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2020-06-18Fixed small bug that was introduced four commits agoRaul Infante-Sainz-4/+4
In Commit 105467fe6402 (Software tarballs are downloaded even if not built), we introduced tests to download the tarballs of software even if they don't need to be built on the respective host. However some small typos in the checks existed that could cause a crash on macOS. In particular in the building of PatchELF and libbsd we had forgot to add the necessary 'x' before the 'yes' in the conditional to check if a we are on macOS or not. With this commit these two checks have been corrected. Also, in the building of 'isl' and 'mpc', we now check for 'host_cc' (signifying that the user wants to use their host C compiler for the high-level step) instead of 'on_mac_os'. The reason is that even on non-macOS systems, a user may not want to build the C compiler from scratch and use the '--host-cc' option. In such cases, they don't need to compile 'isl' and 'mpc'.
2020-06-17Text surrounding software acknowledgements as a configuration fileBoud Roukema-11/+124
Until now, the English texts that embeds the list of software to acknowledge in the paper was hard-wired into the low-level coding ('reproduce/software/shell/configure.sh' to be more specific). But this file is very low-level, thus discouraging users to modify this surrounding text. While the list of software packages can be considered to be 'data' and is fixed, the surrounding text to describe the lists is something the authors should decide on. Authors of a scientific research paper take responsibility for the full paper, including for the style of the acknowledgments, even if these may well evolve into some standard text. With this commit, authors who do *not* modify 'reproduce/software/config/acknowledge_software.sh' will have a default text, with only a minor English correction from earlier versions of Maneage. However, Authors choosing to use their own wording should be able to modify the text parameters in `reproduce/software/config/acknowledge_software.sh` in the obvious way. This is much more modular than asking project authors to go looking into the long and technical 'configure.sh' script. Systematic issues: the file `reproduce/software/config/acknowledge_software.sh` is an executable shell script, because it has to be called by `reproduce/software/shell/configure.sh`, which, in principle, does not yet have access to `GNU make` (if I understand the bootstrap sequence correctly). It is placed in `config/` rather than `shell/`, because the user will expect to find configuration files in `config/`, not in `shell/`. A possible alternative to avoid having a shell script as a configure file would be to let `reproduce/software/config/acknowledge_software.sh` appear to be a `make` file, but analyse it in `configure.sh` using `sed` to remove whitespace around `=`, and adding other hacks to switch from `make` syntax to `shell` syntax. However, this risks misleading the user, who will not know whether s/he should follow `make` conventions or `shell` conventions.
2020-06-17Software tarballs are downloaded even if not builtMohammad Akhlaghi-56/+36
Some low-level software aren't necessary on some operating systems, for example GCC can't be built on macOS, hence we don't build it and the GCC-only dependencies. Also, on GNU/Linux systems users could configure with '--host-cc' to avoid all the time it takes to build GCC when doing a fast test. Until now, in such cases not only was the software not installed, but the tarballs of the software were also not downloaded. Hence making the output of '--dist-software' incomplete (as in bug #58561). With this commit, we now import all the necessary tarballs, when the software isn't necessary for the particular system, it won't be built or cited, but its tarball will be present anyway, thus allowing the output of '--dist-software' to be complete.
2020-06-17Corrected symbolic link to Gnuastro's configuration filesMohammad Akhlaghi-1/+1
Until now, when making the link to Gnuastro's configuration files, the 'configure.sh' script would incorrectly link to the old configuration directory under the 'reproduce/software' directory. With this commit, it is moved to the proper directory under 'reproduce/analysis'.
2020-06-16XLSX I/O properly accounts for local buildMohammad Akhlaghi-2/+2
Until now, when adding the necessary library flags to the build of XLSX I/O, we were effectively over-writing the 'LDFLAGS' variables. So the compiler was effectively not being told where to look for the necessary libraries. With this commit, to fix the problem, we now append the new linking flags to LDFLAGS in XLSX I/O's build, not over-write it.
2020-06-15OpenSSL now built after PerlMohammad Akhlaghi-1/+1
After trying a clean build of Maneage in a Docker image (with a minimal debian:stable-20200607-slim OS), I noticed that the building of OpenSSL is failing because it doesn't find the proper Perl functionality. To fix it, with this commit, Perl is set as a prerequisite of OpenSSL and this fixed the problem.
