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2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-402/+0
Until now, the software building and analysis steps of the pipeline were intertwined. However, these steps (of how to build a software, and how to use it) are logically completely independent. Therefore with this commit, the pipeline now has a new architecture (particularly in the `reproduce' directory) to emphasize this distinction: The `reproduce' directory now has the two `software' and `analysis' subdirectories and the respective parts of the previous architecture have been broken up between these two based on their function. There is also no more `src' directory. The `config' directory for software and analysis is now mixed with the language-specific directories. Also, some of the software versions were also updated after some checks with their webpages. This new architecture will allow much more focused work on each part of the pipeline (to install the software and to run them for an analysis).
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-17/+15
All occurances of "pipeline" have been chanaged to "project" or "template" withint the text (comments, READMEs, and comments) of the template. The main template branch is now also named `template'. This was all because `pipeline' is too generic and couldn't be distinguished from the base, and customized project.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-15/+12
Until now, the files where the people were meant to change didn't have a proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was wrong because the license does not convey copyright ownership. So the name of the file's original author must always be included and when people modify it (and add their own copyright-able modifications). With this commit, the file's original author (and email) are added to the copyright notice and when more than one person modified a file, both names have their individual copyright notice. Based on this, the description for adding a copyright notice in `README-hacking.md' has also been modified.
2019-04-12File is built as a dependency of GCCRaul Infante-Sainz-0/+1
Until now, we did not have `file'. It was in other project, where a problem with `Astrometry-net' software, ends up with the necessity of having `file' into the pipeline. With this commit, we add `file' to the project. Since it is a low level program, it is set in `dependencies-basic.mk' as a prerequisite of GCC.
2019-04-07GNU M4 now built as a dependency of GNU LibtoolMohammad Akhlaghi-0/+1
On some systems, M4 isn't available, so the linking to the host system fails, as a result, we can't build GNU Libtool. The main reason we weren't building M4 was a bug with the most recent GNU C library (http://lists.gnu.org/archive/html/bug-gnulib/2019-04/msg00004.html). But I found a patch used by Arch Linux which fixes the issue and allows M4 to be built. As a result, the pipeline is now building M4 also and the patched M4 tarball is now uploaded to my own webpage as backup. While doing the steps above, I also noticed that we weren't using a tab at the start of the link definitions of `dependencies-basic.mk'. Although its not necessary, to be consistent, its good for the lines to always start with a tab.
2019-04-07Copyright notice added to all files missing oneMohammad Akhlaghi-0/+20
Until now, for short files, we only had a license notice, not an actual copyright notice. With this commit, a copyright notice has also been added. We use this new command to find these files, suggested by `ineiev@gnu.org'.
2019-04-05Imported work on adding Cython and Python's pkgconfig moduleMohammad Akhlaghi-0/+2
This work is now merged, I just added the new argument to the `pybuild' function.
2019-04-05Python cython and pkgconfig packages added for h5pyRaul Infante-Sainz-0/+2
After trying to set the pipeline from scratch with no internet conection (but all tarballs already downladed), `h5py' Python package complained about not having access to download `pkgconfig'. After solving this dependency, it also complained about not having `cython'. With this commit, we add `pkgconfig' (Python) and `cython' to the pipeline in order to be able to install `h5py' properly.
2019-04-04Dependency version LaTeX macros written at the end of configureMohammad Akhlaghi-10/+8
Until now, these versions were written in each run. This was mainly inherited from the old days of the pipeline, where we didn't know the software on the host. But now that we have almost everything under control, we can just write these LaTeX macros at the end of the configure script and make `initialize.mk' simpler and also (very slightly!) speed-up/simplify the processing.
2019-04-04Copyright notice on some of the new filesMohammad Akhlaghi-5/+10
The new files that were just added didn't have a copyright. One has been added for them with this commit.
2019-04-04Numpy and Scipy build on Mac imported into the main branchMohammad Akhlaghi-11/+58
We were developing the build of Numpy and Scipy on Mac in a parallel thread and things seems to be working relatively nice now. There were only two problems: 1) GCC still has some random building issues on Mac. 2) ATLAS shared libraries can't be built on Mac (so we used OpenBLAS to build Numpy and Scipy on both Mac and GNU/Linux). But for now, none of these problems are critical. So, we can progress in one branch. There were only very minor conflicts in the merge.
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.
2019-04-01Added short copyright notice on configuration filesMohammad Akhlaghi-9/+44
A short, all-permisive copyright notice was added to the configuration files that were missing one.
2019-03-29Added copyright information in dependency-versions.mkMohammad Akhlaghi-1/+20
To help make it easier to re-use (like the rest of the "large" files).
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).
2018-12-06Gnuastro'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.
2018-12-04Shared 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.