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2020-05-23Added TeXLive's ulem package to also be builtMohammad Akhlaghi-1/+1
David reported this problem, it happened right after importing IEEEtran, but for some reason, it didn't happen for me.
2020-05-23Corrected name of listings package when installing it with texliveMohammad Akhlaghi-1/+1
When entering the name of the "listings" package, I had forgot to add the final 's', so it wasn't being installed on a clean system! I didn't have a problem until now, because it remained from previous builds.
2020-05-22Re-write of the paper to fit in ~6000 words and IEEE formatMohammad Akhlaghi-1/+3
Following the fact that the DSJ editor decided that this paper doesn't fit into their scope, we decided to submit it to IEEE's Computing in Science and Engineering (CiSE). So with this commit the text was re-written to fit into their style and word-count limitations.
2020-05-02First implementation of style in IEEEtran styleMohammad Akhlaghi-11/+6
The paper is no longer using LuaLaTeX, but raw LaTeX (that saves a DVI), it is so much faster! Initially I had used LuaLaTeX to use special fonts to resemble the CODATA Data Science Journal, but all that overhead is no longer necessary. Therefore I also removed the MANY extra LaTeX packages we were importing. The paper builds and is able to construct one of its images (the git-branching figure) with only 7 packages beyond the minimal TeX/LaTeX installation. Also in terms of processing it is so much faster. The text is just temporary now, and mainly just a place holder. With the next commit, I'll fill it with proper text.
2020-05-01Imported recent changes in Maneage, minor conflicts fixedMohammad Akhlaghi-25/+23
A few small conflicts showed up here and there. They are fixed with this merge.
2020-05-01Fixed OpenSSL deprecation bug on some OSs, causing problems in libgit2Boud Roukema-1/+5
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.
2020-04-28Astropy will no longer be installed by defaultMohammad Akhlaghi-1/+1
Until now Gnuastro and Astropy where installed by default in any clean build of Maneage. Gnuastro is used to do the demonstration analysis that is reported in the paper and Astropy was just there to help in testing the building of the MANY tools it depends on! It (and its dependencies) also had several papers that helped show software citation. However, as Boud suggested in task #15619, the burden of installing them for a new user may be too much and any future changes will cause merge conflicts. It may also give the impression that Maneage is only/mainly written for astronomers. So with this commit, I am removing Astropy as a default target. But we can only remove Gnuastro after we include an alternative analysis in the demonstration `delete-me' files. Following Boud's suggestion in that task, `TARGETS.conf' was also added to the files to be ignored in any future merge (in the checklist of `README-hacking.mk'). The solution was already described there, but mainly focused on the deleted `delete-me' files. So with this commit, I brought out this item as a more prominent item in the list. Maybe we can later add the analysis done in the Maneage paper (not yet published). In terms of testing the software builds, we already have task #15272 (Single target to build all high-level software, for testing) that aims to have a single configure option to install ALL high-level software and we can ask people to try if they like and report errors.
2020-04-27Configuration: improved version separation from tarball nameBoud Roukema-2/+2
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-22/+16
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.
2020-04-17Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-136/+8
A few minor conflicts came up that were easily fixed.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-133/+5
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.
2020-04-13Installation year removed from TeXLive installationMohammad Akhlaghi-6/+6
TeXLive recently transitioned from its 2019 version to its 2020 version thanks to Elham Saremi's trial of the this project. The fact that traditionally Maneage installs all TeXLive packages in a per-year directory is very annoying and required an update in the core Maneage system every year. So I suddently recognized that we can fix this by setting a different name for the directory holding the release year. This has been implemented with this commit. I have also done this change in the main Maneage branch for other projects to also benefit from this correction.
2020-04-13Configure (TeXLive): Year of distribution no longer in directoryMohammad Akhlaghi-6/+6
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.
2020-04-05Building Minizip 1.x instead of Minizip 2.xRaul Infante-Sainz-2/+5
Minizip is a dependency of XLSX I/O and until now, I was just using the most recent version I found (2.9.2), but XLSX I/O is written for the Minizip 1.x series, not 2.x. Somehow it didn't cause a crash on my computer!!! I think XLSX I/O's CMake is instructed to look into system directories by default when it doesn't find the directories in the given places. And because I had installed Minizip on my operating system, it did't complain. Upon trying the build on their systems, Yahya, Raul and Zahra reported a failure in the build of XLSX I/O which was due the to the problem above (we were installing the wrong version of Minizip!). With this commit, this has been fixed by installing the 1.x series of Minizip (whish is actually installed within zlib!). This commit was original done by Mohammad Akhlaghi.
