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2018-11-28Better control of shared library linkingMohammad Akhlaghi-47/+70
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.
2018-11-26Making lock file directoryMohammad Akhlaghi-4/+4
We had forgot to add the rule to build the lock file directory for downloading data. This has been corrected.
2018-11-26High-level dependencies build without system's PATHMohammad Akhlaghi-86/+151
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/+16
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.
2018-11-25Rule of tex/pipeline.tex now defined in paper.mk not top MakefileMohammad Akhlaghi-206/+231
To avoid redundant steps in the the top-level Makefile and make it simpler and easier to follow, we now define the base names of all the Makefiles in the `makesrc' variable of the top-level Makefile. `makesrc' is then used to define the Makefiles to include and the necessary TeX macros at the same time. This is much more clear and obvious than the previous case were we had to list the Makefiles and TeX macro files separately in the top level Makefile.
2018-11-25More generic naming conventionMohammad Akhlaghi-73/+46
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.
2018-11-25Removed mention of extra input dataset in configure scriptMohammad Akhlaghi-5/+0
While preparing the input dataset downloading scripts, we wanted to have two input datasets, but it was too much, so it was ultimately removed. But I had forgot to remove the information about this file in the `./configure' script. So it is removed now.
2018-11-25Instructions on changing input dataset in pipelineMohammad Akhlaghi-5/+11
A step has been added to the checklist to correct the template's input dataset into the custom dataset necessary for each research.
2018-11-25Pipeline now downloads and uses an input datasetMohammad Akhlaghi-100/+414
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.
2018-11-22Minor correction to README-pipeline.mdMohammad Akhlaghi-1/+0
There was an extra line (probably created by Emacs in a wrong command!) in the end of `README-pipeline.md' that has been removed.
2018-11-22Spell check in two READMEsMohammad Akhlaghi-7/+8
A spellcheck was run on the two README files.
2018-11-22Minor edit/correction in README.mdMohammad Akhlaghi-9/+8
The note to the pipeline designers was corrected to display properly on Gitlab.
2018-11-22Placeholder in README.md for pipeline dependenciesMohammad Akhlaghi-9/+15
A placeholder link is now used in `README.md' to encourage the pipeline designers to keep a backup of all the dependencies they use.
2018-11-22Top level READMEs renamed to be similar to actual projectMohammad Akhlaghi-1020/+1010
Until now, were were advising the users to rename the two README files after cloning the project. This was because online Git browsers usually display the `README.md' file, so we wanted the description of the pipeline to be visible in the pipeline, and later when a project adopts it, they can have their own `README.md'. But the problem is that any change in `REAME.md' will later cause conflicts with a project's `README.md'. So we are now using the same naming convention as the papers that use the pipeline.
2018-11-22Checklist defining remote moved to topMohammad Akhlaghi-20/+27
In the checklist, we are now defining the remote host of the repository at an early stage. This is because we will need it in the `README.md' file (which now has a placeholder `XXXXXXX' instead of a valid URL).
2018-11-22README editedMohammad Akhlaghi-23/+29
The README file was edited to be more clear and easy to understand. In particular, it is explained that Git is not necessary for getting the pipeline.
2018-11-22Using .local instead of ./.local in READMEsMohammad Akhlaghi-9/+9
Until now, in the instructions, we were suggesting to run `./.local/bin/make', but the `./' part is extra: this is already a directory and so the shell will be able to find it. So to make things more clear and easy to read/write, we removed the `./' part from the calls to our custom Make installation.
2018-11-22Wget not using server timestampsMohammad Akhlaghi-3/+2
By default, Wget uses the same time stamp for the downloaded file as the server. As a result, if a dependency was previously built before the tarball was uploaded to the server, the pipeline wouldn't recognize that its new and wouldn't re-build it. With this commit, we are adding the `--no-use-server-timestamps' to the call to Wget to fix this problem. I also noticed that (probably as a bug left over from the time we were testing the configure script), we were manually setting the `userread' variable to `n' independent of what the user provided. This has also been fixed.
