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As part of Commit 87b510bc, an Emacs spell check was run on the
paper. However, during the process, the Jupyter add-on name 'nbextensions'
was mistakenly "corrected" to "extension's"! With this commit, it has been
corrected to its correct name.
The commit message was edited to add more clarity/context, also Florian's
name has been added in the acknowledgments by Mohammad.
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Antonio kindly proposed these corrections (mostly in Appendix A, but one
also at the start of Appendix B). They are fixed with this commit.
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While looking at the affiliations, I noticed that "France" was missing in
my Lyon affiliation! Also, for both Boud and myself it was necessary to put
a '.' after 'Univ' because its short for University and not a full word.
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While having a fast glance at Appendix A, I noticed two small parts that
could be improved by adding a 'from' and using 'Maneage' instead of "the
proposed solution". They are corrected with this commit.
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I just(!) noticed that in the CiSE version of the paper, they replaced the
"Towards" (first word in the title) with "Toward" (removing the
's'). According to thorough history provided by the Merriam-Webster
dictionary[1], the difference is mainly because of US/British English.
Also, they have slightly changed the capitalizations of the "long-term"
phrase, from "Long-term" that we had initially used to "Long-Term". I have
no particular opinion on this and accept their judgement.
To keep things in line with the published paper, I am correcting both these
issues in our version of the paper also (that will later go in arXiv).
https://www.merriam-webster.com/words-at-play/toward-towards-usage
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This commit changes the rather confused sentence ending "is, thus, not any
the less valuable as itself" to "often as valuable as the result
itself". This clarifies the intended meaning. The error was unfortunately
missed by the proofreaders of our article.
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In the old versions of this paper, the two components of Figure 1 were
under each other, so we referred to them as "top" and "bottom"! However, we
later put them beside each other (by shrinking the data graph), so they
became "left" and "right".
I just noticed that within the main body of the text, in one place, we were
still mistakenly saying "bottom"! So with this commit, it has been changed
to "right".
Unfortunately this has gone into the final publication on CiSE, but it is
important to fix such minor issues anyway (the good thing with having a Git
history!), we also haven't yet put the final upload on arXiv.
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In the discussion on criteria that Popper lacks, the last mentioned
criteria "including the narrative" is written in such a way that can
confuse readers into thinking that only a single criteria is
lacking. Hyphenating ('including-the-narrative') has been applied to make
the sentence less likely to be misunderstood.
The ending of the first paragraph in the "Generational gaps" item in
Appendix A.G ("... every few years is not practically possible.") sounds
like "not almost possible". So it can cause confusions. Endings that are
much clearer include:
* is impractical.
* is not possible in practice.
* is not practical.
* is not possible practically.
[meaning 2. is less likely in this case]
I've selected the first option, also replacing "they" by "scientists" to
avoid the misinterpretation that "programming languages ... have their own
science field to focus on".
This commit and the previous one were "amended" by Mohammad (compared to
the original commits that Boud had sent).
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This commit does several small copyediting fixes in the body of the
appandices which should improve their readability.
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Based on a reasonable suggestion on ethical reasoning [1], this commit
replaces the git.sdf.org + archive.today pair of URLs in the footnote on
Github's unethical aspects, with a single archive.org URL, which contains
the original URL, making this sufficient for readers wishing to check
either the live or archived versions.
[1] https://social.privacytools.io/@resist1984/106403926114506533
https://social.privacytools.io/@resist1984/106403932399114639
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This commit adds a few sentences in relation to the first known attempt to
store and make available git repository hosting ephemera (GHTorrent,
introduced to us by Roberto Di Cosmo). Since one of the two sponsors of
GHTorrent is Microsoft, both the ethics and practical aspects of this in
the context of reproducibility and scientific ethics as expressed by the
international scientific community are rather unclear, so a link to one of
the well-known lists of practical and ethical issues with Github is
included.
A minor fix is made in 'tex/src/appendix-existing-solutions.tex', since the
word 'data' is plural (singular is 'datum').
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This is the version of the project that will be published in Computing in
Science and Engineering (CiSE), Volume 23, Issue 3, Pages 82--91.
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After going through Boud's corrections and edits in the previous commit, I
thought some minor clarifications would be necessary, and they are
implemented in this commit.
Also, in preparation for submission to the journal, the top-level software
heritage ID has been corrected to the latest commit on Software Heritage.
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This commit makes several copyediting changes to the appendices and to the
supplement.tex introduction to the appendices.
