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Until now, the build strategy of the paper was to have a single output PDF
that either contains (1) the full paper with appendices in the same paper
(2) only the main body of the paper with no appencies.
But the editor in chief of CiSE recently recommended publishing the
appendices as supplements that is a separate PDF (on its webpage). So with
this commit, the project can make either (1) a single PDF (containing both
the main body and the appendices) that will be published on arXiv and will
be the default output (this is the same as before). (2) two PDFs: one that
is only the main body of the paper and another that is only the appendices.
Since the appendices will be printed as a PDF in any case now, the old
'--no-appendix' option has been replaced by '--supplement'. Also, the
internal shell/TeX variable 'noappendix' has been renamed to
'separatesupplement'.
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Since we have a long list of Copyright statements at the top, I thought its
easier to just move the copyright notice to the top of 'paper.tex' also.
In the acknowledgments, the paragraph on Maneage was slighltly summarized
to save a few words and still be clear. Also, the long name of the Japanese
Ministry of Education, Culture, Sports, Science, and Technology, was
summarized to Japanese MEXT.
In the biographies, the '-at' (replacing '@' in the emails) was changed to
'-AT' to be more clear to the eye that its just a place holder.
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As recommended by Lorena Barba (editor in chief of CiSE), we should prepare
the appendices as a separate "Supplement" for the journal. But we also want
them to be appendices within the paper when built for arXiv.
As a first step, with this commit, each appendix has been put in a separate
'tex/src/appendix-*.tex' file and '\input' into the paper. We will then be
able to conditionally include them in the PDF or not.
Also, as recommended by Lorena, the general "necessity for reproducible
research" appendix isn't included (possibly going into the webpage later).
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After adding Mohammadreza as an author of the paper, we forgot to add him
as a copyright holder at the start of the paper.
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This commit makes many small wording fixes, mainly to Appendix A.
It also insert "quotes" around some of the titles fields in
'tex/src/references.tex', since otherwise capitalisation is lost (DNA
becomes Dna; 'of Reinhart and Rogoff' becomes 'of reinhart and rogoff'; and
so on). I didn't do this for all titles, because some Have All Words
Capitalised, which blocks the .bib file from choosing a consistent style.
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Mohammadreza has made significant contributions to the text of the paper
and also the source. However his contributions to the text came after the
initial submission, so until now, he was not added as an author. The reason
we waited for this was that no responses were given by CiSE editors, on the
inquiry of the possibility of adding a new author at this phase.
With this commit, following approval from the editors, Mohammadreza's
information has been added to the manuscript as an author to refrain from
delays in submitting the manuscript revision.
While merging with the 'master' branch, Mohammad also done some minor edits
to the other biographies to follow a similar format.
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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.
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In the first/long draft of this work, we had a good introduction on the
necessity of reproducibility. But we were forced to remove it because of
word-count limits. Having moved a major portion of the previous work into
the appendices, I thought it would be good to put that introduction as a
first appendix also, focused on the necessity for reproducibile research.
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Following Boud's point in the previous commit, I tried to clarify the point
in the text that we are only talking about hand-written source files: in
short, in this part of the paper, we are not talking abou the
version/snapshot for arXiv which needs figures and many extra automatically
built files. We are just talking about the raw, hand-written files. Trying
to convince people how good it is to keep the raw files separate from
automatically generated files ;-).
Also, while looking around in other parts of the main body of the paper, I
tried to edit/clarify a few points and summarize/shorten others.
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This commit fixes 'automaticly', 'mega byte', 'terra byte'.
It also changes 'will be far less than a mega byte' to 'should be
less than a megabyte'. The reason for 'should' is that in some
cases, providing a small data set in the package is useful, as in
[1]. Of course, [1] would be only 0.9 Mb in size, including the
data sets, instead of 1.3 Mb, if the author, whoever that may
happen to be, had excluded the useless (produced) file
'paper-tmp.eps'. :P Case [2] is 0.4 Mb.
These two tar archives are for ArXiv, so they also contain
produced .eps files. So maybe in principle 'far less than'
is right. However, on neither [3] nor [4], trying to follow
the recommendations :), are any of the "useful" versions of
single file archives smaller than the ArXiv version. The
git bundles are bigger because of the git history, and the
'software' archives are 0.5 to 0.6 Gb because they include
almost everything.
However, stating something that is possible in principle but
not done in practice would be misleading. So I would not include
'far less'.
