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2022-08-13IMPORTANT: Software updateMohammad Akhlaghi-4/+10
SUMMARY: This is a software update to make Maneage more portable and up to date. It does not involve any Maneage infrastructure changes. You should just re-build your project to make sure the updated software haven't removed/changed any of their features that you were using. In particular, for Astrometry.net users, please see the respective note in P.S.2 below. Until now, there have been many updates in the software that are built within Maneage. The last software upadte was almost one year ago. With this commit, the software in the P.S.1 have been updated. A description of notable changes in the software environment is given in P.S.2. This software environment has been tested on an Arch GNU/Linux, Debian, CentOS-7 and macOS. This commit is the merging of 24 individual commits by Raul Infante-Sainz (who put a lot of energy on porting the software below for macOS, and updating citations), Boudewijn Roukema (who helped with memory checking for GCC, and testing on Debian and CentOS), Sepideh Eskandarlou (who tested the environment) and myself. Besides the updates in the core software, the followimg improvements have also been implemented in this commit: - When you run './project shell': - A welcome message is printed that will remind the caller that they have entered a new environment, it will print the location of 'HOME' and the location of the shell startup file. - The 'reproduce/software/shell/bashrc.sh' is loaded as a startup file. This allows you to customize your interactive Maneage shell. A default step has already been placed there that will put the git branch name (in green) within the shell prompt (which was purple). This greatly helps when dealing with directories under Git version control. These settings won't bother with Maneage's default operations: through environment variables we make sure that these './project shell' features will not slow-down the calls to the shell within the non-interactive Make calls. - The host's 'COLORTERM' is passed to the Maneage environment. It is used by some programs that can have color outputs on the terminal. - Updates to citations: - Numpy and Scipy (as requested on their pages): https://numpy.org/citing-numpy and https://scipy.org/citing-scipy - Gnuastro: Added https://arxiv.org/abs/1909.11230 which describes major updates to Gnuastro after 10 releases. - When a software's paper is indexed in the SAO/NASA Astrophysics Data System (ADS), Maneage now use the BibTeX entries provided by ADS. This helps to give a unified format to most software, and more information (like ADS+arXiv hyperlinks in the BibLaTeX compilation of the default bibliography). - We were able to build this version of Maneage on a Debian system from 2010 (+12 years ago!). Only three downgrades were necessary in the "basic" software (not affecting the high-level science software!). A description of the necessary downgrades for such old systems has been added in 'README.md'. P.S.1 List of updated software: Basic software: cURL 7.79.1 --> 7.84.0 Dash 0.5.11.5 --> 0.5.11-057cd65 File 5.41 --> 5.42 GNU AWK 5.1.0 --> 5.1.1 GNU Bash 5.1.8 --> 5.2-rc2 GNU Binutils 2.37 --> 2.39 GNU Compiler Collection (GCC) 11.2.1 --> 12.1.0 GNU Findutils 4.8.0 --> 4.9.0 GNU Gzip 1.11 --> 1.12 GNU Help2man 1.48.5 --> 1.49.2 GNU Integer Set Library (ISL) 0.18 --> 0.24 GNU Libtool 2.4.6 --> 2.4.7 GNU Nano 6.0 --> 6.4 GNU Readline 8.1.1 --> 8.2-rc2 GNU libiconv 0.16 --> 0.17 Git 2.36.0 --> 2.37.1 OpenSSL 3.0.0 --> 3.0.5 PatchELF 0.13 --> 0.15.0 Perl 5.34.0 --> 5.36.0 High-level software: Astrometry.net 0.89 --> 0.91 CFITSIO 4.0.0 --> 4.1.0 CMake 3.21.4 --> 3.24.0 GNU Astronomy Utilities (Gnuastro) 0.16.1 --> 0.18 GPL Ghostscript 9.55.0 --> 9.56.1 HDF5 1.10.5 --> 1.13.1 Libjpeg 9d --> 9e Libtiff 4.3.0 --> 4.4.0 OpenBLAS 0.3.18 --> 0.3.21 PLplot n/a --> 5.15.0 Python 3.10.0 --> 3.10.6 SCAMP 2.6.7 --> 2.10.0 SWarp 2.38.0 --> 2.41.5 Util-Linux 2.37.2 --> 2.38.1 Vim 8.2 --> 9.0 WCSLIB 7.7 --> 7.11 X.org packages (used by graphical software like Ghostscript and LaTeX): Fontconfig 2.13.94 --> 2.14.0 LibX11 1.7.2 --> 1.8 LibXCB 1.14 --> 