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2019-10-29Minor edits to suggestion on using shared memoryMohammad Akhlaghi-0/+0
The edits help it be more clear, and remind the reader to delete any remaining file in the RAM in the end.
2019-10-29Suggestion on good usage of /dev/shm in README-hacking.mdMohammad Akhlaghi-0/+0
When you are working with large files and there is some good RAM in the system (large/powerful computers), it is beneficial to work in the shared memory directory and not the actual persistent storage (like HDD or SSD). With this commit, a fully working demo has been added to `README-hacking.md' (under the tips of "Make programming") to show how to effectively work in situations like this.
2019-10-28HEALPix, Autoconf and Automake now in libraryMohammad Akhlaghi-0/+0
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/+0
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/+0
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/+0
With this commit these three software packages are now installable with this template.
2019-10-19Minor improvments in packaging of project with make distMohammad Akhlaghi-0/+0
The steps to package the project have been made slightly more clear and also the temporary directory that is created for packaging is deleted after the tarball is made.
2019-10-11Properly working make clean when in group modeMohammad Akhlaghi-0/+0
Until now, when you ran `make clean', all the directories under `$(BDIR)/tex/' would be deleted except for `macros' and `build'. This was good for the single-user mode. But in group mode, this would delete the user-specific TeX build directory because its called `build-USER', not `build'. With this commit, to fix the problem, we define the new `texbtopdir' and based on the group condition, and use that to specify which directory to not delete.
2019-10-10Including trimspaces from TeXLiveMohammad Akhlaghi-0/+0
Carlos Morales Socorro reported that his LaTeX build was missing the `trimspaces' package, so it is now included in the pipeline.
2019-10-07Software citations now use modern ADS link for adsurlMohammad Akhlaghi-0/+0
Until now, some software were using the depreciated ADS URL (`http://adsabs.harvard.edu....') and some were using the modern one (`http://ui.adsabs.harvard.edu'). With this commit, to be consistent they all link to the modern URL.
2019-10-02Possibile to use download-multi-try script without locksMohammad Akhlaghi-0/+0
Until now, this script would always only work with a file-lock. But in some scenarios, we might want to download in parallel. For example when the system has multiple ports to the internet. With this commit, we have added this feature: when the lockfile name is `nolock', it won't lock and will download in parallel.
2019-10-01Minor corrections in configure and prepare phaseMohammad Akhlaghi-0/+0
Since ImageMagick can take long to build, we are now building it in parallel. Also, the part where we replace an `_' with `\_' in the software version at the end of the configure script was removed. It is more clear/readable that the actual rule that includes such a name deals with the underline (as is the case for `sip_tpv' which already dealt with it). Finally, I noticed that the checks at the start of `top-prepare' were missing new-lines. I had forgot that the Make single-shell variable isn't activated in this stage yet.
2019-10-01Infrastructure to keep preparation resultsMohammad Akhlaghi-0/+0
A special directory is now defined in `initialize.mk' that can be used in both the preparation and build phases. Also, the contents of prepared results can now be conditionally read during `./project make'.
2019-10-01Preparation phase added before final buildingMohammad Akhlaghi-0/+0
In many real-world scenarios, `./project make' can really benefit from having some basic information about the data before being run. For example when quering a server. If we know how many datasets were downloaded and their general properties, it can greatly optmize the process when we are designing the solution to be run in `./project make'. Therefore with this commit, a new phase has been added to the template's design: `./project prepare'. In the raw template this is empty, because the simple analysis done in the template doesn't warrant it. But everything is ready for projects using the template to add preparation phases prior to the analysis.
2019-10-01New versions for ImageMagick, Python, Numpy Scipy and MatplotlibMohammad Akhlaghi-0/+0
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.
