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2021-01-09IMPORTANT: analysis outputs written in BDIR/analysisMohammad Akhlaghi-2/+2
Until now, the build directory contained a 'software/' directory (that hosted all the built software), a 'tex/' subdirectory for the final building of the paper, and many other directories containing intermediate/final data of the specific project. But this mixing of built software and data is against our modularity and minimal complexity principles: built software and built data are separate things and keeping them separate will enable many optimizations. With this commit, the build directory of the core Maneage branch will only contain two sub-directories: 'software/' and 'analysis/'. The 'software/' directory has the same contents as before and is not touched in this commit. However, the 'analysis/' directory is new and everything created in the './project make' phase of the project will be created inside of this directory. To facilitate easy access to these top-level built directories, two new variables are defined at the top of 'initialize.mk': 'badir', which is short for "built-analysis directory" and 'bsdir', which is short for "built-software directory". HOW TO IMPLEMENT THIS CHANGE IN YOUR PROJECT. It is easy: simply replace all occurances of '$(BDIR)' in your project's subMakefiles (except the ones below) to '$(badir)'. To confirm if everything is fine before building your project from scratch after merging, you can run the following command to see where 'BDIR' is used and confirm the only remaning cases. $ grep -r BDIR reproduce/analysis/* --> make/verify.mk: innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \ --> make/initialize.mk:badir=$(BDIR)/analysis --> make/initialize.mk:bsdir=$(BDIR)/software --> make/initialize.mk: $$sys_rm -rf $(BDIR) --> make/top-prepare.mk:all: $(BDIR)/software/preparation-done.mk 'BDIR' should only be present in lines of the files above. If you see '$(BDIR)' used anywhere else, simply change it to '$(badir)'. Ofcourse, if your project assumes BDIR in other contexts, feel free to keep it, it will not conflict. If anything un-expected happens, please post a comment on the link below (you need to be registered on Savannah to post a comment): https://savannah.nongnu.org/task/?15855 One consequence of this change is that the 'analysis/' subdirectory can be optionally mounted on a separate partition. The need for this actually came up for some new users of Maneage in a Docker image. Docker can fix portability problems on systems that we haven't yet supported (even Windows!), or had a chance to fix low-level issues on. However, Docker doesn't have a GUI interface. So to see the built PDF or intermediate data, it was necessary to copy the built data to the host system after every change, which is annoying during working on a project. It would also need two copies of the source: one in the host, one in the container. All these frustrations can be fixed with this new feature. To describe this scenario, README.md now has a new section titled "Only software environment in the Docker image". It explains step-by-step how you can make a Docker image to only host the built software environment. While your project's source, software tarballs and 'BDIR/analysis' directories are on your host operating system. It has been tested before this commit and works very nicely.
2021-01-05Configuration: GNU Binutils linking bug on some systems fixedMohammad Akhlaghi-1/+1
Until now, when building GNU Binutils on GNU Linux operating systems, we would simply put a link to the host's core C library components (the '*crt*' files). However, the symbolic link wasn't "forced"! So if it already existed in the build directory, it would crash. With this commit a '-f' option has been added to the 'ln' command and this fixed the problem. This bug was reported by Zahra Sharbaf.
2021-01-04Building of Less program now uses patchelf to ensure good linkingMohammad Akhlaghi-0/+3
After correctly setting Less to depend on 'ncurses', I noticed its still not linking to Maneage's 'ncurses', but pointing to my host system's 'ncurses' (that happens to have the same version! So it would crash on a system with a different version). This shows that like some other software, we need to manually correct the RPATH inside Less. With this command, the necessary call to 'patchelf' has been added and with it, the installed 'less' command properly linked to Maneage's internal build of 'ncurses'.
2021-01-04Building of less software depends on ncursesMohammad Akhlaghi-1/+1
Until now, the 'less' software package (used to view large files easily on the command-line and used by Git for things like 'git diff' or 'git log') only depended on 'patchelf' (which is a very low-level software). However, as Boud reported in bug #59811 [1], building less would crash with an error saying "Cannot find terminal libraries" in some systems (including the proposed Docker image of 'README.md' which I confirmed afterwards). Looking into the 'configure' script of 'less', I noticed that 'less' is actually just checking for some functions provided by the ncurses library! With this commit, 'less' depends on 'ncurses'. I was able to confirm that with this change, 'less' successfully builds within the Docker image. [1] https://savannah.nongnu.org/bugs/?59811
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-13/+13
Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also.
