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2020-12-28Minor edits, updated citation to published Menke+20 paperMohammad Akhlaghi-1/+3
Some minor edits were made to the paper to shorten it. In particular the example of IPOL was removed from the main body of the paper, and we'll just rely on the more extensive review of IPOL in the appendix. I also updated the referee report to account for the new Appendix A that is just an extended introduction. Also, I noticed that the Menke+20 paper that we replicate here has recently been published in the iScience journal. So its bibliography was updated from the bioarXiv information to the journal information. Also, the number of words (after removing abstract and captions and accounting for figures) is now only printed when the project is built with '--no-appendix'. This was done because this information is extra/annoying/unnecessary for the case where there is an appendix.
2020-11-26All the referee points have been answeredMohammad Akhlaghi-2/+2
There is an answer for all the referee points now. I also did some minor edits in the paper. But we are still over the limit by around 250 words. The only remaining point that is not yet addressed (and has '####' around it) is the discussion on parallelization and its effect on reproducibility.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-5/+7
A new directory has been added at the top of the project's source called 'peer-review'. The raw reviews of the paper by the editors and referees has been added there as '1-review.txt'. All the main points raised by the referees have been listed in a numbered list and addressed (mostly) in '1-answers.txt'. The text of the paper now also includes all the implemented answers to the various points.
2020-11-20Highlighting changes can now be toggled at run-timeMohammad Akhlaghi-3/+14
Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro that defines two LaTeX macros: '\new' and '\tonote'. When '\highlightchanges' was defined, anything that was written within '\new' became dark green (highlighting new things that have been added). Also, anything that was written in '\tonote' was put within a '[]' and became dark red (to show that there is a note here that should be addressed later). When '\highlightchanges' wasn't defined, anything within the '\new' element would be black (like the rest of the text), and the things in '\tonote' would not be shown at all. Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex' (to toggle the modes above) would create a different Git hash and has to be committed. But this different commit hash could create a false sense in the reader that other things have also been changed and the only way they could confirm was to actually go and look into the project history (which they will not usually have time to do, and thus won't be able to trust the two modes of the text). Also, the added highlights and the note highlights were bundeled together into one macro, so you couldn't only have one of them. With this commit, the choice of highlighting either one of the two is now done as two new run-time options to the './project' script (which are passed to the Makefiles, and written into the 'project.tex' file which is loaded into 'paper.tex'). In this way, we can generate two PDFs with the same Git commit (project's state): one with the selected highlights and another one without it. This issue actually came up for me while implementing the changes here: we need to submit one PDF to the journal/referees with highlights on the added features. But we also need to submit another PDF to arXiv and Zenodo without any highlights. If the PDFs have different commit hashes, the referees may associate it with other changes in any part of the work. For example https://oadoi.org/10.22541/au.159724632.29528907 that mentions "Another version of the manuscript was published on arXiv: 2006.03018", while the only difference was a few words in the abstract after the journal complained on the abstract word-count of our first submission (where the commit hashes matched with arXiv/Zenodo).
2020-11-04Appendix of long paper added, optionally we can disable itMohammad Akhlaghi-2/+6
Given the referee reports, after discussing with the editors of CiSE, we decided that it is important to include the complete appendix we had before that included a thorough review of existing tools and methods. However, the appendix will not be published in the paper (due to the strict word-count limit). It will only be used in the arXiv/Zenodo versions of the paper. This actually created a technical problem: we want the commit hash of the project source to remain the same when the paper is built with an appendix or without it. To fix this problem the choice of including an appendix has gone into the 'project' script as a run-time option called '--no-appendix'. So by default (when someone just runs './project make'), the PDF will have an appendix, but when we want to submit to the journal, or when the appendix isn't needed for a certain reason, we can use this new option. The appendix also has its own separate bibliography. Some other corrections made in this commit: 1. Some new references were added that had an '_' in their source, they were corrected in 'references.tex'. 2. I noticed that 'preamble-style.tex' is not actually used in this paper, so it has been deleted.
