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

Age	Commit message (Collapse)	Author	Lines
2020-02-16	Building XLSX I/O and its dependencies: expat and minizip	Mohammad Akhlaghi	-1/+1
	Until now, there was no easy way to read/write `.xlsx' files (Microsoft Excel spreadsheets) within the template. But XLSX I/O provides to simple programs and some libraries to easily convert `.xlsx' files to CSV that can easily be read by any tool. This has also been implemented in the core template branch.
2020-01-18	First set of customizations done	Mohammad Akhlaghi	-2/+2
	The unnecessary parts were removed and the project now runs.
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.
2019-10-30	Tarballs set as order-only prerequisites, not needed for build calls	Mohammad Akhlaghi	-1/+1
	Until now, the tarballs were the first normal prerequisite of the software. As a result if their date changed, the whole software would be re-built. However, for tarballs specifically, we actually check their contents with a checksum, so their date is irrelevant (if its newer than the built program, but has the same checksum, there is no need to re-build the software). Also, calling the tarball name as an argument to the building process (for example `gbuild') was redundant. It is now automatically found from the list of order-only prerequisites within `gbuild' and `cbuild' (similar to how it was previously found in the `pybuild' for Python building). A `README.md' file has also been placed in `reproduce/software/make' to help describe the shared properties of the software building Makefiles. This will hopefully grow much larger in the future.
2019-10-29	lmfit and its dependencies added, Python tarballs as prerequisite	Mohammad Akhlaghi	-1/+1
	Python's `lmfit' module and all its major dependencies (`asteval', `corner', `emcee' and `uncertainties') have been included in the template. While doing this I noticed that if the tarballs are the last prerequisite of each software building rule, then when building in parallel, the template will immediately start building packages as soon as the first one is downloaded. Not like the current way that it will attempt to download several, then start building. For now, this has been implemented in the Python build rules for all the modules and we'll later do the same for the other programs and libraries. This also motivated a simplification of the `pybuild' function: it now internally looks into the prerequisites and selects the tarball from the prerequisite that is in the tarballs directory. This isn't a problem for the build, but I just don't understand why Python can't recognize the version of `emcee', Python reads the version of `emcee' as `0.0.0'! But it doesn't cause any crash in the build, so for now its fine.
2019-06-29	Added citation for TIDES, sorted progs alphabetically	Mohammad Akhlaghi	-2/+2
	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.
2019-06-28	Corrections to basic build	Prasenjit Saha	-1/+1
	Several corrections were necessary in the basic build: 1) the version of GCC on some systems includes an `_' which would cause a crash when building the PDF. 2) libcharset had to be manually added to the Git build.
2019-04-29	Modified copyright information of some files	Raul Infante-Sainz	-0/+1
	With this commit, the copyright information of some files have been modify in order to include the work of Raul Infante-Sainz.
2019-04-22	High-level software now specified in TARGETS.mk	Mohammad Akhlaghi	-0/+41
	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.