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2019-05-21ImageMagick put as prerequisite of MatplotlibRaul Infante-Sainz-0/+1
With this commit, ImageMagick program has been set as prerequisite of Matplotlib Python package. Since some submodules of Matplotlib rely on ImageMagick programs (for example, those to make image animations), and now we have ImageMagick into the project, it is good to install ImageMagick when Matplotlib is requested to be installed.
2019-05-21ImageMagick is now included into the projectRaul Infante-Sainz-0/+13
With this commit, ImageMagick software has been added into the project. This software is useful to deal and treat images from the command line. Since it is widely used and a lot of other programs rely on it, it is worth to have it into the project.
2019-05-21Source directory links to build directory all managed in configureMohammad Akhlaghi-18/+53
Until now, the `tex/build' symbolic link was put in the clone/source tree when the build-directory's `tex' directory was being built. Thanks to Roberto Baena, we just found a bug because of this behavior: when a second group member is trying to build the pipeline, since the build directory's `tex' directory already exists, no `tex/build' will be put in their clone/source directory. As a result, the PDF building will crash. To fix this (and keep things organized), the two `tex/build' and `tex/tikz' links (to the build directory) are now built in the configure step while it is building all the top-level directories. They are no longer built within the Makefiles. Also, a comment was added on top of every directory built during the configuration phase to be clear. This fixes bug #56362.
2019-05-15for-group script using internal chmodMohammad Akhlaghi-1/+1
Until now, the `for-group' script was using the system's `chmod' at the end of its operation. But when `for-group' reaches this level, we already have our own custom `chmod'. With this commit, for a consistent operation, we are now using our custom `chmod' program for this final step.
2019-05-09Typo, space instead of TAB, corrected in recipe of MetastoreMohammad Akhlaghi-27/+27
In the previous commits where Metastore's recipe was updated, all the `TAB's in the recipe were saved as spaces just before the commit (due to a copying and pasting from the terminal, not the text editor). With this commit, I am correcting this.
2019-05-09download-multi-try now starts with a /bin/bash shebangMohammad Akhlaghi-0/+2
Until now, the `download-multi-try' script assumed GNU Bash features (when comparing the number of attempts at downloading), but it didn't explicitly ask the operating system to be run with Bash. As a result, when weaker shells were used (like the default Debian minimalist `dash' shell), the `>' ("larger than" operator in a math context) is interpreted a redirection and two extra files are created: `1' and `maxcount'! With this commit, we now start this script with `/bin/bash'. Ofcourse, this will assume that the host has GNU Bash installed, but we are also making this assumption in the configure script. So atleast for now, Bash (any version) is a critical dependency of this template anyway.
2019-05-09Metastore Git hooks properly written after its installationMohammad Akhlaghi-35/+34
Until now, in the recipe to build Metastore, we would store the current directory in a `current_dir' Bash variable before running `gbuild' to build Metastore. However, in this Makefile, we aren't using `.ONESHELL'. As a result, each un-quoted new-line character creates a new shell and the `current_dir' variable that we used afterwards was empty! This happened because until recently, Metastore was being built in `high-level.mk' (where `.ONESHELL' is activated, because we are using GNU Make to call that Makefile). But in `basic.mk', we are using the host's Make, which may not be GNU Make, so we can't use any GNU-only features. Also, this error was hard to notice, because we weren't using `&&' before writing the final target of Metastore! With this commit, both this issues are addressed: all the lines in the recipe are now quoted in the end with a backslash, and the steps before making the target are separated by `&&', not `;' (which doesn't cause a crash if the command fails). This fixes bug #56295.
2019-05-09Removed extra Binutils from GCC's prerequisitesMohammad Akhlaghi-1/+0
Until this commit, Binutils was brough up as a GCC prerequisite two times: Once as a special (`host_cc') dependency (for when we want to build GCC), another time as a dependency in every build. The first one is now obsolete: on MacOS systems where we don't build Binutils, we define its symbolic links in the same recipe. With this commit, we remove the first one, so Binutils is always a dependency of GCC.
2019-05-08TeXLive csquotes packages (needed by BibLaTeX) has been addedMohammad Akhlaghi-1/+8
In the warnings output by LaTeX during the building of a project, I noticed that `csquotes' is recommended for some features of BibLaTeX (a warning was printed) so it is added with this commit.
