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With the submission of the revision (which highlighted all the relevant
parts to the points the referees raised in the submitted PDF) it is no
longer necessary to highlight these parts.
If we get another revision request, we can add new '\new' parts for
highlighting.
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This commit makes some minor fixes following the hardwired non-numerical
solution to the cross-referencing issue between the main article and the
supplement, such as fixing "lineage like lineage" and missing closing
parentheses.
From Mohammad: while re-basing the commit over the 'master' branch, I also
added Boud'd name at the top of the copyright holders of the appendices.
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Since the addition of the appendix bibliography we hadn't checked the 'make
dist' command, as a result the PDF couldn't be built. With this commit, in
the 'dist' rule, we are now also copying 'appendix.bbl' and the created
tarball could build the PDF properly. Also the 'peer-review' directory is
now also included in the tarball created by './project make dist'.
I also found a small typo in the description of Occam (an 'a' was missing)
and fixed it.
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In preparation for the submission of the revised manuscript, I went through
the full paper and appendices one last time. The second appendix (reviewing
existing reproducible solutions) in particular needed some attention
because some of the tools weren't properly compared with the criteria.
In the paper, I was also able to remove about 30 words, and bring our own
count (which is an over-estimation already) to below 6250.
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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).
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There weren't any conflicts in this merge; either technical conflicts that
can be found by Git, or logical conflicts (that will cause a crash in the
project).
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After correctly setting Less to depend on 'ncurses', I noticed its still
not linking to Maneage's 'ncurses', but pointing to my host system's
'ncurses' (that happens to have the same version! So it would crash on a
system with a different version). This shows that like some other software,
we need to manually correct the RPATH inside Less.
With this command, the necessary call to 'patchelf' has been added and with
it, the installed 'less' command properly linked to Maneage's internal
build of 'ncurses'.
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After going through the publication checklist, some edits were made to make
things more clear. Also, an item was added to remind the project author
that the commit hashes on the uploaded data files should be the same.
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Until now, the description in 'README.md' to build the Dockerfile in
'README.md' had one item per line, thoroughly describing the reason behind
that line. But in many cases, the user is already familiar with Docker (or
has already read through the items) and just wants to have the Dockerfile
ready fast. In these cases, all those extra explanations are annoying.
With this commit, an item '0' has been added at the start of the item list
for summary. It only contains the necessary Dockerfile contents with no
extra explanation.
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Until now, the 'less' software package (used to view large files easily on
the command-line and used by Git for things like 'git diff' or 'git log')
only depended on 'patchelf' (which is a very low-level software).
However, as Boud reported in bug #59811 [1], building less would crash with
an error saying "Cannot find terminal libraries" in some systems (including
the proposed Docker image of 'README.md' which I confirmed
afterwards). Looking into the 'configure' script of 'less', I noticed that
'less' is actually just checking for some functions provided by the ncurses
library!
With this commit, 'less' depends on 'ncurses'. I was able to confirm that
with this change, 'less' successfully builds within the Docker image.
[1] https://savannah.nongnu.org/bugs/?59811
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After his previous two commits, we discussed some of the points and I am
making these edits following those. In particular the last statement about
Madagascar "could have been more useful..." was changed to simply mention
that mixing workflow with analysis is against the modularity principle. We
should not judge its usefulness to the community (which is beyond our scope
and would need an official survey).
A few other minor edits were done here and there to clarify some of the
points.
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With this commit, I have corrected some minor typos of this appendix.
They are very minor corrections.
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With this commit, I have corrected some minor typos of this appendix.
In addition to that, I also put empty lines to separate subsections and
subsubsections appropiately.
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I ran a simple Emacs spell check over the main body and the two
appendices. All discovered typos have been fixed.
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With this commit, I have corrected some minor typos of this appendix. In
addition to that, I also put empty lines to separate subsections and
subsubsections appropiately (5 lines and 1 line, respectively).
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With this commit, I had a look at the paper and correct some minor typos.
When possible, I tried to simplify some phrases to have less number of words.
To do that, I added some hypens when I considered it could be necessary/possible.
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Having entered 2021, it was necessary to update the years of all the
copyright statements.
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There were only three very small conflicts that have been fixed.
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Until now, in the appendices we were simply using '\ref' to refer to
different parts of the published paper. However, when built in
'--supplement' mode, the main body of the paper is a separate PDF and
having links to a separate PDF is not impossible, but far too complicated.
However, having the links adds to the richness of the text and helps point
readers to specific parts of the paper.
With this commit, there is a LaTeX conditional anywhere in the appendices
that we want to refer the reader to sections/figures in the main body. When
building a separate PDF, the resepective section/figure is cited in a
descriptive mode (like "Seciton discussing longevity of tools"). However,
when the appendices go into the same PDF as the main body, the '\ref's
remain.
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Having added/modified text in the supplements, Boud is now a copyright
holder of this file too.
I also added 2021 to the copyright years of paper.tex and supplement.tex.
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This commit does some minor copyediting, especially of the
introduction to the supplement. There's no point complaining to
the reader about the word limit of the journal: s/he is not
interested in that. This is not the right place for discussing
journal policy. The need for summarising content and focussing on
key elements of a cohesive argument is fundamental in a world of
information overload. A&A/MNRAS/ApJ/PRD letters are generally
much worse than normal articles in terms of reproducibility
because they have to omit so many details that the reader has
to read the full articles to really know what is done. But the
reality is that letters get read a lot, because they're short
and snappy.