The ArXiv unofficially increased upload limit of 50 Mb comes from a tweet:
https://nitter.fdn.fr/arxiv/status/1286381643893268483 (archive:
https://archive.today/PdxhT) but not listed on official ArXiv pages. So it
seems safer not to quote a value. The very old value was 0.5 Mb - out of
respect to people with low bandwidth, especially scientists in poor
countries. Tweets are generally not acceptable as "reliable sources" in
en.Wikipedia.
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David made suggested some minor edits that are now implemented (most
importantly that he would not like to be associated with an ORCID ID).
I also "saved" a new Zenodo DOI for the final submission of this paper to
Zenodo, but "after" obtaining the page number information and other minor
things.
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Until now the appendix only touched upon the archival aspects of scholarly
research producs (data, code, narrative). To help in clarity, the context
of this section has been improved, giving more explanations and examples.
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After Boud posted a notice about Maneage in an online forum [1], Rémi
Rampin and Vicky Rampin (from the ReproZip project) replied with some notes
about our review of ReproZip in Appendix B. We are very grateful to both
Rémi and Vicky for looking into it and for their comments, their
contribution has been gratefully acknowledged with this commit.
The relevant comments are listed below and have been addressed in this
commit (see the 'diff' of this commit).
- [Rémi Rampin] ReproZip can capture the build step if you want it to,
it's just another command. So if you want to trace "make" and "pip
install" etc before tracing your actual experiment, you will have all
that build information.
- [Rémi Rampin] Bundle size is easily fixed by not putting terabyte-sized
data in the bundle, which is done by editing a simple configuration
file.
- [Vicky Rampin] Not all the files in the bundle are compiled/binary files
[in relation to the old sentence "ReproZip just copies the
binary/compiled files used in a project"].
[1] https://framapiaf.org/@boud/106296894758145705
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This commit contains minor fixes in Appendix B.
ReproZip: As Vicky Rampin points out [1], ReproZip typically also
includes non-binary files, so I removed "just" and improved
the wording.
Popper: the Popper URL that we gave is obsolete; at Wayback
Machine it redirects to getpopper.io [2], so I've updated this;
and I've fixed up the wording ('off of' only exists in US
English).
[1] https://octodon.social/@VickyRampin/106298214313216228
[2] https://web.archive.org/web/20210425223605/http://falsifiable.us/
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This commit adds a few extremely brief and incomplete paragraphs
on archiving, including URLs, as what is now subsection D of
Appendix A.
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A few days, CiSE gave us a proof of the edited text and formatted
PDF. After comparing the edited text with our text, I noticed some minor
editorial issues that have been corrected in this commit. The parts that
were wrong (or could be improved in the proof) have been listed and will be
submitted to the journal.
In particular, following the recommendation from the editor, the
biographies were extended with a full listing of each author's affiliation,
I also added our ORCID IDs in the biographies.
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Until now, the paragraph impilied implicitly that the 'n2t.net' link is the
only way to access SWHIDs. Also, context/content duality wasn't too clear
in the end where I had mentioned to click on the digital format SWHID.
With this commit, I tried to edit it and avoid these two sources of
confusion.
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The most basic way to resolve a Software Heritage identifier (SWHID) is to
prefix it with 'https://archive.softwareheritage.org'. However, Roberto Di
Cosmo informed me that SWHIDs are also resolved by 'n2t.net' and
'identifiers.org'.
With this commit, on the first occurance of an SWHID, I added some
explanation of how to resolve it by adding 'http://n2t.org' (since it was
the shorter option).
Some further minor edits were made:
- In the manuscript submission information, instead of "published on
IEEE", I wrote "first published online". The journal name is available
on the top of every page and doesn't include "IEEE", so this hopefully
avoids some confusion for people who don't know CiSE is published by
IEEE.
- The URL with the link to Ubuntu images was moved to footnotes to help
the readablity and better type-setting of the paragraph. A minor edit
was then made in that paragraph to shrink the paragraph by two words
that had occupied a whole line in its end.
- The first comment line in the second listing (Git commands to start a
new branch from Maneage) was slightly edited to avoid the term 'main'
(which could be confused with the branch name after 'git checkout -b
main').
- In the acknowledgements, the paragraph on Maneage commit/branch
information was moved at the top so the people and institutions are
acknowledged immediately after each other.
- Some minor edits were made in the Spanish acknowledgements to fit with
new project names.