2020-04-04Building Minizip 1.x instead of Minizip 2.xMohammad Akhlaghi-2/+5
Minizip is a dependency of XLSX I/O and until now, I was just using the most recent version I found (2.9.2), but XLSX I/O is written for the Minizip 1.x series, not 2.x. Somehow it didn't cause a crash on my computer!!! I think XLSX I/O's CMake is instructed to look into system directories by default when it doesn't find the directories in the given places. And because I had installed Minizip on my operating system, it did't complain. Upon trying the build on their systems, Yahya, Raul and Zahra reported a failure in the build of XLSX I/O which was due the to the problem above (we were installing the wrong version of Minizip!). With this commit, this has been fixed by installing the 1.x series of Minizip (whish is actually installed within zlib!).
2020-04-03CMake updated to version 3.17.0Raul Infante-Sainz-2/+2
With this commit, CMake has been updated to its most recent version. This upgrade has been done because in the installation of XLSX I/O on macOS laptop, it crashes complaining about C compiler "not able to compile a simple test program". After a fast search, I found it could be possible to just use the most recent version of CMake to solve the problem. But it didn't work. In any case, it is good to have the most recent version of CMake included.
2020-04-02Imported recent work on Maneage, minor conflicts fixedMohammad Akhlaghi-13/+16
A few minor conflicts occurred and were fixed.
2020-03-17Astroquery updated to version 0.4Raul Infante-Sainz-2/+2
In the last update of Astropy to version 4.0 they removed some things that the previous version of Astroquery needs. As a consequence, it is also necessary to update the Astroquery version to be a ble to run with the Astropy 4.0. With this commit, the update of Astroquery to it most recent version (0.4) has been done.
2020-03-02Described the first analysis phase with a demo subMakefileMohammad Akhlaghi-1/+2
Until now, there was no explanation on an actual analysis phase, therefore with this commit an example scenario with a readable Makefile is included. The Data lineage graph was also simplified to both be more readable, and also to correspond to this new explanation and subMakefile. Some random edits/typos were also corrected and some references added for discussion.
2020-02-24MissFITS is now added to the templateSurena Fatemi-0/+2
MissFITS is package for manipulating FITS files. I added it as my first commit to the project for educational purposes.
2020-02-16Building XLSX I/O and its dependencies: expat and minizipMohammad Akhlaghi-1/+7
Until now, there was no easy way to read/write `.xlsx' files (Microsoft Excel spreadsheets) within the template. But XLSX I/O provides to simple programs and some libraries to easily convert `.xlsx' files to CSV that can easily be read by any tool. This has also been implemented in the core template branch.
2020-02-16XLSX I/O installed with its two dependencies: expat and minizipMohammad Akhlaghi-0/+6
XLSX I/O is a very simple and fast program and library for reading and writing `.xls' and `.xlsx' files (mainly used by Microsoft Excel) to CSV files. It has two separate executables that can be called for an Excel file and will output a CSV plain text file that can then be used within the pipeline with more standard tools.
2020-01-31Configure step: compiler checks done before basic settingsMohammad Akhlaghi-0/+1
Until now, the project would first ask for the basic directories, then it would start testing the compiler. But that was problematic because the build directory can come from a previous setting (with `./project configure -e'). Also, it could confuse users to first ask for details, then suddently tell them that you don't have a working C library! We also need to store the CPATH variable in the `LOCAL.conf' because in some cases, the compiler won't work without it. With this commit, the compiler checking has been moved at the start of the configure script. Instead of putting the test program in the build directory, we now make a temporary hidden directory in the source directory and delete that directory as soon as the tests are done. In the process, I also noticed that the copyright year of the two hidden files weren't updated and corrected them.
2020-01-26General project structure and configuration describedMohammad Akhlaghi-1/+1
In the last few days I have been writing these two sections in the middle of other work. But I am making this commit because it has already become a lot! I am now going onto the description of `./project make'.
2020-01-20IMPORTANT!!! Configuration Makefiles now have a .conf suffixMohammad Akhlaghi-9/+9
Until now, the configuration Makefiles (in `reproduce/software/config/installation' and `reproduce/analysis/config') had a `.mk' suffix, similar to the workhorse Makefiles. Although they are indeed Makefiles, but given their nature (to only keep configuration parameters), it is confusing (especially to early users) for them to also have a `.mk' (similar to the analysis or software building Makefiles). To address this issue, with this commit, all the configuration Makefiles (in those directories) are now given a `.conf' suffix. This is also assumed for all the files that are loaded. The configuration (software building) and running of the template have been checked with this change from scratch, but please report any error that may not have been noticed. THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
2020-01-19GNU Make updated to version 4.3Mohammad Akhlaghi-2/+2
GNU Make 4.3 was just announced, so I have updated it here is well. This was important because until now the installable version was in alpha-mode (4.2.90), now its a stable version.