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In the abstract the repeated benefits of Maneage (which are also mentioned
in the criteria) were removed to fit into CiSE's online submission
guidelines. In Section II (Longevity of existing tools), the paragraph that
itemized the following paragrahs as a numbered list has been removed with
the sentence that repeatedly states the importance of reproducibility in
the sciences and some branches of the industry.
With these changes our approximate automatic count has 6277 words. This is
still very slightly larger than the 6250 word limit of the
journal. However, this count is a definite over-estimation (including many
things like page titles and page numberings from the raw PDF to text
conversion). So the actual count for the journal publication should be less
than this.
A few other tiny corrections were made:
- The year of the paper and copyright in 'README.md' was set to 2021. The
copyright of the rest of the files will be set to 2021 after the next
merge with Maneage soon (the years of core infrastructure copyrights has
already been corrected there).
- Mohammadreza's name was added in 'README.md'.
- The line to import the "necessity" appendix has been commented in the
version to have the full paper in one PDF (to be upladed to arXiv or
Zenodo).
- The supplement PDF now starts with '\appendices' so the sections have
the same labels as the single-PDF version.
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Until now the supplement had no introduction for a random reader to see the
purpose of this "Web extra" supplement.
With this commit, an abstract has been added.
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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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Until now there was only a 'clean' (to delete all files created during the
'make' phase) and the 'distclean' (to delete all files during configuration
and make). But sometimes we don't want to delete all the files created
during the full 'make' phase, we only want to delete the files that were
created by LaTeX for building the paper.
Witht this commit, a new target has been added for this job. You can now
run the following command for this job:
./project make texclean
Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz'
directory under that location is recreated, ready for a future build).
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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.
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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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Until now, there was no warning when the 'maneage' branch didn't exist in
the Git history. This can happen when you forget to push the 'maneage'
branch to a remote for your project, and you later clone your project from
that remote (for example on another computer). We use the 'maneage' branch
to report the latest commit hash and date in the final paper (which can
greatly help future readers). Since we check the 'maneage' branch on every
run of './project make' (in 'initialize.mk') this would result in a printed
statement like this:
fatal: Not a valid object name maneage
Also until now, the description of what to do when TeXLive wasn't installed
properly wasn't complete: it didn't mention that it is necessary to delete
the TeXLive target files. This could confuse users (they would re-run
'./project configure -e', but with no effect).
With this commit, for the 'maneage' branch issue a complete warning will be
printed. Telling the user what to do to get the 'maneage' branch (and thus
fix this warning). Also, the LaTeX macros that go in the paper are now red
when the 'maneage' branch doesn't exist, telling the user to see the
printed warning (thus encouraging the user to get the branch). For the
TeXLive issue, the necessary commands to run are now also printed in the
warning.
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Until now, when building the high-level (optional) software, we would give
both 'CPPFLAGS' and 'C_INCLUDE_PATH' the same value/directory in
'high-level.mk'. But we recently found that on macOS's C compiler
('clang'), if a directory is included in both 'CPPFLAGS' and
'C_INCLUDE_PATH', then that directory is ignored in 'CPPFLAGS' (which has
higher priority). This caused linking problems when the version of a
software on the host was different from the Maneage version.
With this commit, 'C_INCLUDE_PATH' is not set on macOS any more and this
fixed the problem on the reported systems.
This bug was fixed with the help of Mohammad Akhlaghi and Mahdieh Navabi.
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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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Less is rarely used in non-interactive mode and is primarily intended for
interactively viewing large files. So its need within Maneage (for batch
processing) wasn't often felt until now. However, when running './project
shell' (which completely closes-off the outside environment), or building a
Maneage'd project within a minimal container that doesn't have less, it
becomes hard to use Git (and in particular its 'diff' output which depends
on 'less').
With this commit, Less has been added as a dependency of Git in
'basic.mk'. In total its built product is roughly 800KB and builds within a
second or two. So it isn't a burden on any project. But it can be very
useful when the projects are being developed within the Maneage environment
itself.
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In a recent build on a macOS, we recognized that Texinfo needs the
'libintl.h' headers of Gettext. However, Gettext depends on M4, and until
now we had set M4 to depend on Texinfo. Therefore adding Gettext as a
dependency of Texinfo would cause a circular dependency.
On the macOS, we temporarily disabled M4's Texinfo dependency, and the
build went through. I also checked on my GNU/Linux system: temporarily
renamed all Texinfo built files from my system and done a clean build of M4
and it succeeded. To be further safe, I built Maneage from this commit
(where M4 doesn't depend on Texinfo) in a Docker container, and it went
through with no problems. So the current M4 version indeed doesn't need
Texinfo. I think adding Texinfo as a dependency of M4 was a historic issue
from the early days.
In the process, I also cleaned 'basic.mk' a little:
- A "# Level N" comment was added on top of each group of software that
can be built in parallel (generally).
- GNU Nano was moved to the end of the file (to be "Level 6").
- Some comments were edited in some places.
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