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Until now, the SWHIDs were not accessible in the print version of the
paper, they were only hidden as hyper-links within the PDF for readers to
click on. This is not a robust way to use the fruits of Software Heritage
and was kindly highlighted by Roberto Di Cosmo (principle investigator of
Software Heritage) after a first look at the paper.
With this commit, following the recommendation of Roberto, all the URLs are
corrected to print the raw SWHID as a footnote (for example
'swh:1:dir:...', for directories, or 'swh:1:cnt:...', for
contents/files). The click-able link of the SWHID also contains the context
(for example "origin" and etc).
In the process I noticed that the paper submission/acceptance info was not
filled and was also a footnote (which would not be seen if not cited). So
this information (received, accepted and published on IEEE) is now taken
just under the author list on the first page heading.
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The DOI of the paper has been minted by IEEE, so as a step to finalize this
paper, it has been added to the REAMEME.md and the header of all PDF
pages. Along with the DOI in the header, the arXiv and Zenodo links are
also added to the header (they are small, and won't bother the reading).
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Some minor conflicts (all expected from the commit messages in the Maneage
branch) occurred but were easily fixed.
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Summary:
- Use the new name of this variable in your Makefiles.
- In 'metadata.conf', remove fixed URL prefixes for DOIs
('https://doi.org/') or arXiv ('https://arxiv.org/abs').
Until now, the Make variable that would print the general metadata (of
whole project) into each to-be-published dataset was called
'print-copyright'! But it now does much more than simply printing the
copyright, it will also print a lot of metadata like arXiv ID, Zenodo DOI
and etc into plain-text outputs. The out-dated name could thus be
misleading and cause confusions.
With this commit, the variable is therefore called
'print-general-metadata'. After merging your project with the Maneage
branch, please replace any usage of 'print-copyright' to
'print-general-metadata'.
Also with this commit, 'README-hacking.md' mentions 'metadata.conf' and
'print-general-metadata' in the "Publication checklist" section and reminds
you to keep the first up to date, and use the second in your
to-be-published datasets.
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In the project's 'metadata.conf', we also have an option to store the
journal DOI of the project (that will later be printed in the output file
products). So now that the paper's DOI has been set by the journal, it was
time to add it in the project too.
While looking at the usage of the metadata, I noticed that the "Publication
checklist" of 'README-hacking.md' didn't talk about it. In fact, the part
about putting metadata went into a lot of detail without even mentioning
the generic 'print-general-metadata' variable (previously called
'print-copyright') that is created in 'initialize.mk'. So I removed those
extra points and just recommended using this variable for plain-text files
and putting similar info in other formats.
Some other minor changes were made:
- The metadata now doesn't need the fixed 'https://doi.org/' prefix (to
make it consistent with the arXiv identifier). Inside 'initialize.mk',
there are now two variables called 'doi-prefix-url' and
'arxiv-prefix-url' that contain the fixed prefix.
- The 'print-copyright' name was clearly outdated for all the extra
metadata that this variable created (including the copyright). So its
name was changed to 'print-general-metadata'.
The generic Maneage changes will be taken into Maneage after this (they
were tested here).
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In the previous commit, I had forgot to put a '-f' before the 'git add'!
Becauase '.txt' files are set to be ignored in Git by default (they are
marked in '.gitignore').
With this commit this file is now added into the project history.
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The email notice of the final acceptance of this paper in CiSE has been
included in the project and the stylistic points that were raised by the
editor in chief (EiC) have also been implemented. The most important points
were:
- Including citations within the text structure (as if they would be
footnotes), so things like "see \cite{...}" should have been changed.
- Hyperlinks should be printed as footnotes (because the journal gets
actually printed).
Also, to avoid the second listing breaking between pages, it has been moved
to after the next paragraph.
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Being immutable doesn't necessary mean that something is always present, so
an "always present" was also added for the reason we recommend a Git
hash. The end of the sentence was also slightly summarized to allow the
extra few words.
The re-wording of the conclusion of Active papers, was great! I just
changed the "likely" to "possible", because as Konrad mentioned in Commit
a63900bc5a8, he is now using Guix.
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These are minor last minute copyedits for recently added text,
e.g. a git hash is not literally a timestamp.
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Roberto has recently moved to a new position as professor in the
Universidad Internacional de La Rioja. With this commit, his short bio and
email address have thus been updated in the main paper to reflect this.