2020-09-09Imported recent important fixes in Maneage, no conflictsMohammad Akhlaghi-8/+8
There weren't any conflicts in this merge.
2020-09-08Removed all occurances of IFS in low-level scriptsMohammad Akhlaghi-8/+8
Following the previous commit, we recognized that the 'IFS' terms are not necessary and can be even cause problems. So all their occurances in the scripts of Maneage have been removed with this commit.
2020-09-03Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-30/+32
Only two small conflicts came up: * The addition of the hardware architecture macro in 'paper.tex' (which was removed for now, but will be added as the referee has requested within the text). * The usage of "" around directory variables in 'paper.mk'.
2020-08-28Plain text editors: nano in basic, emacs and vim in high-levelMohammad Akhlaghi-11/+13
While a project is under development, the raw analysis software are not the only necessary software in a project. We also need tools to all the edit plain-text files within the Maneaged project. Usually people use their operating system's plain-text editor. However, when working on the project on a new computer, or in a container, the plain-text editors will have different versions, or may not be present at all! This can be very annoying and frustrating! With this commit, Maneage now installs GNU Nano as part of the basic tools. GNU Nano is a very simple and small plain text editor (the installed size is only ~3.5MB, and it is friendly to new users). Therefore, any Maneaged project can assume atleast Nano will be present (in particular when no editor is available on the running system!). GNU Emacs and VIM (both without extra dependencies, in particular without GUI support) are also optionally available in 'high-level.mk' (by adding them to 'TARGETS.conf'). The basic idea for the more advanced editors (Emacs and VIM) is that project authors can add their favorite editor while they are working on the project, but upon publication they can remove them from 'TARGETS.conf'. A few other minor things came up during this work and are now also fixed: - The 'file' program and its libraries like 'libmagic' were linking to system's 'libseccomp'! This dependency then leaked into Nano (which depends on 'libmagic'). But this is just an extra feature of 'file', only for the Linux kernel. Also, we have no dependency on it so far. So 'file' is not configured to not build with 'libseccomp'. - A typo was fixed in the line where the physical core information is being read on macOS. - The top-level directories when running './project shell' are now quoted (in case they have special characters).
2020-08-27Machine architecture and byte-order available as LaTeX macroMohammadreza Khellat-19/+19
Until now, no machine-related specifications were being documented in the workflow. This information can become helpful when observing differences in the outcome of both software and analysis segments of the workflow by others (some software may behave differently based on host machine). With this commit, the host machine's 'hardware class' and 'byte-order' are collected and now available as LaTeX macros for the authors to use in the paper. Currently it is placed in the acknowledgments, right after mentioning the Maneage commit. Furthermore, the project and configuration scripts are now capable of dealing with input directory names that have SPACE (and other special characters) by putting them inside double-quotes. However, having spaces and metacharacters in the address of the build directory could cause build/install failure for some software source files which are beyond the control of Maneage. So we now check the user's given build directory string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(', ')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different directory.
2020-08-20Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-5/+57
Some very minor conflicts came up and were easily corrected. They were mostly in parts that are also shared with the demonstration in the core Maneage branch.
2020-08-13--check-config option now prints names of last 5 installedMohammad Akhlaghi-3/+54
Until now, './project --check-config' would only print the names of the software that were being built. Besides that, it is also useful to know which packages have most recently finished. With this commit, we now print the last 5 built software packages with '--check-config' also, and the output has also been placed in a row of '='s to help separate it in each round. Also some more sanity checks have been added so it doesn't print error messages.
2020-07-04Some command line messages of ./project didn't mention shellMohammad Akhlaghi-2/+3
Until now, the 'shell' mode of the './project' script was missing in the top output of './project --help' and in the error message printed when no operation was given, or when more than one operation was given. This is now corrected.