1.15 XCB-proto 1.14.1 --> 1.15 Xorg-proto 2021.5 --> 2022.1 Python modules: Astropy 5.0 --> 5.1 GalSim 2.3.3 --> 2.3.5 P.S.2: Notable points regarding the software environment: - Two new links from the host's low-level tools are now included in Maneage's build environment: - On GNU/Linux systems, the host's 'ldd' is linked inside the custom environment. This belongs to the GNU C Library (which is not yet installed in Maneage). But helps in checking the linking status of the binaries on GNU/Linux systems. - On macOS: the 'codesign' binary is included, which is used by GNU Emacs on macOS to sign the built executable. - GNU Bison has been moved in basic software (necessary for GNU Binutils). - The Zip and Unzip programs have been moved as high-level software that have to be manually requested when necessary. This is because they are not used by any of the basic software anymore. They were just installed as dependencies of GNU Tar to be close the other compression programs. Also, in the past we would use the original tarballs, and some (for example Numpy) were distributed in Zip format. However, by default, we now use a custom Lzip tarball and don't need Zip or Unzip. This was suggested by Zahra Sharbaf and Raul Infante-Sainz. - Some minor edits in 'reproduce/software/shell/tarball-prepare.sh'. In particular the 'awk' command was effectively just replacing a '_' with '-', so it just uses a simple SED expression instead. - Fixed bug 62700 (https://savannah.nongnu.org/bugs/index.php?62700) by compiling 'xz' with a patched version of the xz source file 'src/liblzma/liblzma.map'. - Astrometry.net doesn't depend on NetPBM any more. NetPBM (and its dependencies) were causing many crashes on macOS and it also a very strange build system that is hard to maintain. Astrometry.net uses it to take images as input. However, it isn't necessary when you provide Astrometry.net with a catalog. Therefore, Raul added some instructions on how to run astrometry from your own custom X-Y catalog. These instruction can be seen on top of the build rule of Astrometry.net in 'reproduce/software/make/high-level.mk'. - h5py has been removed as a dependency of Astropy. It is an optional dependency to write tables into HDF5 format. But since we couldn't get it to build on macOS it has been removed. None of the current Maneage users/developers also use this feature of Astropy! - PLplot is added a new software, but not a default pre-requisite of SCAMP (which can use it to generate figures), because there were many build problems on macOS. Instructions have been added on top of SCAMP on how to add PLplot as a dependency. - With the aim of being able to install Plplot on macOS, we have wrote several lines to fix header problems. However, we didn't succeed. In any case we are leaving these lines in case they are useful in the future. - The '-Wno-nullability-completeness' compiler flag (which is primarily necessary for macOS) is now only added for macOS systems. It was causing many warnings of un-recognized option in GNU/Linux systems. - The 'mkswap' program of Util-Linux has been disabled because it caused crashes on older kernels. Generally, its not necessary for a Maneage project because it needs root permissions to run! - LibXT (of the x.org software) has been added as a dependency of Cairo. - ImageMagick and Lzip were using the host's C++ standard library! But on GNU/Linux we build our own C++ Standard Library with GCC, so with this commit, they properly link with Maneage's C++ standard library. - ImageMagick on macOS couldn't properly link with Maneage's Ghostscript library! This has been fixed using macOS's install_name_tool. - Necessary RAM to build GCC on GNU/Linux systems changed to ~8GB, see https://savannah.nongnu.org/task/?16244#comment12 - Pythran is no longer as prerequisite of Scipy. Until now, Pythran was a prerequisite of Scipy. But we noticed that it is optional and was causing problems on macOS. - The URLs of some of the software have been updated in 'reproduce/software/config/urls.conf'. By default, these are all commented, but they can be useful when searching for new versions or when a project needs custom software that is not (yet) in Maneage.
