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2023-05-23Configuration: portability fixes in Less and WCSLIBHEADmaneageMohammad Akhlaghi-12/+31
SUMMARY: no change is necessary in your project, unless you use the Fortran features of WCSLIB in your project. Until now, there were two compilation failures on recent macOS computers with an M1 CPU: Less would crash because it couldn't find the relevant PCRE (perl-compatible regular expression) libraries and WCSLIB would crash because the LLVM compiler's Fortran features could not be built. With this commit, both issues have been fixed by disabling the relevant feature. Extensive comments have been placed in both places in case your project needs these features, so please see the comments in the relevant part of 'reproduce/software/make/basic.mk' for Less and 'reproduce/software/make/high-level.mk' for WCSLIB. In fact the previous solution (where we would not have Fortran features in WCSLIB on macOS systems was problematic and non-reproducibile (the features of WCSLIB depended on the operating system!). Another minor change was that for macOS, we now directly use the version-string of WCSLIB to fix the internal linking issue there. As a result, WCSLIB is no longer a "Version-dependent build" software (in 'reproduce/software/config/versions.conf'). Recall that these are software that when changing the version, it is also necessary to inspect their build recipe. These two issues and their fix were discovered and fixed with the help of James Robinson.
2023-05-07Copyright years: updated to 2023, accompanied by some minor fixesMohammad Akhlaghi-102/+104
SUMMARY: just house-cleaning, no need to do anything major in your branch. Just update the copyright years in files that you have added. Until now, the latest copyright years of the whole Maneage source code was 2022! As of this commit, we have already moved to 2023 for 5 months! Furthermore, there were a few other minor issues that needed correction: - The URL to download input datasets wasn't quoted in 'initialize.mk' or the download script! As a result, when the input URL had characters that are meaningful to the shell (like '&'), the download command would not work. - The only program that had 'make check' in the 'basic.mk' programs was MPFR. At that stage, we still haven't built our own compiler at this stage, this is not accurate. - The 'pyerfa' and 'extension-helpers' packages in Python need 'setuptools_scm' on some systems. But until now, it was not in the list of their prerequisites. With this commit, all the issues above have been corrected.
2022-09-02Added server authentication and FITS DATASUM for verficiationMohammad Akhlaghi-69/+216
SUMMARY: Nothing special is necessary for your existing projects. This commit just addds two new features (read the commit description for more): 1. To provide a user and password to servers that need authentication before they allow downloading of proprietary data, 2. To use the FITS Standard's DATASUM for file verification (for cases where the file is not static on the server, and is generated upon receiving your download request). Until now, Maneage didn't have any infrastructure for databases that require authentication (through a user or password, when calling 'wget'). Furthermore, when the downloaded file is automatically generated by the server upon request, the server usually adds metadata (like file date, or query number and etc) in the header. Therefore the simple SHA256 checksum of the file would differ on every download! This made it very hard to verify if the data (not headers) are unchanged. With this commit, both these problems have been addressed: - Server authentication: the 'reproduce/software/config/LOCAL.conf' now contains three new variables for this purpose. With them, you can give your username and password, along with the authentication method of the server. The comments on top of these three variables give a full description of their usage. - Verifying only the data in a file (ignoring the headers): The 'reproduce/analysis/config/INPUTS.conf' now accepts two new optional variables for each input file using the FITS standard's DATASUM convention: 'INPUT-%-fitsdatasum' and 'INPUT-%-fitshdu'. If the SHA256 isn't specified for a file, Maneage will use these to verify the file. With the latter, you specify the HDU of the data you want to verify and with the former you give the DATASUM value for that HDU. As the name suggests, this is only valid for FITS files. If we find other formats that support a similar behavior, we can add this feature for those formats also. This is also thoroughly discussed in the comments of 'reproduce/analysis/config/INPUTS.conf'. This commit was done with the help of Pedram Ashofte Ardakani, Sepideh Eskandarlou and Mohammadreza Khellat.
2022-08-13IMPORTANT: Software updateMohammad Akhlaghi-347/+988
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.
2022-07-13Configuration: astropy added as a dependency of astrometry.netMohammad Akhlaghi-0/+1
Until now, astrometry.net didn't explicitly depend on Astropy! However, astrometry.net does depend on it (or pyfits) and will crash later when running if astropy or pyfits aren't installed. We hadn't noticed this until now because of the data reduction projects we had built Astropy independently of astrometry.net! We noticed this bug in a project that didn't use astropy! With this commit, astropy is built as a dependency of astrometry.net and afterwards (during the analysis), astrometry.net was able to run without any crash. This bug was found with the help of Zohreh Ghaffari.
