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2019-04-15Template's main branch is now masterMohammad Akhlaghi-25/+44
Until now, the main template branch was called `template'. However, the standard Git convention is that the main branch of a project be called `master'. Many systems rely on this default and it is also easier for new users (who have been accustomed to this convention). So with this commit, the main template branch is `master', but in `README-hacking.mk', we instruct the users on how to rename it to `template' as part of their customization. This is infact better, because when we are actually developing the template in a separate fork, we can refer/use the `master' branch like any other project. And when we are working on a project that uses this template, we will be referring to the main template branch as `template'.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-360/+429
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-472/+457
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.
2019-04-14Corrected copyright information for .file-metadataMohammad Akhlaghi-1/+2
Since `.file-metadata' is a binary file, we can't include a copyright inside of it so we have to use `README.md' to mention its copyright and license notice. However, this was not done clearly and is now corrected.
2019-04-14Added citation for FFTWMohammad Akhlaghi-1/+21
Until now we weren't including the citation for FFTW (one of the template's optional packages). With this commit, it is added.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-162/+128
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.
2019-04-12Minor typo corrections in previous commitsMohammad Akhlaghi-3/+4
Until now, even though `file' was a dependency of `gcc', it was still listed as a `top-level-programs'. Also, we weren't including the new `tex/dependencies' in the distribution tarball (with `make dist'). With this commit, both issues are solved and also, as a cosmetic change, the GCC prerequisites of the same line-length were ordered alphabetically.
2019-04-12Dependency BibTeX entries included only when necessaryMohammad Akhlaghi-261/+291
Until now, there was a single `tex/src/references.tex' file that housed the BibTex entries for everything (software and non-software). Since we have started to include the BibTeX entry for more software, it will be hard to manage the large (sometime unused) BibTeX entries of the software in the middle of the non-software related citations in the text of the paper. Therefore, with this commit, a `tex/dependencies' directory has been made which has a separate BibTeX entry file for each software that needs one. After the software is built, this file is copied to the new `.local/version-info/cite' directory. At the end, the configure script will concatenate all the files in this directory into one file which will later be used with `tex/src/references.tex' by BibLaTeX. This greatly simplifies managing of citations. Allowing us to focus on the software-building and paper-writing citations separately/cleanly (and thus be more efficient in both).
2019-04-12Imported recent corrections, no conflictsMohammad Akhlaghi-15/+143
Some recent corrections that were done by Raul are now merged into the pipeline. There weren't any conflicts.
2019-04-12File is built as a dependency of GCCRaul Infante-Sainz-2/+12
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.
2019-04-12Fixed some Scipy-related packages citationsRaul Infante-Sainz-13/+43
Until now, the Scipy citation was only one paper and not the correct one (it was the online manual). With this commit, Scipy is properly cited using the two papers. Also some modifications in the `tex/src/references.tex' have been done (remove last page number).
2019-04-12Acknowledged Scipy-related packages: Cython, Matplotlib, Numpy and ScipyRaul Infante-Sainz-11/+97
Until now, name and version of all Python packages were indicated in the final paper, but not the main paper of them (if it exists). With this commit, some Python packages (Cython, Matplotlib, Numpy and Scipy) are now properly acknoledged by citating the source paper. `mpi4py' is also cited although this package is not yet included into the pipeline.
2019-04-12Gnuastro's citation included in its build targetMohammad Akhlaghi-4/+4
With this commit, we are applying the new style of citing software within the build rule of Gnuastro.
2019-04-12Configure script dealing properly with empty software directoriesMohammad Akhlaghi-21/+35
Until now, we hadn't actually tested the case where a whole software directory (Python modules in particular) is empty. So the configure script finished with some errors in this case. With this commit, this step of the configure script was modified to deal with such cases cleanly. Also, in `initialize.mk', I added a `-f' to the symbolic link command, so it doesn't complain if the file link already exists.
2019-04-11.file-metadata also given a copyright in top READMEMohammad Akhlaghi-19/+21
Since `.file-metadata' is a binary file and we couldn't put a copyright notice within it, it has been mentioned in `README.md' to have the same copyright. Also, the copyright modification step in `README-hacking.md' was brought to a later step to be more clear that it should always be done (on new files or files that are changed).
2019-04-11Unzip set as prerequisite of Numpy and SetuptoolsRaul Infante-Sainz-2/+4
Since we mixed the installation of Python packages with all other software, it may occur that some Python packages start to be installed before having installed `unzip'. As a consecuence, they could not be decompressed and the installation will fail. In particular, tarballs of Numpy and Setuptools are .zip files. With this commit, we fix this issue by setting `unzip' as a prerequisit of Numpy and Setuptools.
2019-04-10Imported PatchELF correction, gmp and mpfr also dependencies of AWKMohammad Akhlaghi-63/+53
There weren't any conflicts in this merge. However, while, trying to break a long line into multiple (for better readability), I noticed that the AWK version was mistakenly written as `awk-version' in a few cases, so this was corrected to `gawk-version'. While inspecting the libraries that AWK links to, I noticed that it also links to GNU GMP and GNU MPFR. But since they are built after AWK usually, it was using my host system! So with this commit, AWK has these two libraries as prerequisites. As a result, these two libraries were brought up to the basic program section, and not just GCC prerequisites.