2019-05-06Imported work on X window system for netpbm, no conflictsMohammad Akhlaghi-1/+1
There weren't any conflicts in this merge.
2019-05-06Disabled X Window System in netpbm installation for GNU/Linux systemsRaul Infante-Sainz-1/+1
Until this commit, we were installing `netpbm' without disabling the X Windows System in GNU/Linux. That is the default option in the configure step of `netpbm'. However, we are not installing the necessary libraries (X11) and headers for that. As a consecuence, when testing in a system where we don't have these libraries/headers (Ubuntu 14.04), it crashes. With this commit, we disable the X Windows System option in `netpbm' by giving the answer `none' to one of the last answers to that question in the configure step.
2019-05-05Visual alignment of software version numbers under eachother removedMohammad Akhlaghi-104/+104
Until now the software names and versions in `reproduce/software/config/installation/versions.mk' were placed such that all the versions were placed under each other. This had a visual effect, but since many of the software have shorter names, it could sometimes cause visual confusion on which number belongs to which software. Since we recently removed a similar situation with the backslashes, with this commit, there is only a single space between the variable name, `=' and the version number.
2019-05-05Upgraded to GCC 9.1Mohammad Akhlaghi-27/+28
GCC 9.1 was just released and includes many new optimization features that can benefit projects in this template also. Also, the build directory of GCC has been moved inside the unpacked directory (similar to all the other programs). As a result, while GCC is being built, the `.build/software/build-tmp' directory will only have one directory for GCC. Until now, there was one `gcc-build' directory and one unpacked tarball.
2019-05-02Updated to TeXLive 2019Mohammad Akhlaghi-6/+16
Since we just download the binary source of TeXLive, we need to keep it up to date with the server. So it has been incremented to 2019 (TeXLive 2019 was released April 29th). A note was also added in the Checklist to keep the users informed on how to update TeXLive if necessary.
2019-05-01Disabled X Window System in Cairo installationRaul Infante-Sainz-1/+2
Until this commit, we were installing `cairo' without disabling the X Windows System. That is the default option in the configure step of `cairo'. However, we are not installing the necessaries libraries (X11) and headers for that. As a consecuence, when testing in a system where we don't have these libraries/headers (Ubuntu 14.04), it crashes. With this commit, we disable the X Windows System option in `cairo' configure step by setting the option `--with-x=no'.
2019-05-01Corrected typo in netpbm tarball extensionRaul Infante-Sainz-1/+1
In the last imported work about fixing all backslashes, the extension of `netpbm' tarball was not the correct one. Now we are using `.tar.gz' instead of `.tgz'. With this commit, we fix this typo by replacing the `.tgz' by `.tar.gz' in the rule of `netpbm'.
2019-05-01Problem in generic CMake rule correctedMohammad Akhlaghi-5/+9
In the recent correction of backslashes, I had missed adding an `&&' before the `rm' command of the generic CMake building rule (`cbuild' of `build-rules.mk'). With this commit, this has been corrected. A multi-threaded Make was also added to build OpenMPI (which takes long and is often built alone because it takes so long and other things depend on it) and the HDF5 library.
2019-04-30TAB-typo corrected in rule to build SCAMPMohammad Akhlaghi-1/+1
The TAB character wasn't used in the second line of the recipe to build SCAMP. This has been corrected with this commit.
2019-04-30New rule to build Coreutils, it is now built alongMohammad Akhlaghi-85/+108
Recently, after the installation of Coreutils, we added a step to manually run PatchELF over all the contents of the `$(ibdir)'. However, after a fresh test, this method failed: because while PatchELF was updating `mv', another program that was using `mv' couldn't do so and crashed. To fix this problem, Coreutils is now installed in a dummy directory also and the exact files that need `rpath' are identified and PatchELF is run on them (to be clean). Also, higher-level `basic.mk' software (higher-level than Bash), were re-organized so they depend on Coreutils. With this, we are no sure that when Coreutils is being built, it is the only program that is being built and PatchELF won't interfere with any other program. Also, OpenSSL and CMake were set to be bulit in parallel to speed up their build.