2022-06-19Initialize: including *.conf files from the preparation phaseRaul Infante-Sainz-17/+31
Until now, when some configuration files were generated in the preparation phase, only the auto-generated (in the preparation phase) Makefiles (with the suffix '*.mk') were always included in 'initialize.mk'. As a consequence, if there were any configuration files (with suffix '*.conf'), they would not be automatically added, and it was necessary to manually include them. Since auto-generated configuration files are also one common output of the preparation phase of a project, it is better to include them automatically. With this commit, the '*.conf' configuration files generated in the preparation phase are added by 'initialize.mk' automatically (if necessary). In the process, the comments in the final target of 'reproduce/analysis/make/prepare.mk' were updated to be more clear.
2022-06-11Configuration: replacing hard coded PATH in SConsRaul Infante-Sainz-2/+35
Until now, SCons (a high-level Python package builder) was using the OS PATH when building packages (like Imfit that use SCons), not Maneage's PATH. This happened even though 'reproduce/software/make/high-level.mk' completely removes the host's PATH to avoid any host OS dependency. After some investigation, we recognized that SCons hard-codes operating system directories into its source! This doesn't let the user (Maneage in this case; that builds packages that use SCons) customize the search directories. As a result, even though we have our own linker and compiler in Maneage, SCons would go and use the operating system's linker and compiler, causing a leak in the controlled environment we plan to achieve in Maneage. Not letting users customize such critical components of a software and hard-coding parameters is bad program design! This wasn't noticed until now because most operating systems we tested on were relatively recent and the versions of Maneage's linker and the OS linker weren't too different! However, after testing on a much older operating system (GNU/Linux 4.4.0-143-generic X86_64), the operating system's linker couldn't build Imfit (that uses SCons) and would crash. With this commit, after unpacking SCons's source (but before building or installing it), we have added a step to modify SCons's source and replace the hard-coded PATH directories with Maneage's PATH. This fixed the problem. This bug has been fixed with the help of Mohammad Akhlaghi.
2022-06-11IMPORTANT: download.mk removed, content moved to initialize.mkMohammad Akhlaghi-127/+132
SUMMARY: no special action should be necessary; but its an important update in low-level Maneage infra-structure (related with downloading and setting input checksums). Until now, we had a separate 'download.mk' as one of the default sub-Makefiles that should have been loaded in all the 'top-*.mk' files after 'initialize.mk'. This was due to historic reasons: until Commit 91799fe4b6d, we had to manually make some changes in 'download.mk' for every input file we defined in 'INPUTS.mk' (which was very inconvenient, and not easily possible for a large number of files!). But since Commit 91799fe4b6d, those manual changes are no longer necessary, and a normal user will hardly ever need to touch the contents of 'download.mk' (which also had one effective rule). Furthermore, based on shared projects with Zohre Ghaffari and Sepideh Eskandarlou (which involved a large number of large files), we recognized that it is very inconvenient to download a file once, update its checksum, and re-run Maneage (so the validation works). A robust solution was necesary to let project authors download the data and automatically update the checksum. With this commit, to help in high-level project management in Maneage, the single, and generic rule of 'download.mk' has been moved to 'initialize.mk', enabling us to fully remove this extra sub-Makefile from Maneage's source. Furthermore, with this commit, a usable solution to the automatic updating of the checksum has also been implemented (which has been described in the comments of 'INPUTS.conf'): the users can now set the checksum to '--auto-replace--'. In this case, the download rule (now in 'initialize.mk') will automatically update that line of 'INPUTS.conf' and add the checksum instead. After './project make' is complete, when the user runs 'git diff', they can see all the updated checksums in the source of their project and commit the updated 'INPUTS.conf' into the source so this will not be necessary later. Two other smaller issues have also been addressed in this commit: - There was an extra ',' in the call to 'filter-out' when we defined 'prepare-dep' in 'reproduce/analysis/make/prepare.mk'. This would cause a crash (with Make complaining that there is no rule for target 'initialize.mk,': notice the extra ','). With this commit, that extra ',' has been removed and the problem was solved. - The build recipe of Imfit (in 'reproduce/software/make/high-level.mk'), had two SPACE characters after '--no-openmp' which would make the reading hard. They have been updated to one SPACE.
