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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.
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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"
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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.
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This commit tidies up minor aspects of the language in the text
marked by "\new", e.g. a "wokflow" would be fine for Chinese
cooking, but is a little off-topic for Maneage. :) The word count
is reduced by about 7 words.
I haven't yet got to the serious part: checked that we've responded
to the referees' points, and completing the responses which we
haven't yet done.
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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.
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With this commit, I make several minor changes to the text of the final
paper. They are not important, but minor modifications like avoiding
contractions (don't -> do not, and so on).
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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.
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Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro
that defines two LaTeX macros: '\new' and '\tonote'.
When '\highlightchanges' was defined, anything that was written within
'\new' became dark green (highlighting new things that have been
added). Also, anything that was written in '\tonote' was put within a '[]'
and became dark red (to show that there is a note here that should be
addressed later).
When '\highlightchanges' wasn't defined, anything within the '\new' element
would be black (like the rest of the text), and the things in '\tonote'
would not be shown at all.
Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex'
(to toggle the modes above) would create a different Git hash and has to be
committed.
But this different commit hash could create a false sense in the reader
that other things have also been changed and the only way they could
confirm was to actually go and look into the project history (which they
will not usually have time to do, and thus won't be able to trust the two
modes of the text).
Also, the added highlights and the note highlights were bundeled together
into one macro, so you couldn't only have one of them.
With this commit, the choice of highlighting either one of the two is now
done as two new run-time options to the './project' script (which are
passed to the Makefiles, and written into the 'project.tex' file which is
loaded into 'paper.tex'). In this way, we can generate two PDFs with the
same Git commit (project's state): one with the selected highlights and
another one without it.
This issue actually came up for me while implementing the changes here: we
need to submit one PDF to the journal/referees with highlights on the added
features. But we also need to submit another PDF to arXiv and Zenodo
without any highlights. If the PDFs have different commit hashes, the
referees may associate it with other changes in any part of the work. For
example https://oadoi.org/10.22541/au.159724632.29528907 that mentions
"Another version of the manuscript was published on arXiv: 2006.03018",
while the only difference was a few words in the abstract after the journal
complained on the abstract word-count of our first submission (where the
commit hashes matched with arXiv/Zenodo).
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With the optional appendices added recently to the paper, it was important
to go through them and make them more fitting into the paper.
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Given the referee reports, after discussing with the editors of CiSE, we
decided that it is important to include the complete appendix we had before
that included a thorough review of existing tools and methods. However, the
appendix will not be published in the paper (due to the strict word-count
limit). It will only be used in the arXiv/Zenodo versions of the paper.
This actually created a technical problem: we want the commit hash of the
project source to remain the same when the paper is built with an appendix
or without it.
To fix this problem the choice of including an appendix has gone into the
'project' script as a run-time option called '--no-appendix'. So by default
(when someone just runs './project make'), the PDF will have an appendix,
but when we want to submit to the journal, or when the appendix isn't
needed for a certain reason, we can use this new option. The appendix also
has its own separate bibliography.
Some other corrections made in this commit:
1. Some new references were added that had an '_' in their source, they
were corrected in 'references.tex'.
2. I noticed that 'preamble-style.tex' is not actually used in this paper,
so it has been deleted.
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Before this commit, there were no arguments regarding machine related
specifications in the manuscript. This was needed as Mohammad Akhlaghi came
across a review of the artcile by Dylan Aïssi in which Dylan mentioned the
need for discussing CPU architecture dependence in pursuing a long-trem
archivable workflow.
With this commit, the required argument has been added in Sec.IV POC:
Maneage in the paragraph in which it is explained how 'macro files build
the core skeleton of Maneage'. Furthermore, few typos in different places
have been fixed and the 'pre-make-build.sh' has been updated with the
latest fix in Maneage core project.
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This paper is generally about data analysis pipelines, so the abstract now
starts with "Analysis pipelines" instead of "Reproducible workflows". I
also noticed that the sentence was mistakenly broken into multiple lines.
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Only two small conflicts came up:
* The addition of the hardware architecture macro in 'paper.tex' (which
was removed for now, but will be added as the referee has requested
within the text).
* The usage of "" around directory variables in 'paper.mk'.
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I saw this link today in the news (to be implemented from November 1st,
2020), and because it is directly related to this work, I added it. Many
people assume that simply pushing a Docker image to DockerHub is enough to
preserve it, but ignore how much it costs to maintain the storage and
network capacity.
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Until now, no machine-related specifications were being documented in the
workflow. This information can become helpful when observing differences in
the outcome of both software and analysis segments of the workflow by
others (some software may behave differently based on host machine).
