Installation year removed from TeXLive installation

TeXLive recently transitioned from its 2019 version to its 2020 version
thanks to Elham Saremi's trial of the this project. The fact that
traditionally Maneage installs all TeXLive packages in a per-year directory
is very annoying and required an update in the core Maneage system every
year. So I suddently recognized that we can fix this by setting a different
name for the directory holding the release year. This has been implemented
with this commit.

I have also done this change in the main Maneage branch for other projects
to also benefit from this correction.

4 files changed, 22 insertions, 23 deletions

diff --git a/paper.tex b/paper.tex
index 43413a9..99d9d77 100644
--- a/paper.tex
+++ b/paper.tex
@@ -48,12 +48,12 @@
 %% Abstract
 {\noindent\mpregular
   The era of big data has ushered an era of big responsibility.
-  In the absence of reproducibility, as a test on controlling the data lineage, the result's integrity will be subject to perpetual debate.
-  Maneage (management + lineage) is introduced here as a host to the computational and narrative components of an analysis.
-  Analysis steps are added to a new project with lineage in mind, thus facilitating the project's execution and testing as the project evolves, while being friendly to publishing and archival because it is wholly in machine\--action\-able, and human\--read\-able, plain-text.
-  Maneage is founded on the principles of completeness (e.g., no dependency beyond a POSIX-compatible operating system, no administrator privileges, or no network connection), modular and straight-forward design, temporal lineage and free software.
-  The lineage is not limited to downloading the inputs and processing them automatically, but also includes building the necessary software with fixed versions and build configurations.
-  Additionally, Maneage also builds the final PDF report of the project, establishing direct and automatic links between the data analysis and the narrative, with the precision of a word in a sentence.
+  In the absence of reproducibility, as a test on the reported data lineage, the result's integrity will be subject to perpetual debate.
+  To address this problem, we introduce Maneage (management + lineage) which has already been tested and used in several scientific papers.
+  Maneage is founded on the principles of completeness (e.g., no dependency beyond a POSIX-compatible operating system, no administrator privileges, or no network connection), modular and straight-forward design, temporal lineage and free software, to enable precise reproducibility.
+  The Maneage lineage, or workflow, is in machine\--action\-able, and human\--read\-able, plain-text format, facilitating version-control, publication, archival, or automatic parsing to extract data provenance.
+  The lineage is not limited to high-level processing, but also includes building the necessary software from source with fixed versions and build configurations.
+  Additionally, the project's final visualizations and narrative report are also included, establishing direct, and parse-able, links between the data analysis and the narrative or plots, with the precision of a word in a sentence or a point in a plot.
   Maneage enables incremental projects, where a new project can branch off an existing one, with moderate changes to enable experimentation on published methods.
   Once Maneage is implemented in a sufficiently wide scale, it can aid in automatic and optimized workflow creation through machine learning, or automating data management plans.
   Maneage was a recipient of the research data alliance (RDA) Europe Adoption Grant in 2019.
@@ -86,6 +86,7 @@ What operations were done on those inputs? How were the configurations or traini
 How did the quantitative results get visualized into the final demonstration plots, figures or narrative/qualitative interpretation?
 May there be a bias in the visualization?
 See Figure \ref{fig:questions} for a more detailed visual representation of such questions for various stages of the workflow.
+\tonote{Johan: add some general references.}
 
 In data science and database management, this type of metadata are commonly known as \emph{data provenance}, and the lower-level implementation is \emph{data lineage} (for more on the definitions, see Section \ref{sec:definitions}).
 Data lineage is being increasingly demanded for integrity checking from both the scientific and industrial/legal domains.
@@ -798,13 +799,13 @@ Once the improvements become substantial, new paper(s) will be written to comple
 \section{Discussion}
 \label{sec:discussion}
 
-
-
+\section{Summary and conclusion}
+\label{sec:conclusion}
 
 
 %% Acknowledgements
 \section{Acknowledgments}
-The authors wish to thank Pedram Ashofteh Ardakani, Zahra Sharbaf and Surena Fatemi for their useful suggestions and feedback on Maneage and this paper and to David Valls-Gabaud, Ignacio Trujillo, Johan Knapen, Roland Bacon for their support.
+The authors wish to thank Pedram Ashofteh Ardakani, Elham Saremi, Zahra Sharbaf and Surena Fatemi for their useful suggestions and feedback on Maneage and this paper and to David Valls-Gabaud, Ignacio Trujillo, Johan Knapen, Roland Bacon for their support.
 We also thank Julia Aguilar-Cabello for designing the Maneage logo.
 