2020-06-15Configure script now accounts for non-interactive shellsMohammad Akhlaghi-6/+33
The project configuration requires a build-directory at configuration time, two other directories can optionally be given to avoid downloading the project's necessary data and software. It is possible to give these three directories as command-line options, or by interactively giving them after running the configure script. Until now, when these directories weren't given as command-line options, and the running shell was non-interactive, the configure script would crash on the line trying to interactively read the user's given directories (the 'read' command). With this commit, all the 'read' commands for these three directories are now put within an 'if' statement. Therefore, when 'read' fails (the shell is non-interactive), instead of a quiet crash, a descriptive message is printed, telling the user that cause of the problem, and suggesting a fix. This bug was found by Michael R. Crusoe.
2020-06-14Better description for input data directory, pointing to INPUTS.confMohammad Akhlaghi-19/+13
Until now, the description of the input-data directory at configure time included a description of the input data (created by reading the values of 'INPUTS.conf'). Maintaining this is easy for a single dataset, but it becomes hard for a general project which may need many input datasets. To avoid extra complexity (for maintaining this list), the description now points a user of the project to the 'INPUTS.conf' file and asks them to look inside of it for seeing the necessary data. This infact helps with the users becoming familiar with the internal structure of Maneage and will allow the authors to focus on not having to worry about updating the low-level 'configure.sh' script.
2020-06-14Better explanation in the start of project configurationMohammad Akhlaghi-3/+7
When './project configure' is run, after the basic checks of the compiler, a small statement is printed telling the user that some configuration questions will now be asked to start building Maneage on the system. Until now this description was confusing: it lead the reader to think that the local configuration (which was recommended to read before continuing) is in another file. With this commit, the text has been edited to explictly mention that the description of the steps following this notice should be read carefully. Thus avoiding that confusion. This issue was mentioned by Michael R. Crusoe.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-1/+16
Possible semantic conflicts (that may not show up as Git conflicts but may cause a crash in your project after the merge): 1) The project title (and other basic metadata) should be set in 'reproduce/analysis/conf/metadata.conf'. Please include this file in your merge (if it is ignored because of '.gitattributes'!). 2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if you have added all analysis Makefiles to the '.gitattributes' file (thus not merging any change in them with your branch). For example with this command: git diff master...maneage -- reproduce/analysis/make/initialize.mk 3) The old 'verify-txt-no-comments-leading-space' function has been replaced by 'verify-txt-no-comments-no-space'. The new function will also remove all white-space characters between the columns (not just white space characters at the start of the line). Thus the resulting check won't involve spacing between columns. A common set of steps are always necessary to prepare a project for publication. Until now, we would simply look at previous submissions and try to follow them, but that was prone to errors and could cause confusion. The internal infrastructure also didn't have some useful features to make good publication possible. Now that the submission of a paper fully devoted to the founding criteria of Maneage is complete (arXiv:2006.03018), it was time to formalize the necessary steps for easier submission of a project using Maneage and implement some low-level features that can make things easier. With this commit a first draft of the publication checklist has been added to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018 and zenodo.3872248. To help guide users on implementing the good practices for output datasets, the outputs of the default project shown in the paper now use the new features). After reading the checklist, please inspect these. Some other relevant changes in this commit: - The publication involves a copy of the necessary software tarballs. Hence a new target ('dist-software') was also added to package all the project's software tarballs in one tarball for easy distribution. - A new 'dist-lzip' target has been defined for those who want to distribute an Lzip-compressed tarball. - The '\includetikz' LaTeX macro now has a second argument to allow configuring the '\includegraphics' call when the plot should not be built, but just imported.
2020-06-03README-hacking.md: Improved section on ignoring some files in ManeageMohammad Akhlaghi-2/+2
When some files should not be merged, until now we were suggesting to also add deleted files to the '.gitattributes' file. However, this feature of Git doesn't work for deleted files and they would still show up in the 'master' branch after a merge. So with this commit, we have added a simple AWK command to run after a merge that will automatically detect and delete such files (using the output of 'git status --porcelain'). Also, two minor typos were corrected in the newly added 'servers-backup.conf' file: the copyright year was wrong and there was no new-line at the end of the file (a good convention!).