2020-06-27Imported recent work in master, minor conflict fixed in paper.mkMohammad Akhlaghi-27/+72
Only two conflicts came up in the newly added comments of 'paper.mk' in the Maneage branch. It happened because in this project we don't use 'pdflatex', but 'latex' alone.
2020-06-27IMPORTANT: many improvements to low-level software building phaseMohammad Akhlaghi-22/+63
POSSIBLE EFFECT ON YOUR PROJECT: The changes in this commit may only cause conflicts to your project if you have changed the software building Makefiles in your project's branch (e.g., 'basic.mk', 'high-level.mk' and 'python.mk'). If your project has only added analysis, it shouldn't be affected. This is a large commit, involving a long series of corrections in a differnt branch which is now finally being merged into the core Maneage branch. All changes were related and came up naturally as the low-level infrastructure was improved. So separating them in the end for the final merge would have been very time consuming and we are merging them as one commit. In general, the software building Makefiles are now much more easier to read, modify and use, along with several new features that have been added. See below for the full list. - Until now, Maneage needed the host to have a 'make' implementation because Make was necessary to build Lzip. Lzip is then used to uncompress the source of our own GNU Make. However, in the minimalist/slim versions of operating systems (for example used to build Docker images) Make isn't included by default. Since Lzip was the only program before our own GNU Make was installed, we consulting Antonio Diaz Diaz (creator of Lzip) and he kindly added the necessary functionality to a new version of Lzip, which we are using now. Hence we don't need to assume a Make implementation on the host any more. With this commit, Lzip and GNU Make are built without Make, allowing everything else to be safely built with our own custom version of GNU Make and not using the host's 'make' at all. - Until recently (Commit 3d8aa5953c4) GNU Make was built in 'basic.mk'. Therefore 'basic.mk' was written in a way that it can be used with other 'make' implementations also (i.e., important shell commands starting with '&&' and ending in '\' without any comments between them!). Furthermore, to help in style uniformity, the rules in 'high-level.mk' and 'python.mk' also followed a similar structure. But due to the point above, we can now guarantee that GNU Make is used from the very first Makefile, so this hard-to-read structure has been removed in the software build recipes and they are much more readable and edit-friendly now. - Until now, the default backup servers where at some fixed URLs, on our own pages or on Gitlab. But recently we uploaded all the necessary software to Zenodo (https://doi.org/10.5281/zenodo.3883409) which is more suitable for this task (it promises longevity, has a fixed DOI, while allowing us to add new content, or new software tarball versions). With this commit, a small script has been written to extract the most recent Zenodo upload link from the Zenodo DOI and use it for downloading the software source codes. - Until now, we primarily used the webpage of each software for downloading its tarball. But this caused many problems: 1) Some of them needed Javascript before the download, 2) Some URLs had a complex dependency on the version number, 3) some servers would be randomly down for maintenance and etc. So thanks to the point above, we now use the Zenodo server as the primary download location. However, if a user wants to use a custom software that is not (yet!) in Zenodo, the download script gives priority to a custom URL that the users can give as Make variables. If that variable is defined, then the script will use that URL before going onto Zenodo. We now have a special place for such URLs: 'reproduce/software/config/urls.conf'. The old URLs (which are a good documentation themselves) are preserved here, but are commented by default. - The software source code downloading and checksum verification step has been moved into a Make function called 'import-source' (defined in the 'build-rules.mk' and loaded in all software Makefiles). Having taken all the low-level steps there, I noticed that there is no more need for having the tarball as a separate target! So with this commit, a single rule is the only place that needs to be edited/added (greatly simplifying the software building Makefiles). - Following task #15272, A new option has been added to the './project' script called '--all-highlevel'. When this option is given, the contents of 'TARGETS.conf' are ignored and all the software in Maneage are built (selected by parsing the 'versions.conf' file). This new