2019-04-30Imported some recent/parallel work, conflicts fixedMohammad Akhlaghi-62/+114
Especially because of the new convention regarding backslashes, there were many conflicts that are now fixed. But none were substantial.
2019-04-30End-of-line Backslashs no longer right under each otherMohammad Akhlaghi-792/+795
When we need to quote the new-line character we end the line with a backslash (`\'). Until now, our convention has been to put all such backslashes under each other to help in visual inspection. But this causes a lot of confusion in version control: if only one line's length is larger, the whole block will be marked as changed and thus makes it hard to visually see the actual change. It also makes debuging the code (adding some temporary lines) hard. With this commit, I went through all the files and tried to fix all such cases so only a single white space character is between the last command character and the backslash. Where there was an empty line (ending with a backslash, to help in visually separating the code into blocks), I put the backslash right under the previous line's. This completes task #15259.
2019-04-30Better configure checks to see if GCC can be builtRaul Infante-Sainz-26/+64
Until now, to test if GCC can use `sys/cdefs.h', we were building a small test program using it. But after testing on an Ubuntu 14.04, we noticed that the GCC test during the configure script passes, but GCC still can't be built. After some investigation we noticed its available in other directories, but during the build of GCC, those directories aren't used, and it only assumes it to be under `/usr/include'. So with this commit, we are only checking this particular location for this header, not a test run of GCC. After fixing this, we noticed that GCC's build crashed again because it couldn't link with `libc.a' (or `libc.so'). So we also added a for this library and added a new warning to inform the user what they might be able to do. Finally, we noticed that in one of the last steps of building GCC, we weren't using `&&', but `;', so the GCC name file would be built, even when the GCC build failed.
2019-04-30Running PatchELF on all programs after CoreutilsMohammad Akhlaghi-13/+33
Even though the Coreutils configure script says that it adds `rpath' to its executables, its executables don't have it. As a result, it goes to use the host operating system libraries, causing failures when they don't match with the template. Unfortunately after some tests with the configure script, I couldn't find any way to include `rpath'! Even though `-rpath-link' is present in all linking commands during Coreutils' build, the installed files still don't have it! So I was forced to use PatchELF. However, one problem is that Coreutils installs many programs, not just one like Bash or AWK. As a brute-force solution, with this commit, we are running PatchELF on all the installed programs. It won't hurt those that already have it, but it will fix all those that don't. With this commit, I am also making the following non-related small changes: - In `build-rules.mk', the `&&' characters were placed at the start of the line for better readability. - Bash, Readline and NCURSES are now built in parallel on systems that support it (during `basic.mk').
2019-04-29Added M4 as prerequisite of GMPRaul Infante-Sainz-1/+2
Until this commit, `m4' was not a prerequisite of `gmp'. However, during a test in Ubuntu 14.04 using one single core in the configure step, it crashed complaining about not having `m4' installed. With this commit, we set `m4' as a prerequisite of `gmp'.
2019-04-29Corrected spaces/TAB in some rulesRaul Infante-Sainz-61/+61
In some rules there were some spaces when we should use TAB, and also the other way around. We were using TAB instead using spaces. With this commit, we fix that spaces/TAB in the necessary rules.
2019-04-29Added numpy and six as prerequisites of h5pyRaul Infante-Sainz-2/+4
Until now, we were missing `numpy' and `six' as prerequisites of `h5py'. Because we did the configure step with all cores, `numpy' and `six' allways were built before `h5py' with any crash. However, in a single thread configure run we noticed that we were missing these two dependencies. With this commit, we fix this issue by setting `numpy' and `six' as prerequisites of `h5py'.
2019-04-29Modified copyright information of some filesRaul Infante-Sainz-0/+4
With this commit, the copyright information of some files have been modify in order to include the work of Raul Infante-Sainz.
2019-04-29Modified sip_tpv Python package prerequisitesRaul Infante-Sainz-1/+2
Until this commit, the prerequisites of `sip_tpv' were `mpmath' and `sympy'. However, the real prerequisites of `sip_tpv' are `astropy', `numpy' and `sympy'. With this commit, we fix this issue, and now `mpmath' is only a prerequisite of `sympy'.
2019-04-29Fixed a few architecture remnants in initialize.mkMohammad Akhlaghi-33/+3
In a few cases, `reproduce/analysis/make/initialize.mk' still assumed the old architecture. With this commit, they have been corrected.