2019-09-28Main project script sets executable flags at configure timeMohammad Akhlaghi-0/+0
Until now, when the project's source was downloaded from something like arXiv, in `README.md', we were instructing them to set the executable flags of all the files that need it. But except for `./project', the reader shouldn't have to worry about the project internals! Once its executable, `./project' can easily fix the executable flags of all the files that need it automatically. With this commit, in `README.md', we just instruct the reader to set the executable flag of `./project' and any other file that needs an executable flag is given one at the start of the set of commands for `./project configure'. In customized projects, if an author needs executable flags on any other files, they can easily add it there without involving the user.
2019-09-28Corrected name of SExtractor in its final targetMohammad Akhlaghi-0/+0
Until now we were calling it `Sextractor', but the official way of writing it is `SExtractor'. With this commit, this has been corrected.
2019-09-27Changing to the cloned directory added to README.mdMohammad Akhlaghi-0/+0
Konrad Hinsen pointed out that this part was missing from the instructions in `README.md' after cloning. So it is added.
2019-09-26Minor edits/clarifications in README.mdMohammad Akhlaghi-0/+0
The two modifications to the LaTeX source of an arXiv-downloaded source weren't rendered properly on Gitlab, so they are corrected to be in the same line and not have a separate code-block.
2019-09-26Working project when downloaded from arXivMohammad Akhlaghi-0/+0
Until now, we were assuming that the users would just clone the project in Git. But after submitting arXiv:1909.11230, and trying to build directly from the arXiv source, I noticed several problems that wouldn't allow users to build it automatically. So I tried the build step by step and was able to find a fix for the several issues that came up. The scripting parts of the fix were primarily related to the fact that the unpacked arXiv tarball isn't under version control, so some checks had to be put there. Also, we wanted to make it easy to remove the extra files, so an extra `--clean-texdit' option was added to `./project'. Finally, some manual corrections were necessary (prior to running `./project', which are now described in `README.md'. Most of the later steps can be automated and we should do it later, I just don't have enough time now.
2019-09-26Minor edit in README-hacking.mdMohammad Akhlaghi-0/+0
The description of arXiv:1909.11230 was slightly modified to be in the same format as the other papers.
2019-09-26arXiv:1909.11230 added as example paper using this templateMohammad Akhlaghi-0/+0
This paper was published on arXiv today and is a good example for people to see the application of this system in practice.
2019-09-25Won't copy previous distribution builds in new distributionMohammad Akhlaghi-0/+0
Until now, the pipeline was instructed to only ignore the current temporary project distribution directory. So if there were directories from previous builds, they were wrongly included in the current tarball. With this commit, we don't just ignore the directory of the current distribution, but generally, all directories starting with `paper-v*'.
2019-09-18README.md written to be more generic and easy to customizeMohammad Akhlaghi-0/+0
Until now customizing it was a little more detailed, for example the copyright statement wasn't generic and was about "this template". So the user would have to correct it. With this commit, the copyright statment just says "this project", so it can apply to the raw template and also any customization of it. Also, some minor edits were made in the various parts of the text to make it more clear.
2019-09-16Configure script won't allow build directory to be under sourceMohammad Akhlaghi-0/+0
Users that are not familiar with the file structure of the project may specify the current directory (to-level source directory) as their build-directory. This will cause a crash right after answering the questions, where `rm' will complain about `tex/build' not being deleted because it exists as a directory. To avoid such confusing situtations, the configure script now checks if the build directory is actually a sub-directory of the source. If it is, it will complain with a short message and abort. Also, a `CAUTION' statment has been put in the initial description, right ontop of the question. This bug was reported Carlos Allende Prieto and David Valls-Gabaud.
2019-09-16Git checksum printed even when on a tagMohammad Akhlaghi-0/+0
Until now, when the commit was tagged, `git describe' would just print the tag and no longer the commit checksum. This is bad because the checksum is a much more robust way to confirm the point in history. With this commit the `--long' option has been added to `git describe' to fix this issue. From now on, when we are on a tag, it will print the tag followed by a `-0-' and the first characters of the checksum.