2020-12-09Configuration: not settting C_INCLUDE_PATH on macOSRaul Infante-Sainz-2/+9
Until now, when building the high-level (optional) software, we would give both 'CPPFLAGS' and 'C_INCLUDE_PATH' the same value/directory in 'high-level.mk'. But we recently found that on macOS's C compiler ('clang'), if a directory is included in both 'CPPFLAGS' and 'C_INCLUDE_PATH', then that directory is ignored in 'CPPFLAGS' (which has higher priority). This caused linking problems when the version of a software on the host was different from the Maneage version. With this commit, 'C_INCLUDE_PATH' is not set on macOS any more and this fixed the problem on the reported systems. This bug was fixed with the help of Mohammad Akhlaghi and Mahdieh Navabi.
2020-12-02Less is now built as a basic softwareMohammad Akhlaghi-0/+10
Less is rarely used in non-interactive mode and is primarily intended for interactively viewing large files. So its need within Maneage (for batch processing) wasn't often felt until now. However, when running './project shell' (which completely closes-off the outside environment), or building a Maneage'd project within a minimal container that doesn't have less, it becomes hard to use Git (and in particular its 'diff' output which depends on 'less'). With this commit, Less has been added as a dependency of Git in 'basic.mk'. In total its built product is roughly 800KB and builds within a second or two. So it isn't a burden on any project. But it can be very useful when the projects are being developed within the Maneage environment itself.
2020-12-01Installation: m4 no longer depends on TexinfoMohammad Akhlaghi-29/+67
In a recent build on a macOS, we recognized that Texinfo needs the 'libintl.h' headers of Gettext. However, Gettext depends on M4, and until now we had set M4 to depend on Texinfo. Therefore adding Gettext as a dependency of Texinfo would cause a circular dependency. On the macOS, we temporarily disabled M4's Texinfo dependency, and the build went through. I also checked on my GNU/Linux system: temporarily renamed all Texinfo built files from my system and done a clean build of M4 and it succeeded. To be further safe, I built Maneage from this commit (where M4 doesn't depend on Texinfo) in a Docker container, and it went through with no problems. So the current M4 version indeed doesn't need Texinfo. I think adding Texinfo as a dependency of M4 was a historic issue from the early days. In the process, I also cleaned 'basic.mk' a little: - A "# Level N" comment was added on top of each group of software that can be built in parallel (generally). - GNU Nano was moved to the end of the file (to be "Level 6"). - Some comments were edited in some places.
2020-09-09R is built without tcl/tk (for GUI) dependenceBoud Roukema-0/+19
Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support in some software. But they are not yet natively built within Maneage, primarily because we have higher-priority work right now. GUI tools in general aren't high on our priority list right now because GUI tools are generally good for human interaction (which is contrary to the reproducible philosophy), not automatic analysis (a core concept in reproducibility). So even later, when we do include Tcl/Tk in Maneage, their direct usage will be discouraged. Until this commit, because we don't yet build Tcl/Tk, the default maneage install of the statistical package R failed on a Debian Stretch, with 6227 repeats of the line: '/usr/lib//tcl8.5/tclConfig.sh: line 2: dpkg-architecture: command not found' To fix this problem (atleast until Tcl/Tk is installed within Maneage), R is now configured with the '--without-tcltk' option which fixed the problem. Please see the description above the R installation instructions in 'reproduce/software/make/high-level.mk' for more.