2018-11-22Ghostscript was updated to version 9.26Mohammad Akhlaghi-2/+2
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.
2018-11-21Changing of README files in checklistMohammad Akhlaghi-33/+69
When you point to this project, the `README.md' file is the default file that opens on GitLab and other online git repositories. Since a reproduction pipeline project is different from the actual pipeline, its best for the default text that opens to describe the paper, not the pipeline. The old `README.md' is also kept, but its now called `REAME-pipeline.md'.
2018-11-21Pulling into pipeline branch instead of fetching in README.mdMohammad Akhlaghi-13/+15
In the previous commit, we were recommending to fetch the work from this pipeline. But since we have a separate `pipeline' branch, we can simply checkout to that branch and pull all the recent changes. So with this commit, the steps to get recent updates to the pipeline are updated.
2018-11-21Fetching pipeline updates explained in README.md checklistMohammad Akhlaghi-7/+26
Since working on the pipeline will evolve along with the projects that use it, it can be useful for projects to fetch updates in the pipeline. So the checklist in `README.md' updated to explain how to do this cleanly.
2018-11-21Updated description of Make in README.mdMohammad Akhlaghi-7/+13
Until now, because we didn't build the dependencies internally, it was important for the pipeline to be usable with any version of Make. But because of the new installation of dependencies (including GNU Make), that is no longer the case. So we can safely use GNU Make and this needs to be mentioned in `README.md'.
2018-11-21Modified reproducible paper statement in paperMohammad Akhlaghi-4/+2
Gnuastro is just one of the softwares used in the pipeline, so it is too much to include its version just under the abstract. However, the version of the pipeline is very important as well as the link to it. This change puts more emphasis on these two more important points.
2018-11-20Configure script passes if TeX Live was not finalizedMohammad Akhlaghi-103/+181
When there is a problem in creating the final TeX Live installation, the previous version of the pipeline would not understand and just finish! We would later have problems in building the paper. So the following series of steps were taken: to keep the recipes in a shorter and easier to understand way, the steps to install TeX Live are now one rule (that produce `.local/bin/texlive-ready-tlmgr' when its successful), and the steps to install the necessary packages are in another rule (that produce `.local/bin/texlive-ready' when its successful). When control comes back inside configure, if `.local/bin/texlive-ready' isn't there (something failed during the TeX Live installation, or building packages), then the whole TeX Live installation directory (`.local/texlive') will be deleted along with the two output files. This will help ensure that future steps can check the availablility of a working TeX Live in the pipeline.
2018-11-20Corrected call to nproc in configure scriptMohammad Akhlaghi-1/+1
After installing the basic dependencies, we have access to the internally built `nproc' program (by Coreutils) to find the number of threads we can use for building the high-level batch of dependencies. Unfortunately, I had added an extra `./' before `$instdir' when calling `nproc' so the script failed. This problem is fixed now.
2018-11-20Not including system's libraries in high-level dependenciesMohammad Akhlaghi-6/+10
The system's libraries are no longer used in building the higher-level dependencies. Also, thanks to Raul Infante Sainz, we found out that Bash's build script was still removing the extra directory information (not good!).
2018-11-20GNU Coreutils now built in basic dependenciesMohammad Akhlaghi-52/+52
GNU Coreutils are basic programs that can help in the configuration of higher-level programs. Because of that, it was a dependency of almost all software built in `dependencies.mk'. To make things more clear, easier to read and faster (when building in parallel), the building of Coreutils is now moved to the `dependencies-basic.mk' rules. There, it is built along-side Bash. Since `dependenceis-basic.mk' is run and completed before `dependencies.mk', with this, we can be sure that Coreutils is present by the time we want to build the higher-level programs. Also, Zlib is now added as a dependency of Git also (it is necessary for its build).
2018-11-19Libtool set as Gnuastro dependencyMohammad Akhlaghi-2/+3
Until now, we were building Libtool as a high-level `top-level-programs' software. But all tools that use the `./configure' script already have a version of Libtool in them. So ultimately the `libtool' in the PATH is not used. However, in the case of Gnuastro, we need libtool for running BulidProgram. So in effect, its a dependency of Gnuastro.
