diff options
| -rw-r--r-- | reproduce/analysis/config/INPUTS.mk | 8 | ||||
| -rw-r--r-- | reproduce/analysis/make/download.mk | 12 | ||||
| -rw-r--r-- | reproduce/analysis/make/menke2020.mk | 65 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 1 | ||||
| -rwxr-xr-x | reproduce/software/bash/configure.sh | 15 | ||||
| -rw-r--r-- | tex/src/references.tex | 2 |
6 files changed, 84 insertions, 19 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. diff --git a/tex/src/references.tex b/tex/src/references.tex index 63ea0b2..2a67584 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -22,7 +22,7 @@ month = "Feb", volume = {491}, number = {4}, - pages = {5317-5329}, + pages = {5317}, doi = {10.1093/mnras/stz3111}, archivePrefix = {arXiv}, eprint = {1911.01430}, |