Software Heritage IDs (SWHIDs) now printed in PDF

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.

3 files changed, 15 insertions, 14 deletions

diff --git a/README.md b/README.md
index 549bf5d..3bba825 100644
--- a/README.md
+++ b/README.md
@@ -36,7 +36,7 @@ filesystem is affected.
 
 ```shell
 $ git clone http://git.maneage.org/paper-concept.git
-$ cd maneage-paper
+$ cd paper-concept
 $ ./project configure
 $ ./project make
 ```
diff --git a/paper.tex b/paper.tex
index 2984142..5cdb9df 100644
--- a/paper.tex
+++ b/paper.tex
@@ -43,12 +43,12 @@
   Boudewijn F. Roukema,
   Mohammadreza Khellat,\\
   David Valls-Gabaud,
-  Roberto Baena-Gall\'e
-  \thanks{Manuscript received MM DD, YYYY; revised MM DD, YYYY.}
+  Roberto Baena-Gall\'e\\
+  \footnotesize{Manuscript received June 5th, 2020; accepted April 7th, 2021; published on IEEE April 13th, 2021}
 }
 
 %% The paper headers
-\markboth{Computing in Science and Engineering, Vol. X, No. X, MM 2021: \href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}, \href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}, \href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}%
+\markboth{Computing in Science and Engineering, Vol. 23, No. X, MM 2021: \href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}, \href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}, \href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}%
 {Akhlaghi \MakeLowercase{\textit{et al.}}: \projecttitle}
 
 
@@ -95,7 +95,7 @@ after main body of paper (Appendices \ref{appendix:existingtools} and \ref{appen
   \emph{Reproducibility} ---
   All products in \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}},
   Git history of this paper's source at \href{http://git.maneage.org/paper-concept.git}{\texttt{git.maneage.org/paper-concept.git}},
-  which is also archived in \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=http://git.maneage.org/paper-concept.git}{SoftwareHeritage}.
+  which is also archived in Software Heritage\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:33d24ae2107e25c734067d704cdad9d33013588a;anchor=swh:1:rev:b858c601613d620f5cf4501816e161a2f8f2e100}{swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717}}}.
 \end{abstract}
 
 % Note that keywords are not normally used for peer-review papers.
@@ -336,7 +336,7 @@ Building the core Maneage software environment on an 8-core CPU takes about 1.5
 However, this is only necessary once in a project: the analysis (which usually takes months to write/mature for a normal project) will only use the built environment.
 Hence the few hours of initial software building is negligible compared to a project's life span.
 To facilitate moving to another computer in the short term, Maneage'd projects can be built in a container or VM.
-The \inlinecode{README.md}\footnote{\inlinecode{\label{maneageatswh}\href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=http://git.maneage.org/project.git}{https://archive.softwareheritage.org/browse/origin/directory}\\\href{https://archive.softwareheritage.org/browse/origin/directory/?origin\_url=http://git.maneage.org/project.git}{?origin\_url=http://git.maneage.org/project.git}}} file has thorough instructions on building in Docker.
+The \inlinecode{README.md}\footnote{\inlinecode{\label{maneageatswh}\href{https://archive.softwareheritage.org/swh:1:cnt:66c1d53b2860a40aa9d350048f6b02c73c3b46c8;origin=http://git.maneage.org/project.git}{swh:1:cnt:66c1d53b2860a40aa9d350048f6b02c73c3b46c8}}} file has thorough instructions on building in Docker.
 Through containers or VMs, users on non-Unix-like OSs (like Microsoft Windows) can use Maneage.
 For Windows-native software that can be run in batch-mode, evolving technologies like Windows Subsystem for Linux may be usable.
 
@@ -381,7 +381,7 @@ Other built files (``targets'' in intermediate analysis steps) cascade down in t
 \begin{lstlisting}[
     label=code:topmake,
     caption={This project's simplified \inlinecode{top-make.mk}, also see Figure \ref{fig:datalineage}.\\
-    For full file, see \href{https://archive.softwareheritage.org/browse/content/sha1_git:6b055f75fa8050bbb4dee868ef1fb01e1725407d/?origin_url=http://git.maneage.org/paper-concept.git/&path=reproduce/analysis/make/top-make.mk&revision=e4a5566861bb7b639624c50be45b2a04d0ce9197&snapshot=01ad46a4f2cb90c2998df83dc0f2d9bd3e233710}{SoftwareHeritage}}
+    {\footnotesize (\inlinecode{\href{https://archive.softwareheritage.org/swh:1:cnt:6b055f75fa8050bbb4dee868ef1fb01e1725407d;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:01ad46a4f2cb90c2998df83dc0f2d9bd3e233710;anchor=swh:1:rev:e4a5566861bb7b639624c50be45b2a04d0ce9197;path=/reproduce/analysis/make/top-make.mk}{swh:1:cnt:6b055f75fa8050bbb4dee868ef1fb01e1725407d}})}}
   ]
 # Default target/goal of project.
 all: paper.pdf
@@ -405,7 +405,7 @@ include $(foreach s,$(makesrc), \
 Just before reaching the ultimate target (\inlinecode{paper.pdf}), the lineage reaches a bottleneck in \inlinecode{verify.mk} to satisfy the verification criteria.
 All project deliverables (macro files, plot or table data, and other datasets) are verified at this stage, with their checksums, to automatically ensure exact reproducibility.
 Where exact reproducibility is not possible (for example, due to parallelization), values can be verified by the project authors.
-For example see \href{https://archive.softwareheritage.org/browse/origin/content/?branch=refs/heads/postreferee_corrections&origin_url=https://codeberg.org/boud/elaphrocentre.git&path=reproduce/analysis/bash/verify-parameter-statistically.sh}{verify-parameter-statistically.sh} of \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460}.
+For example see \inlinecode{verify-parameter-statistically.sh}\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a;origin=https://codeberg.org/boud/elaphrocentre.git;visit=swh:1:snp:54f00113661ea30c800b406eee55ea7a7ea35279;anchor=swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e;path=/reproduce/analysis/bash/verify-parameter-statistically.sh}{swh:1:cnt:dae4e6de5399a061ab4df01ea51f4757fd7e293a}}} of \href{https://doi.org/10.5281/zenodo.4062460}{zenodo.4062460}.
 