2022-06-10Configuration: num Apple M1 cores, ImageMagick dep. on GhostScriptRaul Infante-Sainz-4/+15
Until now, we never had the opportunity of testing Maneage in a macOS laptop with an Apple M1 CPU (tested on macOS Monterey; version 12.3). The way of getting the number of cores for this type of CPU is different from other macOSs. It was therefore necessary to change the parameters of the 'sysctl' for properly accounting this CPU. Furthermore, until now, GhostScript and ImageMagick were built independently. However, they were not linked. As a consequence, when trying to obtain an image with the program 'convert' (that belongs to ImageMagick'), it complains about not having some fonts. This can be fixed by letting 'ImakeMagick' know that 'GhostScript' libraries are available. With this commit, GhostScript has been set as a dependency of ImageMagick, and ImageMagick is configured with the '--with-gslib' flag. Furthermore, to read the number of M1 CPU cores, we distinguish between the Apple M1 and all other CPU types. However, Maneage still does not successfully build all the software until the end of the configure step. There are other problems that need to be fixed for Apple's M1.
2022-06-10Housekeeping: some portability issues fixed; four software updatesMohammad Akhlaghi-55/+140
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'.
2022-05-15Configuration: necessary compiler flag added for file in CentOS 7Manuel Solimano-0/+1
Until now, Maneage failed to build the 'file' program on at least one machine running CentOS version 7.9.2009 (with Linux kernel 3.10.0, and GCC 4.8.5) when running './project configure'. With this commit (as suggested by the error message issued by the compiler), the '-std=c99' is passed to the compiler in the 'file' recipe (within 'basic.mk'). This flag puts the compiler in C99 mode, which forces it to compile code according to the 1999 edition of the C standard. This was necessary for older versions of GCC (for example GCC 4.8.5 was released in June 2015); hence why others hadn't reported this issue until now. After this fix, File compiles succesfully on such systems; without causing any problem with newer GCC versions (tested in GCC 12.1.0). This issue was solved with the help of Pedram Ashofte Ardakani and Mohammad Akhlaghi.
2022-05-10initialize.mk: Git call in variable works with LD_LIBRARY_PATHMohammad Akhlaghi-37/+43
Until now, the '$(project-commit-hash)' Make variable of 'initialize.mk' simply called 'git' to find the commit hash. However, due to one of the recent software updates, we noticed that this command is no longer working (and the project commit hash wasn't getting printed in the PDF)! The problem was that Maneage's Git, couldn't find the 'libiconv' library that it was built with. With this commit, the '$(shell' command that calls Git, first exports 'LD_LIBRARY_PATH' to Maneage's software build directory. As a result, the Git command can work and will report the commit as a LaTeX macro to be used in the paper. To avoid relying on PATH outside of Make recipes, we now also directly call the Git executable with Maneage. Some other minor issues have been found and fixed in this commit: - README-hacking.md: some minor edits and typo corrections. - initialize.mk: the '$(curdir)' variable is now used in several places that we were calling 'pwd'. - versions.conf: 'xlsxio-version' now included with other programs. Until now it was commented because GCC 11.1.0 had issues with it. However, GCC 11.2.0 doesn't have a problem any more, so it has been returned to the list of all high-level programs. - xorg.mk: used same format to comment recipe lines as the other Makefiles (a '#' followed by a TAB). - preamble-pgfplots.tex: lines to comment for building an EPS figure with PGFPlots have been re-formatted to be more human-readable.
2022-05-08./project: make clean removes extra tex files in top source directoryPedram Ashofteh Ardakani-0/+6
Until now, the './project make clean' command would only clean (remove) the PDF file from the top source directory. However, if a user would run LaTeX outside of Maneage, many extra latex output such as *.aux, *.log, *.synctex and etc would be produced in the top source directory. These files can interfere with './project make'. With this commit, when './project make clean' is run, any possibly existing LaTeX temporary files will also be deleted from the top source directory. This problem was first reported by Matin Torkian.
