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

Age	Commit message (Collapse)	Author	Lines
2018-11-22	Using .local instead of ./.local in READMEs	Mohammad Akhlaghi	-2/+2
	Until now, in the instructions, we were suggesting to run `./.local/bin/make', but the `./' part is extra: this is already a directory and so the shell will be able to find it. So to make things more clear and easy to read/write, we removed the `./' part from the calls to our custom Make installation.
2018-11-21	Changing of README files in checklist	Mohammad Akhlaghi	-13/+42
	When you point to this project, the `README.md' file is the default file that opens on GitLab and other online git repositories. Since a reproduction pipeline project is different from the actual pipeline, its best for the default text that opens to describe the paper, not the pipeline. The old `README.md' is also kept, but its now called `REAME-pipeline.md'.
2018-11-19	Gzip's tarball in tar.gz instead of tar.lz	Mohammad Akhlaghi	-7/+8
	Until now, we were using a customized `tar.lz' tarball for Gzip. But on systems that don't have GNU Tar, this will cause a problem (non-GNU Tar doesn't recognize `.tar.lz'). So to keep things simple, we are using the customized gzip in `tar.gz' format. After the internal build of GNU Tar and Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work nicely on all the standard compression algorithms and we don't have to modify our commands based on the algorithm (nice feature of GNU Tar).
2018-11-18	Updated README and README.md for new dependency building features	Mohammad Akhlaghi	-5/+13
	The two README files have been updated to explain the new feature of downloading and building dependencies.
2018-11-12	Dependencies built at the start of the pipeline	Mohammad Akhlaghi	-103/+14
	To enable easy/proper reproduction of results, all the high-level dependencies are now built within the pipeline and installed in a fixed directory that is added to the PATH of the Makefile. This includes GNU Bash and GNU Make, which are then used to run the pipeline. The `./configure' script will first build Bash and Make within itself, then it will build All the dependencies are also built to be static. So after they are built, changing of the system's low-level libraries (like C library) won't change the tarballs. Currently the C library and C compiler aren't built within the pipeline, but we'll hopefully add them to the build process also. With this change, we now have full control of the shell and Make that will be used in the pipeline, so we can safely remove some of the generalities we had before.
2018-02-20	Necessary programs checked at configure time	Mohammad Akhlaghi	-9/+4
	The mandatory and optional (for example downloader) dependencies are now checked at configure time so users can know what they may be missing before the processing starts. Since its recommended to be run in parallel, it can be hard to find what you are missing after running the pipeline. As part of these checks, the program to use for downloading is now also set at configure time, it is only used as a pre-defined (in `LOCAL.mk') variable during Make's processing. A small title was also added to discus the pipeline architecture that will be filled in the next commit.
2018-02-15	Configure script starts with bin/bash shebang	Mohammad Akhlaghi	-0/+7
	While trying the pipeline on a remote server (which runs on Debian), the configure script had an `Syntax error: "(" unexpected' error. This is caused by the fact that in the Debian world (and its derivate OSs), the default shell is not Bash but Dash which has much fewer features for fast loading. It was thus necessary to start the configure script explicity with the `/bin/bash' shebang.
2018-02-08	Usage of configure command added to README	Mohammad Akhlaghi	-10/+5
	The README file didn't match the current way to set the top-level directories (through `./configure'), it was still the old-fashioned way of manually finding and opening the file. The explanation is now corrected.
2018-02-08	Adding title and description also mentioned in README.md	Mohammad Akhlaghi	-68/+39
	The first commit didn't have an explanation on correcting the title of the project in the final PDF or the top-level Makefile, so a pointer was added to the list. Also, some extra dependencies were removed from `README' and its paragraphs were scaled to the new width of 75 characters that is defined in `.dir-locals.el' (for Emacs settings, taken from Gnuastro).
2018-02-07	First commit to the reproduction pipeline template	Mohammad Akhlaghi	-0/+153
	Let's start working on this pipeline independently with this first commit. It is based on my previous experiences, but I had never made a skeleton of a pipeline before, it was always within a working analysis. But now that the pipeline has a separate repository for its self, we will be able to work on it and use it as a base for future work and modify it to make it even better. Hopefully in time (and with the help of others), it will grow and become much more robust and useful.