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-rw-r--r--reproduce/analysis/make/demo-plot.mk28
-rw-r--r--reproduce/analysis/make/download.mk86
-rw-r--r--reproduce/analysis/make/format.mk44
-rw-r--r--reproduce/analysis/make/initialize.mk221
-rw-r--r--reproduce/analysis/make/paper.mk130
-rw-r--r--reproduce/analysis/make/prepare.mk47
-rw-r--r--reproduce/analysis/make/top-make.mk20
-rw-r--r--reproduce/analysis/make/top-prepare.mk20
-rw-r--r--reproduce/analysis/make/verify.mk42
9 files changed, 324 insertions, 314 deletions
diff --git a/reproduce/analysis/make/demo-plot.mk b/reproduce/analysis/make/demo-plot.mk
index 53e1918..13b0d45 100644
--- a/reproduce/analysis/make/demo-plot.mk
+++ b/reproduce/analysis/make/demo-plot.mk
@@ -1,7 +1,7 @@
# Second step of analysis:
# Data for plot of number/fraction of tools per year.
#
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -22,16 +22,16 @@
a2mk20f1c = $(tex-publish-dir)/tools-per-year.txt
$(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
- # Remove the (possibly) produced figure that is created from this
- # table: it is created by LaTeX's TiKZ package, and includes
- # multiple files with a fixed prefix.
+# Remove the (possibly) produced figure that is created from this
+# table: it is created by LaTeX's TiKZ package, and includes multiple
+# files with a fixed prefix.
rm -f $(tikzdir)/figure-tools-per-year*
- # Write the column metadata in a temporary file name (appending
- # '.tmp' to the actual target name). Once all steps are done, it is
- # renamed to the final target. We do this because if there is an
- # error in the middle, Make will not consider the job to be
- # complete and will stop here.
+# Write the column metadata in a temporary file name (appending
+# '.tmp' to the actual target name). Once all steps are done, it is
+# renamed to the final target. We do this because if there is an
+# error in the middle, Make will not consider the job to be complete
+# and will stop here.
echo "# Data of plot showing fraction of papers that mentioned software tools" > $@.tmp
echo "# per year to demonstrate the features of Maneage (MANaging data linEAGE)." >> $@.tmp
>> $@.tmp
@@ -48,7 +48,7 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
$(call print-general-metadata, $@.tmp)
- # Find the maximum number of papers.
+# Find the maximum number of papers.
awk '!/^#/{all[$$1]+=$$2; id[$$1]+=$$3} \
END{ for(year in all) \
printf("%-7d%-10.3f%d\n", year, 100*id[year]/all[year], \
@@ -56,7 +56,7 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
}' $< \
>> $@.tmp
- # Write it into the final target
+# Write it into the final target
mv $@.tmp $@
@@ -66,15 +66,15 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
# Final LaTeX macro
$(mtexdir)/demo-plot.tex: $(a2mk20f1c) $(pconfdir)/demo-year.conf
- # Find the first year (first column of first row) of data.
+# Find the first year (first column of first row) of data.
v=$$(awk '!/^#/ && c==0{c++; print $$1}' $(a2mk20f1c))
echo "\newcommand{\menkefirstyear}{$$v}" > $@
- # Find the number of rows in the plotted table.
+# Find the number of rows in the plotted table.
v=$$(awk '!/^#/{c++} END{print c}' $(a2mk20f1c))
echo "\newcommand{\menkenumyears}{$$v}" >> $@
- # Find the number of papers in 1996.
+# Find the number of papers in 1996.
v=$$(awk '$$1==$(menke-demo-year){print $$3}' $(a2mk20f1c))
echo "\newcommand{\menkenumpapersdemocount}{$$v}" >> $@
echo "\newcommand{\menkenumpapersdemoyear}{$(menke-demo-year)}" >> $@
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index ea70fca..7110c8f 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -5,7 +5,7 @@
# recipes in this Makefile all use a single file lock to have one download
# script running at every instant.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -27,70 +27,68 @@
# Download input data
# --------------------
#
-# The input dataset properties are defined in
-# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
-# enable easy processing, so all the extra checks in this rule may seem
-# redundant.
+# 'reproduce/analysis/config/INPUTS.conf' contains the input dataset
+# properties. In most cases, you will not need to edit this rule (or
+# file!). Simply follow the instructions of 'INPUTS.conf' and set the
+# variables names according to the described standards.