2020-01-18Raw draft (until now as a separate repository) importedMohammad Akhlaghi-1/+3
Until now, I was writing the paper without the template. But we will soon be adding a tutorial to the template, and I thought it will be good to have an example demonstration here too. So I just brought the hole project into the template structure, allowing us to add the template analysis later when its ready, and also allowing us to easily reproduce this paper ofcourse (without having to worry about the host's TeXLive installation.
2020-01-18First set of customizations doneMohammad Akhlaghi-3/+4
The unnecessary parts were removed and the project now runs.
2020-01-18Added mweights as a TeXLive packageMohammad Akhlaghi-1/+2
After a new rebuild of the project, I noticed that we now need to also build the `mweights' package.
2020-01-13Updated verion of Astropy to 4.0 the most recent oneRaul Infante-Sainz-2/+2
Newer versions of Astropy package has been released. With this commit, it has been updated. It has been increased from v3.2.1 to v4.0
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-14/+14
Now that its 2020, its necessary to include this year in the copyright statements.
2019-12-14Core R package is now in templateMohammad Akhlaghi-0/+2
With this commit, we now have the core R interpretter within the template. We should later include instructions to install R packages (possibly in a separate top-level Makefile like Python).
2019-12-13Necessary TeXLive packages installed: pdfescape letltxmacro bitsetMohammad Akhlaghi-1/+1
Recent builds of the template need these three packages to build the PDF. This was reported by Hamed Altafi.
2019-12-04Added pdftexmcds to the TeXlive packages to installMohammad Akhlaghi-1/+1
Until now we weren't including this package, but Alberto Madrigal recently reported that his build of the template failed because it needed it. With this commit, it is now being installed with the template.
2019-12-04Updated verions of Ghostscript and GnuastroMohammad Akhlaghi-4/+4
Newer versions of these packages have recently come out with major improvements, so they have been updated in the template.
2019-11-06GNU Project Debugger (GDB) and Pexpect can now be builtMohammad Akhlaghi-0/+4
These two packages are necessary to build the GNU C Library.
2019-11-06Perl is now built as a basic dependency of the templateMohammad Akhlaghi-0/+2
Perl is necessary to build Texinfo and later to build LaTeX. Until now we were just using the host operating system's installation of Perl, but in some instances that Perl can be too old and not suppor the features necessary. With this commit, Perl is now built from source during the basic installation step of the template. This was reported by Idafen Santana PĂ©rez, after trying the pipeline on an Amazon AWS EC2 system (a Linux distro by Amazon for its cloud services).
2019-11-03Corrected build of log4cxx by re-building the tarball usedMohammad Akhlaghi-2/+2
When building the log4cxx tarball from its Git history, I noticed that files with very long names are not packaged by tar (because by default Automake uses the ancient v7 tar format that only supports file names less than 99 characters). So I build the tarball with the `tar-ustar' option to Automake (by modifying the log4cxx source) and the resulting tarball was able to compile and run successfully. This has been described above the rule to build log4cxx and I also sent an email to their developing mailing list to inform them of this problem. If they address it, I will remove the note on the necessary corrections.
2019-10-31Minor corrections in distribution and autoconf prerequisite of automakeMohammad Akhlaghi-0/+2
Some minor corrections were made in the template: - When making the distribution, `.swp' files (created by Vim) are also removed. - Autoconf is set as a prerequisite of Automake I was also trying to add the Apache log4cxx, but its default 0.10.0 tarball needs some patches, so I have just left it half done until someone actually needs it and we apply the patch.
2019-10-30Tarballs set as order-only prerequisites, not needed for build callsMohammad Akhlaghi-1/+1
Until now, the tarballs were the first normal prerequisite of the software. As a result if their date changed, the whole software would be re-built. However, for tarballs specifically, we actually check their contents with a checksum, so their date is irrelevant (if its newer than the built program, but has the same checksum, there is no need to re-build the software). Also, calling the tarball name as an argument to the building process (for example `gbuild') was redundant. It is now automatically found from the list of order-only prerequisites within `gbuild' and `cbuild' (similar to how it was previously found in the `pybuild' for Python building). A `README.md' file has also been placed in `reproduce/software/make' to help describe the shared properties of the software building Makefiles. This will hopefully grow much larger in the future.