2020-06-02Core software build before using Make to build other softwareMohammad Akhlaghi-341/+601
Until now, Maneage would only build Flock before building everything else using Make (calling 'basic.mk') in parallel. Flock was necessary to avoid parallel downloads during the building of software (which could cause network problems). But after recently trying Maneage on FreeBSD (which is not yet complete, see bug #58465), we noticed that the BSD implemenation of Make couldn't parse 'basic.mk' (in particular, complaining with the 'ifeq' parts) and its shell also had some peculiarities. It was thus decided to also install our own minimalist shell, Make and compressor program before calling 'basic.mk'. In this way, 'basic.mk' can now assume the same GNU Make features that high-level.mk and python.mk assume. The pre-make building of software is now organized in 'reproduce/software/shell/pre-make-build.sh'. Another nice feature of this commit is for macOS users: until now the default macOS Make had problems for parallel building of software, so 'basic.mk' was built in one thread. But now that we can build the core tools with GNU Make on macOS too, it uses all threads. Furthermore, since we now run 'basic.mk' with GNU Make, we can use '.ONESHELL' and don't have to finish every line of a long rule with a backslash to keep variables and such. Generally, the pre-make software are now organized like this: first we build Lzip before anything else: it is downloaded as a simple '.tar' file that is not compressed (only ~400kb). Once Lzip is built, the pre-make phase continues with building GNU Make, Dash (a minimalist shell) and Flock. All of their tarballs are in '.tar.lz'. Maneage then enters 'basic.mk' and the first program it builds is GNU Gzip (itself packaged as '.tar.lz'). Once Gzip is built, we build all the other compression software (all downloaded as '.tar.gz'). Afterwards, any compression standard for other software is fine because we have it. In the process, a bug related to using backup servers was found in 'reproduce/analysis/bash/download-multi-try' for calling outside of 'basic.mk' and removed Bash-specific features. As a result of that bug-fix, because we now have multiple servers for software tarballs, the backup servers now have their own configuration file in 'reproduce/software/config/servers-backup.conf'. This makes it much easier to maintain the backup server list across the multiple places that we need it. Some other minor fixes: - In building Bzip2, we need to specify 'CC' so it doesn't use 'gcc'. - In building Zip, the 'generic_gcc' Make option caused a crash on FreeBSD (which doesn't have GCC). - We are now using 'uname -s' to specify if we are on a Linux kernel or not, if not, we are still using the old 'on_mac_os' variable. - While I was trying to build on FreeBSD, I noticed some further corrections that could help. For example the 'makelink' Make-function now takes a third argument which can be a different name compared to the actual program (used for examle to make a link to '/usr/bin/cc' from 'gcc'. - Until now we didn't know if the host's Make implementation supports placing a '@' at the start of the recipe (to avoid printing the actual commands to standard output). Especially in the tarball download phase, there are many lines that are printed for each download which was really annoying. We already used '@' in 'high-level.mk' and 'python.mk' before, but now that we also know that 'basic.mk' is called with our custom GNU Make, we can use it at the start for a cleaner stdout. - Until now, WCSLIB assumed a Fortran compiler, but when the user is on a system where we can't install GCC (or has activated the '--host-cc' option), it may not be present and the project shouldn't break because of this. So with this commit, when a Fortran compiler isn't present, WCSLIB will be built with the '--disable-fortran' configuration option. This commit (task #15667) was completed with help/checks by Raul Infante-Sainz and Boud Roukema.
2020-05-28Fixed TeXLive crash because of differing local and server versionsRaul Infante-Sainz-3/+80
Until this commit, when the user had a previous TeXLive tarball already present (in their software-tarball directory) compared to the CTAN server, the project crashed in the configure phase. This was because TeXLive is updated yearly and we don't yet install TeXLive from source (currently we use its own package manager, but we plan to fix this in task #15267). With this commit, we fix the problem by checking the cause of the crash during the installation of TeX. If the crash is due to this particular error, we ignore the old tarball and download the new one and install it (the old one is still kept in '.build/software/tarballs', but will get a '-OLD' in its name. This probem was recurrent, and every year that TeXLive is updated, the previous tarball had to be removed manually! But with this commit, this is done automatically. The detection and fix of this bug has been possible with the help of Mohammad Akhlaghi, thanks!
2020-05-25Unified reference to GNU/Linux and free softwareMohammad Akhlaghi-8/+8
One of the main reasons to building Maneage is to properly acknowledge/attribute the authors of software in research. So we have adopted a standard of never referring to the GNU-based operating systems running the Linux kernel simply as "Linux", we avoid terms like "Open Sourse" and use Free Software instead (in the same spirit). With this commit, a few instances of the cases above have been corrected, they had slipped through our fingers when we initially imported them into the project. In the special case of the "Journal for Open Source Software", we simply replaced it with its abbreviation (JOSS). This was done because in effect we were generally using journal name abbreviations in almost all the citations already. To avoid any inconsistancies, the names of the three other journals that weren't abbreviated are also abbreviated.