#
-# In a real project, you will need more than one dataset. In that case,
-# just add them to the target list and add an `elif' statement to define it
-# in the recipe.
-#
-# Files in a server usually have very long names, which are mainly designed
-# for helping in data-base management and being generic. Since Make uses
-# file names to identify which rule to execute, and the scope of this
-# research project is much less than the generic survey/dataset, it is
-# easier to have a simple/short name for the input dataset and work with
-# that. In the first condition of the recipe below, we connect the short
-# name with the raw database name of the dataset.
+# TECHNICAL NOTE on the '$(foreach, n ...)' loop of 'inputdatasets': we are
+# using several (relatively complex!) features particular to Make: In GNU
+# Make, '.VARIABLES' "... expands to a list of the names of all global
+# variables defined so far" (from the "Other Special Variables" section of
+# the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only
+# used for input files, we find all the variables that contain the input
+# file name (the '%' is the filename). Finally, using the
+# pattern-substitution function ('patsubst'), we remove the fixed string at
+# the start and end of the variable name.
#
# Download lock file: Most systems have a single connection to the
# internet, therefore downloading is inherently done in series. As a
# result, when more than one dataset is necessary for download, if they are
# done in parallel, the speed will be slower than downloading them in
-# series. We thus use the `flock' program to tie/lock the downloading
+# series. We thus use the 'flock' program to tie/lock the downloading
# process with a file and make sure that only one downloading event is in
# progress at every moment.
$(indir):; mkdir $@
downloadwrapper = $(bashdir)/download-multi-try
-inputdatasets = $(indir)/menke20.xlsx
+inputdatasets = $(foreach i, \
+ $(patsubst INPUT-%-sha256,%, \
+ $(filter INPUT-%-sha256,$(.VARIABLES))), \
+ $(indir)/$(i))
$(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
- # Set the necessary parameters for this input file.
- if [ $* = menke20.xlsx ]; then
- localname=$(MK20DATA); url=$(MK20URL); mdf=$(MK20MD5);
- else
- echo; echo; echo "Not recognized input dataset: '$*'."
- echo; echo; exit 1
- fi
+# Set the necessary parameters for this input file as shell variables
+# (to help in readability).
+ url=$(INPUT-$*-url)
+ sha=$(INPUT-$*-sha256)
- # Download (or make the link to) the input dataset. If the file
- # exists in `INDIR', it may be a symbolic link to some other place
- # in the filesystem. To avoid too many links when using these files
- # during processing, we'll use `readlink -f' so the link we make
- # here points to the final file directly (note that `readlink' is
- # part of GNU Coreutils). If its not a link, the `readlink' part
- # has no effect.
+# Download (or make the link to) the input dataset. If the file
+# exists in 'INDIR', it may be a symbolic link to some other place in
+# the filesystem. To avoid too many links when using these files
+# during processing, we'll use 'readlink -f' so the link we make here
+# points to the final file directly (note that 'readlink' is part of
+# GNU Coreutils). If its not a link, the 'readlink' part has no
+# effect.
unchecked=$@.unchecked
- if [ -f $(INDIR)/$$localname ]; then
- ln -fs $$(readlink -f $(INDIR)/$$localname) $$unchecked
+ if [ -f $(INDIR)/$* ]; then
+ ln -fs $$(readlink -f $(INDIR)/$*) $$unchecked
else
touch $(lockdir)/download
$(downloadwrapper) "wget --no-use-server-timestamps -O" \
$(lockdir)/download $$url $$unchecked
fi
- # Check the md5 sum to see if this is the proper dataset.
- sum=$$(md5sum $$unchecked | awk '{print $$1}')
- if [ $$sum = $$mdf ]; then
+# Check the checksum to see if this is the proper dataset.
