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2019-01-19Some typos corrected in README-pipeline.mdMohammad Akhlaghi-3/+3
In a few cases, I had used a signle quote to close `. This would not display properly on the Gitlab webpage, so they are corrected.
2019-01-18Sanity check to run the Make with proper group permissionsMohammad Akhlaghi-73/+225
If the `./for-group' script is not used properly, it can lead to the whole pipeline being re-run. Therefore it is important to do a sanity check immediately at the start of Make's processing and inform the user if there is a problem. With this commit, `./for-group' exports the `reproducible_paper_for_group' variable which is used by both the initial `./configure' script, and later in each call to Make. The `./configure' script will use it to write a value in `reproduce/config/pipeline/LOCAL.mk' and Make will use it to compare with the value in `reproduce/config/pipeline/LOCAL.mk'. If there is an inconsistency, Make will not even attempt to build anything and will just print a message and abort.
2019-01-17Added Gnuastro in paragraph with all programsMohammad Akhlaghi-14/+15
Until now, Gnuastro was only mentioned in the first acknowledgments section, but not in the paragraph with all the program names. But these two are not mutually exclusive. All the software should be mentioned in the last paragraph and those that need special mention can be mentioned before it.
2019-01-17README-pipeline.md referenced in README.mdMohammad Akhlaghi-1/+3
Until now, there was no reference to `README-pipeline.md' within the `README.md' file. Since `README.md' is the first file that someone reads and the basic perpose and structure of the pipeline is described in `README-pipeline.md', it was necessary to bring it up there.
2019-01-15Many network-related libraries ignored in Wget and cURLMohammad Akhlaghi-10/+45
Wget and cURL depend on many network related libraries by default and if they are present on the host operating system, they will be linked with. This causes problems for the pipeline when these libraries are updated on the host system. With this commit, I went through the configure time options of both Wget and cURL and removed any library that didn't seem related to merely downloading of files (possibly with SSL, because we do build OpenSSL in the pipeline). Also, I noticed a new version of cURL has come, so that is also updated.
2019-01-14Links to the built libncursesw corrected after its buildMohammad Akhlaghi-5/+3
In a previous implementation, we were using a `target' variable to define the final target of several links, but with the new `sov' solution, we just used its base name. However, we had forgot to correct two instances of `target'. This is corrected now. Also, the step to clean all already built outputs of the NCURSES library has been simplified to a platform independent wildcard.
2019-01-14Better linking of different NCURSESW namesMohammad Akhlaghi-45/+50
On Mac OS systems, the full version number is not used in the filename given to libncurses. For example for version 6.1, it is called `libncursesw.6.dylib'. So a more generic and easier to maintain and read script is now used to be able to make links for both Mac and GNU/Linux systems. In short, instead of checking if we are in Mac every time, we just set the suffixes at the start based on the machine once as variables and use those to define the links.
2019-01-14Fixed call to sed in the standard GNU Build systemMohammad Akhlaghi-4/+5
The call to SED in `dependencies-build-rules.mk' had the file name before the options. On some verions of SED, this would cause problems. So the filename is now given after the options.
2019-01-14ConvertType's --colormap option added, necessary from Gnuastro 0.8Mohammad Akhlaghi-1/+1
The new `--colormap' option was added to the call to Gnuastro's ConvertType program. Since Gnuastro 0.8, ConvertType needs this option for converting a single-channel dataset to a color-supporting format.
2019-01-14GNU NCURSES and GNU Readline also built before GNU BashMohammad Akhlaghi-65/+179
Readline is a prerequisite of Bash and AWK, while NCURSES is a prerequisite of Readline. With the recent update of GNU Bash (and thus GNU Readline) on my host operating system, the pipeline crashed and I noticed this hole in the pipeline. In particular, AWK (which linked with Readline 7.0) would complain about not finding it and abort.
2019-01-10Minor typo correction in comment of for-group scriptMohammad Akhlaghi-3/+2
A minor typo was fixed to help in readability.