2019-09-16Distribution tarball now builds in arXivMohammad Akhlaghi-0/+0
`./project make dist' will package all the LaTeX-specific files (and analysis source files) into one `tar.gz' file that is ready to upload to servers like arXiv. However, it wasn't updated for some time, so running it would complain about not having a `configure' script in the top of the project. With this commit, it now works with the new file-structure of the project and also copies all the BibLaTeX source files and `paper.bbl' into the top tarball directory, which allows arXiv to build the paper as intended. The output of `./project make dist' has been uploaded and tested on arXiv and it is built by arXiv perfectly. Also, a short description of all the special `make' targets was added to the output of `./project --help'.
2019-09-15Minor edits on the git bundle suggestion of README-hacking.mdMohammad Akhlaghi-0/+0
After a re-read on Gitlab, it has been slightly edited to be more clear.
2019-09-15Added tip on bundling Git history in one fileMohammad Akhlaghi-0/+0
When you want to publish your project, it is very convenient to have a single file that contains the whole history. So a tip is added to `README-hacking.md' that describes how to do this with `git bundle'.
2019-09-15BibLaTeX configured to only print initials of given namesMohammad Akhlaghi-0/+0
Until now, we weren't explicitly asking for BibLaTeX to build the citations with only initial of the author's given names. Therefore when one BibTeX entry had a full given name and another had only initials, this would also be reflected in the paper's bibliography. With this commit, the `giveninits=true' option is given to BibLaTeX to always only print the initial character of an author's given name.
2019-09-15SExtractor BibTex entry updated with ADS's exported formatMohammad Akhlaghi-0/+0
Until now the SExtractor BibTeX entry has the first-name and family name in the same field, while the family-name should be in curly braces. Also, it was missing an ADS URL. So the default ADS generated BibTeX entry for SExtractor is now used instead of the old one.
2019-09-07Updates in BibLaTeX preambleMohammad Akhlaghi-0/+0
In some cases, users of the template may not need the other template headers, they may only want `preamble-biblatex.tex'. But `xcolor' needs to be loaded before being able to load the various colors we use in the references. So to be self-consistent, it is loaded. Also, the default style was also printing the month of the publication which is not common. So a line was added to clear the `month' field before building the Bibliography.
2019-09-06Updated versions of several softwareMohammad Akhlaghi-0/+0
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.
2019-08-22Adding fpack and funpack in the installation of CFITSIORaul Infante-Sainz-0/+0
Until this commit, `fpack' and `funpack' were not installed by default with the installation of CFITSIO. It is necessary to explicity do a `make fpack' and `make funpack' to have them installed. With this commit, these two programs have been added.
2019-08-22Fixed typo in beautifulsoup4 Python package checksum nameRaul Infante-Sainz-0/+0
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.
2019-08-21Using libgit2 implementation of libconv with the option -DUSE_ICONV=OFFRaul Infante-Sainz-0/+0
When trying to install `libgit2' on my macOS system, it complains about not finding `_iconv*' functions! But apparently `libgit2' has its own implementation of `libiconv' that it uses if it can't find `libiconv' on macOS. So, the solution to this problem was to add `-DUSE_ICONV=OFF' to the configuration options of `libgit2'. I reported this issue that now is fixed thanks to the help of Mohammad Akhlaghi.
2019-08-01Updated version of mpi4py doesn't conflict with OpenMPIMohammad Akhlaghi-0/+0
Until now, in version 3.0.1, mpi4py couldn't be built with the most recent version of OpenMPI. However, after trying the next version (3.0.2), I noticed that it builds successfully without a problem.
2019-08-01Typo in previous commit correctedMohammad Akhlaghi-0/+0
After making the previous commit, I noticed an extra line (redundantly defining a wrong `BASH_ENV') that should have been deleted. It has been corrected.