2019-04-10Using bin executable in patchelf for awk and bashRaul Infante-Sainz-11/+12
Until this commit, we were using the target (version number of the program) in the `patchelf' for `awk' and `bash'. This makes an incorrect linking in libraries because the target is not the bin program but just a plain text containing the version number of the program. With this commit we fix this issue by setting in the patchelf of `awk' and `bash' the bin executable, and not the target (version number).
2019-04-08for-group: Options passed to configure or makeMohammad Akhlaghi-10/+17
Until now, the `for-group' script could only two options to Make and didn't pass anything to `./configure'. With this commit, any thing given after the first two tokens to `for-group' is passed directly to `./configure' or Make. Also, the test for the existance of the group has been modified to avoid making a temporary file.
2019-04-08Using Clang on Mac OS systems for pkg-configMohammad Akhlaghi-2/+10
Yahya Sefidbakht reported the following error when building Pkg-config on his Mac OS system (using GCC, not Clang). It is apparently because his version of GCC doesn't support some speical feature on Mac that is necessary to build Glib as part of Pkg-config. With this commit, on Mac systems, for pkg-config we are explicity asking to build with Clang (through the `CC' flag).
2019-04-07Configure script using our build programs in final stepsMohammad Akhlaghi-35/+44
In order to get a consistent final result, in its later steps, the configure script uses our own build of the basic command-line tools (like `cat', `awk'). Also, a correction was made to the short option parsing errors when an unwanted argument is given, and the `-?*' was changed to `-'?'*' to avoid un-necessary shell interpretation (for example giving unreasonable results).
2019-04-07GNU M4 now built as a dependency of GNU LibtoolMohammad Akhlaghi-65/+77
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.
2019-04-07Corrections in configure script and astroquery, astropy rulesMohammad Akhlaghi-19/+24
The step where we check the possibility of using `sys/cdefs.h' was still using `$$' for shell variables (in Make), not `$' (for the shell). This was corrected. Also, since Astropy needs two citations, the `,' in the citation command would conflict with Make's parsing. So we just used an `echo' command to re-write the version info. In Astroquery, the prerequisite list was just reordered by length to be more clear to the eye.
2019-04-07Using gnuastro name for Gnuastro's target, not astnoisechiselMohammad Akhlaghi-9/+9
Until recently we were using an actual installed executable file for the programs. So for Gnuastro, the target was called `astnoisechisel'. But recently, this approach was changed and the target for each software is a simple text file with the official software name and version. So with this commit, we are simply using `gnuastro' for Gnuastro, not `astnoisechisel'.
2019-04-07--host-cc configure option to avoid building GCC, M4 mandatoryMohammad Akhlaghi-36/+73
In some cases (specially when debugging the pipeline), its very time-consuming to install GCC. With this commit, a `--host-cc' option has been added to avoid building the C compiler when necessary. The test to see if `sys/cdefs.h' is available on the system (necessary to build GCC) has also been moved to the configure script to print a more visible warning and also use the new `host_cc' variable to let `dependencies-basic.mk' know that GCC shouldn't be built. Finally, we are having problems installing M4 from source, so it has been set as a mandatory dependency.
2019-04-07Copyright notice added to all files missing oneMohammad Akhlaghi-13/+46
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'.
2019-04-05GCC not building on GNU/Linux system with incomplete complierMohammad Akhlaghi-12/+38
On some GNU/Linux distros, the compiler is separated into `multilib' mode (for 32-bit and 64-bit support) and by default the extra component of the compiler is not installed! In such systems for now, we are just creating symbolic links to the host's compiler (similar to Mac). While testing, I noticed that we weren't passing a "$downloader" option to the downloading script of `dependencies.mk' and `dependencies-python.mk'. Also, I noticed that the Cython and Python-pkg-config packages didn't have setuptools as a dependency! Both have now been fixed. Also, Cython's tarball name is now all small-caps (as in all the other tarballs).
2019-04-05Imported work on adding Cython and Python's pkgconfig moduleMohammad Akhlaghi-3/+19
This work is now merged, I just added the new argument to the `pybuild' function.
2019-04-05Software acknowledgement section is automatically generatedMohammad Akhlaghi-504/+416
Until now, management of the software names and versions in the paper was done manually (a macro had to be defined in `initialize.mk', then used in `paper.tex', so they had to be manually set in two places). Managing this was not easy. To fix this, with this commit, each software building rule's target is a text file that contains its human-readable name and its version. In the end, the configure script sorts them by their name and writes them into a LaTeX input file that we can easily import as a file into the main paper.
2019-04-05Python cython and pkgconfig packages added for h5pyRaul Infante-Sainz-3/+17
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-150/+241
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/+68
The new files that were just added didn't have a copyright. One has been added for them with this commit.
2019-04-04Better option checks and values in the configure scriptMohammad Akhlaghi-27/+29
Double quotes were placed around the checked values so they can have space within them. Also, some checks were added for options that don't accept a value.
