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

Age	Commit message (Collapse)	Author	Lines
2018-02-19	Added tips section on version control with tagging	Mohammad Akhlaghi	-8/+37
	In the "Tips" section of `README.md', a section on version control was added and a first tip regarding tags was added to guide (new) users on how to effectively define and use tags. As a result, in the checklist, adding a `v0' tag is now also suggested. Some minor typos were also fixed.
2018-02-15	Gnuastro's memory mapping is now a local variable	Mohammad Akhlaghi	-8/+14
	As described in the commens above `MINMAPSIZE' of `LOCAL.mk.in', the amount of memory to map to HDD/SSD or keep in RAM is a local issue and not relevant to the pipeline's results. So it is now defined in a `gnuastro-local.conf' file. To keep the Makefiles clean, this file is created by the `./configure' script. To do this cleanly, the `./configure' script was also almost fully re-written with better functionality now.
2018-02-14	Sanity checks added, local settings now in LOCAL.mk.in	Mohammad Akhlaghi	-18/+18
	The choice of whether or not to make a PDF is now also a local system issue, not a general pipeline issue. So it has been put in the new `LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local settings (things that when changed should not be version-controlled) should be defined in this file. A sanity check was added to find if `./configure' has been run before `make' or not (using the `LOCAL.mk' file which is an output of the configuration step). If `LOCAL.mk' doesn't exist, an error will be printed informing the user that `./configure' needs to be run first. The configure script also provides more clear and hopefully better information on its purpose and what must be done. Since `make clean', it is executed even when `./configure' hasn't been run, it will only delete the build directory and its contents when local configuration has been done. A `distclean' target was also added which will first "clean" the pipeline, then delete the `LOCAL.mk.in' file. To allow rules like `make' to be run even if `BDIR' isn't defined (`./configure' hasn't been run yet), a fake `BDIR' is defined in such cases.
2018-02-10	Minor typo corrections in README.md	Mohammad Akhlaghi	-21/+22
	While going over parts of the text, some minor typos were found and corrected.
2018-02-10	Corrected tips title to be more clear	Mohammad Akhlaghi	-6/+6
	The title "Tips on using the pipeline" was a little generic and could be confused with people who want to reproduce the result, not the designers of the pipeline. So it was changed to "Tips on expanding this template (designing your pipeline)". Some minor edits were also made to its first paragraph.
2018-02-08	Minor typos corrected in README.md	Mohammad Akhlaghi	-70/+75
	Some minor typos were found and corrected. In other cases, the text was slightly edited to be more clear.
2018-02-08	Instructions to delete README.md before starting	Mohammad Akhlaghi	-0/+5
	`README.md' is for this pipeline, not the research project that is using it. Therefore it might be confused with the `README' that is devoted to the research project. So in the checklist, a point was added to delete this file before making the first new commit.
2018-02-08	Basic titles now corrected after copyright in README.md	Mohammad Akhlaghi	-18/+16
	The basic title, short description and author section of the checklist was moved immediately after copyright because it is more related to it. The description of Gnuastro is now before `README' because the user will confront Gnuastro in `README' and this will provide a good introduction on what to do with it.
2018-02-08	Moved creation of a new Git repo to the end of the checklist	Mohammad Akhlaghi	-23/+30
	The creation of a new Git repo is now moved to the end of the checklist. It was not in place as the third step before. Now, the user makes all the standard changes and just before they start going into the details of their research, they define their new repository.
2018-02-08	Minor edits in README.md	Mohammad Akhlaghi	-4/+7
	The description of adding a title and authors was made slightly more clear.
2018-02-08	Adding title and description also mentioned in README.md	Mohammad Akhlaghi	-1/+22
	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/+400
	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.