2020-05-23New software: Valgrind and PatchBoud Roukema-1/+105
With this commit, Maneage now includes instructions to build the memory tracing tool Valgrind and the program 'patch' (to apply corrections/patches in text files and in particular the sources of programs). For this version of Valgrind, some patches were necessary for an interface with OpenMPI 2.x (which is the case now). Also note that this version of Valgrind's checks can fail with GCC 10.1.x (when using '--host-cc'), and the failures aren't due to internal problems but due to how the tests are designed (https://bugs.gentoo.org/707598). So currently if any of Valgrind's checks fail, Maneage still assumes that Valgrind was built and installed successfully. While testing on macOS, we noticed that it needs the macOS-specific 'mig' program which we can't build in Maneage. DESCRIPTION: The mig command invokes the Mach Interface Generator to generate Remote Procedure Call (RPC) code for client-server style Mach IPC from specification files. So a symbolic link to the system's 'mig' is now added to the project's programs on macOS systems. This commit's build of Patch and Valgrind has been tested on two GNU/Linux distributions (Debian and ArchLinux) as well as macOS. Work on this commit started by Boud Roukema, but also involved tests and corrections by Mohammad Akhlaghi and Raul Infante-Sainz.
2020-05-22Software citation: removed abstract entry from BibTeX infoMohammad Akhlaghi-7/+0
Until now, two of the software BibTeX sources (Matplolib and Sympy) had an "abstract" entry that was long, not similar to the rest, and not relevant in this context, so they are removed with this commit.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-87/+130
In time, some of the copyright license description had been mistakenly shortened to two paragraphs instead of the original three that is recommended in the GPL. With this commit, they are corrected to be exactly in the same three paragraph format suggested by GPL. The following files also didn't have a copyright notice, so one was added for them: reproduce/software/make/README.md reproduce/software/bibtex/healpix.tex reproduce/analysis/config/delete-me-num.conf reproduce/analysis/config/verify-outputs.conf
2020-05-08Added the option -e in the configure Gnuastro warning messageRaul Infante-Sainz-1/+1
Until this commit, when the version of Gnuastro doesn't match with the version that the project was designed to use, the warning message saying how to run the configure step was not showing the option `-e'. This situation is normal when updating the version of Gnuastro to the most recent one (with the project already configured). However, the use of this option is more convenient than giving the top-build directory, etc, every time. With this commit, the warning message has been changed in order show also the option `-e' in the re-configure of the project.
2020-05-08Installing Scamp with the option --enable-plplot=noRaul Infante-Sainz-1/+3
Until this commit, Scamp was installed with the option `--enable-plplot=yes' (the default). However, Maneage does not have PLplot included. As it is possible to install Scamp without PLplot (in that case it won't generate plots), with this commit this option has been set to `no'. As a consequence, Scamp will be installed even if the host system does not have PLplot without crashing (but it won't make any plot).
2020-05-08GNU Gettext built as a dependency of BashRaul Infante-Sainz-98/+69
Until now Maneage used the host's GNU Gettext if it was present. Gettext is a relatively low-level software that enables programs to print messages in different languages based on the host environment. Even though it has not direct effect on the running of the software for Maneage and the lanugage environment in Maneage is pre-determined, it is necessary to have it because if the basic programs see it in the host they will link with it and will have problems if/when the host's Gettext is updated. With this commit (which is actually a squashed rebase of 9 commits by Raul and Mohammad), Gettext and its two extra dependencies (libxml2 and libunistring) are now installed within Maneage as a basic software and built before GNU Bash. As a result, all programs built afterwards will successfully link with our own internal version of Gettext and libraries. To get this working, some of the basic software dependencies had to updated and re-ordered and it has been tested in both GNU/Linux and macoS. Some other minor issues that are fixed with this commit - Until this commit, when TeX was not installed, the warning message saying how to run the configure step in order to re-configure the project was not showing the option `-e'. However, the use of this option is more convenient than entering the top-build directory and etc every time. So with this commit, the warning message has been changed in order use the option `-e' in the re-configure of the project. - Until now, on macOS systems, Bash was not linking with our internally built `libncurses'. With this commit, this has been fixed by setting `--withcurses=yes' for Bash's configure script.
2020-05-06Corrected latex citation of sip_tpv program (no more \ before _)Mohammad Akhlaghi-1/+1
Until now there we had manually inserted a `\' before the `_' of sip_tpv program. However, we also recently added a step in the configure script to add a `\' before every `_' when writing the final LaTeX macro. This was because some C compilers (when the host's is used) have an `_' in their version that we had no control over. With this commit, the `\' is removed from `sip_tpv' in its build-rule and we let the backslash be inserted automatically.
