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2019-04-23Python package mpmath added into the templateRaul Infante-Sainz-0/+16
With this commit, we add `mpmath' Python package into the template. This package is a prerequisite of `sympy', a package to do symbolic mathematics. The motivation of adding this package is because it is a dependency of `sympy', which is more widely used into the Python science community.
2019-04-22High-level software now specified in TARGETS.mkMohammad Akhlaghi-8/+7
Until now, to specify which high-level software you want the project to contain, it was necessary to go into the `high-level.mk' Makefile that is complicated and can create bugs. With this commit, a new `reproduce/software/config/installation/TARGETS.mk' file has been created that is easily/cleanly in charge of documenting the final high-level software that must be built for the project. Also, until now, FFTW was set as a dependency of Numpy while we couldn't actually get Numpy to use it! It was just there for future reference and to justify its build rule. But now that many software won't be built and there is no problem with having rules even though a project might not use them, it has been removed.
2019-04-16Symbolic link to Python created, using `python' instead of `pythonX'Raul Infante-Sainz-9/+10
Until this commit, we were using `python3' when calling Python (because we were using Python version 3.6.8). This will force us to change the name in the future. For example, when `python4' were available and into the pipeline. With this commit, at the end of the Python installation it creates a symbolic link to the Python bin executable with the new name `python'. As a consecuence, whatever version of Python was installed, into the project we will use allways `python' to invoke it.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+506
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).