2022-04-20Updated Git, Coreutils and Emacs, new script to prepare tarballsPedram Ashofteh Ardakani-8/+192
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/
2022-04-15./project: new --refresh-bib to force-build bibliographyPedram Ashofteh Ardakani-0/+2
Until now, the bibliography was only re-built when 'tex/src/references.tex' was modified. This is useful in many regular cases because building the bibliography can slow down the build and it is in-efficient to built it in every edit of the text of the paper. However, it can be inconvenient when a change in the paper's bibliography is necessary, without actually editing 'references.tex' (for example when you are removing a citation from the text). This happens because Make is only sensitive to file modification time. In this case, Make does not see the need to create a new 'bib' file because the 'tex/src/reference' is not changed, and only the 'paper.tex' is changed. Make is totally 'blind' to the new 'citation' defined in 'paper.tex'. As a workaround, until now users were forced to manually change the 'tex/src/references.tex' file modification date: either by altering the content, or using the 'touch' command. With this commit, the '--refresh-bib' is added to './project' arguments to address this issue. It will just 'touch' the 'tex/src/references.tex' file before calling Make. In effect, this will 'force' Make to create the bibliography file, even if 'tex/src/references.tex' hasn't been updated.
2022-04-15IMPORTANT: more generic, robust and secure INPUTS.conf and download.mkMohammad Akhlaghi-112/+126
SUMMARY: it is necessary to update your 'INPUTS.conf' and 'download.mk'. Until now, adding an input file involved several steps that needed manual (and inconvenient!) intervention: for every file, you needed to define four variables in 'INPUTS.conf', and in 'reproduce/analysis/make/download.mk' you had to use a (complex for large number of files) shell 'if/elif/else' condition to link the names of the input files to those variables. Besides inconvenience, this could cause bugs (typos!). Furthermore, a basic MD5 checksum was used for verifying the files. With this commit, a new structure has been defined for 'INPUTS.conf' that (thanks to some pretty useful GNU Make features), removes the need for users to manually edit 'reproduce/analysis/make/download.mk', and reduces the number of variables necessary for each file to three (from four). Furthermore, we now use the SHA256 checksum for input data validation. Regarding the trick used in 'INPUTS.conf' (form the newly added description in 'download.mk'): In GNU Make, '.VARIABLES' "... expands to a list of the names of all global variables defined so far" (from the "Other Special Variables" section of the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only used for input files, we find all the variables that contain the input file names (the '%' is the filename). Finally, using the pattern-substitution function ('patsubst'), we remove the fixed string at the start and end of the variable name. Steps you need to take: - INPUTS.conf: translate your old format to the new format (after carefully reading the description in the comments at the start of the file). After applying the new standards, you don't need to use the variables of 'INPUTS.conf' directly in your Makefiles! For example if one of your input datasets is called 'abc.fits', the checksum variable will be 'INPUT-abc.fits-sha256' and in your high-level Makefiles, you can simply set '$(indir)/abc.fits' as a prerequisite (like you probably did already). - reproduce/analysis/make/download.mk: for the definition and rule of 'inputdatasets', simply use the Maneage branch, and remove anything you had added in your project. In the process, I also noticed that 'README-hacking.md' still referred to 'master' as the main project branch, while we have used 'main' in the paper (and is the common convention with Git).
2022-03-10Bug fix: wrong definition of the prepare directory is correctedRaul Infante-Sainz-1/+1
Until now, the definition of the prepare directory was wrong (not in the 'analysis' directory of the build directory). I noticed this after an update of the Maneage branch of one project that requires the prepare step. With this commit, this problem has been fixed.