 \begin{figure*}[t]
   \begin{center} \includetikz{figure-branching}{scale=1}\end{center}
@@ -445,7 +445,7 @@ The analysis can benefit from the powerful and portable job management features
 
 To satisfy the recorded history criterion, version control (currently implemented in Git) is another component of Maneage (see Figure \ref{fig:branching}).
 Maneage is a Git branch that contains the shared components (infrastructure) of all projects (e.g., software tarball URLs, build recipes, common subMakefiles, and interface script).
-The core Maneage git repository is hosted at \inlinecode{\href{http://git.maneage.org/project.git}{git.maneage.org/project.git}} (archived at \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=http://git.maneage.org/project.git}{Software Heritage}).
+The core Maneage git repository is hosted at \inlinecode{\href{http://git.maneage.org/project.git}{git.maneage.org/project.git}} (archived at Software Heritage\footnote{\inlinecode{\href{https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:33d24ae2107e25c734067d704cdad9d33013588a;anchor=swh:1:rev:b858c601613d620f5cf4501816e161a2f8f2e100}{swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717}}}).
 Derived projects start by creating a branch and customizing it (e.g., adding a title, data links, narrative, and subMakefiles for its particular analysis, see Listing \ref{code:branching}).
 There is a thoroughly elaborated customization checklist in \inlinecode{README-hacking.md}.
 
@@ -459,7 +459,7 @@ Generally, any Git flow (branching strategy) can be used by the high-level proje
 Low-level improvements in Maneage can thus propagate to all projects, greatly reducing the cost of project curation and maintenance, before \emph{and} after publication.
 
 Finally, a snapshot of the complete project source is usually $\sim100$ kilo-bytes.
-It can thus easily be published or archived in many servers, for example, it can be uploaded to arXiv (with the \LaTeX{} source\cite{akhlaghi19, infante20, akhlaghi15}), published on Zenodo and archived in SoftwareHeritage.
+It can thus easily be published or archived in many servers, for example, it can be uploaded to arXiv (with the \LaTeX{} source\cite{akhlaghi19, infante20, akhlaghi15}), published on Zenodo and archived in Software Heritage.
 
 \begin{lstlisting}[
     label=code:branching,
@@ -579,6 +579,7 @@ Alice Allen,
 Pedram Ashofteh Ardakani,
 Roland Bacon,
 Michael R. Crusoe,
+Roberto Di Cosmo,
 Antonio D\'iaz D\'iaz,
 Surena Fatemi,
 Fabrizio Gagliardi,
@@ -598,7 +599,7 @@ Elham Saremi,
 Yahya Sefidbakht,
 Zahra Sharbaf,
 Nadia Tonello,
-Ignacio Trujillo
+Ignacio Trujillo,
 Lourdes Verdes-Montenegro
 and Peter Wittenburg
 for their useful help, suggestions, and feedback on Maneage and this paper.
diff --git a/tex/src/supplement.tex b/tex/src/supplement.tex
index 2c70855..3873eb6 100644
--- a/tex/src/supplement.tex
+++ b/tex/src/supplement.tex
@@ -40,12 +40,12 @@
   Boudewijn F. Roukema,
   Mohammadreza Khellat,\\
   David Valls-Gabaud,
-  Roberto Baena-Gall\'e
-  \thanks{Manuscript received MM DD, YYYY; revised MM DD, YYYY.}
+  Roberto Baena-Gall\'e\\
+  \footnotesize{Manuscript received June 5th, 2020; accepted April 7th, 2021; published on IEEE April 13th, 2021}
 }
 
 %% The paper headers
-\markboth{Computing in Science and Engineering, Vol. X, No. X, MM 2021: \href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}, \href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}, \href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}%
+\markboth{Computing in Science and Engineering, Vol. 23, No. X, MM 2021: \href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}, \href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}, \href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}%
 {Akhlaghi \MakeLowercase{\textit{et al.}}: \projecttitle}