Described the first analysis phase with a demo subMakefile

Until now, there was no explanation on an actual analysis phase, therefore
with this commit an example scenario with a readable Makefile is included.
The Data lineage graph was also simplified to both be more readable, and
also to correspond to this new explanation and subMakefile.

Some random edits/typos were also corrected and some references added for
discussion.

5 files changed, 13 insertions, 12 deletions

diff --git a/reproduce/analysis/config/INPUTS.mk b/reproduce/analysis/config/INPUTS.mk
index 9332df3..b1cf546 100644
--- a/reproduce/analysis/config/INPUTS.mk
+++ b/reproduce/analysis/config/INPUTS.mk
@@ -9,7 +9,7 @@
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
 
-MK20DATA = menke-etal-2020.xlsx
+MK20DATA = menke20.xlsx
 MK20MD5  = 8e4eee64791f351fec58680126d558a0
 MK20SIZE = 1.9MB
 MK20URL  = https://www.biorxiv.org/content/biorxiv/early/2020/01/18/2020.01.15.908111/DC1/embed/media-1.xlsx
diff --git a/reproduce/analysis/make/menke2020.mk b/reproduce/analysis/make/analysis-1.mk
index 4dd9897..9d0018e 100644
--- a/reproduce/analysis/make/menke2020.mk
+++ b/reproduce/analysis/make/analysis-1.mk
@@ -20,10 +20,10 @@
 
 # Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a
 # simple plain-text file that is easy to use.
-mk20dir = $(BDIR)/menke2020
-mk20tab3 = $(mk20dir)/table-3.txt
-$(mk20dir):; mkdir $@
-$(mk20tab3): $(indir)/menke-etal-2020.xlsx | $(mk20dir)
+a1dir = $(BDIR)/analysis-1
+mk20tab3 = $(a1dir)/menke20-table-3.txt
+$(a1dir):; mkdir $@
+$(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
 
         # Set a base-name for the table-3 data.
 	base=$(basename $(notdir $<))-table-3
@@ -62,7 +62,7 @@ $(mk20tab3): $(indir)/menke-etal-2020.xlsx | $(mk20dir)
 
 
 # Main LaTeX macro file
-$(mtexdir)/menke2020.tex: $(mk20tab3) | $(mtexdir)
+$(mtexdir)/analysis-1.tex: $(mk20tab3) | $(mtexdir)
 
         # Count the total number of papers in their study.
 	v=$$(awk '!/^#/{c+=$$2} END{print c}' $(mk20tab3))
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index 7e61cb8..e4f2ccd 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -49,11 +49,11 @@
 # progress at every moment.
 $(indir):; mkdir $@
 downloadwrapper = $(bashdir)/download-multi-try
-inputdatasets = $(indir)/menke-etal-2020.xlsx
+inputdatasets = $(indir)/menke20.xlsx
 $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
         # Set the necessary parameters for this input file.
-	if   [ $* = menke-etal-2020.xlsx ]; then
+	if   [ $* = menke20.xlsx ]; then
 	  origname=$(MK20DATA); fullurl=$(MK20URL); mdf=$(MK20MD5);
 	else
 	echo; echo; echo "Not recognized input dataset: '$*.fits'."
@@ -93,5 +93,5 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 #
 # It is very important to mention the address where the data were
 # downloaded in the final report.
-$(mtexdir)/download.tex: $(pconfdir)/INPUTS.mk | $(mtexdir)
-	echo > $@
+$(mtexdir)/download.tex: $(indir)/menke20.xlsx | $(mtexdir)
+	echo "\newcommand{\menketwentyurl}{$(MK20URL)}" > $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 29bcd83..6dd322f 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -113,7 +113,7 @@ endif
 makesrc = initialize \
           download \
           verify \
-          menke2020 \
+          analysis-1 \
           paper
 
 
diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive.mk
index c918748..6760eba 100644
--- a/reproduce/software/config/installation/texlive.mk
+++ b/reproduce/software/config/installation/texlive.mk
@@ -23,4 +23,5 @@ texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xcolor \
                    trimspaces pdftexcmds pdfescape letltxmacro bitset \
                    mweights \
                             \
-                   alegreya enumitem fontspec lastpage listings
+                   alegreya enumitem fontspec lastpage listings environ \
+                   tcolorbox