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2019-02-20Installed astroquery in the pipelineRaul Infante-Sainz-50/+297
All dependencies for building astroquery package have been done. Until nowthe Python dependencies were built in the same Makefile as the high level libraries and programs. But, because astroquery has many dependencies we split the Python and Python packages installation in a new Makefile. The installation of differents packages are done using Python and not pip, because we found some problems when doing it with pip. Apparently there are some interferences between the packages installed by the pip of the system and the pip installed as part of Python in the pipeline.
2019-02-13Imported recent work on building Python within the pipelineMohammad Akhlaghi-22/+72
Raul Infante-Sainz added the building of Python (along with the Numpy and Astropy packages) into the pipeline. That work is now being merged into the main pipeline branch. There was only this small problem that needed to be fixed: the Python tarball's name after unpacking is actually `Python-X.X.X' (with a captial P), not `python-X.X.X'. This has been corrected with this merge.
2019-02-13Minor cosmetic corrections in software tarball downloading ruleMohammad Akhlaghi-3/+3
The zip program wasn't placed correctly (in alphabetical order) and its URL command had the wrong indentation! Both have no effect at all on the processing and are only cosmetic (to help in readability).
2019-02-13Astropy installed in the pipelineRaul Infante-Sainz-31/+58
Astropy was added and one very important thing is that we have to use the pypi tarball (https://pypi.org/) (which is bootstrapped) and not the github tarball.
2019-02-07Numpy is now in the pipelineRaul Infante-Sainz-3/+20
Python needs some packages to be really useful. Numpy is the most important package for using Python and a lot of other packages depend on it. In this commit we add numpy to the pipeline. The tarball of numpy right now is fossies.
2019-02-07Python is now in the pipelineRaul Infante-Sainz-1/+8
Many projects use Python so it is necessary include it in the pipeline.
2019-02-06Minor correction in description of downloading wrapperMohammad Akhlaghi-3/+3
In the example running code of the wrapper script, I had just written `./download-multi-try', but this script is meant to be run from the top of the project directory. This could cause confusion. So the example script now starts with `/path/to/download-multi-try'.
2019-02-06Removed .sh suffix in download wrapper scriptMohammad Akhlaghi-2/+4
We don't have a `.sh' suffix in the other scripts of `reproduce/src/bash', so it was also removed from this script.
2019-02-06Wrapper script for multiple attempts at downloading inputsMohammad Akhlaghi-2/+110
Until now, downloading was treated similar to any other operation in the Makefile: if it crashes, the pipeline would crash. But network errors aren't like processing errors: attempting to download a second time will probably not crash (network relays are very complex and not reproducible and packages get lost all the time)! This is usually not felt in downloading one or two files, but when downloading many thousands of files, it will happen every once and a while and its a real waste of time until you check to just press enter again! With this commit we have the `reproduce/src/bash/download-multi-try.sh' script in the pipeline which will repeat the downoad several times (with incrasing time intervals) before crashing and thus fix the problem.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-44/+79
In order to collaborate effectively in the project, even project members that don't necessarily want (or have the capacity) to do the whole analysis must be able to contribute to the project. Until now, the users of the distributed tarball could only modify the text and not the figures (built with PGFPlots) of the paper. With this commit, the management of TeX source files in the pipeline was slightly modified to allow this as cleanly as I could think of now! In short, the hand-written TeX files are now kept in `tex/src' and for the pipeline's generated TeX files (in particular the old `tex/pipeline.tex'), we now have a `tex/pipeline' symbolic-link/directory that points to the `tex' directory under the build directory. When packaging the project, `tex/pipeline' will be a full directory with a copy of all the necessary files. Therefore as far as LaTeX is concerned, having a build-directory is no longer relevant. Many other small changes were made to do this job cleanly which will just make this commit message too long! Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as in the standard GNU Build system).
2019-02-05Ability to package project into tarball or zip fileMohammad Akhlaghi-20/+121
With this commit, it is now possible to package the project into a tarball or zip file, ready to be distributed to collaborators who only want to modify the final paper (and not do the analysis technicalities), or for uploading to sites like arXiv, or online LaTeX sharing pages.