option was added to confirm the extensive changes made in all the software building recipes and is great for development/testing purposes. - Many of the software hadn't been tested for a long time! So after using the newly added '--all-highlevel', we noticed that some need to be updated. In general, with this commit, 'libpaper' and 'pcre' were added as new software, and the versions of the following software was updated: 'boost', 'flex', 'libtirpc', 'openblas' and 'lzip'. A 'run-parts.in' shell script was added in 'reproduce/software/shell/' which is installed with 'libpaper'. - Even though we intentionally add the necessary flags to add RPATH inside the built executable at compilation time, some software don't do it (different software on different operating systems!). Until now, for historical reasons this check was done in different ways for different software on GNU/Linux sytems. But now it is unified: if 'patchelf' is present we apply it. Because of this, 'patchelf' has been put as a top-level prerequisite, right after Tar and is installed before anything else. - In 'versions.conf', GNU Libtool is recognized as 'libtool', but in 'basic.mk', it was 'glibtool'! This caused many confusions and is corrected with this commit (in 'basic.mk', it is also 'libtool'). - A new argument is added to the './project' script to allow easy loading of the project's shell and environment for fast/temporary testing of things in the same environment as the project. Before activating the project's shell, we completely remove all host environment variables to simulate the project's environment. It can be called with this command: './project shell'. A simple prompt has also been added to highlight that the user is using the Maneage shell!
2020-06-17Text surrounding software acknowledgements as a configuration fileBoud Roukema-5/+6
Until now, the English texts that embeds the list of software to acknowledge in the paper was hard-wired into the low-level coding ('reproduce/software/shell/configure.sh' to be more specific). But this file is very low-level, thus discouraging users to modify this surrounding text. While the list of software packages can be considered to be 'data' and is fixed, the surrounding text to describe the lists is something the authors should decide on. Authors of a scientific research paper take responsibility for the full paper, including for the style of the acknowledgments, even if these may well evolve into some standard text. With this commit, authors who do *not* modify 'reproduce/software/config/acknowledge_software.sh' will have a default text, with only a minor English correction from earlier versions of Maneage. However, Authors choosing to use their own wording should be able to modify the text parameters in `reproduce/software/config/acknowledge_software.sh` in the obvious way. This is much more modular than asking project authors to go looking into the long and technical 'configure.sh' script. Systematic issues: the file `reproduce/software/config/acknowledge_software.sh` is an executable shell script, because it has to be called by `reproduce/software/shell/configure.sh`, which, in principle, does not yet have access to `GNU make` (if I understand the bootstrap sequence correctly). It is placed in `config/` rather than `shell/`, because the user will expect to find configuration files in `config/`, not in `shell/`. A possible alternative to avoid having a shell script as a configure file would be to let `reproduce/software/config/acknowledge_software.sh` appear to be a `make` file, but analyse it in `configure.sh` using `sed` to remove whitespace around `=`, and adding other hacks to switch from `make` syntax to `shell` syntax. However, this risks misleading the user, who will not know whether s/he should follow `make` conventions or `shell` conventions.
2020-06-17New target --dist-software to package all necessary software tarballsMohammad Akhlaghi-0/+3
When publishing a project, it is necessary to also publish the source code of all necessary software of the project. We had recently added a new './project make' target called 'dist-software' for this job, but had forgotten to add it in the output of './project --help'! There was also a small bug inside of it that didn't allow the successful copying of the created tarball to the top project directory. With this commit, an explanation for this target has been added in the output of './project --help' and that bug has been fixed.
2020-06-16Using type to see if pdftotext exists or notMohammad Akhlaghi-1/+1
Until now we were using 'which' for this job, but throughout Maneage, we have used 'type', so to help in consistancy, we also use 'type' for this final command for this project also.