+ sum=$$(sha256sum $$unchecked | awk '{print $$1}')
+ if [ $$sum = $$sha ]; then
mv $$unchecked $@
echo "Integrity confirmed, using $@ in this project."
else
echo; echo;
- echo "Wrong MD5 checksum for input file '$$localname':"
+ echo "Wrong SHA256 checksum for input file '$*':"
echo " File location: $$unchecked"; \
- echo " Expected MD5 checksum: $$mdf"; \
- echo " Calculated MD5 checksum: $$sum"; \
+ echo " Expected SHA256 checksum: $$sha"; \
+ echo " Calculated SHA256 checksum: $$sum"; \
echo; exit 1
fi
@@ -104,7 +102,7 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
# It is very important to mention the address where the data were
# downloaded in the final report.
$(mtexdir)/download.tex: $(indir)/menke20.xlsx | $(mtexdir)
- echo "\newcommand{\menketwentyxlsxname}{$(MK20DATA)}" > $@
- echo "\newcommand{\menketwentychecksum}{$(MK20MD5)}" >> $@
- echo "\newcommand{\menketwentybytesize}{$(MK20SIZE)}" >> $@
- echo "\newcommand{\menketwentyurl}{$(MK20URL)}" >> $@
+ echo "\newcommand{\menketwentyxlsxname}{menke20.xlsx}" > $@
+ echo "\newcommand{\menketwentychecksum}{$(INPUT-menke20.xlsx-sha256)}" >> $@
+ echo "\newcommand{\menketwentybytesize}{$(INPUT-menke20.xlsx-size)}" >> $@
+ echo "\newcommand{\menketwentyurl}{$(INPUT-menke20.xlsx-url)}" >> $@
diff --git a/reproduce/analysis/make/format.mk b/reproduce/analysis/make/format.mk
index fd4060a..979475f 100644
--- a/reproduce/analysis/make/format.mk
+++ b/reproduce/analysis/make/format.mk
@@ -6,7 +6,7 @@
# because it provides interesting statistics about tools and methods used
# in scientific papers.
#
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -28,13 +28,13 @@ mk20tab3 = $(a1dir)/table-3.txt
$(a1dir):; mkdir $@
$(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
- # Set a base-name for the table-3 data.
+# Set a base-name for the table-3 data.
base=$(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.
+# 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=$$(pwd)
cd $(indir)
xlsxio_xlsx2csv $(notdir $<)
@@ -42,12 +42,12 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
rm $(notdir $<).*.csv
cd $$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.
+# 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_PAPERS_WITH_TOOLS [counter, i16] Number of papers with an identified tool." >> $@.tmp
@@ -56,9 +56,9 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
awk 'NR>1{printf("%-10d%-10d%-10d%-10d %s\n", $$2, $$3, $$3*$$NF, $$(NF-1), $$1)}' \
FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp
- # Set the temporary file as the final target. This was done so if
- # there is any possible crash in the steps above, this rule is
- # re-run (its final target isn't rebuilt).
+# Set the temporary file as the final target. This was done so if
+# there is any possible crash in the steps above, this rule is re-run
+# (its final target isn't rebuilt).
mv $@.tmp $@
@@ -68,19 +68,19 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
# Main LaTeX macro file
$(mtexdir)/format.tex: $(mk20tab3)
- # Count the total number of papers in their study.
+# Count the total number of papers in their study.
v=$$(awk '!/^#/{c+=$$2} END{print c}' $(mk20tab3))
echo "\newcommand{\menkenumpapers}{$$v}" > $@
- # Count how many unique journals there were in the study. Note that
- # the `31' comes because we put 10 characters for each numeric
- # column and separated the last numeric column from the string
- # column with a space. If the number of numeric columns change in
- # the future, the `31' also has to change.
+# Count how many unique journals there were in the study. Note that
+# the `31' comes because we put 10 characters for each numeric column
+# and separated the last numeric column from the string column with a
+# space. If the number of numeric columns change in the future, the
+# `31' also has to change.
v=$$(awk 'BEGIN{FIELDWIDTHS="41 10000"} !/^#/{print $$2}' \
$(mk20tab3) | uniq | wc -l)
echo "\newcommand{\menkenumjournals}{$$v}" >> $@
- # Count how many rows the original catalog has.
