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Thanks to Boud's corrections, I see that the sentence can be confusing and
not convey the point I wanted to make properly, so I am clarifying it
here. The main point is that this principle complements the definition of
reproducibility, not the other principls.
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These tiny language edits add 1 word in length.
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Boud has contributed a lot to Maneage over the last few years and with the
last few commits he also contributed significantly to this paper, so I am
moving him to third author.
Thanks to Boud, I also remembered that even though I done the most
important parts of Maneage in Lyon, I hadn't added it as an affiliation for
myself, so I added it. Maneage became a separate project in Lyon.
Finally, I tried to decrease the length of the acknowledgments by adding
some abbreviations that were shared between various parts.
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Unfortunately, adding in my name/affiliations/acknowledgments
adds about 90 words to the text. We don't really know if these
are counted by the editor in the 8000-word limit.
I changed `funded' to `funded/supported'. I only get funding from
one out of the three sources I acknowledge, but it's important to
acknowledge all three.
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While looking over the PDF, a few small edits were made to be more clear.
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The conflict was only on the list of existing tools and that was easily
corrected.
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Following Boud's great corrections, I was able to futher summarize this
section, decreasing roughly 150 more words from this section.
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Until now the list of existing tools was written in one line which made it
hard to read and follow, especially since we added links. It is now
expanded into a one-line per item which makes to no difference in the final
PDF.
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Reduction by 15 words.
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Reduction by 7 words.
For a regular GNU/Linux of other unix-like system user, the bit
about ISO C compilers even existing for Microsoft systems more or
less says "despite there being no point ever trying to do science
on a Microsoft system, you *could* hypothetically compile and run
any ISO C program on it". Interesting, but not directly of
interest to this user, who is unlikely to actually want to do it.
A Microsoft user who thinks that s/he can do science on a
Microsoft system will typically think "Microsoft is good, so of
course I can run anything I want on it". So the message here
could more likely be seen as provocative rather than useful,
since this user is unaware of the fundamental problems of
Microsoft as an authoritarian, manipulative, centralised
organisation providing bad software.
So either way, the parenthesis about Microsoft can be safely
removed given the space constraints.
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Reduction by 5 words.
The term "exploratory research" is intended in the specific sense
listed at en.Wikipedia:
https://en.wikipedia.org/wiki/Exploratory_research
to distinguish it from hypothesis testing. The final phases of clinical
(medical) research, for example, to test whether a candidate SARS-CoV-2
vaccine is (i) effective and (ii) safe in homo sapiens, cannot accept the
exploratory methods that are acceptable in astronomy, or in other
exploratory research (which is acceptable in the early stages of medical
research).
Clinical trial registration is aimed at *preventing* scientists from
modifying their methods in a given project:
https://en.wikipedia.org/wiki/Clinical_trial_registration
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One superfluous word was removed.
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Minor wording changes - reduction by 10 words.
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Minor wording improvements; reduction by 10 words.
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For consistency, the principles should either all be nouns, or
all be adjectives. Most are nouns, so this commit switches the
adjectives to nouns.
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Compression by about 40 words. Updating python2 to python3
is often nothing more than modifying print statements, so
removing this doesn't weaken the text by much.
Re-creation helps avoid thinking of watching movies, going to
the beach, reading a novel, when seeing the word "recreation":
https://en.wiktionary.org/wiki/recreation#Usage_notes
The matplotlib sentence was not so clear: now it's a bit shorter
and hopefully clearer.
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Word-length reduction (8 words) of the first part of 3 Principles.
Change in meaning: we can argue that *results* are not part of
science, but science needs aims as well as methods; hypotheses
are needed too, but these overlap between the aims and
methods. So I put "primarily".
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In this commit, the URLs for the 19 "earlier solutions" at the
beginning of "3 Principles" are recovered from
tex/src/paper-long.tex and put behind the package names
as clickable words.
To reduce the chance that these are interpreted as references,
"Project1 (yyy1), Project2 (yyy1)" is changed to "yyy1: Project1,
Project2". We cannot add full references because of the 8000-word
space constraint.
With a minor word improvement, this commit overall reduces the word
count very slightly, by 9, according to
pdftotext paper.pdf |wc paper.txt
before and after the commit.
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Scalability is not just on the size of the project, but also its
complexity, so I added an `and/or complex' to the description of the
scalability principle.
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Someone reading the principles section until now would think that IPOL is
an almosts perfect solution, and for its usecase it certainly is. However,
this is only because of the nature of its work: it only focuses on
algorithms, not usage/analysis which cannot be done in raw ISO C.
So with this commit, I added a new principle on Scalability and discussed
this limitation of IPOL there. To avoid simply lengthening the text, to add
this new principle, I had to remove/summarize some parts that seemed
redundant. In the process, I also removed some of the existing tools (at
the start of the principles section) that had several others in the same
time frame, I have already mentioned (through the "and many more") that
this list is not complete.
Also, the list of people to thank in the acknowledgments is now put in a
one-line per name to be more easily maintainable: Boud and Mohammad-reza
were added, and given that I have sent the paper to several other people
for feedback, I expect the list to get longer.
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A few more minor language edits. For parseable vs parseable, see
https://en.wiktionary.org/wiki/parsable which recommends `parsable`
for formal usage.
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These are mostly minor language edits. There is one significant fix: the
word `typically' in `a non-free software project typically' cannot be
distributed by the project. There is a whole range of licences between
strictly free software definition, strictly OSI open-source definition, and
fully closed source. For example, software with a no-commercial usage
licence (similar to CC-BY-NC) can be publicly redistributed on any server,
as long as there is no requirement of payment or no requirement of payment
that is "commercial" (according to lawyers' interpretation of when a
payment is commercial).