2019-08-01Bash startup script for every recipeMohammad Akhlaghi-0/+0
Until now the only way to define the environment of the Make recipes was through the exported Make variables (mostly in `initialize.mk' for the analysis steps for example). However, there is only so much you can do with environment variables! In some situations you want slightly more complicated environment control, like setting an alias or running of scripts (things that are commonly done in the `~/.bashrc' file of users to configure their interactive, non-login shells). With this commit, a `reproduce/software/bash/bashrc.sh' has been defined for this job (which is currently empty!). Every major Make step of the project adds this file as the `BASH_ENV' environment variable, so the shell that is created to execute a recipe first executes this file, then the recipe. Each top-level Makefile also defines a `PROJECT_STATUS' environment variable that enables users to limit their envirnoment setup based on the condition it is being setup (in particular in the early phase of `basic.mk', where the user can't make any assumption about the programs and has to write a portable shell script).
2019-07-31GCC: libstdc++ has a link to libiconvMohammad Akhlaghi-0/+0
After adding the libiconv library to the template, the C++ library uses three of its functions (`libiconv', `libiconv_open' and `libiconv_close'). However, it doesn't explicity link with it inside its shared library! I tried by exporting `LIBS=-liconv' before the GCC configure script but it crashed as soon as it went on to the second GCC building stage (because this environment variable was no longer present there). I also tried adding the C++ configure option of `--enable-cstdio' to the GCC configure options (so it doesn't use iconv according to the manual), but it made no change. With this commit, as a brute-force solution, `patchelf --add-needed' is run on the installed `libstdc++.so', so `libiconv.so' is explicitly included inside the `libstdc++' shared library. This bug was found by Roberto Baena Galle while trying to load Matplotlib (which needed the C++ library). This fixes bug #56702.
2019-07-29Checking software tarball checksums before building softwareMohammad Akhlaghi-0/+0
Until now, there was no check on the integrity of the contents of the downloaded/copied software tarballs, we only relied on the tarball name. This could be bad for reproducibility and security, for example on one server the name of a tarball may be the same but with different content. With this commit, the SHA512 checksums of all the software are stored in the newly created `checksums.mk' (similar to how the versions are stored in the `versions.mk'). The resulting variable is then defined for each software and after downloading/copying the file we check to see if the new tarball has the same checksum as the stored value. If it doesn't the script will crash with an error, informing the user of the problem. The only limitation now is a bootstrapping problem: if the host system doesn't already an `sha512sum' executable, we will not do any checksum verification until we install our `sha512sum' (as part of GNU Coreutils). All the tarballs downloaded after GNU Coreutils are built will have their checksums validated. By default almost all GNU/Linux systems will have a usable `sha512sum' (its part of GNU Coreutils after all for a long time: from the Coreutils Changelog file atleast since 2013). This completes task #15347.
2019-07-28Corrected typo in environment before running makeMohammad Akhlaghi-0/+0
We recently moved the system's `rm' program absolute address to a shell variable that is found during the `./project' script. But I had forgot to account for the difference between the Make and Bash variable naming differences. I had also forgot to add a value to the HOME variable. With this commit both are corrected: the system's `rm' path is now called `sys_rm' and the HOME variable is set.
2019-07-28Single wrapper instead of old ./configure, Makefile and ./for-groupMohammad Akhlaghi-0/+0
Until now, to work on a project, it was necessary to `./configure' it and build the software. Then we had to run `.local/bin/make' to run the project and do the analysis every time. If the project was a shared project between many users on a large server, it was necessary to call the `./for-group' script. This way of managing the project had a major problem: since the user directly called the lower-level `./configure' or `.local/bin/make' it was not possible to provide high-level control (for example limiting the environment variables). This was especially noticed recently with a bug that was related to environment variables (bug #56682). With this commit, this problem is solved using a single script called `project' in the top directory. To configure and build the project, users can now run these commands: $ ./project configure $ ./project make To work on the project with other users in a group these commands can be used: $ ./project configure --group=GROUPNAME $ ./project make --group=GROUPNAME The old options to both configure and make the project are still valid. Run `./project --help' to see a list. For example: $ ./project configure -e --host-cc $ ./project make -j8 The old `configure' script has been moved to `reproduce/software/bash/configure.sh' and is called by the new `./project' script. The `./project' script now just manages the options, then passes control to the `configure.sh' script. For the "make" step, it also reads the options, then calls Make. So in the lower-level nothing has changed. Only the `./project' script is now the single/direct user interface of the project. On a parallel note: as part of bug #56682, we also found out that on some macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set to blank. This is no problem because RPATH is automatically set in macOS and the executables and libraries contain the absolute address of the libraries they should link with. But having `DYLD_LIBRARY_PATH' can conflict with some low-level system libraries and cause very hard to debug linking errors (like that reported in the bug report). This fixes bug #56682.