With this commit, the host machine's 'hardware class' and 'byte-order' are
collected and now available as LaTeX macros for the authors to use in the
paper. Currently it is placed in the acknowledgments, right after
mentioning the Maneage commit.
Furthermore, the project and configuration scripts are now capable of
dealing with input directory names that have SPACE (and other special
characters) by putting them inside double-quotes. However, having spaces
and metacharacters in the address of the build directory could cause
build/install failure for some software source files which are beyond the
control of Maneage. So we now check the user's given build directory
string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(',
')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different
directory.
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Until now, the replicated plot had the width of the full page and the data
lineage graph was under it. Together they were covering more than half of
the height of the page! But the plot showing the number of papers with
tools really doesn't have too much detail, and all the space was being
wasted.
With this commit, the plot is now much much thinner and the data lineage
graph has been fitted to the right of it.
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To help in the documentation, the Git hash of the Maneage branch commit
that the project has most recently merged with (or branched from) is now
also provided as a LaTeX macro ('\maneageversion').
It is calculated in 'reproduce/analysis/make/initialize.mk' (in the recipe
to 'initialize.tex').
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In the previous commit, the modified abstract of the acknowledgments only
included the URL of Maneage, but its more formal to cite the Maneage paper,
the URL is already present in the paper.
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Until now, the acknowledgment section didn't contain the new name of
Maneage and it also included an acknowledgment of Gnuastro (which is not
appropriate for a general project which may not use Gnuastro).
With this commit this is fixed.
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This was pointed out by Mervyn O'Luing.
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Mervyn had read the paper and provided some interesting thoughts that I
tried to implement. Mervyn's comments are shown below. I just haven't
addressed the last point yet, because I am affraid it may make the text too
long (we are already on the boundary of the word-limit). We have already
discussed that it is a good research topic, and have hopefully triggered
the curiosity of the readers to test it ;-).
-------------------
Page 2: Regarding Criterion 1: Completeness. A project must be self
contained? So this includes not requiring root or administrator
privileges. This suggests that the project is only made open after the
development has been completed?
Regarding Criterion 5: 'a clerk can do it' -- in the pc world that we live
in could this be taken as a disparaging comment?
Page 5: 'The C library is linked with all programs, and this dependence can
hypothetically hinder exact reproducibility of results, but we have not
encountered this so far.' - what do you think might happen if this does
affect reproducibility? Do you have a plan to deal with this? Or are you
going to wait until you hear of such cases as the number will probably be
small? Have you done probability analysis to show that the rates are likely
to be very small? Or should you have a disclaimer with maneage?
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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).
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I visited the AMIGA group in January this year and we had some very useful
discussion on Maneage.
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After going through Terry's corrections, some things were clarified
more. Technically, I realized that many new-lines were introduced and
corrected them. Also, in Roberto's biography, I noticed that compared to
the others it has too much non-reproducibility details, so I removed the
redundant parts for this paper.
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Terry is an astronomer at IAC's Scientific Editorial Service and kindly
agreed to review this paper for us and actually pushed this commit. I am
just adding a commit message here.
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Marios had read the first draft of the paper (Commit f990bba) and provided
valuable feedback (shown below) that ultimately helped in the current
version. But because of all the work that was necessary in those days, I
forgot to actually thank him in the acknowledgment, while I had implemented
most of his thoughts.
Following Marios' thoughts on the Git branching figure, with this commit, I
am also adding a few sentences at the end of the caption with a very rough
summary of Git.
I also changed the branch commit-colors to shades of brown (incrementally
becoming lighter as higher-level branches are shown) to avoid the confusion
with the blue and green signs within the schematic papers shown in the
figure.
Marios' comments (April 28th, 2020, on Commit f990bba)
------------------------------------------------------
I think the structure of the paper is more or less fine. There are two
places that I thought could be improved:
1) Section 3 (Principles) was somewhat confusing to me in the way that it
was structured. I think the main source of confusion is the mixing of what
Maeage is about and what other programs have done. I would suggest to
separate the two. I would have short intro for the section, similar to what
you have now. However, I would suggest to highlight the underlying goals
motivating the principles that follow: reproducibility, open science,
something else? Then I would go into the details of the seven principles.
Some of the principles are less clear to me than others. For example, why
is simplicity a guiding principle? Then some other principles appear to be
related, for example modularity, minimal complexity and scalability to my
eyes are not necessarily separate.
Finally, I would separate the comparison with other software and either
dedicate a section to that somewhere toward the end of the paper (perhaps a
subsection for section 5) or at least condense it and put it as a closing
paragraph for Section 3. As it is now I think it draws focus from Maneage
and also includes some repetitions.