2019-04-27Astrometry-net installation modified to avoid two reporting stepsRaul Infante-Sainz-0/+8
Until this commit, we had a problem in the installation of Astrometry-net in Mac OS systems. During the runing of the Makefile, it stopped at the reporting stage because it tried to do a couple of steps that in Mac OS are not possible: $ cat /proc/cpuinfo $ free The reason is that `/proc/cpuinfo' and `free' doesn't exist in Mac OS. With this commit, we override these two steps. Since they are only for reporting, they are not mandatory. So, we avoid doing them by using `sed' before running the Makefile.
2019-04-27Libpng updated (version 1.6.37)Raul Infante-Sainz-3/+1
Until this commit, we were using `libpng' version 1.4.22 (out dated). The reason is that with `libpng` versions > 1.5, there was some problems with `netpbm'. But we have update `netpbm' version and now there is no conflict betweem them. With this commit, we increase the version of `libpng' to have the most recent one.
2019-04-27Modified netpbm installation answers for Mac OS systemsRaul Infante-Sainz-8/+8
Until now, we installed `netpbm' by setting the default paths to libraries and headers. That worked fine for GNU/Linux systems, however, in Mac OS systems we have to explicity say to `netpbm' questions what are the paths to the libraries and headers. We found this problem because we tried to run `solve-field' to obtain the astrometry of some images, and then it goes to use `pnmfile', a program that failed because it was not properly linked with `libnetpmb'. With this commit, we fix this problem by answering properly the questions in the configure step of `netpbm' and setting explicity where we want to place the libraries and headers. With this commit, we also update `netpbm' version. To do that, we have to download the last version, for which it doesn't exist a tarball. So, we built this tarball and put it in the Mohammad's webpage.
2019-04-27Lack of semicolons in Binutils installation rule for Mac OS fixedRaul Infante-Sainz-7/+7
Until this commit, in Mac OS we were installing `binutils' as symbolic links of various programs (`as', `ar', `ld', `nm',` ps' and `ranlib'). However, there was a missing semicolon at the end of each line. As a consecuence, the installation of `binutils' on Mac OS systems failed. With this commit, we fix this problem by typing a semicolon at the end of each makelink line.
2019-04-25Added --enable-single option in FFTW installationRaul Infante-Sainz-1/+1
Until this commit, FFTW was installed by default, without the single precission option. However, when installing `sextractor' in a new system we found an error in the installation complaining about not having single precission files of FFTW. More explicity the error was: "FFTW single precision library files not found in [...]". With this commit, we fix this problem by passing the option `--enable-single' in the installation of FFTW.
2019-04-24Added copyright notice for sip_tpv.texMohammad Akhlaghi-1/+7
The BibTeX data for `sip_tpv' didn't have a copyright notice, so one was added for it.
2019-04-24Imported work on mpmath, SymPy and sip_tpv, no conflictsMohammad Akhlaghi-0/+68
There wasn't any conflict in this merge.
2019-04-24Added paper citation of sip_tpv Python packageRaul Infante-Sainz-4/+22
Until now, we were not citing the paper of `sip_tpv' package. With this commit, we have been fix this issue.
2019-04-24Removed sip_tpv from TARGETS, now it is an optional packageRaul Infante-Sainz-1/+1
With this commit, we let the Python package `sip_tpv' to be optional in order to not install it by default. It is a very specific package and I forgot to remove it from `TARGETS.mk' in the previous commit.
2019-04-23Python package sip_tpv added into the templateRaul Infante-Sainz-1/+10
With this commit, we add `sip_tpv' Python package into the template. This is a small package to convert SIP distorsion coefficients into PV distorsion coefficients, and the other way around. This package is useful in a astronomical context, specially when `swarp' is going to be used in order to resample images. The reason is that `swarp' only can understand PV distorsion coefficients.
2019-04-23Python package SymPy added into the templateRaul Infante-Sainz-6/+29
With this commit, we add `sympy' Python package into the template. This is a package to do symbolic mathematics. The motivation is that it is a prerequisite of `sip_tpv' Python package, which is useful to convert SIP distorsion coefficients into PV coefficients (in the context of astronomical images). However, the availability of `sympy' in the template will be useful for anyone interested in this package.