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Until now, we were primarily linking people to the Gitlab fork of this
paper. However, since this paper is part of Maneage, its main repository is
on Maneage's own server at http://git.maneage.org/paper-concept.git
With this commit therefore, all the gitlab.com URLs have been corrected to
owr own Git server.
While looking into Git-related points, I also noticed that in the demo code
listing showing how to clone Maneage and start a new project, we were using
Git's old/depreciated 'master' name. Git (and almost all common
repositories) now use 'main' as the default branch name, so this has also
been corrected here.
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I attended one of Peter Wittenburg's talks in the context of RDA on the
Canonical Workflow Frameworks for Research (CWFR). Afterwards I got in
touch with him about Maneage and this paper. He kindly read the paper was
very supportive of it with positive/encouraging feedback.
It was thanks to that discussion that I added CWFR in the discussion (in
the previous commit). But since that commit was focused on IAA's
suggestions, I am acknowledging Peter here.
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The AMIGA team at the Instituto Astrofísica Andalucía (IAA) are very active
proponents of reproducibility. They had already provided very constructive
comments after my visit there and many subsequent interactions. So until
now, the whole team's contributions were acknowledged.
Since the last submission, several of the team members were able to kindly
invest the time in reading the paper and providing very useful comments
which are now being implemented. As a result, I was able to specifically
thank them in the paper's acknowledgments (Thanks a lot AMIGA!). Below, I
am listing the points in the order that is shown in 'git log -p -1' for
this commit.
- Javier Moldón: "PM is not defined. First appearance in the first page".
Thanks for noticing this Javier, it has been corrected.
- Javier Moldón: "In Section III. PROPOSED CRITERIA FOR LONGEVITY and
Appendix B, you mention the FAIR principles as desirable properties of
research projects and solutions, respectively which is good, but may
bring confusion. Although they are general enough, FAIR principles are
specifically for scientific data, not scientific software. Currently,
there is an initiative promoted by the Research Data Alliance (RDA),
among others, to create FAIR principles adapted to research software, and
it is called FAIR4RS (FAIR for Research Software). More information here:
https://www.rd-alliance.org/groups/fair-4-research-software-fair4rs-wg. In
2020 there was a kick-off meeting to divide the work in 4 WG. There is
some more information in this talk:
https://sorse.github.io/programme/workshops/event-016/. I have been
following the work of WG1, and they are about the finish the first
document describing how to adapt the FAIR principles to software. Even if
all this is still work in progress, I think the paper would benefit from
mentioning the existence of this effort and noticing the diferences
between Data and Software FAIR definitions."
Thanks for highlighting this Javier, a footnote has been added for this
(hopefully faithfully summarizing it into one sentence due to space
limitations).
- Sebastian Luna Valero: "Would it be a good idea to define long-term as a
period of time; for example, 5 years is a lot in the field of computer
science (i.e. in terms of hardware and software aging), but maybe that is
not the case in other domains (e.g. Astronomy)."
Thanks Sebastian, in section 2, we do give longevity of the various
"tools" in rough units of years (this was also a suggestion by a
referee). But of course the discussion there is very generic, so going
into finer detail would probably be too subjective and bore the reader.
- Sebastian Luna Valero: "Why do you use git commit eeff5de instead of git
tags or releases for Maneage? Shown for example in the abstract of the
paper: "This paper is itself written with Maneage (project commit
eeff5de)."
Thanks for raising this important point, a sentence has been added to
explain why hashes are objective and immutable for a given history, while
tags can easily be removed or changed, or not cloned/pushed at all.
- Susana Sanchez Exposito: "We think interoperability with other research
projects would be important, do you have any plans to make maneage
interoperable with, for example, the Common Workflow Language (CWL)?".
Thanks a lot for raising this point Susana. Indeed, in the future I
really do hope we can invest enough resources on this. In the discussion,
I had already touched upon research objects as one method for
interoperability, there was also a discussion on such generic standards
in Appendix A.D.10. But to further clarify this point (given its
importance), I mentioned CWL (and also the even more generic CWFR) in the
discussion.
- Sebastian Luna Valero: "Regarding Apache Taverna, please see:"
https://github.com/apache/incubator-taverna-engine/blob/master/README.md
Thanks a lot for this note Sebastian! I didn't know this! I wrote this
section (and visited their webpage) before their "vote"! It was a
surprize to see that their page had changed. I have modified the
explanation of Taverna to mention that it has been "retired" and use the
Github link instead.