2) Section 4 (Maneage) was at times confusing because it is written, I
think in part as a demonstration of Maneage (i.e., including examples that
showed how Maneage was used to write this or other papers) and a
manual/description of the software. I wonder whether these two aspects can
be more cleanly separated. Perhaps it would be possible to first have a
section 4 where each of the modules/units of Maneage are listed and
explained and then have the following section discuss a working example of
Maneage using this or another paper.
3) I found Figure 7 [the git branching figure] and its explanation not very
intuitive. This probably has to do with my zero knowledge of github and how
versioning there works, but perhaps the description can be a bit more "user
friendly" even for those who are not familiar with the tool.
4) I find Section 6 to be rather inconsequential. It does not add anything
and it more or less is just a summary of what was discussed. I would
personally remove it and include a very short summary of the
ideals/principles/goals of Maneage at the beginning of Section 5, before
the discussion.
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The default 'paper.tex' starts by defining some macros and comments
describing them. Until now, the text was not too clear and could be
confusing for someone that is not at all familiar with Maneage.
With this commit, the comments have been edited to be more clear for a
first-time reader. For example they all start with FULL CAPS
summaries.
Two other small things were corrected in 'tex/src/preamble-necessary.tex':
- Until now 'project.tex' was included in this preamble. However, because
of its importance in Maneage, and prominent place in the demonstration
plot of the paper introducing Maneage, it is now included directly in
'paper.tex'. This also allows users to safely ignore/delete this
preamble file if their LaTeX style is different.
- I noticed that some macros for some astronomical software names from the
very first commits in Maneage were still present here! They are no
longer used, so they have been removed.
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Until now, we were saying "POSIX is defined by the IEEE", but in issue #12,
Michael Crusoe pointed out that this is not accurate. It is actually
jointly developed and operated by the IEEE, The Open Group and ISO/IEC JTC
1/SC 22, which together form the Austin Group.
So the sentence was modified to say tha the IEEE (potential publisher of
this paper) is part of the Austin Group that develops the POSIX standard.
Thanks a lot for bringing this up Michael.
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Until now, we were using three EPS (created from SVG) that were downloaded
from https://www.flaticon.com. Therefore it was necessary to acknowledge
the creators and put a link to the webpage. This consumed space in the
caption and decreased the originality of the plot.
Another problem was that the "collaboration" icon (with three people in it)
had arrows, and some of those arrows pointed downwards, make ambiguity in
relation to the top-ward arrows under the commits.
With this commit, three alternative icons are added that I made from
scratch, using Inkscape. The collaboration icon now is two figures and two
speech-bubbles, without any arrows.
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Recently, by default, Maneage will not take the title directly in the PDF,
the title should be given in the 'metdata.conf' file and it is passed onto
LaTeX as a variable. So the comment to "add project title" in the listing
could be confusing. To avoid confusing, I edited it to "Set your name as
author". The comments above the '\title' part is very complete and users
will clearly be able to modify the title if they want.
Also, we had an extra ')' in the line just under it which is now corrected.
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The text of the default paper hadn't been changed for a very long time! In
this time, three papers using Maneage have been published (which can be
very good as an example), Maneage also now has a webpage!
With these commit these examples and the webpage have been added and
generally it was also polished a little to hopefully be more useful.
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Two words were corrected in the text that made the sentences grammatically
wrong (they were actually typos! historically they were correct, but we
later changed the later part of the sentence without fixing the first
part).
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The git history of the project is now archived on SoftwareHeritage and a
link to it as was added in the "Reproducible supplement" tag just under the
abstract.
Also, some corrections were also made in the text. In particular, the part
explaining the separation of software and data reproducibility was slightly
clarified to be more clear
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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.
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Upon submission to CiSE we were informed that the abstract has to be less
than 150 words to be processed. So with this commit, I am shrinking the
abstract slightly, trying to remove some points that are less important and
trying to shrink some of the sentences.
Also, to avoid confusion and be more clear, the term "temporal provenance"
has been replaced by "Recorded history".
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Until now, when the figures were built directly from EPS
('\newcommand{\makepdf}{}' was commented), they would take the full
line-width becoming a little too large! I noticed this after letting arXiv
build the PDF.
With this commit, the 'includetikz' tool takes a second argument to be a
parameter given to 'includegraphics' (which is scale in this case).
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Everything else regarding the submission to arXiv and Zenodo has been
complete, so I done a final read, making some minor edits to hopefully make
the text easier to read.
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All the steps following the to-be-added (in 'README-hacking.md')
publication checklist prior to the final check from new clone have been
added:
- 'README.md' file has been set.
- "Reproducible supplement" was added just above the keywords, pointing to
Zenodo.
