of a working
TeX Live in the pipeline.
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The system's libraries are no longer used in building the higher-level
dependencies. Also, thanks to Raul Infante Sainz, we found out that Bash's
build script was still removing the extra directory information (not
good!).
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GNU Coreutils are basic programs that can help in the configuration of
higher-level programs. Because of that, it was a dependency of almost all
software built in `dependencies.mk'. To make things more clear, easier to
read and faster (when building in parallel), the building of Coreutils is
now moved to the `dependencies-basic.mk' rules. There, it is built
along-side Bash. Since `dependenceis-basic.mk' is run and completed before
`dependencies.mk', with this, we can be sure that Coreutils is present by
the time we want to build the higher-level programs.
Also, Zlib is now added as a dependency of Git also (it is necessary for
its build).
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Until now, we were building Libtool as a high-level `top-level-programs'
software. But all tools that use the `./configure' script already have a
version of Libtool in them. So ultimately the `libtool' in the PATH is not
used. However, in the case of Gnuastro, we need libtool for running
BulidProgram. So in effect, its a dependency of Gnuastro.
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When the C compiler is not GNU GCC, linking with GNU Binutils is going to
cause problems. So until the time that we can include GCC into this
pipeline, its best to avoid Binutils also.
Also, for building CMake, we were relying on an installed CMake, but now,
we are using its own `./bootstrap' script, so it can be built even if the
host system doesn't have CMake.
Also, for TeX Live, we are now setting a custom file as main target to
avoid complications with symbolic links as targets in Make.
Finally, when the user says they don't want to re-write an existing
configuration file, no extra notices will be printed and the configure
script will immediately start building programs.
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After going through the checklist for starting a new project based on the
pipeline, I noticed some parts that could be modified to be more
clear. They are now applied.
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Until now, we were using a customized `tar.lz' tarball for Gzip. But on
systems that don't have GNU Tar, this will cause a problem (non-GNU Tar
doesn't recognize `.tar.lz'). So to keep things simple, we are using the
customized gzip in `tar.gz' format. After the internal build of GNU Tar and
Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work
nicely on all the standard compression algorithms and we don't have to
modify our commands based on the algorithm (nice feature of GNU Tar).
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The two README files have been updated to explain the new feature of
downloading and building dependencies.
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Since the final product of the pipeline is a LaTeX-created PDF file, it was
necessary to also have LaTeX within the pipeline. With this commit, TeX
Live is also built as part of the configuration and all the necessary
packages to build the PDF are also installed and mentioned in the paper
along with their versions.
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TeX Live is now also downloaded and built by the reproduction
pipeline. Currently on the basic (TeX and LaTeX) source is built but no
extra packages, so the PDF building will fail. We'll add them in the next
commit.
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If the Makefile `$(static_build)' variable in
'/reproduce/src/make/dependencies-build-rules.mk' isn't defined (by
mistake), it will default to blank space, then the Shell will complain
about a bad formatted operator (needing two operands). So an `x' was added
before it and before `yes' which will allow us to safely pass such cases
without a terrible crash.
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