2022-03-07paper.tex: fix double dash that was not showing up in output pdfPedram Ashofteh Ardakani-5/+5
Until now, the 'double dash' (i.e. \texttt{--}) in the default 'paper.tex' would only print one (longer) dash in the output pdf. With this commit, the double dashes are replaced with '-{}-' in the LaTeX source as a workaround suggested by Stefan Kottwitz in [1]. [1] https://latex.org/forum/viewtopic.php?f=44&t=4670&start=0
2022-01-21IMPORTANT: Updates to almost all softwareMohammad Akhlaghi-1813/+2760
This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2
2021-10-01Configuration: GCC not linking to system libunwind (crashed GCC's build)Boud Roukema-1/+10
This commit provides a hack/correction to the unwrapped GCC source files that sym-links the generic file 'libgcc/unwind-generic.h' to the two directories in which a file includes "unwind.h" or <unwind.h>. The aim is that the gcc compilation system uses this header file from the internal gcc source files instead of searching for a system-level file 'unwind.h'. This commit also unaliases two 'ls' commands in some build recipes of 'basic.mk' in case the host system (normally at user level) has aliased the command to something like 'ls -F'. In the situation that sometimes occurs of library files being given executable status, the '-F' decorative option could lead to an asterisk being included in a string that is not expected to contain asterisks. If the system shell does not contain the 'alias' command at all, then a fallback of 'true' should provide safe behaviour. The notation of the 'sed' command is also clarified. This solves bug #61240: https://savannah.nongnu.org/bugs/index.php?61240
2021-07-12Configuration: fixed bugs in building of OpenSSL and GettextMohammad Akhlaghi-4/+5
Until now, the 'RPATH' variable (specifying where to look for shared libraries) wasn't being set in the 'libcrypto' library of OpenSSL (it was only set for the 'libssl' library). Also, Gettext used the host Emacs for some operations during installation that could cause the following crash (because we are giving priority to local libraries, which the host Emacs doesn't recognize): emacs: /BDIR/libcrypto.so.1.1: version `OPENSSL_1_1_1b' not found (required by /lib64/libk5crypto.so.3) With this commit both these bugs have been fixed: 1) Patchelf is run on the 'libcrypto' library also and 2) we pass the '--without-emacs' configuration option to the configure script of Gettext. These bugs were found by Elham Saremi.
2021-06-25Configuration: New check to see if /dev/shm allows executionBoud Roukema-27/+61
On systems that allow it (like GNU/Linux systems), Maneage will build the necessary software in shared memory (a directory that is actually in the RAM, not on an SSD/HDD, on GNU/Linux systems, it is '/dev/shm'). This allows Maneage to operate faster and not harm the HDD/SSD with all the temporary writing of many small files. Until now, we would only check that this directory exists and that it has enough space. However, some systems also set the 'noexec' flag on shared memory for security reasons [1]. This causes Maneage to crash upon building of the software in later phases. With this commit, at the very start of the configuration step, and after all other shared-memory checks are done, a dummy executable script file is created there and its execution is tested. If it doesn't work, shared memory will not be used at all. In the process, the steps dealing with the software building directory in the configure script have been brought in one place and comments were added to further clarify every step. This commit was initially done by Boud Roukema and later edited by Mohammad Akhlaghi. [1] https://web.archive.org/web/20210624192819/https://serverfault.com/questions/72356/how-useful-is-mounting-tmp-noexec
2021-06-03Update publications: Peper+Roukema publishedBoud Roukema-18/+22
This commit updates some of the publication data in README-hacking.md : Peper+Roukema (2021) is now published in MNRAS and Akhlaghi+ (2021) is published online and very close to getting a conventional volume and page number. :) See task https://savannah.nongnu.org/task/?15736 for ideas of how to make a more systematic publication list instead one managed by prose text. There are already too many non-automated places for publication lists where we have to copy/paste our publication data again and again and again and ... This commit also adds the softwareheritage ID that we have in the content of Akhlaghi+2021 (without the extra context, because as a URL that's very long). There are plenty of arguments to be made each way for different versions of the swh IDS. One advantage of the 'rev' ID is that the hash is the original (full) git hash, which is what I've done for the elaphrocentre and subpoisson papers.
2021-06-03Configuration: improved warning when TeX Live couldn't be installedBoud Roukema-8/+12
Once a year, the texlive update system becomes incompatible with the version from the previous year. Since a texlive install failure is considered non-fatal by 'high-level.mk', so until now, the user could miss the printed message and mistakenly believe that the configure is valid. This commit explicitly adds a 10-second delay that should be enough for a user who does the 'configure --existing-conf' step alone to notice that there is a TeX Live problem. It also adds the explicit instruction of how to allow an update from an earlier year's texlive installer to the warning message (by deleting '.build/software/tarballs/install-tl-unx.tar.gz'). I had to rediscover this a few times for old Maneage installs. Also, a few lines in 'reproduce/software/shell/configure.sh' were indented with a TAB (that is not recommended because TAB is displayed with different widths on different browsers). So while doing this commit, those TABs were also converted to a space.
2021-04-25README.md: edited steps to only build software env in Docker imageMohammad Akhlaghi-76/+151
Until now, while the series of steps mentioned in 'README.md' were complete, they had some implicit thing in them that made it a little hard to run as a checklist (the commands to do some basic things weren't included). Also, it was recommending to run a long 'docker run ...' command, which wasn't too user friendly. With this commit, the series of steps is now a complete checklist, containing every step. Also, the checklist now recommends putting the long 'docker run' command inside a script called 'docker-run' that will also do a 'sudo' internally (thus making things very easy for a first-time user). Also, since the 'docker-run' script contains host OS-specific directory names, it should not be under control, so it has been added to the '.gitignore' file in case users decide to keep this same name (which is recommended).