2019-01-10cURL added as a dependency of GitMohammad Akhlaghi-1/+3
Git needs cURL in its build. Until now, by chance cURL was always built before Git, but while building this pipeline on a system, Git was built before cURL and we found the problem. I also noticed that we hadn't added `Your name <your@email.address>' to the `for-group' script. This has been corrected now.
2019-01-10ccache ignored and disabledMohammad Akhlaghi-3/+16
ccache is a super annoying program in the context of the reproduction pipeline. On systems that use it, the `gcc' and `g++' that are found in PATH are actually calls to `ccache' (so it can manage their call)! Two steps have been taken to ignore and disable ccache (if it isn't ignored properly!): 1) when making symbolic links to compilers, if a directory containing `ccache' is present in the PATH, it is first removed, then we look for the low-level programs that we won't be building. 2) The `CCACHE_DISABLE' environment variable is set to 1 where necessary (with the other environment variables).
2019-01-10Wrapper script to allow groups working in the build directoryMohammad Akhlaghi-0/+87
On large projects, its often necessary to share the build directory between the various users of the pipeline. To simplify the process a `for-group' script is now added to the pipeline which is just a wrapper over the `./configure' and `.local/bin/make' commands to make sure that the group owner of the outputs and the permission flags are set properly.
2019-01-08Updated versions of core GNU programsMohammad Akhlaghi-7/+7
During the last month, several core GNU programs were updated, so their versions in the pipeline have also been updated.
2019-01-08When installing Bash, check if the sh link is already presentMohammad Akhlaghi-2/+7
After installing Bash, we would just blindly try to build the $(ibdir)/sh' symbolic link. But that could fail if it already existed. To make things clean, we now remove any link first before attempting to make a new one.
2019-01-02Copyright year updated to 2019Mohammad Akhlaghi-9/+9
Since the current implementation of this pipeline officially started in 2018, all the files only had 2018 in their copyright years. This has now been corrected to 2018-2019.
2019-01-01--with-pc-path for pkg-config configurationMohammad Akhlaghi-1/+1
By giving this option specifically at the build time of Pkg-config, we'll ensure that any package that uses pkg-config will first look into our locally installed build.
2018-12-31Updated Gzip and Gnuastro versions to standard buildsMohammad Akhlaghi-24/+25
Both Gzip and Gnuastro were being bootstrapped personally from their Git repository until now. But fortunately a new release of both came out last week and so to make things standard we are now using their standard tarballs. I also noticed that we weren't checking the version of Gzip or mentioning it in the acknowledgement section. This was also corrected.
2018-12-27Igoring .texlive* in the top build directoryMohammad Akhlaghi-0/+1
As part of the pipeline, `.texlive2018' may be created. So it is added to `.gitignore'.
2018-12-27Corrected typo in README-pipeline.mdMohammad Akhlaghi-1/+1
A closing double-quotation was missing in the command to read about Automatic variables in Make.
2018-12-19Removed temporary file for testing Bzip2's versionMohammad Akhlaghi-6/+7
Bzip2's verison is found differently from the other programs (because it writes no standard error, not standard output!). So a custom function is written for it which includes creating a temporary file. But we had forgot to delete that file after the version is found.
2018-12-18Forced linking of bin/sh and verbose Make in GitMohammad Akhlaghi-3/+4
While checking the build of the previous commit, a failure happened when linking `reproduce/build/dependencies/installed/bin/sh' with the built Bash (because the symbolic link already existed!). So a `-f' flag was added to `ln' to just change it without complaining. I also noticed that the Git build was also not in verbose mode. So this has also been corrected.
2018-12-18Gzip compiles in verbose mode to be clear and help in debugsMohammad Akhlaghi-1/+1
While we were testing this pipeline on a Mac OS system, we found and reported a problem in Gzip's build (bug #33689). However, since the Gzip build is not verbose, it was necessary to run its `make' with `V=1'. Generally, since almost all the programs are built in verbose mode (where you can see the compilation commands), we have also set this flag in any build to be clear and make it easier to spot bugs in the future.