2020-06-09Two minor corrections to avoid warnings in make and make cleanMohammad Akhlaghi-5/+10
There were two small warnings that are removed with this commit: - In the end, when we print the number of words in the PDF, we hadn't accounted for the fact that 'paper.pdf' doesn't always exist (for example when './project make clean' is run). So a check was added to only print the number of words when a PDF exists. - I noticed that the '$(texdir)/to-publish' directory was being built both in 'initialize.mk' and in 'demo-plot.mk'. So the one in 'demo-plot.mk' has been removed.
2020-06-09Imported Maneage, minor conflicts fixed, a bug found and fixedMohammad Akhlaghi-1/+2
Some minor conflicts came up in 'initialize.mk' and 'verify.mk'. For the former, I chose the version on Maneage, for the latter, I kept the 'master' version on the checksums of this project, but kept the Maneage version for the rest of the improvements there (like printing the verified files as LaTeX comments in 'verify.tex'. While testing the conflicts, I noticed a bug (in the LaTeX macro for the number of years in the Menke+20 paper) in the previous build, thanks to the verification step :-)! Fortunately it wasn't actually printed in the PDF, so a normal reader won't recognize. The bug was caused by the recently added meta-data/commented lines in the 'tools-per-year.txt' file: when calculating the number of years studied in that paper, we were simply counting all the lines and we had forgot to correct this after adding comments. As a result, the un-used LaTeX macro file was saying that they have studied 47 years instead of the real 31 years! This element was actually used in the very first (+40 page!) draft of the paper that was summarized to fit into the journal limits.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-1/+2
Possible semantic conflicts (that may not show up as Git conflicts but may cause a crash in your project after the merge): 1) The project title (and other basic metadata) should be set in 'reproduce/analysis/conf/metadata.conf'. Please include this file in your merge (if it is ignored because of '.gitattributes'!). 2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if you have added all analysis Makefiles to the '.gitattributes' file (thus not merging any change in them with your branch). For example with this command: git diff master...maneage -- reproduce/analysis/make/initialize.mk 3) The old 'verify-txt-no-comments-leading-space' function has been replaced by 'verify-txt-no-comments-no-space'. The new function will also remove all white-space characters between the columns (not just white space characters at the start of the line). Thus the resulting check won't involve spacing between columns. A common set of steps are always necessary to prepare a project for publication. Until now, we would simply look at previous submissions and try to follow them, but that was prone to errors and could cause confusion. The internal infrastructure also didn't have some useful features to make good publication possible. Now that the submission of a paper fully devoted to the founding criteria of Maneage is complete (arXiv:2006.03018), it was time to formalize the necessary steps for easier submission of a project using Maneage and implement some low-level features that can make things easier. With this commit a first draft of the publication checklist has been added to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018 and zenodo.3872248. To help guide users on implementing the good practices for output datasets, the outputs of the default project shown in the paper now use the new features). After reading the checklist, please inspect these. Some other relevant changes in this commit: - The publication involves a copy of the necessary software tarballs. Hence a new target ('dist-software') was also added to package all the project's software tarballs in one tarball for easy distribution. - A new 'dist-lzip' target has been defined for those who want to distribute an Lzip-compressed tarball. - The '\includetikz' LaTeX macro now has a second argument to allow configuring the '\includegraphics' call when the plot should not be built, but just imported.
2020-06-03Imported recent updated in Maneage, minor conflict fixedMohammad Akhlaghi-8/+11
The minor conflict was with 'reproduce/software/make/high-level.mk', and in particular because we implemented the fix to Maneage's Task #15664 in this project first. After it was moved to the main Maneage branch some minor stylistic corrections were done to it, thus causing the conflict. To resolve the conflict, I simply imported the full Maneage version of the file with this command: git checkout maneage -- reproduce/software/make/high-level.mk The other conflicts were due to the deleted files (that were resolved as described in 'README-hacking.md') and the LaTeX files that I had told '.gitattributes' to ignore from the Maneage branch.
