5 files changed, 83 insertions, 18 deletions
diff --git a/reproduce/analysis/config/INPUTS.mk b/reproduce/analysis/config/INPUTS.mk
index 6ddaec7..9332df3 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.
 
-WFPC2IMAGE = WFPC2ASSNu5780205bx.fits
-WFPC2MD5   = a4791e42cd1045892f9c41f11b50bad8
-WFPC2SIZE  = 62kb
-WFPC2URL   = https://fits.gsfc.nasa.gov/samples
+MK20DATA = menke-etal-2020.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/download.mk b/reproduce/analysis/make/download.mk
index 7c290f4..7e61cb8 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -49,12 +49,12 @@
 # progress at every moment.
 $(indir):; mkdir $@
 downloadwrapper = $(bashdir)/download-multi-try
-inputdatasets = $(foreach i, wfpc2, $(indir)/$(i).fits)
-$(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
+inputdatasets = $(indir)/menke-etal-2020.xlsx
+$(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
         # Set the necessary parameters for this input file.
-	if   [ $* = wfpc2 ]; then
-	  origname=$(WFPC2IMAGE); url=$(WFPC2URL); mdf=$(WFPC2MD5);
+	if   [ $* = menke-etal-2020.xlsx ]; then
+	  origname=$(MK20DATA); fullurl=$(MK20URL); mdf=$(MK20MD5);
 	else
 	echo; echo; echo "Not recognized input dataset: '$*.fits'."
 	echo; echo; exit 1
@@ -72,7 +72,7 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
 	else
 	  touch $(lockdir)/download
 	  $(downloadwrapper) "wget --no-use-server-timestamps -O" \
-	                     $(lockdir)/download $$url/$$origname $@
+	                     $(lockdir)/download $$fullurl $@
 	fi
 
         # Check the md5 sum to see if this is the proper dataset.
@@ -94,4 +94,4 @@ $(inputdatasets): $(indir)/%.fits: | $(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 | $(mtexdir)
-	echo "\\newcommand{\\wfpctwourl}{$(WFPC2URL)}" > $@
+	echo > $@
diff --git a/reproduce/analysis/make/menke2020.mk b/reproduce/analysis/make/menke2020.mk
new file mode 100644
index 0000000..df87080
--- /dev/null
+++ b/reproduce/analysis/make/menke2020.mk
@@ -0,0 +1,65 @@
+# Use the data from Menke 2020 (DOI:10.1101/2020.01.15.908111) as a
+# demonstration analysis for this paper. This is a relevant paper because
+# it provides good statistics about the status of reproducibility in
+# scientific publications.
+#
+# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details. See <http://www.gnu.org/licenses/>.
+
+
+
+
+# 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 | $(mk20dir)
+
+        # Set a base-name for the table-3 data.
+	base=$(basename $(notdir $<))-table-3
+
+        # Unfortunately XLSX I/O only works when the input and output are
+        # in the directory it is running. So first, we need to switch to
+        # the input directory, run it, then put our desired output where we
+        # want and delete the extra files.
+	topdir=$$(pwd)
+	cd $(indir)
+	xlsxio_xlsx2csv $(notdir $<)
+	cp $(notdir $<)."Table 3 All by journal by year".csv $$base.csv
+	rm $(notdir $<).*.csv
+	cd $$topdir
+
+        # Read the necessary information. Note that we are dealing with a
+        # CSV (comma-separated value) file. But when there are commas in a
+        # string, quotation signs are put around it. The `FPAT' values is
+        # fully described in the GNU AWK manual. In short, it ensures that
+        # if there is a comma in the middle of double-quotes, it doesn't
+        # count as a delimter.
+	echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp
+	echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp
+	echo "# Column 3: NUM_ID_TOOLS [counter, i16] Number of software/tools that were identified." >> $@.tmp
+	awk 'NR>1{printf("%-6d%-5d%d\n", $$2, $$3, $$(NF-1)*$$NF)}' \
+	    FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp
+
+        # Set the temporary file as the final target. This was done so if
+        # there is any possible crash in the steps above, this rule is
+        # re-run (its final target isn't rebuilt).
+	mv $@.tmp $@
+
+
+
+
+
+# Main LaTeX macro file
+$(mtexdir)/menke2020.tex: $(mk20tab3) | $(mtexdir)
+	touch $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index acbbafa..29bcd83 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -113,6 +113,7 @@ endif
 makesrc = initialize \
           download \
           verify \
+          menke2020 \
           paper
 
 
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 08f2609..f7fa9c8 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -299,10 +299,10 @@ if [ x"$input_dir" = x ]; then
 else
     indir=$input_dir
 fi
-wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.mk)
-wfpc2md5=$(awk  '!/^#/ && $1=="WFPC2MD5"   {print $3}' $adir/INPUTS.mk)
-wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE"  {print $3}' $adir/INPUTS.mk)
-wfpc2url=$(awk  '!/^#/ && $1=="WFPC2URL"   {print $3}' $adir/INPUTS.mk)
+mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.mk)
+mk20md5=$(awk  '!/^#/ && $1=="MK20MD5"  {print $3}' $adir/INPUTS.mk)
+mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.mk)
+mk20url=$(awk  '!/^#/ && $1=="MK20URL"  {print $3}' $adir/INPUTS.mk)
 if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
     cat <<EOF
 
@@ -315,10 +315,9 @@ please specify the directory hosting them on this system. If you don't,
 they will be downloaded automatically. Each file is shown with its total
 volume and its 128-bit MD5 checksum in parenthesis.
 
-  $wfpc2name ($wfpc2size, $wfpc2md5):
-    A 100x100 Hubble Space Telescope WFPC II image used in the FITS
-    standard webpage as a demonstration of this file format.
-    URL: $wfpc2url/$wfpc2name
+  $mk20name ($mk20size, $mk20md5):
+    Supplementary dataset to http://dx.doi.org/10.1101/2020.01.15.908111
+    URL: $mk20url
 
 NOTE I: This directory, or the datasets above, are optional. If it doesn't
 exist, the files will be downloaded in the build directory and used.