2018-11-19Removed GNU Binutils, CMake's built with its own bootstrapMohammad Akhlaghi-123/+132
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.
2018-11-19Minor corrections for easy applying of checklistMohammad Akhlaghi-30/+38
After going through the checklist for starting a new project based on the pipeline, I noticed some parts that could be modified to be more clear. They are now applied.
2018-11-19Gzip's tarball in tar.gz instead of tar.lzMohammad Akhlaghi-59/+73
Until now, we were using a customized `tar.lz' tarball for Gzip. But on systems that don't have GNU Tar, this will cause a problem (non-GNU Tar doesn't recognize `.tar.lz'). So to keep things simple, we are using the customized gzip in `tar.gz' format. After the internal build of GNU Tar and Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work nicely on all the standard compression algorithms and we don't have to modify our commands based on the algorithm (nice feature of GNU Tar).
2018-11-18Building dependencies on single thread for debuggingMohammad Akhlaghi-2/+2
To help in debugging on other systems, the building of dependencies is only done on a single thread.
2018-11-18Updated README and README.md for new dependency building featuresMohammad Akhlaghi-9/+26
The two README files have been updated to explain the new feature of downloading and building dependencies.
2018-11-18Pipeline also installs TeX live and necessary packagesMohammad Akhlaghi-52/+143
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-15/+63
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.
2018-11-17Corrected typo in previous commitMohammad Akhlaghi-1/+1
In the previous commit, for testing the static build, I had added a `-ljunk' option to the compiler. But I had forgot to remove it! It is removed now.
2018-11-16Minor correction in shell's if statementMohammad Akhlaghi-2/+2
If the Makefile `$(static_build)' variable in '/reproduce/src/make/dependencies-build-rules.mk' isn't defined (by mistake), it will default to blank space, then the Shell will complain about a bad formatted operator (needing two operands). So an `x' was added before it and before `yes' which will allow us to safely pass such cases without a terrible crash.
2018-11-16Configure script checks if static libraries will be builtMohammad Akhlaghi-8/+110
The default Mac compiler has problems building static libraries. Since we are not yet building the GNU C Compiler as part of the pipeline, we'll have to rely on the host system's compiler. Therefore, a check is now added a the start of the configure script that will build a minimal program with the `-static' flag and if it fails, it will print a warning. Afterwards, none of the dependencies will be built with the `-static' flag.
2018-11-15Minor corrections in paper's textMohammad Akhlaghi-7/+8
Some minor corrections have been made in the paper's text to make things easier to read and be more formal.
2018-11-15Fixed small typo (missed a semi-colon)Mohammad Akhlaghi-2/+2
A semi-colon was missed in defining the link for `zlib'. It is now added.
2018-11-15Binutils and other compressors also included in pipelineMohammad Akhlaghi-80/+164
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-24/+23
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-99/+125
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.
2018-11-14Configuration stops if a dependency cannot be builtMohammad Akhlaghi-49/+103
Until now, we used semicolons in Make's Call function definitions to build the programs with GNU build system or CMake. Therefore, if any step of the process failed, the rest would be ignorant to it and pass. Now, we use `&&' to separate the different processing steps. In this way, we can be sure that if any of them fails (during configuration, or building for example), the pipeline will also stop and not continue to the next command (in the same recipe). Since the two Make Call functions were identical in the two `dependencies-basic.mk' and `dependencies.mk', they are now in one file to be imported in both. This bug was found by Raul Infante Sainz.
2018-11-14All used software with versions, acknowledgedMohammad Akhlaghi-3/+35
All the used software are now acknowledged in the template paper along with their versions. This section is also mentioned in the check list, so users don't delete it by mistake.
2018-11-14./configure and building of Bash and Make with more basic toolsMohammad Akhlaghi-262/+410
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-52/+89
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-26/+44
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.
2018-11-12System's environment (including PATH) only available for LaTeXMohammad Akhlaghi-5/+12
The system's environment is now removed from the internal processing of the pipeline, except for LaTeX.