2020-05-29pdftotext only called if present in system, minor editMohammad Akhlaghi-4/+6
David and Raul had both reported that because 'pdftotext' wasn't available on their system, the project failed (even though the PDF was built!). So with this commit, we first check if the system has 'pdftotext' and call it only if its is available. Some minor edits were made, building upon Boud's previous commit.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-8/+11
In time, some of the copyright license description had been mistakenly shortened to two paragraphs instead of the original three that is recommended in the GPL. With this commit, they are corrected to be exactly in the same three paragraph format suggested by GPL. The following files also didn't have a copyright notice, so one was added for them: reproduce/software/make/README.md reproduce/software/bibtex/healpix.tex reproduce/analysis/config/delete-me-num.conf reproduce/analysis/config/verify-outputs.conf
2020-05-22Re-write of the paper to fit in ~6000 words and IEEE formatMohammad Akhlaghi-0/+5
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.
2020-04-25IMPORTANT: Primary Maneage repositories are now under maneage.orgMohammad Akhlaghi-1/+1
Until now, the primary Maneage URLs were under GitLab, but since we now have a dedicated URL and Git repository, its better to transfer to this as soon as possible. Therefore with this commit, throughout Maneage, any place that Maneage was referenced through GitLab has been corrected. Please correct your project's remote to point to the new repository at `git.maneage.org/project.git', and please make sure it follows the `maneage' branch. There is no more `master' branch on Maneage.
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-8/+8
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.
2020-02-29IMPORTANT: re-preparation can only be done with --prepare-redoMohammad Akhlaghi-5/+19
Until now, the preparation phase was always executed before the final build phase when running `./project make'. But when it becomes necessary, project preparation can be slow and will un-necessarily slow down the project while the project is growing (focus is on the analysis that is done after preparation). With this commit, preparation will be done automatically the first time that the project is run (`.build/software/preparation-done.mk' doesn't exist). However, after preperation is complete once, future runs of `./project make' won't do preparation any more (by calling `top-prepare.mk'). They will directly call `top-make.mk' for the analysis. To manually invoke preparation after the first attempt, the `./project make' script should be run with the new `--prepare-redo' option. Also, since the preparation phase is now automatically done before the analysis phase, the long notice that describes running `./project make' at the end of the preparation phase has been removed in `top-prepare.mk'. It now just prints a short line, saying the preparation has been complete. Finally, when the project has not been run with the proper group configuration, it ends with an `exit 1' so the main `./project' script doesn't proceed any further.
2020-02-01Better message for analysis when configuration wasn't completeMohammad Akhlaghi-4/+13
Until now, when `./project make' was run after an insuccessful run of `./project configure', it would just say to run `./project configure'. But for a first time user, this could be confusing because when the configuration is done in parallel, the error message can be very high on the command-line outputs and not seen clearly. With this commit, the error message is more complete and describes the problem and what the users should do in which circumstance.
2020-02-01IMPORTANT: reproduce/software/bash renamed to reproduce/software/shellMohammad Akhlaghi-2/+2
Until now the shell scripts in the software building phase were in the `reproduce/software/bash' directory. But given our recent change to a POSIX-only start, the `configure.sh' shell script (which is the main component of this directory) is no longer written with Bash. With this commit, to fix that problem, that directory's name has been changed to `reproduce/software/shell'.
2020-01-27Initial scripts compatible with Dash (minimalistic POSIX)Mohammad Akhlaghi-5/+5
Until now, the initial project scripts were primarily tested with GNU Bash. But Bash is not generally available on all systems (it has many features beyond POSIX). Because of this, effectively we were imposing the requirement on the user that they must have Bash installed. We recently started this with setting the shebang of `project' and `reproduce/software/bash/configure.sh' to `/bin/sh'. After doing so, Raul and Gaspar reported an error on their systems. To fix the problem, I installed Dash (a minimalist POSIX-compliant shell) on my computer and temporarily set the shebangs to `/bin/dash', ran the project configuration step and fixed all issues that came up. With this commit, it can go all the way to building GCC on my system's Dash. After this stage (when `high-level.mk' is called), there is no problem, because we have our own version of GNU Bash and that installed version is used. Probably some more issues still remain and will hopefully be found in the future. While doing this, I also noticed the following two minor issues: - The `./project configure' option `--input-dir' was not recognized because it was mistakenly checking `--inputdir'. It has been corrected. - The test C programs now use the `<<EOF' method instead of `echo'. - In `basic.mk', the extra space between `syspath' and `:=' was removed (it was an ancient relic!).