2020-05-06Software are rebuilt automatically with change of versionMohammad Akhlaghi-227/+232
Until now, when you changed the version of a software in an already-built system, its tarball would be downloaded, but it wouldn't actually build. The only way would be to force the build by deleting the main target of that file (under `.local/version-info/TYPE/PROGRAM'). This was because the tarballs were an order-only prerequisite which was implemented some time ago based on some theoretical argument that if the tarball dates changes, the software should not be rebuilt (because we check the checksum). However, the problems this causes are more than those it solves: Users may forget to delete the main target of the program and mistakenly think that they are using the new version. The fact that all the numbers going into the paper also contain this number further hides this. With this commit, tarballs are no longer order-only and any time a version of a software is updated, it will be automatically built and not cause confusion and manual intervention by the users. As a result of this change, I also had to correct the way we find the tarball from the list of prerequisites.
2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-1/+16
Until this commit, the configure step would fail with an error when compiling libgit2 on a test system. The origin of this bug, on the OS that was tested, appears to be that in OpenSSL Version 1.1.1a, openssl/ec.h fails to include openssl/openconf.h. The bug is described in more detail at https://savannah.nongnu.org/bugs/index.php?58263 With this commit, this is fixed by manually inserting a necessary components. In particular, `sed` is used to insert a preprocessor instruction into `openssl/openconf.h`, defining `DEPRECATED_1_2_0(f)`, for an arbitrary section of code `f`, to include that code rather than exclude it or warn about it. This commit is valid provided that openssl remains at a version earlier than 1.2.0. Starting at version 1.2.0, deprecation warnings should be run normally. We have thus moved the version of OpenSSL in `versions.conf' to the section for programs that need to be manually checked for version updates with a note to remind the user when reaching that version. Other packages that use OpenSSL may benefit from this commit, not just libgit2.
2020-04-29Reactivated --host-cc config option to use host C compilerMohammad Akhlaghi-5/+23
Until now, if GCC couldn't be built for any reason, Maneage would crash and the user had no way forward. Since GCC is complicated, it may happen and is frustrating to wait until the bug is fixed. Also, while debugging Maneage, when we know GCC has no problem, because it takes so long, it discourages testing. With this commit, we have re-activated the `--host-cc' option. It was already defined in the options of `./project', but its affect was nullified by hard-coding it to zero in the configure script on GNU/Linux systems. So with this commit that has been removed and the user can use their own C compiler on a GNU/Linux operating system also. Furthermore, to inform the user about this option and its usefulness, when GCC fails to build, a clear warning message is printed, instructing the user to post the problem as a bug and telling them how to continue building the project with the `--host-cc' option.
2020-04-28Better explanation at the end of the configurationMohammad Akhlaghi-4/+8
Until now, at the end of the configuration step, we would tell the user this: "To change the configuration later, please re-run './project configure', DO NOT manually edit the relevant files". However, as Boud suggested in Bug #58243, this is against our principle to encourage users to modify Maneage. With this commit, that explanation has been expanded by a few sentences to tell the users what to change and warn them in case they decide to change the build-directory.
2020-04-28Astropy will no longer be installed by defaultMohammad Akhlaghi-1/+1
Until now Gnuastro and Astropy where installed by default in any clean build of Maneage. Gnuastro is used to do the demonstration analysis that is reported in the paper and Astropy was just there to help in testing the building of the MANY tools it depends on! It (and its dependencies) also had several papers that helped show software citation. However, as Boud suggested in task #15619, the burden of installing them for a new user may be too much and any future changes will cause merge conflicts. It may also give the impression that Maneage is only/mainly written for astronomers. So with this commit, I am removing Astropy as a default target. But we can only remove Gnuastro after we include an alternative analysis in the demonstration `delete-me' files. Following Boud's suggestion in that task, `TARGETS.conf' was also added to the files to be ignored in any future merge (in the checklist of `README-hacking.mk'). The solution was already described there, but mainly focused on the deleted `delete-me' files. So with this commit, I brought out this item as a more prominent item in the list. Maybe we can later add the analysis done in the Maneage paper (not yet published). In terms of testing the software builds, we already have task #15272 (Single target to build all high-level software, for testing) that aims to have a single configure option to install ALL high-level software and we can ask people to try if they like and report errors.