- Sebastian Luna Valero: "Page 21: 'logevity' should be 'longevity'."
Thanks a lot for noticing this! It has been corrected :-).
- Javier Moldón: "There is a nice diagram in Johannes Köster's article on
data processing with snakemake that I find very interesting to show some
key aspects of data workflows: see Fig 1 in
https://www.authorea.com/users/165354/articles/441233-sustainable-data-analysis-with-snakemake "
This is indeed a nice diagram! I tried to cite it, but as of today, this
link is not a complete paper (with no abstract and many empty section
titles). If it was complete, I would certainly have cited it in
Snakemake's discussion.
- Javier Moldón: "Regarding the problem mentioned in the introduction about
PM not precisely identified all software versions, I would like to
mention that with Snakemake, even if the analysis are usually constructed
using other package managers such as conda, or containers, you don't need
to depend on online servers or poorly-documented software versions, as
you can now encapsulate an analysis in a tarball containing all the
software needed. You still have long-term dependency problems (as you
will need to install snakemake itself, and a particular OS), but at least
you can keep the exact software versions for a particular platform."
Thanks for highlighting this Javier. This is indeed better than nothing,
we have already discussed the dangers of this "black box" approach of
archiving binaries in many contexts, and many package managers have
it. So while I really appreciate the point (I didn't know this), to avoid
lengthening the paper, I think its fine to not mention it in the paper.
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Konrad had kindly gone through the paper and the appendices with very good
feedback that is now being addressed in the paper (thanks a lot Konrad!):
- IPOL recently also allows Python code. So the respective parts of the
description of IPOL have been updated. To address the dependency issue, I
also added a sentence that only certain dependencies (with certain
versions) are acceptable.
- On Active Papers (AP: which is written by Konrad) corrections were made
based on the following parts of his comments:
- "The fundamental issue with ActivePapers is its platform dependence on
either Java or Python, neither of which is attractive."
- "The one point which is overemphasized, in my opinion, is the necessity
to download large data files if some analysis script refers to it. That
is true in the current implementation (which I consider a research
prototype), but not a fundamental feature of the approach. Implementing
an on-demand download strategy is not particularly complicated, it just
needs to be done, and it wasn't a priority for my own use cases."
- "A historical anecdote: you mention that HDF View requires registering
for download. This is true today, but wasn't when I started
ActivePapers. Otherwise I'd never have built on HDF5. What happened is
that the HDF Group, formerly part of NCSA and thus a public research
infrastructure, was turned into a semi-commercial entity. They have
committed to keeping the core HDF5 library Open Source, but not any of
the tooling around it. Many users have moved away from HDF5 as a
consequence. The larger lesson is that Richard Stallman was right: if
software isn't GPLed, then you never know what will happen to it in the
future."
- On Guix, some further clarification was added to address Konrad's quote
below (with a link to the blog-post mentioned there). In short, I
clarified that I mean storing the Guix commit hash with any respective
high-level analysis change is the extra step.
- "I also looked at the discussion of Nix and Guix, which is what I am
mainly using today. It is mostly correct as well, the one exception
being the claim that 'it is up to the user to ensure that their created
environment is recorded properly for reproducibility in the
future'. The environment is *recorded* in all detail,
automatically. What requires some effort is extracting a human-readable
description of that environment. For Guix, I have described how to do
this in a blog post
(https://guix.gnu.org/en/blog/2020/reproducible-computations-with-guix/),
and in less detail in a recent CiSE paper
(https://hal.archives-ouvertes.fr/hal-02877319). There should
definitely be a better user interface for this, but it's no more than a
user interface issue. What is pretty nice in Guix by now is the user
interface for re-creating an environment, using the "guix time-machine"
subcommand."
- The sentence on Software Heritage being based on Git was reworded to fit
this comment of Konrad: "The plural sounds quite optimistic. As far as I
know, SWH is the only archive of its kind, and in view of the enormous
resources and long-time commitments it requires, I don't expect to see a
second one."
- When introducing hashes, Konrad suggested the following useful paper that
shows how they are used in content-based storage:
DOI:10.1109/MCSE.2019.2949441
- On Snakemake, Konrad had the following comment: "[A system call in Python
is] No slower than from bash, or even from any C code. Meaning no slower
than Make. It's the creation of a new process that takes most of the
time." So the point was just shifted to the many quotations necessary for
calling external programs and how it is best suited for a Python-based
project.