2019-04-04Corrected typo in GCC build recipeMohammad Akhlaghi-3/+2
For the tests, we had just set an absurd value for a test in the GCC build recipe to always fail, but we had forgot to fix it. It is now corrected. Also the order of making `g++' and `gfortran' was reversed for easier readablility (it doesn't matter which one is done first, it only matters that `gcc' be done last).
2019-04-04Configure script also accepts short options with no delimiterMohammad Akhlaghi-13/+28
Until now, the short options to the configure script needed a delimiter (either white-space or an `=') between the name and value. With this commit, for short options, it also accepts the value immediately touching the option name. Also, when trying to fine the absolute address of a given path, a check was added to abort if it doesn't exist.
2019-04-04--existing-conf doesn't take any values in configure scriptMohammad Akhlaghi-7/+7
Until now we were (wrongly) assuming that the configure script's `--existsing-conf' option takes a value, while this is not the case.
2019-04-04Numpy and Scipy build on Mac imported into the main branchMohammad Akhlaghi-217/+508
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.
2019-04-04Using host GCC on Mac, defining compilers in HDF5 libraryRaul Infante-Sainz-9/+12
We wer not able to build `gcc' on Mac, so we are using links to the host compilers. In this commit we also found that on Mac the HDF5 library needs an explicit definition of the compilers.
2019-04-04Better option-reading in configure, using .build to access BDIRMohammad Akhlaghi-279/+157
Until now, the steps to manage the command-line options of the configure script were limited (couldn't accept an equal sign or space between the option name and value). With this commit, it can now also accept optional equal signs between the option name and value. Thus not causing many confusions. Also, it is more logically consistent for the link to the build-directory to be placed in the top directory (as a hidden file like `.local' until now), and not as a visible directory like `reproduce/build' (which we used until now). Therefore, with this commit, the link to easily access the build-directory is `.build' in the top source directory. Finally, because `minmapsize' is too specific to Gnuastro and has now been given its default value at the start of the configure script, the description for `minmapsize' has been removed (to not confuse users who don't use Gnuastro). If anyone is familiar enough with Gnuastro to change it, they already know it from its book.
2019-04-03OpenMPI, HDF5 libraries added for h5pyMohammad Akhlaghi-3/+46
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.
2019-04-02Python packages are installed as high level program dependenciesRaul Infante-Sainz-87/+30
Until this commit, the installation of all Python packages were done in a separate Makefile. With this commit, the pipeline install Python packages as part of the hight level software. All Python packages rules them remain in a separate Makefile, but this Makefile is included in the high level dependency `reproduce/src/make/dependencies.mk'.
2019-04-02Numpy and Scipy using OpenBLAS instead of ATLASRaul Infante-Sainz-24/+54
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.
2019-04-02.gitignore with copyright using better search for copyright noticeMohammad Akhlaghi-0/+16
In the previous commit, a copyright notice was added after a systematic search of the version controlled files. However, we missed `.gitignore' (because we were discarding those with the `*.git*' pattern to avoid files in the `.git' directory). This has been fixed by using this command (in the top project directory) instead: for f in $(find ./ -type f); do \ if [[ $f != ./.git/* ]]; then \ n=$(grep -i copyright $f | wc -l); \ echo "$n $f"; \ fi; \ done | awk '$1==0'
2019-04-02Copyright notice added to remaining filesMohammad Akhlaghi-11/+37
After doing a systematic search for files without a copyright notice, a few more were found that didn't have a notice. So a notice was added for them. I used this Bash command to find the files: for f in $(find ./ -type f); do \ if [[ $f != *.git* ]]; then \ n=$(grep -i copyright $f | wc -l); \ echo "$n $f"; \ fi; \ done | awk '$1==0'
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).
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-8/+202
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-03-29Disabling ATLAS shared libraries on Mac OSRaul Infante-Sainz-42/+26
The Makefile that build the shared libraries comes from Arch Linux so it does not work easily on Mac. But the full ATLAS build goes successfully for static libraries. For now we are disabling shared libraries on Mac. Python was built explicity with `clang' on Mac.
2019-03-28Configure script now has optionsMohammad Akhlaghi-40/+254
With the options, it is now possible to run the configure script more easily after the initial run. The `--help' option provides a nice and complete introduction along with a listing of the input options and the `-j' option can be use to manually set the number of threads.
2019-03-28flock is now built in configure, to allow serial downloadsMohammad Akhlaghi-42/+104
Until now, we were using `flock' (file-lock) for downloading the input datasets in series. But we couldn't do this when downloading the software tarballs because `flock' wasn't yet available. Generally, unlike processing, downloading is much better done in series than in parallel. To enable serial downloads of the software also, with this commit we are installing `flock' in the configure script (not in a Makefile). As a result, besides `flock', we can also benefit from the other good features of the `reproduce/src/bash/download-multi-try' script *(for example attempting download again after some time). Some GNU mirrors may have problems at the time of download, so with this commit, we are using the main GNU FTP server for GNU programs.