2020-04-28Configration bug fixed: other problematic software names from tarballBoud Roukema-5/+4
Similar to the previous commit (e43e3291483699), following a change made yesterday in the identification of software names from their tarballs, a few other problematic names are corrected with this commit: `apr-util', HDF5, TeX Live's installation tarball and `rpcsvc-proto'. Even though we have visually checked the list of software, other unidentified similar cases may remain and will be fixed when found in practice.
2020-04-28Configration bug fixed: identify pkg-config from its tarball nameBoud Roukema-1/+1
Until Commit 3409a54 (from yesterday), pkg-config was found correctly in `reproduce/software/make/basic.mk` by searching for `pkg`. However, commit a21ea20 made an improvement in the regular expression for relating package names and download filenames, and the string `pkg-config` with the new regex no longer simplifies to `pkg`. The result of this was that the basic.mk could not find `pkg-config` in the list of packages, since it was still listed as `pkg`. This blocked downloading for a system without pkg-config preloaded. With this commit (of just a few bytes), the bug is fixed.
2020-04-27Aborting with informative error when GNU gettext not foundMohammad Akhlaghi-1/+39
Until now, we wouldn't explicity check for GNU gettext. If it was present on the system, we would just add a link to it in Maneage's installation directory. However, in bug #58248, Boud noticed that Git (a basic software) actually needs it to complete its installation. Unfortunately we haven't had the tiem to include a build of Gettext in Maneage. Because it is mostly available on many systems, it hasn't been reported too commonly, it also has many dependencies which make it a little time consuming to install. So with this commit, we actually check for GNU gettext right after checking the compiler and if its not available an informative error message is written to inform the user of the problem, along with suggestions on fixing it (how to install GNU gettext from their package manager).
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-27/+36
Until now, the sed script for determining URL download rules in the three software building Makefiles (`basic.mk', `high-level.mk' and `python.mk') considered package names such as `fftw-3...` and `fftw2-2.1...` to be identical. As the example above shows, this would make it hard to include some software that may hav conflicting non-number names. With this commit, the SED script that is used to separate the version from the tarball name only matches numbers that are after a dash (`-'). Therefore considers `fftw-3...` and `fftw-2...` to be identical, but `fftw-3-...` and `fftw2-2.1...` to be different. As a result of this change, the `elif' check for some of the other programs like `m4', or `help2man' was also corrected in all three Makefiles. While doing this check on all the software, we noticed that `zlib-version' is being repeated two times in `version.conf' so it was removed. It caused no complications, because both were the same number, but could lead to bugs later.
2020-04-26Configure.sh: build directory checked for ability to modify permissionsPedram Ashofteh Ardakani-11/+81
Until now we only checked for the existance and write-ability of the build directory. But we recently discovered that if the specified build-directory is in a non-POSIX compatible partition (for example NTFS), permissions can't be modified and this can cause crashs in some programs (in particular, while building Perl, see [1]). The thing that makes this problem hard to identify is that on such partitions, `chmod' will still return 0 (so it was hard to find). With this commit, a check has been added after the user specifies the build-directory. If the proposed build directory is not able to handle permissions as expected, the configure script will not continue and will let the user know and will ask them for another directory. Also, the two printed characters at the start of error messages were changed to `**' (instead of `--'). When everything is good, we'll use `--' to tell the user that their given directory will be used as the build directory. And since there are multiple checks now, the final message to specify a new build directory is now moved to the end and not repeated in every check. [1] https://savannah.nongnu.org/support/?110220
2020-04-20Configuration: current directory printed properly in stdoutMohammad Akhlaghi-9/+9
Until now, the message that we printed just before starting to build software didn't actually print the current directory, but only `pwd'. With this commit, this is fixed (it uses the `currentdir' variable that is already found before).
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-111/+84
Until now, throughout Maneage we were using the old name of "Reproducible Paper Template". But we have finally decided to use Maneage, so to avoid confusion, the name has been corrected in `README-hacking.md' and also in the copyright notices. Note also that in `README-hacking.md', the main Maneage branch is now called `maneage', and the main Git remote has been changed to `https://gitlab.com/maneage/project' (this is a new GitLab Group that I have setup for all Maneage-related projects). In this repository there is only one `maneage' branch to avoid complications with the `master' branch of the projects using Maneage later.
2020-04-18Properly adding libiconv to the libraries that libstdc++ links withMohammad Akhlaghi-1/+4
Of the GCC dynamically linked libraries we need to manually add RPATH to all and for `libstdc++' we also need to tell it to link with `libiconv'. Until now, the conditional to check for libstdc++ was not working and thus libiconv wasn't been added to it. With this commit the conditional has been corrected and is now working. Also, to help in reading the logs, an echo statement was added after every call to PatchELF.