In addition some minor typos that I found during the process are also
fixed.
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When built in 'group' mode, the write permissions of all created files will
be activated for a certain group of users in the host operating system. The
user specifies the name of the group with the '--group' option at configure
time. At the very start, the './project' script checks to see if the given
group name actually exists or not (to avoid hard-to-debug errors popping up
later).
Until now, the checking 'sg' command (that was used to build the project
with group-writable permissions) would always fail due to the excessive
number of redirections. Therefore, it would always print the error message
and abort.
With this commit, the output of 'sg' is no longer re-directed (which also
helps users in debuggin). If the group does actually exist, it will just
print a small statement saying so, and if it fails, the error message is
printed. This fixed the problem, allowing maneage to be built in
group-mode.
I also noticed that the variable name keeping the group name
('reproducible_paper_group_name') used the old name for the project (which
was "Reproducible paper template"! So it has been changed/corrected to
'maneage_group_name'.
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In the previous commit, some Gnuastro-specific initializations were
removed but a few more cases remained that are removed with this
commit.
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Until now, the './project' script included an '--minmapsize' option which
is an option to one of the original programs that was used in Maneage
(Gnuastro). Such an option doesn't exist in many other programs, so it is
not a suitable option for the generic Maneage project (and can just cause
confusion). It was also not used in any part of Maneage any more!
With this commit, this option is removed from the core Maneage './project'
script and if any project uses it, they can implement it in their own
branch.
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Until now the SWIG software would use the host operating system's packages
to find the TCL configuraiton (which we don't install yet in Maneage). In
particular, you can see the error during its configuration here:
....
checking for pkg-config... pkg-config
checking for Tcl configuration... found /usr/lib/tclConfig.sh
/usr/lib/tclConfig.sh: line 2: dpkg-architecture: command not found
/usr/lib//tcl8.6/tclConfig.sh: line 2: dpkg-architecture: com. not found
With this commit, TCL has been disabled when building SWIG with the
'--without-tcl' option. Later, when we add TCL in Maneage, we can remove
this option.
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With a recent update of macOS systems (macOS Big Sur 11.2.3 and Xcode
12.4), there are many warnings when building C programs (for example the
simple program we compile to check the compiler, or some of the software
like `gzip'). It prints hundreds of warning lines for every source file
that are irrelevant for our builds, but really clutters the output.
With this commit, these warnings are disabled by adding
`-Wno-nullability-completeness' to the 'CPPFLAGS' environment
variable. This has also been added to the very first check of the C
compiler in the configure step.
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Until now, each time there was a problem in the configuration of Maneage'd
projects and debugging was necessary, we had to take the following changes:
- Run the configuration on a single thread ('-j1') to see the building of
only the problematic software.
- Disable the Zenodo check manually by commenting those parts of
'reproduce/software/shell/configure.sh'. Because the internet connection
wastes a few seconds and is thus very annoying during repeated runs!
- Manually remove the '-k' option that was passed to Make (when building
the software). With the '-k', Make keeps going with the execution of
other targets if something crashes and this usually causes confusions
during the debugging.
Doing the manual changes within the code was both very annoying and prone
to errors (forgetting to correct it!).
With this commit, the existing '--debug' option has been generalized to the
software configuration phase of Maneage also. Until now, it was only
available in the analysis phase (and would directly be passed to the 'make'
command that would run the analysis). When this option is used, and the
project is in the software configuration phase, the Zenodo check won't be
done, it will use one single thread ('-j1'), and it will stop the execution
as soon as an error occurs (Make is not run with '-k').
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Until now when making a link to the system's 'dl' and 'pthread' libraries
we were simply linking the installed location on the system (in
'/usr/lib'). However, in some systems, these may themselves be links to
other locations and this could cause linking problems.
With this commit, we now use 'realpath' to extract the absolute address of
the final file that the libraries may link to, and directly link to them.
A minor cosmetic correction was also made in the build rule for CFITSIO:
the long line was broken into two!
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Until now, important LaTeX packages like 'caption' (for managing figure
captions), 'hyperref' (for managing links) and 'xcolor' (for managing
colors) were being loaded inside the optional
'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove
this file from loading when you use custom journal sytels. However, these
packages will often be necessary after loading special journal styles also.
With this commit, these packages are now loaded into LaTeX as part of the
'tex/src/preamble-project.tex' file. This file is in charge of LaTeX
settings that are custom to the project and independent of its style.