+# Count how many rows the original catalog has.
v=$$(awk '!/^#/{c++} END{print c}' $(mk20tab3))
echo "\newcommand{\menkenumorigrows}{$$v}" >> $@
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index bc73df8..7f0c514 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
# Project initialization.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -25,10 +25,10 @@
# Basic directories that are used throughout the project.
#
# Locks are used to make sure that an operation is done in series not in
-# parallel (even if Make is run in parallel with the `-j' option). The most
+# parallel (even if Make is run in parallel with the '-j' option). The most
# common case is downloads which are better done in series and not in
# parallel. Also, some programs may not be thread-safe, therefore it will
-# be necessary to put a lock on them. This project uses the `flock' program
+# be necessary to put a lock on them. This project uses the 'flock' program
# to achieve this.
#
# To help with modularity and clarity of the build directory (not mixing
@@ -43,7 +43,7 @@ bsdir=$(BDIR)/software
texdir = $(badir)/tex
lockdir = $(bsdir)/locks
indir = $(badir)/inputs
-prepdir = $(padir)/prepare
+prepdir = $(badir)/prepare
mtexdir = $(texdir)/macros
installdir = $(bsdir)/installed
bashdir = reproduce/analysis/bash
@@ -56,10 +56,10 @@ pconfdir = reproduce/analysis/config
# Preparation phase
# -----------------
#
-# This Makefile is loaded both for the `prepare' phase and the `make'
+# This Makefile is loaded both for the 'prepare' phase and the 'make'
# phase. But the preparation files should be dealt with differently
-# (depending on the phase). In the `prepare' phase, the main directory
-# should be created, and in the `make' phase, its contents should be
+# (depending on the phase). In the 'prepare' phase, the main directory
+# should be created, and in the 'make' phase, its contents should be
# loaded.
#
# If you don't need any preparation, please simply comment these lines.
@@ -87,6 +87,14 @@ endif
# (independent parts of the paper can be added to it independently). To fix
# this problem, when we are in a group setting, we'll use the user's ID to
# create a separate LaTeX build directory for each user.
+#
+# The same logic applies to the final paper PDF: each user will create a
+# separte final PDF (for example 'paper-user1.pdf' and 'paper-user2.pdf')
+# and no 'paper.pdf' will be built. This isn't a problem because
+# 'initialize.tex' is a .PHONY prerequisite, so the rule to build the final
+# paper is always executed (even if it is present and nothing has
+# changed). So in terms of over-all efficiency and processing steps, this
+# doesn't change anything.
ifeq (x$(GROUP-NAME),x)
texbtopdir = build
else
@@ -104,7 +112,7 @@ tikzdir = $(texbdir)/tikz
# ---------------------------
#
# Before defining the local sub-environment here, we'll need to save the
-# system's environment for some scenarios (for example after `clean'ing the
+# system's environment for some scenarios (for example after 'clean'ing the
# built programs).
curdir := $(shell echo $$(pwd))
@@ -117,16 +125,16 @@ curdir := $(shell echo $$(pwd))
#
# We want the full recipe to be executed in one call to the shell. Also we
# want Make to run the specific version of Bash that we have installed
-# during `./project configure' time.
+# during './project configure' time.
#
# Regarding the directories, this project builds its major dependencies
# itself and doesn't use the local system's default tools. With these
# environment variables, we are setting it to prefer the software we have
# build here.
#
-# `TEXINPUTS': we have to remove all possible user-specified directories to
-# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'),
-# we are also going to overwrite `TEXINPUTS' just before `pdflatex'.
+# 'TEXINPUTS': we have to remove all possible user-specified directories to
+# avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'),
+# we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'.
.ONESHELL:
.SHELLFLAGS = -ec
export TERM=xterm
@@ -144,12 +152,12 @@ export LD_LIBRARY_PATH := $(installdir)/lib
# will be empty.
export CPATH := $(SYS_CPATH)
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
-# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because
+# OpenMPI can depend on an existing 'ssh' or 'rsh' binary. However, because
# of security reasons, its best to not install them, disable any
# remote-shell accesss through this environment variable.
export OMPI_MCA_plm_rsh_agent=/bin/false
@@ -163,7 +171,7 @@ export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Python enviroment
# -----------------
#
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
# have found several other Python-related environment variables on some
# systems which might interfere. To be safe, we are removing all their
# values.
@@ -187,10 +195,10 @@ export MPI_PYTHON3_SITEARCH :=
# directories (or possible sub-directories) for individual steps will be
# defined and added within their own Makefiles.
#
-# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the
+# The '.SUFFIXES' rule with no prerequisite is defined to eliminate all the
# default implicit rules. The default implicit rules are to do with
-# programming (for example converting `.c' files to `.o' files). The
-# problem they cause is when you want to debug the make command with `-d'
+# programming (for example converting '.c' files to '.o' files). The
+# problem they cause is when you want to debug the make command with '-d'