[1] https://zenodo.org/record/3951152/files/subpoisson-252cf1c-arXiv.tar.gz
[2] https://zenodo.org/record/4062461/files/elaphrocentre-724a7c8-arXiv.tar.gz
[3] https://zenodo.org/record/3951152
[4] https://zenodo.org/record/4062461
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This commit fixes the labels alliez19, claerbout1992, schwab2000
which were multiply defined. The problem was using \citeappendix
instead of \cite for these in the appendix, even though they
are first used in the official part of the article.
You must do './project make clean' before recreating the pdf
in order for this to compile correctly. (Otherwise you'll waste
time re-using old files; this means that one of our 'make'
dependencies could in principle be improved.)
With this change, these references in the pdf are (for me)
correct clickable links back to [5], [1], [11], respectively.
[If you use xpdf (poppler library), remember the 'b' key for
navigate back from a clicked internal link quickly.]
This way you can quickly navigate between the appendix text
and the references used, and you avoid LaTeX warning about
'multiply defined labels'.
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This commit provides a little bit of minor copyediting, mainly in
the appendices, based on and around changing the casual 'isn't',
'don't' and other contractions with 'not' to a less casual style
of language. A few of the changes aim to improve the meaning in
tiny ways.
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The sentence sounds better with 'the'.
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It was recently announced by both RedHat[1] and CentOS[2] that CentOS 8
(which was meant to end LTS at 2030) will be terminated 8 years early (by
the end of 2021). This is a perfect example of the longevity issues when
relying on third-party providers.
With this commit, I added this as a parenthesis after mentioning Ubuntu's
LTS web address. Some minor edits were also done in other parts of this
paragraph.
[1] https://www.redhat.com/en/blog/centos-stream-building-innovative-future-enterprise-linux
[2] https://blog.centos.org/2020/12/future-is-centos-stream
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Today, Richard Stallman sent a mail in 'info-gnu@gnu.org' (GNU's public
announcements mailing list) about proprietary obsolescence (or planned
obsolescence) [1]. After looking into it, I saw there is actually a
Wikipedia page for this concept. Since it direclty relates to our Free
software criteria, I thought its good to use this technical term there.
[1] https://www.gnu.org/proprietary/proprietary-obsolescence.html
[2] https://en.wikipedia.org/wiki/Planned_obsolescence
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I just remembered that in the paragraph we compare with Jupyter, another
important point is that with based on the modularity principle, people can
choose their favorite text editor and aren't limited to one. I also tried
to remove redundant parts to avoid adding too many extra words.
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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 ;-).
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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.
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While going through Mohammad-reza's recent two commits, I noticed that we
had missed an importnat discussion on modularity in this version of the
paper (discussing how file management should also be modular resulting in
cheaper archival, and thus better longevity), so a few sentences were added
under criteria 2 (Modularity).
Mohammad-reza's edits were also generally very good and helped clarify many
points. I only reset the part that we discuss the problems with POSIX, and
not being able to produce bitwise reproducible software (which systems like
Guix work very hard at, and thus need root permissions). I felt the edit
missed the main point here (that while bitwise reproducibility of the
software is good, it is not always necessary).
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Before this commit, there were discussions in different sections related to
POSIX compliance and features. Since the relevant Cmpleteness criterion has
been changed to execution within a Unix-like OS, such dicussions had to be
modifies as well.
With this commit, the parts that were related to condition (1) of the
Completeness criterion have been modified to be relevant to new Unix-like
OS requirement. Also, few spelling problems were fixed.
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Before this commit, condition (1) for the Completeness criterion was
referring to POSIX compliance. POSIX is a very detailed dynamic standard
which goes under revision continuously and not a lot of operating systems,
GNU/Linux included are completely/officially POSIX-compliant. Furthermore,
not all sections of the huge 4000 pages standard are really important
specifically to the current Maneage functionality.
With this commit, condition (1) has been replaced by a looser condition of
execution within a Unix-like OS. Also since the term environment might have
been mistaken with the term "Operating Environment", it was replaced by the
unmistakable term "environment variables" in conditions (3) and (5). Last
but not least, condition (2) was made more restrict by adding ASCII
encoding as the condition for storing the plain text files.
TO-DO:
POSIX could contain valuable ideas regarding portability of programming
practices. These can be taken advantage of later in providing necessary and
sufficient conditions for project completeness. Another idea could be to
make LFS construct or something else as a sharp definition for what we mean
by minimal Unix-like OS.