2020-08-28Plain text editors: nano in basic, emacs and vim in high-levelMohammad Akhlaghi-6/+64
While a project is under development, the raw analysis software are not the only necessary software in a project. We also need tools to all the edit plain-text files within the Maneaged project. Usually people use their operating system's plain-text editor. However, when working on the project on a new computer, or in a container, the plain-text editors will have different versions, or may not be present at all! This can be very annoying and frustrating! With this commit, Maneage now installs GNU Nano as part of the basic tools. GNU Nano is a very simple and small plain text editor (the installed size is only ~3.5MB, and it is friendly to new users). Therefore, any Maneaged project can assume atleast Nano will be present (in particular when no editor is available on the running system!). GNU Emacs and VIM (both without extra dependencies, in particular without GUI support) are also optionally available in 'high-level.mk' (by adding them to 'TARGETS.conf'). The basic idea for the more advanced editors (Emacs and VIM) is that project authors can add their favorite editor while they are working on the project, but upon publication they can remove them from 'TARGETS.conf'. A few other minor things came up during this work and are now also fixed: - The 'file' program and its libraries like 'libmagic' were linking to system's 'libseccomp'! This dependency then leaked into Nano (which depends on 'libmagic'). But this is just an extra feature of 'file', only for the Linux kernel. Also, we have no dependency on it so far. So 'file' is not configured to not build with 'libseccomp'. - A typo was fixed in the line where the physical core information is being read on macOS. - The top-level directories when running './project shell' are now quoted (in case they have special characters).
2020-08-27Machine architecture and byte-order available as LaTeX macroMohammadreza Khellat-4/+4
Until now, no machine-related specifications were being documented in the workflow. This information can become helpful when observing differences in the outcome of both software and analysis segments of the workflow by others (some software may behave differently based on host machine). With this commit, the host machine's 'hardware class' and 'byte-order' are collected and now available as LaTeX macros for the authors to use in the paper. Currently it is placed in the acknowledgments, right after mentioning the Maneage commit. Furthermore, the project and configuration scripts are now capable of dealing with input directory names that have SPACE (and other special characters) by putting them inside double-quotes. However, having spaces and metacharacters in the address of the build directory could cause build/install failure for some software source files which are beyond the control of Maneage. So we now check the user's given build directory string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(', ')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different directory.
2020-08-08Software tarballs saved as symlinks if already in filesystemMohammad Akhlaghi-2/+7
Until now, if the software source tarballs already existed on the system they would be copied inside the project. However, the software source tarballs are sometimes/mostly larger than their actual product and can consume significant space (~375 MB in the core branch!). With this commit, when the software are present on the system, their symbolic link will be placed in 'BDIR/software/tarballs', not a full copy. Also, because the tarballs in software tarball directory may themselves be links, we use 'realpath' to find the final place of the actual file and link to that location. Therefore if 'realpath' can't be found (prior to installing Coreutils in Maneage), we will copy the tarballs from the given software tarball directory. After Maneage has installed Coreutils, the project's own 'realpath' will be used. Of course, if the software are downloaded, their full downloaded copy will be kept in 'BDIR/software/tarballs', nothing has changed in the downloading scenario.
2020-08-08IMPORTANT: New software versions (17 basic, 16 high-level and 7 Python)Mohammad Akhlaghi-28/+81