- A link to the to-be-uploaded data underlying the plot was added in the
caption of the tools-per-year plot.
- A new meta-data configuration file was added to store basic project
metadata to be used throughout the project. This will later be taken
into Maneage. For examle the project title is now stored here and
written into the paper's LaTeX source and output datasets automatically.
- Verification was activated and plot's data and LaTeX macro files are now
automatically verified.
- A complete metadata was added for the data underlying the plot.
- A generic function was added in 'initialize.mk' that will automatically
write project info and copyright in all plain-text outputs.
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I noticed that we hadn't include the publication of the workflow and the
advantage that Maneage provides in this regard. So it was added at the end
of the proof-of-concept section. However, it was necessary to summarize
some other parts to not increase the wordcount.
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These are some corrections that David sent to me by email and I am
committing here.
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Antonio Diaz Diaz (author of the Lzip program/library), has had a very
supportive role in what became Maneage in the last 4 years. For example I
really started to appreciate the value of simplicity and archivability
while reading Lzip's documentation.
Fortunately he also read a recent version of the paper that was again very
supportive. Some of the minor points he raised had already been fixed, but
using 'supplier' instead of 'server' (in the Free Software) criterion was
new so I implemented it here with this commit. With this, I am also
thanking him for all his wonderful support and encouragement in the last 4
years.
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Boud's point about a "random reader" not being a good example case was
correct. But "user" also gives it a software perspective that is ofcourse
not wrong, its can just be confusing. So I thought of changing it to
"interested reader".
In the part about the C-library dependency of high-level software, from
Boud's correction, I found out that it is very hard to convey what I wanted
to say (that separating errors due to C-library implementation and
measurement errors will be easy, because they should be on much different
scales). But I then corrected it to give it a slightly better tone while
mentioning the same thing: that with Maneage we can now accurately measure
the effect of the C library.
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Changes with this commit are mostly minor and obvious. Some worth
commenting on include:
* `technologies develop very fast` - As a general statement, this
is too jargony, since technology is much wider than just
`software`; `some technologies` makes it clear that we're referring
to the specific case of the previous sentence
* `in a functional-like paradigm, enabling exact provenance` -
While `make` is not an imperative programming language, I don't
see how `make` is `like` a functional programming language.
Classifying it as a declarative and a dataflow programming
language and as a metaprogramming language would seem to go in
the right direction [1-3]. I also couldn't see how the language
type relates to tracking exact provenance.
But since we don't want to lengthen the text, my proposal is to
put `and efficient in managing exact provenance` without trying
to explain this in terms of a taxonomy of programming languages.
[1] https://en.wikipedia.org/wiki/Functional_programming
[2] https://en.wikipedia.org/wiki/Comparison_of_multi-paradigm_programming_languages
[3] https://en.wikipedia.org/wiki/Dataflow_programming
* `A random reader` - In the scientific programming context, `random`
has quite specific meanings which we are not using here; a `reader`
has not necessarily tried to reproduce the project. So I've proposed
`A user` here - with the idea that a `user` is more likely to be someone
who has done `./project configure && ./project make`.
* `studying this is another research project` - the present tense `is`
doesn't sound so good; I've put what seems to be about the shortest
natural equivalent.
Pdf word count: 5856
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An "internally" was added to the part about core GNU tools accounting for
the differences between POSIX-compatible systems. One extra word was also
removed in the next sentence.
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Hopefully, it is more to the point with these few word-corrections.
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Konrad raised some very interesting points in particular about the
limitations of POSIX as a fuzzy standard that does not guaratee
reproducibility. A relatively long paragraph was thus added in the
discussion to address this important point.
In order to fit it in, the paragraph on "unwanted competition" was removed
since the POSIX issue was much more relevant for a curious
reader. Throughout the text, some other parts were edited to decrease the
length of the paper while making it easier to read.
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Some of the redundant sentences have been removed and some minor edits
made.
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The changes in this commit are best shown with `git diff --word-diff`
or `git patch --word-diff`. There are about half a dozen changes
of 1-2 words or a comma, the reasons should be obvious.
The sentence with "can not just" seems to be correct formally, but
"can not only" seems to me better to warn the reader that this
is a phrase of the form "can not only do X but can also do Y";
"can not just" sounds a bit like "You cannot just enter the room
without knocking" - it doesn't require a second part.
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One major point was that following Konrad's suggestion the issue of not
being familiar with the Lisp/Scheme framework of GWL is now removed. We
actually mention the main problem we have had with Guix, but also highlight
that their solution was one of the main inspirations for this work.
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Until this commit, there was only a small description of me. With this
commit, I have added a small paragraph with my biography. I know we are
very restricted because of the word limit so I tried to be very short!
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