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Some minor conflicts that came up during the merge were fixed.
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Until now, Maneage only provided the commit hashes (of the project and
Maneage) as LaTeX macros to use in your paper. However, they are too
cryptic and not really human friendly (unless you have access to the Git
history on a computer).
With this commit, to make things easier for the readers, the date of both
commits are also available as LaTeX macros for use in the paper. The date
of the Maneage commit is also included in the acknowledgements.
Also, the paragraph above the acknowledgements has been updated with better
explanation on why adding this acknowledgement in the science papers is
good/necessary.
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This only concerns the TeX sources in the default branch. In case you don't
use them, there should only be a clean conflict in 'paper.tex' (that is
obvious and easy to fix). Conflicts may only happen in some of the
'tex/src/preamble-*.tex' files if you have actually changed them for your
project. But generally any conflict that does arise by this commit with
your project branch should be very clear and easy to fix and test.
In short, from now on things will even be easier: any LaTeX configuration
that you want to do for your project can be done in
'tex/src/preamble-project.tex', so you don't have to worry about any other
LaTeX preamble file. They are either templates (like the ones for PGFPlots
and BibLaTeX) or low-level things directly related to Maneage. Until now,
this distinction wasn't too clear.
Here is a summary of the improvements:
- Two new options to './project make': with '--highlight-new' and
'--highlight-notes' it is now possible to activate highlighting on the
command-line. Until now, there was a LaTeX macro for this at the start
of 'paper.tex' (\highlightchanges). But changing that line would change
the Git commit hash, making it hard for the readers to trust that this
is the same PDF. With these two new run-time options, the printed commit
hash will not changed.
- paper.tex: the sentences are formatted as one sentence per line (and one
line per sentence). This helps in version controlling narrative and
following the changes per sentence. A description of this format (and
its advantages) is also included in the default text.
- The internal Maneage preambles have been modified:
- 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have
been merged into one preamble file called
'tex/src/preamble-maneage-default-style.tex'. This helps a lot in
simply removing it when you use a journal style file for example.
- Things like the options to highlight parts of the text are now put in
a special 'tex/src/preamble-maneage.tex'. This helps highlight that
these are Maneage-specific features that are independent of the style
used in the paper.
- There is a new 'tex/src/preamble-project.tex' that is the place you
can add your project-specific customizations.
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These can help a first-time reader of 'paper.tex'.
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Until now, the Maneage-only features of LaTeX where mixed with
'tex/src/preamble-project.tex' (which is reserved for project-specific
things). But we want to move the highlighting features (that have started
here) into the core Maneage branch, so its best for these Maneage-specific
features to be in a Maneage-specific preamble file.
With this commit, a hew 'tex/src/preamble-maneage.tex' has been created for
this purpose and the highlighting modes have been put in there. In the
process, I noticed that 'tex/src/preamble-project.tex' doesn't have a
copyright! This has been corrected.
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Roberto sent me his summarized CV which is now being included and I also
removed the extra statements about non-degree things from Raul and my own
biography (like mentioning Gnuastro, and scientific interests). To be
short, we are only mentioning degrees and positions. For Raul, I added his
M.Sc institute.
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After Mohammad-reza sent me his commit on an improved definition for
longevity, we had an indepth discussion (through a video-conference) to
avoid complexities in the terminology, while staying on point and
word-count.
In this commit/merge, I am including the improved version of the definition
of longevity, and the newly added term "functionality" (instead of
"usability" that Mohammad-reza was originally complaining to).
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The paragraph was slightly shortened, while keeping the main points.
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Before this commit, Longetivity was defined on the basis of the term
usability. Although the scope and context of the term has been mentioned
right after its use, this could have caused confusion with the keyword
"usability" in the field of software engineering.
With this commit, Longetivity definition has been rephrased in a way that
it would not require "usability". Furthermore, since longetivity would
logically require the availability of the machines and platforms during the
time of re-use, this has been explicitly mentioned in the definition.
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Following Boud's great suggestion, I also summarized my CV to be less
than 40 words.
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Following Boud's great suggestion, I also summarized my CV to be less than
40 words.
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This commit provides shorter CVs for me (Boud) + David
in order to get closer to the 6500 word limit. Our CVs
are the least significant part of the paper.
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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.
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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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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.
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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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