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2019-04-07Copyright notice added to all files missing oneMohammad Akhlaghi-0/+2
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'.
2019-04-04Better option-reading in configure, using .build to access BDIRMohammad Akhlaghi-1/+1
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.
2019-04-02.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'
2019-03-19Minor corrections: typo and adding file to .gitignoreMohammad Akhlaghi-0/+1
The LaTeX macro for libgit2 was not properly used in `paper.tex'. On Mac systems, after browsing the directory, a `.DS_Store' file was created. So to keep things clean on those systems, it is added to the files to be ignored by Git.
2019-02-13Astropy installed in the pipelineRaul Infante-Sainz-0/+1
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.
2019-02-07Python is now in the pipelineRaul Infante-Sainz-1/+2
Many projects use Python so it is necessary include it in the pipeline.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-1/+1
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-0/+4
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.
2018-12-27Igoring .texlive* in the top build directoryMohammad Akhlaghi-0/+1
As part of the pipeline, `.texlive2018' may be created. So it is added to `.gitignore'.
2018-11-12Dependencies built at the start of the pipelineMohammad Akhlaghi-0/+3
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.
2018-02-15Ignoring .nfs* files from GitMohammad Akhlaghi-0/+1
On some servers, `.nfs*' files are also created during the processing, so to keep the Git repo clean (avoid an un-necessary `-dirty' prefix), we are adding these files to the `.gitignore'.
2018-02-15Wildcard for mmap files made more genericMohammad Akhlaghi-1/+1
In some systems, the fact that `.gnuastro' and `reproduce/config/gnuastro' are the same is not recognized by Git in `.gitignore' and so the `mmap' files will be treated as un-commit files. So we now simply ignore all files starting with `mmap_*' and removed the directory information before it.
2018-02-15Gnuastro's memory mapping is now a local variableMohammad Akhlaghi-4/+8
As described in the commens above `MINMAPSIZE' of `LOCAL.mk.in', the amount of memory to map to HDD/SSD or keep in RAM is a local issue and not relevant to the pipeline's results. So it is now defined in a `gnuastro-local.conf' file. To keep the Makefiles clean, this file is created by the `./configure' script. To do this cleanly, the `./configure' script was also almost fully re-written with better functionality now.
2018-02-14Sanity checks added, local settings now in LOCAL.mk.inMohammad Akhlaghi-1/+1
The choice of whether or not to make a PDF is now also a local system issue, not a general pipeline issue. So it has been put in the new `LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local settings (things that when changed should not be version-controlled) should be defined in this file. A sanity check was added to find if `./configure' has been run before `make' or not (using the `LOCAL.mk' file which is an output of the configuration step). If `LOCAL.mk' doesn't exist, an error will be printed informing the user that `./configure' needs to be run first. The configure script also provides more clear and hopefully better information on its purpose and what must be done. Since `make clean', it is executed even when `./configure' hasn't been run, it will only delete the build directory and its contents when local configuration has been done. A `distclean' target was also added which will first "clean" the pipeline, then delete the `LOCAL.mk.in' file. To allow rules like `make' to be run even if `BDIR' isn't defined (`./configure' hasn't been run yet), a fake `BDIR' is defined in such cases.
2018-02-07First commit to the reproduction pipeline templateMohammad Akhlaghi-0/+14
Let's start working on this pipeline independently with this first commit. It is based on my previous experiences, but I had never made a skeleton of a pipeline before, it was always within a working analysis. But now that the pipeline has a separate repository for its self, we will be able to work on it and use it as a base for future work and modify it to make it even better. Hopefully in time (and with the help of others), it will grow and become much more robust and useful.