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

Age	Commit message (Collapse)	Author	Lines
2021-01-04	Edits in the answers to the referee report	Mohammad Akhlaghi	-262/+305
	Given the new appendix/supplement structure, it was necessary to go through the answers and correct them. I also generally edited them and added a top-level letter to the editors (to directly copy-paste into the webpage).
2020-12-28	Minor edits, updated citation to published Menke+20 paper	Mohammad Akhlaghi	-42/+38
	Some minor edits were made to the paper to shorten it. In particular the example of IPOL was removed from the main body of the paper, and we'll just rely on the more extensive review of IPOL in the appendix. I also updated the referee report to account for the new Appendix A that is just an extended introduction. Also, I noticed that the Menke+20 paper that we replicate here has recently been published in the iScience journal. So its bibliography was updated from the bioarXiv information to the journal information. Also, the number of words (after removing abstract and captions and accounting for figures) is now only printed when the project is built with '--no-appendix'. This was done because this information is extra/annoying/unnecessary for the case where there is an appendix.
2020-12-02	Minor edits in newly added parts on statistical verification	Mohammad Akhlaghi	-6/+6
	Thanks a lot Boud for adding that script in your own project and linking it here. Since the raw file (without context of the whole project) is very hard to understand for the users, I switched the URL to the navigable URL the link is actually on the filename. It will always show the most recent version of this script, not the particular snapshot of now. But infact that is better, since we can make it better and improve it over time. Maybe even by the end of this paper's referee review will be able to include it in Maneage's core branch. I also removed the link to this discussion at the first paragraph of Section IV (proof of concept). Since that is just the introduction, and going into this level of detail there could be confusing for the readers. Having the name of the script in the proper place is more direct and understandable for the readers. Thanks again Boud for the nice work on this ;-).
2020-12-02	URL of statistical verification	Boud Roukema	-7/+10
	This commit adds the SWH URL of the statistical verification script to the paper and tidies up the corresponding answer in '1-answer.txt'. The script file includes more extensive documentation than the earlier 'make' version of the method.
2020-11-27	Merged with Boud's corrected answers (generally very similar)	Mohammad Akhlaghi	-107/+155
	The only issue that still remains is how to address statistical reproducibility, and I am in touch with Boud to do this in the best way possible (it has been highlighted with '#####'s in the answers.
2020-11-26	All the referee points have been answered	Mohammad Akhlaghi	-34/+68
	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.
2020-11-26	All questions have now been responded to	Boud Roukema	-104/+170
	This commit is intended to be submittable quality. Point 56 was removed, and the later points renumbered, because it was a point of Reviewer 5 described what we have done - it was not a criticism to respond do. :) The current word count (without abstract and references) is 6091.
2020-11-25	Points 33-35 handled in answer to reviewers	Boud Roukema	-14/+27
	This commit only modifies "peer-review/1-answer.txt", giving answers to Reviewer 4; these mostly take into account David's email list of proposed answers. No changes are done to "paper.tex".
2020-11-25	Reviewer points 16 to 32	Boud Roukema	-31/+42
	Copyediting of points 16 to 32 (paper.tex + peer-review/1-answer.txt) is done in this commit. TODO list: 2. paper lacking focus 9. tidy up README-hacking.md for appearance on website App B.G. similar to Figure ?? - ref missing 29. website: README-hacking.md and tutorial "on same page"
2020-11-25	Reviewer points 1-15; appendix clickable links	Boud Roukema	-63/+78
	This commit updates "paper.tex" and "peer-review/1-answer.txt" for the first 15 (out of 59!) reviewer points, excluding points 2 (not yet done) and 9 (README-hacking.md needs tidying). A fix to "reproduce/analysis/make/paper.mk" for the links in the appendices is also done in this commit (the same algorithm as for paper.tex is added). The links in the appendices are not (yet) clickable.
2020-11-24	List of answers - minor copyedit	Boud Roukema	-18/+21
	This commit does a minor copyedit of "peer-review/1-answer.txt", mostly just at the top, plus some hashes to highlight an unanswered concern; and removes the @ symbols (and full stops) from email addresses in the peer review email in order to reduce our feeding of email harvesters (spiders that collect email addresses for spammers).
2020-11-23	Minor edits and corrections	Mohammad Akhlaghi	-5/+8
	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.
2020-11-23	Minor corrections to referees answer	Raul Infante-Sainz	-6/+13
	With this commit, I am just adding several minor corrections to the answer to the referees. They are very minor typos. I would only emphasize the fact that in Maneage there is the "Minimal complexity" criteria, and because of that, even if the project is not able to be executed in the future, the interested reader could have a look at the analysis steps (because it is in plain text). Note that I put "Raul" at the beginning of the line, so my name should have to be removed in the final document to be sent to the referees.
2020-11-23	First draft of all the points addressed by the referees	Mohammad Akhlaghi	-0/+1828
	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.