2021-04-17IMPORTANT: print-general-metadata new name for print-copyrightMohammad Akhlaghi-77/+115
Summary: - Use the new name of this variable in your Makefiles. - In 'metadata.conf', remove fixed URL prefixes for DOIs ('https://doi.org/') or arXiv ('https://arxiv.org/abs'). Until now, the Make variable that would print the general metadata (of whole project) into each to-be-published dataset was called 'print-copyright'! But it now does much more than simply printing the copyright, it will also print a lot of metadata like arXiv ID, Zenodo DOI and etc into plain-text outputs. The out-dated name could thus be misleading and cause confusions. With this commit, the variable is therefore called 'print-general-metadata'. After merging your project with the Maneage branch, please replace any usage of 'print-copyright' to 'print-general-metadata'. Also with this commit, 'README-hacking.md' mentions 'metadata.conf' and 'print-general-metadata' in the "Publication checklist" section and reminds you to keep the first up to date, and use the second in your to-be-published datasets.
2021-03-28Configuration: corrected check of group nameMohammad Akhlaghi-11/+11
When built in 'group' mode, the write permissions of all created files will be activated for a certain group of users in the host operating system. The user specifies the name of the group with the '--group' option at configure time. At the very start, the './project' script checks to see if the given group name actually exists or not (to avoid hard-to-debug errors popping up later). Until now, the checking 'sg' command (that was used to build the project with group-writable permissions) would always fail due to the excessive number of redirections. Therefore, it would always print the error message and abort. With this commit, the output of 'sg' is no longer re-directed (which also helps users in debuggin). If the group does actually exist, it will just print a small statement saying so, and if it fails, the error message is printed. This fixed the problem, allowing maneage to be built in group-mode. I also noticed that the variable name keeping the group name ('reproducible_paper_group_name') used the old name for the project (which was "Reproducible paper template"! So it has been changed/corrected to 'maneage_group_name'.
2021-03-26Initialization: removed other Gnuastro-specific featuresMohammad Akhlaghi-8/+3
In the previous commit, some Gnuastro-specific initializations were removed but a few more cases remained that are removed with this commit.
2021-03-26./project: unused --minmapsize option is removedMohammad Akhlaghi-6/+0
Until now, the './project' script included an '--minmapsize' option which is an option to one of the original programs that was used in Maneage (Gnuastro). Such an option doesn't exist in many other programs, so it is not a suitable option for the generic Maneage project (and can just cause confusion). It was also not used in any part of Maneage any more! With this commit, this option is removed from the core Maneage './project' script and if any project uses it, they can implement it in their own branch.
2021-03-24Maneage installation: removed TCL as a dependency of SWIGMohammad Akhlaghi-1/+2
Until now the SWIG software would use the host operating system's packages to find the TCL configuraiton (which we don't install yet in Maneage). In particular, you can see the error during its configuration here: .... checking for pkg-config... pkg-config checking for Tcl configuration... found /usr/lib/tclConfig.sh /usr/lib/tclConfig.sh: line 2: dpkg-architecture: command not found /usr/lib//tcl8.6/tclConfig.sh: line 2: dpkg-architecture: com. not found With this commit, TCL has been disabled when building SWIG with the '--without-tcl' option. Later, when we add TCL in Maneage, we can remove this option.
2021-03-20Configuration: nullability-completeness warnings suppressedRaul Infante-Sainz-3/+13
With a recent update of macOS systems (macOS Big Sur 11.2.3 and Xcode 12.4), there are many warnings when building C programs (for example the simple program we compile to check the compiler, or some of the software like `gzip'). It prints hundreds of warning lines for every source file that are irrelevant for our builds, but really clutters the output. With this commit, these warnings are disabled by adding `-Wno-nullability-completeness' to the 'CPPFLAGS' environment variable. This has also been added to the very first check of the C compiler in the configure step.