It was a long time that the Maneage software versions hadn't been updated. With this commit, the versions of all basic software were checked and 17 of that had newer versions were updated. Also, 16 high-level programs and libraries were updated as well as 7 Python modules. The full list is available below. Basic Software (affecting all projects) --------------------------------------- bash 5.0.11 -> 5.0.18 binutils 2.32 -> 2.35 coreutils 8.31 -> 8.32 curl 7.65.3 -> 7.71.1 file 5.36 -> 5.39 gawk 5.0.1 -> 5.1.0 gcc 9.2.0 -> 10.2.0 gettext 0.20.2 -> 0.21 git 2.26.2 -> 2.28.0 gmp 6.1.2 -> 6.2.0 grep 3.3 -> 3.4 libbsd 0.9.1 -> 0.10.0 ncurses 6.1 -> 6.2 perl 5.30.0 -> 5.32.0 sed 4.7 -> 4.8 texinfo 6.6 -> 6.7 xz 5.2.4 -> 5.2.5 Custom programs/libraries ------------------------- astrometrynet 0.77 -> 0.80 automake 0.16.1 -> 0.16.2 bison 3.6 -> 3.7 cfitsio 3.47 -> 3.48 cmake 3.17.0 -> 3.18.1 freetype 2.9 -> 2.10.2 gdb 8.3 -> 9.2 ghostscript 9.50 -> 9.52 gnuastro 0.11 -> 0.12 libgit2 0.28.2 -> 1.0.1 libidn 1.35 -> 1.36 openmpi 4.0.1 -> 4.0.4 R 3.6.2 -> 4.0.2 python 3.7.4 -> 3.8.5 wcslib 6.4 -> 7.3 yaml 0.2.2 -> 0.2.5 Python modules -------------- cython 0.29.6 -> 0.29.21 h5py 2.9.0 -> 2.10.0 matplotlib 3.1.1 -> 3.3.0 mpi4py 3.0.2 -> 3.0.3 numpy 1.17.2 -> 1.19.1 pybind11 2.4.3 -> 2.5.0 scipy 1.3.1 -> 1.5.2
2020-08-02OpenMPI build with slurm compatibilityBoud Roukema-1/+4
Prior to this commit, compilation of OpenMPI used the default OpenMPI choices of deciding which libraries should be used in relating to a job scheduler [1] (such as Slurm [2]). Given that the user on a multi-user cluster has to accept the sysadmin's choice of a job scheduler, the question of whether to (1) link with OpenMPI's own libraries (and increase the reproducibility of the science project) or rather (2) link with the sysadmin managed libraries (more likely to be compatible with the host's job scheduler), is an open question of which the best strategy for reproducibility needs to be debated and studied. In this commit, strategy (1) is adopted. The options '--withpmix=internal' and '--with-hwloc=internal' are added to the configure command. The working assumption is that the Maneage version of OpenMPI is likely to be modern enough to be compatible with the native job scheduler such as Slurm. Compilation without any 'pmix' option gave a fail in at least one case; it appears that an external pmix library was sought by the configure script. As of OpenMPI 4.0.1, the internal libevent library is used by default, so there appears to be no option to force it to be chosen internally. This commit also includes the option '--without-verbs'. This option removes a library related to "infiniband", "verbs", "openib" and "BTL"; this library appears to be deprecated. See [3], [4] for discussion. Please add feedback and discussion to the Maneage task about openmpi linking strategies (1) (internal) and (2) (external) at Savannah [5]. [1] https://en.wikipedia.org/wiki/Job_scheduler#Batch_queuing_for_HPC_clusters [2] https://en.wikipedia.org/wiki/Slurm_Workload_Manager - To avoid a name clash, 'slurm-wlm' is the metapackage in Debian for the client commands, the compute node daemon, and the central node daemon. An unrelated package 'slurm' also exists. [3] https://www-lb.open-mpi.org/faq/?category=openfabrics#ofa-device-error [4] https://www-lb.open-mpi.org/faq/?category=building [5] https://savannah.nongnu.org/task/index.php?15737
2020-07-07Fixed typo that lead to crash when building healpyMarius Peper-1/+1
Until now, if a project needed the healpy software package, Maneage would crash with the following error message (abridged for full name in build directory). This was caused by a typo in the version of 'healpix' (the dependency of 'healpy'). make: *** No rule to make target '.../version-info/proglib/healpix-' With this commit, the typo in line 334 of 'python.mk' is fixed, so that when '$(ipydir)/healpy-$(healpy-version)' gets called it correctly searches for a rule to make '$(ibidir)/healpix-$(healpix-version)'.
2020-07-05Configure script prefers clang for macOS systemsMohammad Akhlaghi-0/+1
In the previous commit (Commit 1bc00c9: Only using clang in macOS systems that also have GCC) we set the used C compiler for high-level programs to be 'clang' on macOS systems. But I forgot to do the same kind of change in the configure script (to prefer 'clang' when we are testing for a C compiler on the host). With this commit, the compiler checking phases of the configure script have been improved, so on macOS systems, we now first search for 'clang', then search for 'gcc'. While doing this, I also noticed that the 'rpath' checking command was done before we actually define 'instdir'!!! So in effect, the 'rpath' directory was being set to '/lib'! So with this commit, this test has been taken to after defining 'instdir'.