2020-01-23Hashbangs of project and configure.sh set to /bin/shMohammad Akhlaghi-1/+1
Until now, the hashbang of these two shell scripts was set to `/bin/bash', hence assuming that GNU Bash exists on the host system! But this is an extra requirement on the host operating system and these two scripts should be written such that they operate on a POSIX shell (the generic `/bin/sh' which can point to any shell program). With this commit this has been implemented! We may confront some errors as the system is run on other systems, but we should fix such errors and work hard to make these two scripts as POSIX-compatible as possible (runnable on any shell, so as not to force users to install Bash before running the project). This completes Task #15525.
2020-01-23IMPORTANT: Project preparation is now also done with project makeMohammad Akhlaghi-60/+22
Until now, the main commands to run the project were these: `./project configure' (to build the software), `./project prepare' (to possibly arrange input datasets and build special configuration Makefiles) and finally `./project make' to run the project. The main logic behind the "prepare" phase `top-prepare.mk' is to build configuration files that can be fed into the "make" step and optimize its operation. For example when the total number of necessary inputs for the majority of the analysis is not as large as the total number of inputs. With "prepare" (when necessary), you go through the raw inputs, select the ones that are necessary for the rest of the project. The output of `top-prepare.mk' is a configuration file (a Make variable) that keeps the IDs (numbers, names, etc). That configuration file would then be used in the `top-make.mk' to identify the lower level targets and allow optimal project organization and management. But the last two are both part of the analysis, and while they indeed need different calls to Make to be executed, many projects don't actually need a preparation phase: ultimately, its an implementation choice by the project developers and doesn't concern the project users (or the developers when they are running it). To avoid confusing the users, or simply annoying them when a projet doesn't need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk' Makefiles are called with the single `./project make' command and `./project prepare' has been dropped. I noticed this while writing the paper on this system.
2020-01-19New --check-config option to ./project to check software build statusMohammad Akhlaghi-0/+42
Until now, it was necessry to run a long `while true' loop to see what is currently being built at configure time. So with this commit, a new `--checkconfig' option has been added to `./project' that can be called to run that loop and make it easier to check.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-1/+1
Now that its 2020, its necessary to include this year in the copyright statements.
2019-11-24Project's Makefiles run with no builtin rules or variablesMohammad Akhlaghi-1/+2
Until now, after removing all environment variables, we were just giving Make the top Makefile to execute. By default, for every target, Make will try many built-in rules (which is good when compiling programs, but redundant in other cases). All these checkings also populate the debugging output of Make (with `-d'). So its easier and slightly faster to just tell Make to ignore builtin rules and variables. With this commit, to address this issue, the `project' script runs `.local/bin/make' with `--no-builtin-rules' and `--no-builtin-variables'.
2019-10-01Infrastructure to keep preparation resultsMohammad Akhlaghi-1/+1
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-31/+97
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.
2019-09-28Main project script sets executable flags at configure timeMohammad Akhlaghi-0/+20
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.
2019-09-26Working project when downloaded from arXivMohammad Akhlaghi-0/+13
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.
2019-09-16Distribution tarball now builds in arXivMohammad Akhlaghi-11/+20
`./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'.
2019-07-28Corrected typo in environment before running makeMohammad Akhlaghi-1/+1
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/+291
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.