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2020-02-01IMPORTANT: reproduce/software/bash renamed to reproduce/software/shellMohammad Akhlaghi-66/+0
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'.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-1/+1
Now that its 2020, its necessary to include this year in the copyright statements.
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.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+66
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).