2020-04-17Replaced name of directory under akhlaghi.org as backup serverMohammad Akhlaghi-17/+17
Until now, when a the raw tarball of some software wasn't usable, I would put it under my own webpage, or `akhlaghi.org/reproduce-software'. That same address was also used as a backup server. However, now the project has a proper name: Maneage. So I changed the directory on my own server to `akhlaghi.org/maneage-software'. With this commit, this new address has replaced the old one. But to avoid crashes in projects that haven't yet merged with the main Maneage branch, the old `reproduce-software' still works (its actually a symbolic link to the new directory now).
2020-04-17Removed confusing comment in configure.sh, and extra variableMohammad Akhlaghi-12/+2
In the previous commit, we remove the `-static' flag from building PatchELF because it wasn't necessary any more. Howver, the comment for the check still included it and could be confusing. This is corrected with this commit. Also, we don't need the `good_static_libc' variable (that was only defined to pass onto PatchELF). This has also been corrected.
2020-04-17Patchelf is now built dynamicallyMohammad Akhlaghi-11/+2
Until a few commits ago, PatchELF was built statically because it was used to patch `libstdc++' at the end of the GCC building phase, but PatchELF also depends on `libstdc++', so it would crash. However, recently when patching the GCC libraries, we don't directly apply Patchelf to the library, first we copy it to a temporary place, do the patching, then put it in its proper place. So the problem above won't happen any more. With this commit, I am thus removing the static flag from patchelf and letting it built dynamically all the time. The main problem was that some systems don't have a static C++ library, so PatchELF couldn't be built statically. Instead of adding more checks, we just fixed the core foundation of the problem.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-155/+27
Until now the software configuration parameters were defined under the `reproduce/software/config/installation/' directory. This was because the configuration parameters of analysis software (for example Gnuastro's configurations) were placed under there too. But this was terribly confusing, because the run-time options of programs falls under the "analysis" phase of the project. With this commit, the Gnuastro configuration files have been moved under the new `reproduce/analysis/config/gnuastro' directory and the software configuration files are directly under `reproduce/software/config'. A clean build was done with this change and it didn't crash, but it may cause crashes in derived projects, so after merging with Maneage, please re-configure your project to see if anything has been missed. Please let us know if there is a problem.
2020-04-13Configure (TeXLive): year correction also in high-level packagesMohammad Akhlaghi-1/+1
In the previous commit, I removed the year from the basic installation of TeXLive packages, but I forgot to correct this in the high-level TeXLive packages! This is corrected with this commit.
2020-04-13Configure (TeXLive): Year of distribution no longer in directoryMohammad Akhlaghi-12/+10
It is this time of year again: TeXLive has transitioned to its 2020 release and the year is imprinted into the installation directory of TeXLive. Until now, we have had to manually change this year and it caused complications and was very annoying. With this commit, the explicit year has been removed from TeXLive's installation and we now simply put a `maneage' instead of the year. I tried this on another system and it worked nicely. Until the time that we can fully install LaTeX packages from source tarballs, this is the best thing we could do for now.