2021-03-20Configuration: --debug option available in this phase alsoRaul Infante-Sainz-13/+40
Until now, each time there was a problem in the configuration of Maneage'd projects and debugging was necessary, we had to take the following changes: - Run the configuration on a single thread ('-j1') to see the building of only the problematic software. - Disable the Zenodo check manually by commenting those parts of 'reproduce/software/shell/configure.sh'. Because the internet connection wastes a few seconds and is thus very annoying during repeated runs! - Manually remove the '-k' option that was passed to Make (when building the software). With the '-k', Make keeps going with the execution of other targets if something crashes and this usually causes confusions during the debugging. Doing the manual changes within the code was both very annoying and prone to errors (forgetting to correct it!). With this commit, the existing '--debug' option has been generalized to the software configuration phase of Maneage also. Until now, it was only available in the analysis phase (and would directly be passed to the 'make' command that would run the analysis). When this option is used, and the project is in the software configuration phase, the Zenodo check won't be done, it will use one single thread ('-j1'), and it will stop the execution as soon as an error occurs (Make is not run with '-k').
2021-02-12Installation: minor correction in links to system librariesMohammad Akhlaghi-2/+6
Until now when making a link to the system's 'dl' and 'pthread' libraries we were simply linking the installed location on the system (in '/usr/lib'). However, in some systems, these may themselves be links to other locations and this could cause linking problems. With this commit, we now use 'realpath' to extract the absolute address of the final file that the libraries may link to, and directly link to them. A minor cosmetic correction was also made in the build rule for CFITSIO: the long line was broken into two!
2021-01-12Default LaTeX preamble: some packages moved to preamble-project.texMohammad Akhlaghi-70/+42
Until now, important LaTeX packages like 'caption' (for managing figure captions), 'hyperref' (for managing links) and 'xcolor' (for managing colors) were being loaded inside the optional 'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove this file from loading when you use custom journal sytels. However, these packages will often be necessary after loading special journal styles also. With this commit, these packages are now loaded into LaTeX as part of the 'tex/src/preamble-project.tex' file. This file is in charge of LaTeX settings that are custom to the project and independent of its style. Several other small corrections are made with this commit: - I noticed that './project make texclean' crashes if no PDF exists in the working directory! So a '-f' was added to the 'rm' command of the 'texclean' rule. - As part of the LaTeX Hyperref, we can set general metadata or properties for the PDF (that aren't written into the printable PDF, but into the file metadata). They can be viewed in many PDF viewers as PDF properties. Until now, we were only using the '\projecttitle' macro here to write the paper's title. However, thanks to the recently added 'reproduce/analysis/config/metadata.conf', we now have a lot of useful information that can also go here. So the 'metadata-copyright-owner' is now used to define the PDF author, and the project's 'metadata-git-repository' and commit hash are written into the PDF subject. But to import these, it was necessary to define them as LaTeX macros, hence the addition of these macros in 'initialize.mk'. - Some extra packages that aren't necessary to build the default PDF were removed in 'preamble-project.tex'.
2021-01-10make dist: removing temp files moved after project-specific filesMohammad Akhlaghi-6/+7
Until now, when you ran './project make dist', first it would delete the temporary files (like files ending in '~' or '.swp' created by some editors), then it had a place to add project-specific operations for the distribution. However, in the process of cleaning the temporary files, it would 'cd' into the directory that would later be packaged. So project-specific operations would first have to 'cd' back into the top source directory. This was prone to hard-to-find bugs. With this commit, to avoid the problem the project-specific operations are now placed before the cleaning phase. This is also technically good because in the project-specific operations there may also be temporary files that shouldn't go into the distribution tarball.
2021-01-09IMPORTANT: analysis outputs written in BDIR/analysisMohammad Akhlaghi-66/+211
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'.
2021-01-04README-hacking.md: edits and improvements to publication checklistMohammad Akhlaghi-23/+40
After going through the publication checklist, some edits were made to make things more clear. Also, an item was added to remind the project author that the commit hashes on the uploaded data files should be the same.
2021-01-04README.md: summary Dockerfile with all necessary lines in one stepMohammad Akhlaghi-0/+26
Until now, the description in 'README.md' to build the Dockerfile in 'README.md' had one item per line, thoroughly describing the reason behind that line. But in many cases, the user is already familiar with Docker (or has already read through the items) and just wants to have the Dockerfile ready fast. In these cases, all those extra explanations are annoying. With this commit, an item '0' has been added at the start of the item list for summary. It only contains the necessary Dockerfile contents with no extra explanation.
