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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2020-03-02 02:55:00 +0000
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2020-03-02 02:55:00 +0000
commite9c81f9f40187bc4701ac539d110003e92b9ca69 (patch)
treee3929f2a116cf1bc790eaf88883e0315ef0ffa6c /reproduce/analysis
parentf51082b27e47e552658000689161c150d9c9a70e (diff)
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.
Diffstat (limited to 'reproduce/analysis')
-rw-r--r--reproduce/analysis/config/INPUTS.mk2
-rw-r--r--reproduce/analysis/make/analysis-1.mk (renamed from reproduce/analysis/make/menke2020.mk)10
-rw-r--r--reproduce/analysis/make/download.mk8
-rw-r--r--reproduce/analysis/make/top-make.mk2
4 files changed, 11 insertions, 11 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