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2019-04-03OpenMPI, HDF5 libraries added for h5pyMohammad Akhlaghi-1/+3
After trying the build a system with no Python library, I noticed that Python's HDF5 module (`h5py') needs the HDF5 library and OpenMPI (to work in parallel). So they were added. Finally `h5py' uses the `mpi4py' module to communicate with OpenMPI, so it was also added. However, for some reason, mpi4py doesn't work with this version of OpenMPI (as described in the comments above). So for now, h5py doesn't use it and can only work on a single thread, while the HDF5 C library links with OpenMPI with no problem.
2019-04-02Numpy and Scipy using OpenBLAS instead of ATLASRaul Infante-Sainz-14/+8
We could not get ATLAS shared libraries on Mac (while the static ATLAS libraries are built and can be used successfully on Mac). So, the pipeline now builds OpenBLAS, which both Numpy and Scipy can use on Mac and GNU/Linux. We also added FFTW as a dependency of Numpy. Altough Numpy is not linking to FFTW for some reason. However, since FFTW is a low level library used by many programs, we have kept it as a dependency of Numpy anyway for now.
2019-03-22H5py added and setuptools as main Python module dependencyRaul Infante-Sainz-0/+1
In this commit we add `h5py' Python package. We also include `setuptools' as a main dependency of Python because with the previous commit it (as well as `pip') is no longer installed with Python. Numpy version also has been incremented.
2019-03-21ATLAS and Scipy working on GNU/LinuxRaul Infante-Sainz-1/+48
Numpy needs ATLAS as shared libraries. So we also need to build Python with shared libraries. We also need to define site.cfg for numpy and scipy so we define a master template: `reproduce/config/pipeline/dependency-numpy-scipy.cfg' Also `Openssl' did not have rpath so we added with this commit.
2019-03-20Including ATLAS in the pipeline, not yet completeRaul Infante-Sainz-9/+12
An initial installation of atlas is now included in the pipeline, but we are still trying to make it compile and build smoothly. In the process, we found that GCC also needs some modifications (for example rpath issues).
2019-03-07Several new Python packages added for full buildMohammad Akhlaghi-0/+7
To ensure that we have all the necessary Python dependencies, I done an offline build and noticed that several packages were also necessary for the `./configure' step to finish (`libffi', `asn1crypto', `cffi', `jeepney', `pycparser' and `secretstorage'). With this commit they are added.
2019-03-06Astroquery, astropy, matplotlib and numpy are now in the pipelineRaul Infante-Sainz-5/+4
Until this commit, we had some of the python packages intalled but they did not work properly because of the `PYTHONPATH' variables. That is, the pipeline's `python' was the `python' of the system instead of the pipeline's `python'. With this commit this issue has been fixed by setting the correct `PYTHONPATH'. In this commit we also modify the installation of `bzip2' because `CMake' was complaining about some libraries built statically.
2019-02-28Python installation and related packages have been splitRaul Infante-Sainz-3/+5
Until now the installation of Python and its packages (numpy, astropy, astroquery, etc.) were done in the same `makefile'. With this commit the installation of Python and its packages have been split and now it is independent of the other programs. The installation of all Python packages needs to be written explicitely because pip is not used anymore.
2019-02-21Matplotlib is now in the pipelineRaul Infante-Sainz-0/+6
As matplotlib is a general package for plotting and it is widely used in science, we have added it to the pipeline. When installing a dependency of matplotlib `python-dateutil', we found a conflict in the download of the tarball. This is because the name has a dash (-) in the middle. In addition, the name starts with 'python', so it is the same as the python itself. Now it is possible to install any package with any name, just adding an elif in before the URL direction.
2019-02-20Installed astroquery in the pipelineRaul Infante-Sainz-0/+17
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.
2019-02-13Astropy installed in the pipelineRaul Infante-Sainz-46/+53
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-0/+1
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-0/+1
Many projects use Python so it is necessary include it in the pipeline.
2019-02-05Ability to package project into tarball or zip fileMohammad Akhlaghi-0/+2
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-24/+1
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-1/+1
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.
2019-01-22Updated to newly modified version of metastoreMohammad Akhlaghi-1/+1
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.
2019-01-22Using fork of metastore to work when getpwuid isn't usableMohammad Akhlaghi-1/+1
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-0/+1
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-0/+1
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).
2019-01-21Patchelf also built to manually set RPATH in Bash and AWKMohammad Akhlaghi-0/+1
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.
2019-01-18Sanity check to run the Make with proper group permissionsMohammad Akhlaghi-0/+24
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-1/+1
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.
2019-01-14GNU NCURSES and GNU Readline also built before GNU BashMohammad Akhlaghi-0/+2
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.
2019-01-08Updated 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.
2018-12-31Updated Gzip and Gnuastro versions to standard buildsMohammad Akhlaghi-2/+2
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.
2018-12-13Minor update in checklist, incremented Gnuastro versionMohammad Akhlaghi-1/+1
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.
2018-12-11Updated the version of GitMohammad Akhlaghi-1/+1
The version of Git was updated to the most recent version (2.20.0).
2018-12-04Shared library absolute address fixed in Libgit2 and WCSLIB on Mac OSMohammad Akhlaghi-2/+10
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.
2018-12-03Preference for shared library linkingMohammad Akhlaghi-1/+1
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.
2018-12-02Wget and OpenSSL now installed as a basic dependencyMohammad Akhlaghi-0/+2
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.