2020-07-05Only using clang in macOS systems that also have GCCMohammad Akhlaghi-27/+58
Until now, when Maneage was built on a macOS that had both a clang and GCC, we would make links to both. But this cause many conflicts in some high-level programs (for example Numpy and etc, all the programs where we have explicity set 'export CC=clang' before the build recipe). This happens because the GCC that is built on a macOS isn't complete for some operations. To fix this problem, when we are on a macOS, we explicity set 'gcc' to point to 'clang' and 'g++' to point to 'clang++'. We also don't link to the host's C-preprocessor ('cpp') on macOS systems because this is only a GNU feature and using the GNU CPP is also known to have some basic problems. For example this was reported by Mahdieh Nabavi (which was the main trigger for this work): ld: Symbol not found: ___keymgr_global Referenced from: /Users/Mahdieh/build/software/installed/bin/cpp Expected in: /usr/lib/libSystem.B.dylib Also, to avoid linking to another link on the host tools (in the 'makelink' function of 'basic.mk'), we are now using 'realpath'.
2020-07-01Properly accounting for space characters in host's PATHMohammad Akhlaghi-12/+20
Until now, when reading the host's PATH environment variable we weren't accounting for directory names with a space character. This was most prominently visible in the 'low-level-links' step where we put links to some core system components into the project's build directory (mainly for prorietary systems like macOS). To address the problem, double quotations have been placed around the part that we extract 'ccache' from the PATH, and the part where we make the symbolic link. In the process the comments above 'makelink' were made more clear and 'low-level-links' now depends on 'grep' (which is the highest-level program it uses). This bug was reported by Mahdieh Navabi.
2020-07-01Minor typo corrected in referencing LibidnRaul Infante-Sainz-1/+2
Until this commit, once Libidn was installed, insted of its own name and version, the name and version of Libjpeg were saved (in the target if Libidn). This robably come from a copy/paste of the rule. With this commit, this minor bug has been corrected. I also added my name as an author of `reproduce/software/make/xorg.mk' Makefile since I added some code there.
2020-06-30Proper deletion of util-linux source after successfully building itMohammad Akhlaghi-1/+3
After recently adding util-linux to Maneage build-tree, we had forgot to delete the unpacked and built source directory after it was installed! This has been corrected with this commit.
2020-06-30Core Xorg libraries necessary for Ghostscript now includedMohammad Akhlaghi-47/+322
Until now, in order to build Ghostscript, the project used the host's Xorg libraries. This was because we hadn't yet added the necessary build rules for them. With this commit, the instructions to build the necessary Xorg libraries for Ghostscript have also been added. Also, the shared Ghostscript library has been built with this commit and two sets of standard fonts are also included, setting us on the path to build TeXLive from source later. This task was done with the help and support of Raul Infante-Sainz.
2020-06-27IMPORTANT: many improvements to low-level software building phaseMohammad Akhlaghi-2091/+2002
POSSIBLE EFFECT ON YOUR PROJECT: The changes in this commit may only cause conflicts to your project if you have changed the software building Makefiles in your project's branch (e.g., 'basic.mk', 'high-level.mk' and 'python.mk'). If your project has only added analysis, it shouldn't be affected. This is a large commit, involving a long series of corrections in a differnt branch which is now finally being merged into the core Maneage branch. All changes were related and came up naturally as the low-level infrastructure was improved. So separating them in the end for the final merge would have been very time consuming and we are merging them as one commit. In general, the software building Makefiles are now much more easier to read, modify and use, along with several new features that have been added. See below for the full list. - Until now, Maneage needed the host to have a 'make' implementation because Make was necessary to build Lzip. Lzip is then used to uncompress the source of our own GNU Make. However, in the minimalist/slim versions of operating systems (for example used to build Docker images) Make isn't included by default. Since Lzip was the only program before our own GNU Make was installed, we consulting Antonio Diaz Diaz (creator of Lzip) and he kindly added the necessary functionality to a new version of Lzip, which we are using now. Hence we don't need to assume a Make implementation on the host any more. With this commit, Lzip and GNU Make are built without Make, allowing everything else to be safely built with our own custom version of GNU Make and not using the host's 'make' at all. - Until recently (Commit 3d8aa5953c4) GNU Make was built in 'basic.mk'. Therefore 'basic.mk' was written in a way that it can be used with other 'make' implementations also (i.e., important shell commands starting with '&&' and ending in '\' without any comments between them!). Furthermore, to help in style uniformity, the rules in 'high-level.mk' and 'python.mk' also followed a similar structure. But due to the point above, we can now guarantee that GNU Make is used