paper-concept.git - Paper (Towards Long-term and Archivable Reproducibility)

Age	Commit message (Collapse)	Author	Lines
2020-05-22	Re-write of the paper to fit in ~6000 words and IEEE format	Mohammad Akhlaghi	-0/+0
	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.
2020-05-01	Imported recent changes in Maneage, minor conflicts fixed	Mohammad Akhlaghi	-1/+1
	A few small conflicts showed up here and there. They are fixed with this merge.
2020-04-26	verify-outputs.conf: typo correction in comment to avoid confusion	Boud Roukema	-1/+1
	Until now, the comment in the file said that setting the `verify-outputs` variable to `yes` disables the verification. Looking at `reproduce/analysis/make/verify.mk` shows that the opposite is true. With this commit, the word `disable` is replaced with `enable` so that the user is not confused by the conflict between the source code in the other file and this comment.
2020-04-17	Imported recent work in Maneage, minor conflicts fixed	Mohammad Akhlaghi	-0/+128
	A few minor conflicts came up that were easily fixed.
2020-04-17	IMPORTANT: software config directly under reproduce/software/config	Mohammad Akhlaghi	-0/+128
	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.
2020-04-02	Imported recent work on Maneage, minor conflicts fixed	Mohammad Akhlaghi	-1/+0
	A few minor conflicts occurred and were fixed.
2020-03-23	Analysis and configuration file sections complete	Mohammad Akhlaghi	-0/+3
	With this commit a description of these two important parts have been added to the project, along with several figures showing various parts of the files that are discussed. I also done some other restructuring of the figures and files to make things fit better into the the description of the paper.
2020-03-02	Described the first analysis phase with a demo subMakefile	Mohammad Akhlaghi	-1/+1
	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.
2020-02-16	Menke+2020 data is now imported and ready for later steps in plain text	Mohammad Akhlaghi	-4/+4
	The main problems with this dataset was the names of the journals (which sometimes have single quotes or apostrophes in them that is really annoying for SED)! But ultimately, for the simple study we want to do here, the journal names are irrelevant, so in the end I just ignored the names. Later we can set an identifier for the journals if necessary. But now we have the basic information in a way that is usable in a plot to show in this paper.
2020-01-20	IMPORTANT!!! Configuration Makefiles now have a .conf suffix	Mohammad Akhlaghi	-1/+0
	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.
2020-01-18	First set of customizations done	Mohammad Akhlaghi	-3/+1
	The unnecessary parts were removed and the project now runs.
2020-01-01	Verification of output values and data added within template	Mohammad Akhlaghi	-0/+3
	Until now, the only verification that the template provided was the published PDF. Users had to manually compare the published and generated PDFs (numbers, plots, tables) and see if they obtained the same result. However, this type of manual verification is not good and is prone to frustration and missing important differences. With this commit, a new Makefile has been added in the analysis steps: `verify.mk'. It provides facilities to easily verify the results that go into the paper. For example tables that go into making the paper's plots, or the LaTeX macros that blend into the text. See the updated parts in `README-hacking.md` for a more complete explanation. This completes task #15497.
2020-01-01	Copyright statements updated to include 2020	Mohammad Akhlaghi	-2/+2
	Now that its 2020, its necessary to include this year in the copyright statements.
2019-06-29	Added citation for TIDES, sorted progs alphabetically	Mohammad Akhlaghi	-1/+1
	While reviewing Prasenjit's commits, I noticed that we had forgot to add the citation for TIDES, also to make things clear, the program/library build rules are now sorted alphabetically. Finally, I noticed that after building the TiKZ PDF figures, it is crashing (like on Prasenjit's computer). After looking around, I noticed its because we were setting the of the `TEXINPUTS' environment variable to be the installed TeX Live directory (which was ultimately redundant because by default TeX will look into where it was installed). The important thing is just that we remove any possible value the host system has, not to set new directories.
2019-06-28	tides library added	Prasenjit Saha	-1/+1
	TIDES is an ODE integrator with multiple-precision arithmetic.
2019-04-15	New architecture to separate software-building and analysis steps	Mohammad Akhlaghi	-0/+38
	Until now, the software building and analysis steps of the pipeline were intertwined. However, these steps (of how to build a software, and how to use it) are logically completely independent. Therefore with this commit, the pipeline now has a new architecture (particularly in the `reproduce' directory) to emphasize this distinction: The `reproduce' directory now has the two `software' and `analysis' subdirectories and the respective parts of the previous architecture have been broken up between these two based on their function. There is also no more `src' directory. The `config' directory for software and analysis is now mixed with the language-specific directories. Also, some of the software versions were also updated after some checks with their webpages. This new architecture will allow much more focused work on each part of the pipeline (to install the software and to run them for an analysis).