2018-11-29GCC is now installed by the pipelineMohammad Akhlaghi-0/+6
The pipeline now installs GCC and all its necessary prerequisites.
2018-11-28Better control of shared library linkingMohammad Akhlaghi-1/+2
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.
2018-11-26High-level dependencies build without system's PATHMohammad Akhlaghi-0/+2
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.
2018-11-26sh executable now available in PATHMohammad Akhlaghi-1/+1
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.
2018-11-25More generic naming conventionMohammad Akhlaghi-27/+0
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.
2018-11-25Pipeline now downloads and uses an input datasetMohammad Akhlaghi-6/+16
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.
2018-11-22Ghostscript was updated to version 9.26Mohammad Akhlaghi-1/+1
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.
2018-11-19Removed GNU Binutils, CMake's built with its own bootstrapMohammad Akhlaghi-1/+0
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.
2018-11-18Pipeline also installs TeX live and necessary packagesMohammad Akhlaghi-0/+15
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.
2018-11-17TeX Live also built within the pipeline (no extra packages yet)Mohammad Akhlaghi-1/+30
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.
2018-11-15Binutils and other compressors also included in pipelineMohammad Akhlaghi-0/+4
To have better control over the build, GNU Binutils, Bzip2, GNU Gzip, and XZ Utils have also been added to the pipeline. Some other minor cleanups and fixes were also implemented throughout the process.
2018-11-15Static linking flag added to LDFLAGS, using special Bash scriptMohammad Akhlaghi-1/+1
Until now, when a package was to be built statically, we were adding the `--static' option to `CFLAGS'. This was the wrong place to put it! It should be in the linking step (thus `LDFLAGS'). Also, based on Bash's configure script, we are now using the more generic form of `-static' (single dash, not double dash). On the other hand, the `--disable-shared' option isn't available in many of the packages and it is highly redundant with the `-static' option, so it has been removed to avoid an extra warning in such packages.
2018-11-14Lzip and Tar also built as basic dependenciesMohammad Akhlaghi-0/+2
To ensure the easy unpacking and building of the programs, Lzip and Tar are now also build during the initial setup phase. Some minor corrections were also applied to make things cleaner and smoother.
2018-11-14./configure and building of Bash and Make with more basic toolsMohammad Akhlaghi-89/+4
After a test by Raúl Infante Sainz, we found out that the configure script and the Make script for Bash and Make are making too many assumptions on more recent versions of both. As a result, it couldn't be built. Therefore, the `configure' script was modified to not use more recent tools like `readlink' (to find the absolute address of a relative one). It was also re-organized to not have to read the configuration parameters from a text file. The parameters are directly read from the command-line and are written into the proper file afterwards. This removes the need to opening a text editor by the user (which also caused problems on Raúl's system). To fix the Make version issue, the building of Bash and Make are now done in a new Makefile (`reproduce/src/make/dependencies-basic.mk'). This file doesn't make many of the assumptions that were made in `dependencies.mk'. So it should hopefully work on any version of Make. To help in debugging, for now, the Makefile of configure, are asked to work on one thread (the `-j' option is commented in the `configure'). But after checks, we'll fix this.
2018-11-13Most library versions are now also checkedMohammad Akhlaghi-2/+2
All the libraries that define their version string as a macro in their headers are now also checked in `reproduce/src/make/initialize.mk'. Also, the CFITSIO tarball now follows the same versioning style as the rest of the tarballs: a script is added to convert the version string into what is included in the tarball.
2018-11-13Version of programs checked on each run of pipelineMohammad Akhlaghi-4/+8
The version of all programs is now checked in `reproduce/make/src/initialize.mk' and the pipeline won't complete if any of the program versions change from those listed in `reproduce/config/pipeline/dependency-versions.mk'. Since the pipeline is systematically checking all program versions, we don't need Gnuastro's `--onlyversion' option any more. So it (and all references to it) have been removed.
2018-11-12Libcurl, Git, CMake, TIFF, Zlib also built at configure timeMohammad Akhlaghi-20/+26
During the configuration step several new programs that were necessary for a more complete controlled environment are now also downloaded and built statically.
2018-11-12Dependencies built at the start of the pipelineMohammad Akhlaghi-14/+33
To enable easy/proper reproduction of results, all the high-level dependencies are now built within the pipeline and installed in a fixed directory that is added to the PATH of the Makefile. This includes GNU Bash and GNU Make, which are then used to run the pipeline. The `./configure' script will first build Bash and Make within itself, then it will build All the dependencies are also built to be static. So after they are built, changing of the system's low-level libraries (like C library) won't change the tarballs. Currently the C library and C compiler aren't built within the pipeline, but we'll hopefully add them to the build process also. With this change, we now have full control of the shell and Make that will be used in the pipeline, so we can safely remove some of the generalities we had before.
2018-02-27Default PDF now uses PGFPlots and BibLaTeXMohammad Akhlaghi-0/+2
Making plots and including references are integral parts of a scientific paper. Therefore to demonstrate how cleanly they can be used within the pipeline, they are now used to produce the final PDF. To use PGFPlots a random dataset is made (using AWK's random function) and is plotted using PGFPlots. The minimum and maximum values of the dataset are also included in the text to further show how such calculations can go into the macros and text. For the references, the NoiseChisel paper was added as a reference to cite when using this pipeline along with the MUSE UDF paper I, which uses this pipeline for two sections. Following this discussion, citation is also discussed in `README.md` and the NoiseChisel paper is also added as a published work with a reproduction pipeline.