2019-02-01Group name is now part of the local configurationMohammad Akhlaghi-18/+23
Until now, the group name to build the project actually went into the Git source of the project! This doesn't allow exact reproducibility on different machines (where the group name may be different). With this commit, the `for-group' script has been modified to accept the group name as its first argument and pass that onto `configure' and Make. This is much better now, because not only the existance of a group installation is checked, but also the name of the group. It also made things simpler (in particular in `LOCAL.mk.in').
2019-01-24Updated fork of metastore allows building on macOSMohammad Akhlaghi-3/+19
I recently found another fork of metastore that allows its build on macOS systems (https://github.com/mpctx/metastore). So I forked it into my own fork with several other corrections (mostly cosmetic!), so it is now much better suited for this pipeline. Raul Infante-Sainz has already tested the building of metastore on his macOS. In a previous test, we also noticed that libbsd should not be built on Mac systems, so it is now a conditional prerequisite to metastore.
2019-01-23Removing files ending with a ~ in the git checkout hookMohammad Akhlaghi-3/+18
While editing files, some editors create temporary `~' files that can cause problems in metastore's ability to delete their host directory if its not on the other branch. With this commit, a `find' call was added to the post checkout Git hook to remove such temporary files before metastore is called. Also, some comments were added to both git hooks to make them easier to understand for a beginner.
2019-01-23Corrections in metastore's git hooksMohammad Akhlaghi-3/+3
Two corrections were made in the Git hooks of Metastore. 1) The shebang at the start of the scripts now uses the absolute adress of our installed bash, not the relative `.local/bin/bash'. Note that it is possible to use Git within subdirectories and in that scenario, the `.local' will fail. 2) The `$$user' section was removed from the command to find the user's group. With the user as an argument, `groups' may print the user's name first, then their list of groups. When this happens, the script would be just repeating the user's name. But the raw `groups' command will list the groups of the running user.
2019-01-23Corrected check for patchelf when building BashMohammad Akhlaghi-6/+9
Until now, the check to see if the patchelf program should be used or not (for GNU/Linux vs. Mac installations) was mistakenly added over the step that we define the `sh' symbolic link, not over the call to patchelf. This is corrected with this commit.
2019-01-22Updated to newly modified version of metastoreMohammad Akhlaghi-7/+2
In this version, too many extra notices (just regarding a change from branch to branch) are not printed with `-q'. Instead only a one line statement is printed that it is saved or applied.
2019-01-22Not checking metastore's version temporarilyMohammad Akhlaghi-2/+7
Until we see what happens with the pull request of our suggested features in metastore, its version isn't written directly into the executable, so we won't actually check it, but write the version directly into the paper.
2019-01-22Using fork of metastore to work when getpwuid isn't usableMohammad Akhlaghi-16/+36
After testing the built of Metastore on a server, I noticed that because its `/etc/passwd' doesn't have the list of users, the `getpwuid' call within metastore failed and wouldn't let it finish. So I looked into the code and was able to implement a solution to this problem by adding two options to it for default values for the user and group. Also, file attributes are not necessary in our (current) use case of metastore and caused crashes on our server, so they are also disabled.
2019-01-21Libbsd added as a dependency of MetastoreMohammad Akhlaghi-2/+18
Metastore depends on `bsd/string.h' to work properly (atleast on GNU/Linux systems). The first system I tried building with had that library, so I didn't notice! With this commit, we also build `libbsd' as part of the pipeline. Also, I couldn't find libbsd's version in any of its installed headers, so like Libjpeg, we can't actually check and will directly write our internal version into the paper.