2020-04-12Configure (numpy): added --std=c99 to CFLAGS to fix errorMohammad Akhlaghi-0/+1
Elham Saremi recently reported the following errors when building Numpy in numpy/core/src/npysort/radixsort.c.src: "error: 'for' loop initial declarations are only allowed in C99 or C11 mode". After some searching, I found Issue 14147[1] on Numpy's main repository about the same problem. As described there, apparently Numpy needs C99 compiler, but doesn't check for it or set it manually (for some strange reason, leaving it to the packagers to check if they want!!!). Any way, after a check with Elham, we were able to fix it by adding the `--std=c99' to CFLAGS of Numpy's build and with this commit, it is now being implemented in the core Maneage to not cause a problem in any other project. [1] https://github.com/numpy/numpy/issues/14147
2020-04-06Astropy now depending on the Expat library to fix internal conflictRaul Infante-Sainz-10/+26
Until now, Astropy was instructed to build its own internal copy of the Expat library. However, with the recent commits before, Maneage now includes an installation of Expat and Astropy can't keep the two (its internal version and the project's version) separate, so they conflict and don't let Astropy get built. With this commit, the problem is fixed by setting the Expat library as an explicit dependency of Astropy and asking Astropy to ignore its internal copy. While doing this, I recognized that it is much easier and elegant to add steps in various stages of the `pybuild' function through hooks instead of variables. So the fifth argument of the `pybuild' function was removed and now it actually checks if hooks are defined as functions and if so, they will be called. The `pyhook_after' function was also implemented in the installation of `pybind11' (which needed it, given that the 5th argument of `pybuild' was removed) and after doing a test-build, I noticed that two lines were not ending with a `\' in `boost' (a dependency of `pybind11'). Commit written originally by Mohammad Akghlaghi
2020-04-05Commenting version numbers with an underscore for LaTeXRaul Infante-Sainz-1/+3
Until now we would simply return the version numbers as they were written into the separate files and situations can happen where the version numbers contain an underscore (`_'). However, this character is a methematical character in LaTeX, causing LaTeX to complain and abort. With this commit, a step has been added at the end of the configure script to convert any possible `_' to `\_'. Once it is commented (a backslash is put behind it), the underscore will be printed as it is in the final PDF. This commit was originally written by Mohammad Akhlaghi
2020-04-05The build of M4 and XLSX I/O on macOS has been fixedRaul Infante-Sainz-6/+37
Until now, the M4 that was built on macOS had internal problems (as discussed in #1): it would simply print `Abort trap: 6' in the output and abort. After looking at the build of Homebrew, I noticed that they apply a patch (correct one line) to fix this problem. To be able to apply that patch on macOS systems, I had fully open up the build recipe of M4 and atleast on the testing system, it was built successfully. Also, after successfully building M4, and thus Autoconf and thus Minizip, we were able to build XLSX I/O on a macOS and found out that the internal library's full address wasn't being put in the libraries and executables. With this commit, we now use macOS's `install_name_tool' to correct the positions of the two `libxlsxio_*' libraries in all its executables. This commit was originally written by Mohammad Akhlaghi
2020-04-05Including version number of Minizip in its installation targetRaul Infante-Sainz-1/+1
Until this commit, only the word `Minizip' was written into the Minizip installation target (without the version number of Minizip). With this commit, this minor bug has been fixed by using the appropiate Make variable: `$(minizip-version)'.
2020-04-05Building Minizip 1.x instead of Minizip 2.xRaul Infante-Sainz-17/+67
Minizip is a dependency of XLSX I/O and until now, I was just using the most recent version I found (2.9.2), but XLSX I/O is written for the Minizip 1.x series, not 2.x. Somehow it didn't cause a crash on my computer!!! I think XLSX I/O's CMake is instructed to look into system directories by default when it doesn't find the directories in the given places. And because I had installed Minizip on my operating system, it did't complain. Upon trying the build on their systems, Yahya, Raul and Zahra reported a failure in the build of XLSX I/O which was due the to the problem above (we were installing the wrong version of Minizip!). With this commit, this has been fixed by installing the 1.x series of Minizip (whish is actually installed within zlib!). This commit was original done by Mohammad Akhlaghi.
2020-04-03CMake updated to version 3.17.0Raul Infante-Sainz-2/+2
With this commit, CMake has been updated to its most recent version. This upgrade has been done because in the installation of XLSX I/O on macOS laptop, it crashes complaining about C compiler "not able to compile a simple test program". After a fast search, I found it could be possible to just use the most recent version of CMake to solve the problem. But it didn't work. In any case, it is good to have the most recent version of CMake included.
2020-04-01Removed multiple tabs in MissFITS tarball definitionRaul Infante-Sainz-1/+1
With this commit, multiples tabs in the definition of MissFITS tarball have been removed. Now they are white spaces.
2020-03-20Adding PyYAML, Html5lib, and Beautifulsoup4 as prerequsites of AstropyRaul Infante-Sainz-4/+4
Until this commit, PyYAML was not set as prerequisite of Astropy. This package is an optional dependency of Astropy for some particular functions. However, we have already included PyYAML into this project so it is available. With this commit, PyYAML has been set as a prerequisite of Astropy. In addition to this, Html5lib and Beautifulsoup4 have been also added as prerequsites of Astropy (and removed from Astroquery prerequisites). I noticed that both of them are optional dependencies of Astropy.
2020-03-17Astroquery updated to version 0.4Raul Infante-Sainz-3/+3
In the last update of Astropy to version 4.0 they removed some things that the previous version of Astroquery needs. As a consequence, it is also necessary to update the Astroquery version to be a ble to run with the Astropy 4.0. With this commit, the update of Astroquery to it most recent version (0.4) has been done.