2019-04-23Python package mpmath added into the templateRaul Infante-Sainz-1/+19
With this commit, we add `mpmath' Python package into the template. This package is a prerequisite of `sympy', a package to do symbolic mathematics. The motivation of adding this package is because it is a dependency of `sympy', which is more widely used into the Python science community.
2019-04-23Bash updated with patched tarball (version 5.0.7)Mohammad Akhlaghi-5/+27
Until now we were using the official tarball of GNU Bash. However, Bash is distributed using patches, not a public version controlled history. So to implement newer features of Bash, its necessary to apply those patches and make the tarball ourselves. With this commit, we have done just that: we used the 7 patches that have been released since version 5.0.0 and made a tarball to use for this template. The instructions on how to make the patched tarball are also given above the Bash build rule.
2019-04-23Awk, coreutils and sed are now prerequisites of metastoreRaul Infante-Sainz-2/+9
Until now, `metastore' did not depend on the necessaries programs that we use to install it (`awk', `coreutils' and `sed'). They are not official dependencies of `metastore', but we need them to install it. With this commit, we put these programs as prerequisites of `metastore' in order to be able to install it without any problem.
2019-04-22High-level software now specified in TARGETS.mkMohammad Akhlaghi-207/+259
Until now, to specify which high-level software you want the project to contain, it was necessary to go into the `high-level.mk' Makefile that is complicated and can create bugs. With this commit, a new `reproduce/software/config/installation/TARGETS.mk' file has been created that is easily/cleanly in charge of documenting the final high-level software that must be built for the project. Also, until now, FFTW was set as a dependency of Numpy while we couldn't actually get Numpy to use it! It was just there for future reference and to justify its build rule. But now that many software won't be built and there is no problem with having rules even though a project might not use them, it has been removed.
2019-04-22Git, Metastore, cURL and Libbsd moved to basic softwareMohammad Akhlaghi-119/+126
Git and Metastore are very basic and fundamental tools for the template, so to keep things clean (let the `high-level.mk' software only represent optional software in the template), these two software (and their dependencies: `cURL' and `Libbsd') will now be built in `basic.mk'.
2019-04-22Imported recent work on several astronomy packagesMohammad Akhlaghi-30/+286
With this commit, Raul's work on the installation of several astronomy software is implemented in the main template.
2019-04-22Removed ATLAS as a prerequisite of ScampRaul Infante-Sainz-4/+12
Until this commit, ATLAS was a prerequisite of Scamp. The documentation says that. However, we have been able to install Scamp without having ATLAS installed. As a consecuence, ATLAS does not have to be a prerequisite of Scamp anymore. With this commit, we remove ATLAS as prerequisite of Scamp. We also put available software in the template as optional because not all people are going to use these software.
2019-04-22SCAMP and cdsclient have been added into the projectRaul Infante-Sainz-5/+64
With this commit, we add SCAMP into the project. This program is part of the Astromatic software and the main purpose is to make the fine astrometry and the distorsion correction astronomical images. In principle, SCAMP needs ATLAS library to be able to work (that is what the documentation says). However, we had some problems with ATLAS libraries on Mac OS system, and due to that, we set the option `--enable-openblas' in the configure step. By doing that, we are be able to install SCAMP with no problems. One dependency of SCAMP is `cdsclient', it has been also added with this commit. The `cdsclient' package is a set of C and shell routines which can be built on Unix stations or PCs running Linux, which once compiled allow to query some databases located at CDS or on mirrors over the network.
2019-04-17SExtractor is now included into the projectRaul Infante-Sainz-1/+37
With this commit, we add SExtractor to be installed into the project. It is a widely used program to detect object and build catalogues from astronomical images. We had some problems when installing it because it could not link with some ATLAS libraries. But, since we have OpenBLAS installed, we can use it to override the problem with ATLAS.
2019-04-17Corrected bibtex entry for Astrometry-net and SwarpRaul Infante-Sainz-13/+12
Until now, there were erros in the citation of Astrometry-net and Scamp papers. With this commit, we fix these problems. The Swarp bibtex has also been modify to follow the stetic of the citation style we have right now in the project. We also added the `dependency-bib.tex' as a prerequisite of `paper.bbl'.