2019-10-29lmfit and its dependencies added, Python tarballs as prerequisiteMohammad Akhlaghi-5/+15
Python's `lmfit' module and all its major dependencies (`asteval', `corner', `emcee' and `uncertainties') have been included in the template. While doing this I noticed that if the tarballs are the last prerequisite of each software building rule, then when building in parallel, the template will immediately start building packages as soon as the first one is downloaded. Not like the current way that it will attempt to download several, then start building. For now, this has been implemented in the Python build rules for all the modules and we'll later do the same for the other programs and libraries. This also motivated a simplification of the `pybuild' function: it now internally looks into the prerequisites and selects the tarball from the prerequisite that is in the tarballs directory. This isn't a problem for the build, but I just don't understand why Python can't recognize the version of `emcee', Python reads the version of `emcee' as `0.0.0'! But it doesn't cause any crash in the build, so for now its fine.
2019-10-28HEALPix, Autoconf and Automake now in libraryMohammad Akhlaghi-0/+8
The tarball of HEALPix includes multiple languages and doesn't include the ready-to-run GNU Build System by default, we actually have to build the `./configure' script for the C/C++ libraries. So it was necessary to also include GNU Autoconf and GNU Automake as prerequisites of HEALPix. However, the official GNU Autoconf tarball (dating from 2012) doesn't build on modern systems, so I just cloned it from its source and bootstrapped it and built its modern tarball which we are using here.
2019-10-24Several more LSST pipeline dependencies are addedMohammad Akhlaghi-0/+18
The following software are added with this commit: eigency, esutil, flake8, future, galsim, lsstdesccoord, pybind11 and pyflakes.
2019-10-24APR, APR Utility, Boost and Eigen are now availableMohammad Akhlaghi-0/+8
As part of an effort to bring in all the dependencies of the LSST Science pipeline (which includes the last commit), these software are now available in the template.
2019-10-24GNU Bison, GNU Help2man and Flex are now availableMohammad Akhlaghi-0/+6
With this commit these three software packages are now installable with this template.
2019-10-10Including trimspaces from TeXLiveMohammad Akhlaghi-1/+2
Carlos Morales Socorro reported that his LaTeX build was missing the `trimspaces' package, so it is now included in the pipeline.
2019-10-01New versions for ImageMagick, Python, Numpy Scipy and MatplotlibMohammad Akhlaghi-10/+10
It was some time since these three software were not updated! With this commit the template now uses the most recent stable release of these packages. Also, the hosting server for ImageMagick was moved to my own webpage because unfortunately ImageMagick removes its tarballs from its own version.
2019-09-06Updated versions of several softwareMohammad Akhlaghi-21/+21
New versions of astropy, bash, cmake, curl, findutils, gawk, gcc, ghostscript, git, make, gsl had recently come so they are updated with this commit. About GNU Findutils and GNU Make: I was bootstrapping (building the tarball of) these two separately separately because their standard tarball release had problems on some systems. Both have been updated now so I am no longer using my own webpage as their main URL. A special note about GNU Make. I just noticed that during bootstrapping, GNU Make would use the fixed version string of `4.2.90' for any commit!!! But fortunately they have officially released their 4.2.90 version, so we are safely using their own webpage. The only difference is the compression format. My old bootstrapped build was `tar.lz', but the standard release is `tar.gz'. Also, all the basic programs (installed in `.local/bin') in `basic.mk' are now existance-only dependencies (after a `|'). Because later programs just use them at a very basic level, so there is no need to rebuild everything when Bash gets updated for example.
2019-08-22Fixed typo in beautifulsoup4 Python package checksum nameRaul Infante-Sainz-2/+2
Until this commit, the name of the variable for `beautifulsoup4' checksum was wrong, and because of that, it was not able to install it. With this commit, `beautifulsoup-checksum' has been replaced for `beautifulsoup4-checksum' in the `reproduce/software/make/python.mk' Makefile, and the problem has been fixed. This was not noticed previously because this Python package is only installed when some high level programs are requested to be installed. With this commit the version of `imagemagick' program has been also updated because the previous version is not available in the official website anymore.
2019-08-21Gnuastro's configuration file updated for version 0.10Mohammad Akhlaghi-2/+8
Recently the version of Gnuastro in the template was updated to version 0.10. However, I had forgot to update the `gnuastro.conf' file to fit with the necessary new features of this version. The new general Gnuastro configuration file is now added instead. This bug was reported by Deepak.