from the very first Makefile, so this hard-to-read structure has been removed in the software build recipes and they are much more readable and edit-friendly now. - Until now, the default backup servers where at some fixed URLs, on our own pages or on Gitlab. But recently we uploaded all the necessary software to Zenodo (https://doi.org/10.5281/zenodo.3883409) which is more suitable for this task (it promises longevity, has a fixed DOI, while allowing us to add new content, or new software tarball versions). With this commit, a small script has been written to extract the most recent Zenodo upload link from the Zenodo DOI and use it for downloading the software source codes. - Until now, we primarily used the webpage of each software for downloading its tarball. But this caused many problems: 1) Some of them needed Javascript before the download, 2) Some URLs had a complex dependency on the version number, 3) some servers would be randomly down for maintenance and etc. So thanks to the point above, we now use the Zenodo server as the primary download location. However, if a user wants to use a custom software that is not (yet!) in Zenodo, the download script gives priority to a custom URL that the users can give as Make variables. If that variable is defined, then the script will use that URL before going onto Zenodo. We now have a special place for such URLs: 'reproduce/software/config/urls.conf'. The old URLs (which are a good documentation themselves) are preserved here, but are commented by default. - The software source code downloading and checksum verification step has been moved into a Make function called 'import-source' (defined in the 'build-rules.mk' and loaded in all software Makefiles). Having taken all the low-level steps there, I noticed that there is no more need for having the tarball as a separate target! So with this commit, a single rule is the only place that needs to be edited/added (greatly simplifying the software building Makefiles). - Following task #15272, A new option has been added to the './project' script called '--all-highlevel'. When this option is given, the contents of 'TARGETS.conf' are ignored and all the software in Maneage are built (selected by parsing the 'versions.conf' file). This new option was added to confirm the extensive changes made in all the software building recipes and is great for development/testing purposes. - Many of the software hadn't been tested for a long time! So after using the newly added '--all-highlevel', we noticed that some need to be updated. In general, with this commit, 'libpaper' and 'pcre' were added as new software, and the versions of the following software was updated: 'boost', 'flex', 'libtirpc', 'openblas' and 'lzip'. A 'run-parts.in' shell script was added in 'reproduce/software/shell/' which is installed with 'libpaper'. - Even though we intentionally add the necessary flags to add RPATH inside the built executable at compilation time, some software don't do it (different software on different operating systems!). Until now, for historical reasons this check was done in different ways for different software on GNU/Linux sytems. But now it is unified: if 'patchelf' is present we apply it. Because of this, 'patchelf' has been put as a top-level prerequisite, right after Tar and is installed before anything else. - In 'versions.conf', GNU Libtool is recognized as 'libtool', but in 'basic.mk', it was 'glibtool'! This caused many confusions and is corrected with this commit (in 'basic.mk', it is also 'libtool'). - A new argument is added to the './project' script to allow easy loading of the project's shell and environment for fast/temporary testing of things in the same environment as the project. Before activating the project's shell, we completely remove all host environment variables to simulate the project's environment. It can be called with this command: './project shell'. A simple prompt has also been added to highlight that the user is using the Maneage shell!
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'.
2020-06-17Software 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.
2020-06-16XLSX 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.
2020-06-02Core software build before using Make to build other softwareMohammad Akhlaghi-237/+282
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-3/+3
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-0/+37
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.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-52/+92
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
2020-05-08Installing 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-53/+58
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-0/+11
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-4/+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.
2020-04-28Configration 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.
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-25/+34
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.
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-66/+48
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).
2020-04-17Patchelf 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-14/+16
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-6/+4
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
2020-04-05The 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