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These are important aspects that are highly relevant to Maneage: its
philosophy (the former) and usability (the latter). To add them, I tried to
summarize some other parts of the paper.
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Three such cases and they are fixed.
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A few minor issues were found and fixed in the text. I also tried to
shorten it a little further.
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I forgot to put these in the last commit! They are now implemented.
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I had another look at the text and tried to summarize it a little more
while also fixing several typos that I had just discovered! In the process,
I noticed that we hadn't actually put a link to Maneage's main Git
repository! So we now have the URL as a `git clone' command.
Also, I thought that its better to show the `TARGETS.conf' file (which we
actually talk about) in the file architecture instead of `LOCAL.conf.in'
(which we don't talk about any more!).
Finally, to be more similar with DSJ, the bibliography is now in normal
font size, not footnotesize.
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In the introduction I had mistakenly put "metadata" instead of "workflow",
its corrected with this commit.
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Ryan O'Connor is from RDA and my principle contact for the grant. He also
kindly went over the first draft of the paper and gave useful and
encouraging comments.
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This was only relevant for the submitted version, so I am committing it
until the next submission.
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After the submission and reading through the text another time I found some
typo corrections and fixed them. Also now that David is an author, I
removed him from the people to acknowledge (David brought this up himself,
thanks David ;-)).
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Since the journal doesn't accept supplementary files during initial
submission, I have put this link on the PDF for the referee and editors to
access if they want.
Also the `tex/img' file was added to the distribution tarball.
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Thanks David ;-)! I tried to implement as many as I could. For the time
being, I just removed teh `~' between "Section" and its number, and removed
the italics on software names. Let's see what the journal editors say about
it. Otherwise, most of the suggestions were very good and indeed made the
text much better to read.
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David submitted these comments by email, I (Mohammad) am committing it into
the project.
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To make the text easier to read and further comply with the author
guideline, the text was shrank a little more and the two final sections
were also added on "Competing interest" and "Author contributions".
I also found the CODATA logo on Wikipedia in SVG format (vector graphics),
so I replaced the previous pixelated PNG format with the PDF (converted
from SVG).
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I removed the part emphasizing one journal, but about the comment at the
end of the conclusion (to say some negative things): we have already done
that in the discussion, mentioning the caveats ;-). But you are right, we
should summarize the caveats is well.
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With this commit, minor typos have been fixed from Section 4 to 6. The
majority of them are minor corrections (typos/spelling). I added just a
couple of comments/suggestions in red. If you think they are necessary
try to fit with the latest modifications. If not, just ignore them.
Really nice paper, congratulations to all contributors!!
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With this commit, just minor typos have been fixed (I am rushing over
the text since we are out of time!). There are also a suggestion in
order to remove a couple of phrases to try to be more aseptic when
comparing with another project. But there is only an idea, take it or
not as you consider.
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A first draft for these was added and will probably become much better in
the next few iterations.
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I went through the whole paper and tried to decrease its size even futher,
also a first draft of the summarized discussion has been added.
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TeXLive recently transitioned from its 2019 version to its 2020 version
thanks to Elham Saremi's trial of the this project. The fact that
traditionally Maneage installs all TeXLive packages in a per-year directory
is very annoying and required an update in the core Maneage system every
year. So I suddently recognized that we can fix this by setting a different
name for the directory holding the release year. This has been implemented
with this commit.
I have also done this change in the main Maneage branch for other projects
to also benefit from this correction.
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Thanks Roberto, they are now implemented.
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I corrected bugs, typos, double words, and punctuations along the whole
text. I do some comments which are always highlighted with \hl{this is my
comment}, so you can identify them easily in the pdf. If you want to
remove, then you can do it easily with Ctrl+R since I think you never used
\hl. Finally, I added my name as coauthor but, please, feel free to remove
it if you want.
Note from Mohammad: since there were two other suggested commits before
this that were already merged, I rembased Roberto's commits and fixed a few
minor conflicts.
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There weren't any conflicts in this merge.
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With this commit, a short line telling that Maneage has tutorials
showing the workflow in a practical way has been added. Because of we
are near to the limit of words, I have added just a very short line. The
sentence does not specify any file name since the tutorial(s) is not
included (it will be in a near future).
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With this commit, I have included a small line to recognize Julia
Aguilar-Cabello as the designer of the Maneage's logo.
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The contents until two commits ago when I started to summarize the paper
are now in a new and shorter format: previously the discussion started on
page 25, but now it starts on page 17. It is still a little longer than
8000 words, but not as significantly as before. I will add the discussion
and also try to summarize it futher before submission.
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As described in the previous commit, we had to shorten the paper to roughly
8000 words (which is significant decrease!). With this commit, I am
committing the current version of the summarized paper, where the
introduction, defintions and principles have now been summarized. I am now
summarizing the rest (describing Maneage and the discussion).
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We just recently recognied that the final paper should not be longer than
8000 words. The easiest way was just to start a new `paper.tex' and bring
in parts from the original/long version. We can use all the hard work that
went into writing the long paper later (possibly in a manual for
Maneage). So I don't want to suddenly distroy its history at this point.
To let Git know about renaming the original `paper.tex' to
`tex/src/paper-long.tex', I am making this commit. This commit doesn't have
any `paper.tex' and only records the fact that it has been renamed. In the
next commit, I'll re-create `paper.tex' which will host the short/final
version. But thanks to this commit, if we later make any changes to long
version, Git will know that it was originally the main `paper.tex'.
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