2018-12-13Added extra note to the input datasets directoryMohammad Akhlaghi-1/+4
To make things clear for a user of the pipeline its mentioned that the given input directory is only read and nothing is written to it.
2018-12-13Minor update in checklist, incremented Gnuastro versionMohammad Akhlaghi-3/+3
A minor correction was made in the checklist (since we only have one `foreach' loop in the top-level Makefile) and also the version of Gnuastro was incremented.
2018-12-13Fixed numthreads in dependencies alsoMohammad Akhlaghi-7/+8
Some problems with using the number of threads in dependency building were fixed.
2018-12-11Updated the version of GitMohammad Akhlaghi-1/+1
The version of Git was updated to the most recent version (2.20.0).
2018-12-11Passing -j build options to dependency building bottle-necksMohammad Akhlaghi-3/+11
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).
2018-12-11Removed extra line on Gnuastro from checklistMohammad Akhlaghi-1/+0
An extra line regarding the removal of Gnuastro in the checklist was removed (we don't report the Gnuastro version at the start of the paper any more).
2018-12-06Added generic copying/license file to topMohammad Akhlaghi-0/+674
As is common in most projects, a generic "COPYING" file has been added in the top directory to mark the license of the whole project.
2018-12-06Edited README.md to show example dependency repositoryMohammad Akhlaghi-3/+3
To help and be more clear a link to this pipeline's dependency repository has been added to `README.md'.
2018-12-06Gnuastro's special BuildProgram configuration file addedMohammad Akhlaghi-0/+9
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.
2018-12-05CFITSIO configure script looks for our build of cURL on Mac OSMohammad Akhlaghi-3/+20
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).
2018-12-05Updated README.mdMohammad Akhlaghi-15/+15
The README.md file was updated to reflect recent changes in the pipeline (especially regarding the downloader).
2018-12-05Corrected comment on downloader in configure scriptMohammad Akhlaghi-12/+5
The comment above the downloader section of the configure script was not up to date with how the pipeline uses a downloader during configuration and building now. So it was updated.
2018-12-05Configuring on multiple threadsMohammad Akhlaghi-2/+2
Until now we had constrained the configuration step to one thread to easily see failures on other systems. But with most tests passing successfully now, we are using the total number of available threads.
2018-12-05Forgotten line break comment addedMohammad Akhlaghi-6/+4
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.
2018-12-04Shared library absolute address fixed in Libgit2 and WCSLIB on Mac OSMohammad Akhlaghi-26/+67
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.
2018-12-04Removed already built symbolic links to OS toolsMohammad Akhlaghi-0/+2
`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.
2018-12-04Low-level links nolonger a prerequisite of programsMohammad Akhlaghi-11/+8
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.
2018-12-04Link to `sw_vers' for Mac OS systems also createdMohammad Akhlaghi-0/+3
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'.
2018-12-04Configure script for GNU Build system now an input argumentMohammad Akhlaghi-8/+10
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.
2018-12-03Checking Mac OS host for configuring OpenSSLMohammad Akhlaghi-3/+32
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.
2018-12-03Added rpath in basic dependencies, remove input if download failsMohammad Akhlaghi-4/+9
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.
2018-12-03Gnuastro's dependencies fully sorted by build timeMohammad Akhlaghi-4/+9
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.
2018-12-03Gnuastro's dependencies sorted by length of buildMohammad Akhlaghi-1/+1
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.
2018-12-03Minor typo correction in building CoreutilsMohammad Akhlaghi-1/+1
We were missing a `\' at the end of the `$(call' function of Coreutils to connect the two lines. It has been fixed now.
2018-12-03Trusted CA certificates also downloaded for Wget usageMohammad Akhlaghi-11/+22
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.
2018-12-03Preference for shared library linkingMohammad Akhlaghi-87/+132
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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