Several other small corrections are made with this commit:
- I noticed that './project make texclean' crashes if no PDF exists in the
working directory! So a '-f' was added to the 'rm' command of the
'texclean' rule.
- As part of the LaTeX Hyperref, we can set general metadata or properties
for the PDF (that aren't written into the printable PDF, but into the
file metadata). They can be viewed in many PDF viewers as PDF
properties. Until now, we were only using the '\projecttitle' macro here
to write the paper's title. However, thanks to the recently added
'reproduce/analysis/config/metadata.conf', we now have a lot of useful
information that can also go here. So the 'metadata-copyright-owner' is
now used to define the PDF author, and the project's
'metadata-git-repository' and commit hash are written into the PDF
subject. But to import these, it was necessary to define them as LaTeX
macros, hence the addition of these macros in 'initialize.mk'.
- Some extra packages that aren't necessary to build the default PDF were
removed in 'preamble-project.tex'.
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Until now, when you ran './project make dist', first it would delete the
temporary files (like files ending in '~' or '.swp' created by some
editors), then it had a place to add project-specific operations for the
distribution.
However, in the process of cleaning the temporary files, it would 'cd' into
the directory that would later be packaged. So project-specific operations
would first have to 'cd' back into the top source directory. This was prone
to hard-to-find bugs.
With this commit, to avoid the problem the project-specific operations are
now placed before the cleaning phase. This is also technically good because
in the project-specific operations there may also be temporary files that
shouldn't go into the distribution tarball.
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There was a single conflict in the comments of one part of 'configure.sh'
that has been fixed.
There was also a single place that needed to convert 'BDIR' to 'badir' in
this project (so after the merge, it also built easily).
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Until now, the build directory contained a 'software/' directory (that
hosted all the built software), a 'tex/' subdirectory for the final
building of the paper, and many other directories containing
intermediate/final data of the specific project. But this mixing of built
software and data is against our modularity and minimal complexity
principles: built software and built data are separate things and keeping
them separate will enable many optimizations.
With this commit, the build directory of the core Maneage branch will only
contain two sub-directories: 'software/' and 'analysis/'. The 'software/'
directory has the same contents as before and is not touched in this
commit. However, the 'analysis/' directory is new and everything created in
the './project make' phase of the project will be created inside of this
directory.
To facilitate easy access to these top-level built directories, two new
variables are defined at the top of 'initialize.mk': 'badir', which is
short for "built-analysis directory" and 'bsdir', which is short for
"built-software directory".
HOW TO IMPLEMENT THIS CHANGE IN YOUR PROJECT. It is easy: simply replace
all occurances of '$(BDIR)' in your project's subMakefiles (except the ones
below) to '$(badir)'. To confirm if everything is fine before building your
project from scratch after merging, you can run the following command to
see where 'BDIR' is used and confirm the only remaning cases.
$ grep -r BDIR reproduce/analysis/*
--> make/verify.mk: innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \
--> make/initialize.mk:badir=$(BDIR)/analysis
--> make/initialize.mk:bsdir=$(BDIR)/software
--> make/initialize.mk: $$sys_rm -rf $(BDIR)
--> make/top-prepare.mk:all: $(BDIR)/software/preparation-done.mk
'BDIR' should only be present in lines of the files above. If you see
'$(BDIR)' used anywhere else, simply change it to '$(badir)'. Ofcourse, if
your project assumes BDIR in other contexts, feel free to keep it, it will
not conflict. If anything un-expected happens, please post a comment on the
link below (you need to be registered on Savannah to post a comment):
https://savannah.nongnu.org/task/?15855
One consequence of this change is that the 'analysis/' subdirectory can be
optionally mounted on a separate partition. The need for this actually came
up for some new users of Maneage in a Docker image. Docker can fix
portability problems on systems that we haven't yet supported (even
Windows!), or had a chance to fix low-level issues on. However, Docker
doesn't have a GUI interface. So to see the built PDF or intermediate data,
it was necessary to copy the built data to the host system after every
change, which is annoying during working on a project. It would also need
two copies of the source: one in the host, one in the container. All these
frustrations can be fixed with this new feature.
To describe this scenario, README.md now has a new section titled "Only
software environment in the Docker image". It explains step-by-step how you
can make a Docker image to only host the built software environment. While
your project's source, software tarballs and 'BDIR/analysis' directories
are on your host operating system. It has been tested before this commit
and works very nicely.
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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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