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2021-04-09Changed all gitlab.com URLs to git.maneage.orgMohammad Akhlaghi-1/+1
Until now, we were primarily linking people to the Gitlab fork of this paper. However, since this paper is part of Maneage, its main repository is on Maneage's own server at http://git.maneage.org/paper-concept.git With this commit therefore, all the gitlab.com URLs have been corrected to owr own Git server. While looking into Git-related points, I also noticed that in the demo code listing showing how to clone Maneage and start a new project, we were using Git's old/depreciated 'master' name. Git (and almost all common repositories) now use 'main' as the default branch name, so this has also been corrected here.
2021-01-03Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-1/+1
There were only three very small conflicts that have been fixed.
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-1/+1
Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also.
2020-11-26All the referee points have been answeredMohammad Akhlaghi-1/+1
There is an answer for all the referee points now. I also did some minor edits in the paper. But we are still over the limit by around 250 words. The only remaining point that is not yet addressed (and has '####' around it) is the discussion on parallelization and its effect on reproducibility.
2020-11-23Minor edits and correctionsMohammad Akhlaghi-1/+1
Raul's added point on the answer to the referee was very good, so I edited it a little to be more clear (and removed his name). Also, after looking in a few parts of the text, I fixed a few typos.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-1/+1
A new directory has been added at the top of the project's source called 'peer-review'. The raw reviews of the paper by the editors and referees has been added there as '1-review.txt'. All the main points raised by the referees have been listed in a numbered list and addressed (mostly) in '1-answers.txt'. The text of the paper now also includes all the implemented answers to the various points.
2020-06-28Zenodo identifier is extracted automatically from metadata.confMohammad Akhlaghi-1/+1
Until now, the Zenodo identifier was manually written in the paper. But now we have the Zenodo DOI in 'metadata.conf', so its much more robust to get it from there (in case updated versions of the paper is published).
2020-06-09Imported Maneage, minor conflicts fixed, a bug found and fixedMohammad Akhlaghi-0/+25
Some minor conflicts came up in 'initialize.mk' and 'verify.mk'. For the former, I chose the version on Maneage, for the latter, I kept the 'master' version on the checksums of this project, but kept the Maneage version for the rest of the improvements there (like printing the verified files as LaTeX comments in 'verify.tex'. While testing the conflicts, I noticed a bug (in the LaTeX macro for the number of years in the Menke+20 paper) in the previous build, thanks to the verification step :-)! Fortunately it wasn't actually printed in the PDF, so a normal reader won't recognize. The bug was caused by the recently added meta-data/commented lines in the 'tools-per-year.txt' file: when calculating the number of years studied in that paper, we were simply counting all the lines and we had forgot to correct this after adding comments. As a result, the un-used LaTeX macro file was saying that they have studied 47 years instead of the real 31 years! This element was actually used in the very first (+40 page!) draft of the paper that was summarized to fit into the journal limits.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-0/+25
Possible semantic conflicts (that may not show up as Git conflicts but may cause a crash in your project after the merge): 1) The project title (and other basic metadata) should be set in 'reproduce/analysis/conf/metadata.conf'. Please include this file in your merge (if it is ignored because of '.gitattributes'!). 2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if you have added all analysis Makefiles to the '.gitattributes' file (thus not merging any change in them with your branch). For example with this command: git diff master...maneage -- reproduce/analysis/make/initialize.mk 3) The old 'verify-txt-no-comments-leading-space' function has been replaced by 'verify-txt-no-comments-no-space'. The new function will also remove all white-space characters between the columns (not just white space characters at the start of the line). Thus the resulting check won't involve spacing between columns. A common set of steps are always necessary to prepare a project for publication. Until now, we would simply look at previous submissions and try to follow them, but that was prone to errors and could cause confusion. The internal infrastructure also didn't have some useful features to make good publication possible. Now that the submission of a paper fully devoted to the founding criteria of Maneage is complete (arXiv:2006.03018), it was time to formalize the necessary steps for easier submission of a project using Maneage and implement some low-level features that can make things easier. With this commit a first draft of the publication checklist has been added to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018 and zenodo.3872248. To help guide users on implementing the good practices for output datasets, the outputs of the default project shown in the paper now use the new features). After reading the checklist, please inspect these. Some other relevant changes in this commit: - The publication involves a copy of the necessary software tarballs. Hence a new target ('dist-software') was also added to package all the project's software tarballs in one tarball for easy distribution. - A new 'dist-lzip' target has been defined for those who want to distribute an Lzip-compressed tarball. - The '\includetikz' LaTeX macro now has a second argument to allow configuring the '\includegraphics' call when the plot should not be built, but just imported.