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
2021-01-02./project make: new texclean targetMohammad Akhlaghi-1/+7
Until now there was only a 'clean' (to delete all files created during the 'make' phase) and the 'distclean' (to delete all files during configuration and make). But sometimes we don't want to delete all the files created during the full 'make' phase, we only want to delete the files that were created by LaTeX for building the paper. Witht this commit, a new target has been added for this job. You can now run the following command for this job: ./project make texclean Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz' directory under that location is recreated, ready for a future build).
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-87/+87
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.
2020-12-14Better warnings when maneage branch not present and PDF not builtMohammad Akhlaghi-12/+31
Until now, there was no warning when the 'maneage' branch didn't exist in the Git history. This can happen when you forget to push the 'maneage' branch to a remote for your project, and you later clone your project from that remote (for example on another computer). We use the 'maneage' branch to report the latest commit hash and date in the final paper (which can greatly help future readers). Since we check the 'maneage' branch on every run of './project make' (in 'initialize.mk') this would result in a printed statement like this: fatal: Not a valid object name maneage Also until now, the description of what to do when TeXLive wasn't installed properly wasn't complete: it didn't mention that it is necessary to delete the TeXLive target files. This could confuse users (they would re-run './project configure -e', but with no effect). With this commit, for the 'maneage' branch issue a complete warning will be printed. Telling the user what to do to get the 'maneage' branch (and thus fix this warning). Also, the LaTeX macros that go in the paper are now red when the 'maneage' branch doesn't exist, telling the user to see the printed warning (thus encouraging the user to get the branch). For the TeXLive issue, the necessary commands to run are now also printed in the warning.
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/+13
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.
2020-12-01README-hacking.md: recommended to push maneage after mergingMohammad Akhlaghi-4/+11
Until now at the end of the updating process, we hadn't explicity talked about pushing the branches. So people would usually only push their 'master' branch to their remote. While the merged 'master' branch does contain the commits from the core Maneage branch, having a no-updated 'maneage' branch reference on their remote can be confusing. With this commit, at the end of the process to merge with the 'maneage' branch we explicitly recommend to push both the 'master' and 'maneage' branches.
2020-12-01Default paper: macros available for date of commits citedMohammad Akhlaghi-5/+12
Until now, Maneage only provided the commit hashes (of the project and Maneage) as LaTeX macros to use in your paper. However, they are too cryptic and not really human friendly (unless you have access to the Git history on a computer). With this commit, to make things easier for the readers, the date of both commits are also available as LaTeX macros for use in the paper. The date of the Maneage commit is also included in the acknowledgements. Also, the paragraph above the acknowledgements has been updated with better explanation on why adding this acknowledgement in the science papers is good/necessary.
2020-12-01IMPORTANT: organizational improvements in Maneage TeX sourcesMohammad Akhlaghi-334/+298
This only concerns the TeX sources in the default branch. In case you don't use them, there should only be a clean conflict in 'paper.tex' (that is obvious and easy to fix). Conflicts may only happen in some of the 'tex/src/preamble-*.tex' files if you have actually changed them for your project. But generally any conflict that does arise by this commit with your project branch should be very clear and easy to fix and test. In short, from now on things will even be easier: any LaTeX configuration that you want to do for your project can be done in 'tex/src/preamble-project.tex', so you don't have to worry about any other LaTeX preamble file. They are either templates (like the ones for PGFPlots and BibLaTeX) or low-level things directly related to Maneage. Until now, this distinction wasn't too clear. Here is a summary of the improvements: - Two new options to './project make': with '--highlight-new' and '--highlight-notes' it is now possible to activate highlighting on the command-line. Until now, there was a LaTeX macro for this at the start of 'paper.tex' (\highlightchanges). But changing that line would change the Git commit hash, making it hard for the readers to trust that this is the same PDF. With these two new run-time options, the printed commit hash will not changed. - paper.tex: the sentences are formatted as one sentence per line (and one line per sentence). This helps in version controlling narrative and following the changes per sentence. A description of this format (and its advantages) is also included in the default text. - The internal Maneage preambles have been modified: - 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have been merged into one preamble file called 'tex/src/preamble-maneage-default-style.tex'. This helps a lot in simply removing it when you use a journal style file for example. - Things like the options to highlight parts of the text are now put in a special 'tex/src/preamble-maneage.tex'. This helps highlight that these are Maneage-specific features that are independent of the style used in the paper. - There is a new 'tex/src/preamble-project.tex' that is the place you can add your project-specific customizations.