2019-01-21Metastore package now installed to allow keeping file meta-dataMohammad Akhlaghi-19/+130
The pipeline heavily depends on file meta data (and in particular the modification dates), for example the configuration-Makefiles within the pipeline are set as prerequisites to the rules of the pipeline. However, when Git checks out a branch, it doesn't preserve the meta-data of the files unique to that branch (for example program source files or configuration-Makefiles). As a result, the rules that depend on them will be re-done. This is especially troublesome in the scenario of this reproducible paper project because we commonly need to switch between branches (for example to import recent work in the pipeline into the projects). After some searching, I think the Metastore program is the best solution. Metastore is now built as part of the pipeline and through two Git hooks, it is called by Git to store the original meta-data of files into a binary file that is version controlled (and managed by Metastore).
2019-01-21Separate LaTeX build directory for each user in group scenarioMohammad Akhlaghi-7/+43
When building in group mode, users can manage them selves to work on independent analysis steps and thus not cause conflicts. However, until now, there was no way to avoid conflicts in building the final paper. To fix this problem, when we are in group mode, the pipeline will create a separate LaTeX build director for each user and also a separate PDF file for each user. This will ensure that their compilations don't conflict.
2019-01-21Patchelf also built to manually set RPATH in Bash and AWKMohammad Akhlaghi-92/+123
With the current build system, Bash and AWK don't write RPATH into the executables. This causes many problems in the pipeline (for example when using the `$(shell)' function in Make which doesn't have `LD_LIBRARY_PATH'). After consulting the Bash and Make mailing lists, so far, the best solution was to use the Patchelf program to manually write RPATH in these executables. With this commit, Patchelf is now installed in the pipeline and used in Bash and AWK to fix this problem.
2019-01-20Cleaner, more managable, build of BashMohammad Akhlaghi-6/+10
The build of bash has been made a little cleaner to help in readability and management of the code.
2019-01-20Removed webp and zstd as dependencies of libtiffMohammad Akhlaghi-1/+2
The TIFF library can optionally depend on webp [1] and zstd [2]. But these aren't commonly used in scientific datasets so to avoid a longer build and managing of extra dependencies (atleast for now!), we are disabling them. The problem is that they cause a dependency on the host system and if they are updated/removed, the relevant pipeline programs will crash. [1] https://en.wikipedia.org/wiki/WebP [2] https://en.wikipedia.org/wiki/Zstandard
2019-01-20Corrected copyright typo in dependencies-basic.mkMohammad Akhlaghi-1/+2
In the previous commit, the copyright year and owner were mistakenly modified. They are corrected now.
2019-01-20Bash is built with its own libreadline, not using oursMohammad Akhlaghi-104/+113
While working on a pipeline based on this, I noticed many linking errors of our installed Bash, complaining that it can't link with libreadline. This was while readline was present in the proper directory and the Bash within a recipe would work properly. After some investigation, I found out that this is because Make's `foreach' function (which was used to define the targets) was apparently calling Bash without setting `LD_LIBRARY_PATH', causing this error. To avoid such sitations, Bash now uses its internal build of readline and we no longer ask it to link with the installed readline.
2019-01-20Corrected symbolic links to the extra pkgconfigs of ncursesMohammad Akhlaghi-6/+6
The targets of the links to have the extra common `ncurses' packages were previously just `pkgconfig/*.pc'! But this would only work when run within the `installed/lib' directory, not any other! So the targets for these packages now use an absolute address.
2019-01-18Sanity check to run the Make with proper group permissionsMohammad Akhlaghi-12/+60
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.
2019-01-15Many network-related libraries ignored in Wget and cURLMohammad Akhlaghi-9/+44
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-46/+157
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.
2019-01-10cURL added as a dependency of GitMohammad Akhlaghi-1/+2
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).
2019-01-08When 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-8/+8
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-2/+3
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.
2018-12-19Removed 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.
2018-12-13Fixed numthreads in dependencies alsoMohammad Akhlaghi-7/+7
Some problems with using the number of threads in dependency building were fixed.
2018-12-11Passing -j build options to dependency building bottle-necksMohammad Akhlaghi-3/+10
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).
2018-12-05CFITSIO 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).
2018-12-05Forgotten 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-22/+54
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.