2019-07-26Better explanation of suggested commit messages in REAME-hacking.mdMohammad Akhlaghi-0/+0
Until now the description of the commit message guidelines wasn't clear enough and could cause confusion, in particular because it didn't describe why some basic formatting issues are mandatory. With this commit, it is explained that the main reason we require contributors for follow this format is "consistency" within the project. Also generally it was edited to become more elaborate and explain the points more clearly. I also ran a spell check over the whole file and fixed a few typos. This correction was suggested by Mohammad-reza Khellat.
2019-07-26PatchELF built statically and updatedMohammad Akhlaghi-0/+0
Until now, like all other software, PatchELF would install with dynamic linking. However, PatchELF links with `libstdc++' so on one system, I noticed that PatchELF gives a segmentation fault and corrupts `libstdc++' while correcting its RPATH (after installing GCC). The solution is to build PatchELF statically. With this commit, we force PatchELF to be built statically (it only installs on GNU/Linux systems anyway, so there is no problem with static linking on macOS). This solved the problem on that system. While looking at its documentation, I also noticed that a new version of PatchELF has been released after almost three years, so it has been updated in the template also. This fixes bug #56673.
2019-07-25Updated version of WCSLIB to 6.3, previously 6.2Mohammad Akhlaghi-0/+0
Some bugs have been fixed in the new version of WCSLIB, so it has been updated in the template.
2019-07-25Corrected preparation to build software in shared memoryMohammad Akhlaghi-0/+0
The previous implementation of using shared memory to build software was edited to be more clear and less prone to errors.
2019-07-24libgit2 updated to version 0.28.2, from 0.26.0Mohammad Akhlaghi-0/+0
More than two releases and bug fixes have been made to libgit2. So we are now using a more recent version in the template.
2019-07-24Temporary software building done in shared memory if availableMohammad Akhlaghi-0/+0
Until now, the template would unpack the software and build them directly in the build directory of each project. After installation, the whole unpacked directory is deleted. However, building the software involves the reading and writing of millions of files, so on the long run, it can be bad for the non-volatile memory (HDDs or SSDs), it can also be slightly slow. To fix this, if the system has a shared-memory directory (commonly named `/dev/shm'), we can do the temporary building of the software there. The great thing about this unique directory is that it is actually in the RAM, not on the HDD/SSD. This can slightly improve the speed (not much probably), but more importantly it will not do any long-term harm to the host's HDDs/SSDs. With this commit, when there is a shared memory directory mounted in `/dev/shm', and it has enough space (currently set to 2GB), the `./configure' script will make `.build/software/build-tmp' as a symbolic link to a fixed directory there. Otherwise, it will just build it as a directory in the project's shared directory. The structure has been defined in such a way that we can later easily add different standard shared-memory locations (for different operating systems). This completes task #15336.
2019-07-15Minor corrections in configure and high-levelMohammad Akhlaghi-0/+0
Configure script: when `texlive-ready-tlmgr' is not created, it is similar to not having installed TeXLive. A check was added so in this scenario the `./configure' script doesn't crash. high-level.mk: `cairo' and `pixman' are now installed in parallel and with `V=1' (so the full compilation and linking command is printed).