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2020-03-23Analysis and configuration file sections completeMohammad 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.
2020-03-02Described the first analysis phase with a demo subMakefileMohammad 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.
2020-02-16Menke+2020 data is now imported and ready for later steps in plain textMohammad 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.
2020-01-18First set of customizations doneMohammad Akhlaghi-3/+1
The unnecessary parts were removed and the project now runs.
2020-01-01Verification of output values and data added within templateMohammad 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.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-2/+2
Now that its 2020, its necessary to include this year in the copyright statements.
2019-06-29Added citation for TIDES, sorted progs alphabeticallyMohammad 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.
2019-06-28tides library addedPrasenjit Saha-1/+1
TIDES is an ODE integrator with multiple-precision arithmetic.
2019-04-15New architecture to separate software-building and analysis stepsMohammad 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).