2022-06-10Housekeeping: some portability issues fixed; four software updatesMohammad Akhlaghi-39/+77
Until now, there were several portability issues in Maneage: 1. Maneage would crash on older operating systems (checked on Debian 6), where Wget didn't have the '--no-use-server-timestamps'. 2. On a Linux kernel 2.6.32 (of the same Debian 6 above) some features in 'util-linux' (like 'swapon' or 'libmount') wouldn't build and wouldn't let 'util-linux' complete. These features need root permissions to be useful, so the wouldn't be used in Maneage any way! But they wouldn't let Maneage get built 3. The './project shell' command would still read the host's '~/.bashrc', letting the host environment leak-in to Maneage's interactive shell. 4. The building of Flex 2.64 wouldn't complete due to a segmentation fault an Ubuntu, but NetPBM (which depends on Flex) would crash with a wrong usage of 'yyunput'. This had actually caused a non-update to Flex in a previous Maneage software update. 5. The update Astrometry.net would assume SExtractor's executable name is 'source-extractor'; causing a crash in usage. This forced the users to manually create a 'source-extractor' symbolic link in the '.local/bin' directory. 6. The 'reproduce/software/shell/tarball-prepare.sh' script (that is used for making Maneage-standard tarballs) wouldn't accept option values with an '=' between the option name and value! It also didnt' print sufficiently informative messages and errors (for example it would say "skipping ..." (making the user think there is a problem!), but it was actually that the file already existed! 7. The 'reproduce/analysis/make/prepare.mk' and 'reproduce/analysis/make/verify.mk' Makefiles that needed to reject some of the 'makesrc' sub-Makefiles would simply substitute their names with nothing. But this would cause problems when the name is part of the name of another sub-Makefile. 8. On the Debian 6 system mentioned above the raw 'df' command's output wasn't in the expected format; so Maneage would fail to properly detect the free space in the disk. With these commit, all the issues above have been solved: for 1, A check has been added to avoid using that option. For 2, those 'util-linux' features have been disabled. For 3, the '--norc' and '--noprofile' options have beed added to the call to Bash. For 4, see below. For 5, the symbolic link is now automatically made with SExtractor. For 6, the option reading components of that script have been fully re-written and more robust sanity checks are also added, with more informative warnings. For 7, the 'subst' function of Make was replaced with 'filter-out' and this fixed the problem. For 8, 'df' is called with the '-P' option so it has a unified format in all versions. For 4, the versions of 'flex' and 'netpbm' have been updated. Since they were the dependency of 'astrometrynet', that has also been updated. In the process, we discovered that 'lzip' has a new version which claims to be faster, so that is also updated. lzip 1.22 --> 1.23 astrometrynet 0.85 --> 0.89 flex 2.6.4 --> 2.6.4-410-74a89fd netpbm 10.73.39 --> 10.73.39 NetPBM needed some manual manipulation in its source (to remove the extra line), so the necessary steps have been added to its build recipe in 'reproduce/software/make/high-level.mk'.
2022-04-20Updated Git, Coreutils and Emacs, new script to prepare tarballsPedram Ashofteh Ardakani-0/+181
Until now, one had to follow the instructions from [1] to prepare a standard software tarball before merging with the low-level tarballs-software repository [2]. The script only worked for '.tar.gz' suffix and was only available as a comment on Savannah (in [1]). With this commit, the script has been imported into Maneage as 'reproduce/software/shell/tarball-prepare.sh' to simplify future software updates. It work with all supported '.tar.*' suffixes (of the upstream tarball repository) and will convert the tarballs to Maneage's standard format. Also, this script has a minimal argument parser and can skip the tarballs that are already unpacked, allowing faster tests. This script was used to update the versions of: Coreutiles 9.0 --> 9.1 Git 2.34 --> 2.36 Emacs 27.2 --> 28.1 The main motive behind this update was Git which announced a vulnerability issue [3] and suggested an update to the latest version as soon as possible. More detail is described in this github blog [4], but in summary, it was a security issue on multi-user systems that has been found and fixed by Git developers. Since Maneage is often installed on such shared systems, it was important to make this update. GNU Coreutils and GNU Emacs were also updated because they are also commonly used. The following improvements have also done with this commit: - .gitignore: ignore emacs auto-save files (that end with a '#') - README-hacking.md: In the checklist for updating the Maneage branch, the no-longer-necessary '--decorate' option of Git was removed from the command to check the general branch history. [1] https://savannah.nongnu.org/task/?15699 [2] https://git.maneage.org/tarballs-software.git/ [3] https://lore.kernel.org/git/xmqqv8veb5i6.fsf@gitster.g/ [4] https://github.blog/2022-04-12-git-security-vulnerability-announced/