 Work on the reproducible paper template has been funded by the Japanese Ministry of Education, Culture, Sports, Science, and Technology ({\small MEXT}) scholarship and its Grant-in-Aid for Scientific Research (21244012, 24253003), the European Research Council (ERC) advanced grant 339659-MUSICOS, European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No 721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P.
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index ce4e488..29afbfe 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -324,7 +324,7 @@ $(packagecontents): paper.pdf | $(texdir)
         # file. TIP: you can use the same strategy for other LaTeX packages
         # that may cause problems on the arXiv server.
 	cp tex/build/build/paper.bbl $$dir/
-	tltopdir=.local/texlive/2019/texmf-dist/tex/latex
+	tltopdir=.local/texlive/maneage/texmf-dist/tex/latex
 	find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
 	     | xargs -0 cp -t $$dir
 
diff --git a/reproduce/software/config/installation/texlive.conf b/reproduce/software/config/installation/texlive.conf
index 2e86ac4..b5075c6 100644
--- a/reproduce/software/config/installation/texlive.conf
+++ b/reproduce/software/config/installation/texlive.conf
@@ -9,19 +9,19 @@
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
 selected_scheme scheme-basic
-TEXDIR @installdir@/texlive/2019
-TEXMFCONFIG @installdir@/texlive2019/texmf-config
+TEXDIR @installdir@/texlive/maneage
+TEXMFCONFIG @installdir@/texlive-maneage/texmf-config
 TEXMFLOCAL @installdir@/texlive/texmf-local
-TEXMFSYSCONFIG @installdir@/texlive/2019/texmf-config
-TEXMFSYSVAR @installdir@/texlive/2019/texmf-var
-TEXMFVAR @installdir@/texlive2019/texmf-var
+TEXMFSYSCONFIG @installdir@/texlive/maneage/texmf-config
+TEXMFSYSVAR @installdir@/texlive/maneage/texmf-var
+TEXMFVAR @installdir@/texlive-maneage/texmf-var
 instopt_adjustpath 0
 instopt_adjustrepo 1
 instopt_letter 0
 instopt_portable 0
 instopt_write18_restricted 1
 tlpdbopt_autobackup 1
-tlpdbopt_backupdir @installdir@/texlive/2019/backups
+tlpdbopt_backupdir @installdir@/texlive/maneage/backups
 tlpdbopt_create_formats 1
 tlpdbopt_desktop_integration 1
 tlpdbopt_file_assocs 1
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index cdaaf7d..b0847a9 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -1261,12 +1261,10 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
         # don't want the configure script to fail if it can't run.
 	if ./install-tl --profile=texlive.conf -repository $(tlmirror); then
 
-          # Put a symbolic link of the TeX Live executables in `ibdir'. The
-          # main problem is that the year and build system (for example
-          # `x86_64-linux') are also in the directory names, making it hard
-          # to be generic. We are using wildcards here, but only in this
-          # Makefile, not in any other.
-	  ln -fs $(idir)/texlive/20*/bin/*/* $(ibdir)/
+          # Put a symbolic link of the TeX Live executables in `ibdir' to
+          # avoid all the complexities of its sub-directories and additions
+          # to PATH.
+	  ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
 
           # Register that the build was successful.
 	  echo "TeX Live is ready." > $@
@@ -1326,7 +1324,7 @@ $(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf
 
           # Make a symbolic link of all the TeX Live executables in the bin
           # directory so we don't have to modify `PATH'.
-	  ln -fs $(idir)/texlive/20*/bin/*/* $(ibdir)/
+	  ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
 
           # Get all the necessary versions.
 	  texlive=$$(pdflatex --version | awk 'NR==1' | sed 's/.*(\(.*\))/\1/' \