# option: they add too many extra checks that make it hard to find what you
# are looking for in the outputs.
.SUFFIXES:
@@ -201,8 +209,11 @@ $(lockdir): | $(bsdir); mkdir $@
# Version and distribution tarball definitions
-project-commit-hash := $(shell if [ -d .git ]; then \
- echo $$(git describe --dirty --always --long); else echo NOGIT; fi)
+project-commit-hash := $(shell \
+ if [ -d .git ]; then \
+ export LD_LIBRARY_PATH="$(installdir)/lib"; \
+ echo $$($(installdir)/bin/git describe --dirty --always --long); \
+ else echo NOGIT; fi)
project-package-name := maneaged-$(project-commit-hash)
project-package-contents = $(texdir)/$(project-package-name)
@@ -213,10 +224,10 @@ project-package-contents = $(texdir)/$(project-package-name)
# High-level Makefile management
# ------------------------------
#
-# About `.PHONY': these are targets that must be built even if a file with
+# About '.PHONY': these are targets that must be built even if a file with
# their name exists.
#
-# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because
+# Only '$(mtexdir)/initialize.tex' corresponds to a file. This is because
# we want to ensure that the file is always built in every run: it contains
# the project version which may change between two separate runs, even when
# no file actually differs.
@@ -229,14 +240,20 @@ texclean:
mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
clean:
- # Delete the top-level PDF file.
+# Delete the top-level PDF file.
rm -f *.pdf
- # Delete all the built outputs except the dependency
- # programs. We'll use Bash's extended options builtin (`shopt') to
- # enable "extended glob" (for listing of files). It allows extended
- # features like ignoring the listing of a file with `!()' that we
- # are using afterwards.
+# Delete possible LaTeX output in top directory. This can happen when
+# the user has run LaTeX with applications other than maneage. For
+# example, when opening 'paper.tex' file with 'texstudio' and
+# executing 'build'.
+ rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf
+
+# Delete all the built outputs except the dependency programs. We'll
+# use Bash's extended options builtin ('shopt') to enable "extended
+# glob" (for listing of files). It allows extended features like
+# ignoring the listing of a file with '!()' that we are using
+# afterwards.
shopt -s extglob
rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
@@ -244,14 +261,13 @@ clean:
rm -rf $(bsdir)/preparation-done.mk
distclean: clean
- # Without cleaning the Git hooks, we won't be able to easily
- # commit or checkout after this task is done. So we'll remove them
- # first.
+# Without cleaning the Git hooks, we won't be able to easily commit
+# or checkout after this task is done. So we'll remove them first.
rm -f .git/hooks/post-checkout .git/hooks/pre-commit
- # We'll be deleting the built environent programs and just need the
- # `rm' program. So for this recipe, we'll use the host system's
- # `rm', not our own.
+# We'll be deleting the built environent programs and just need the
+# 'rm' program. So for this recipe, we'll use the host system's 'rm',
+# not our own.
$$sys_rm -rf $(BDIR)
$$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
@@ -268,15 +284,15 @@ distclean: clean
# without having to worry about the technicalities of the analysis.
$(project-package-contents): paper.pdf | $(texdir)
- # Set up the output directory, delete it if it exists and remake it
- # to fill with new contents.
+# Set up the output directory, delete it if it exists and remake it
+# to fill with new contents.
dir=$@
rm -rf $$dir
mkdir $$dir
curdir=$$(pwd)
- # Build a small Makefile to help in automatizing the paper building
- # (including the bibliography).
+# Build a small Makefile to help in automatizing the paper building
+# (including the bibliography).
m=$$dir/Makefile
echo "paper.pdf: paper.tex paper.bbl" > $$m
printf "\tlatex -shell-escape -halt-on-error paper\n" >> $$m
@@ -291,94 +307,92 @@ $(project-package-contents): paper.pdf | $(texdir)
printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n" >> $$m
printf "\trm -f *.blg *.log *.out *.run.xml\n" >> $$m
- # Copy the top-level contents (see next step for `paper.tex').
+# Copy the top-level contents (see next step for 'paper.tex').
cp COPYING project README.md README-hacking.md $$dir/
- # Since the packaging is mainly intended for high-level building of
- # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
- # the paper. This will disable usage of TiKZ.
+# Since the packaging is mainly intended for high-level building of
+# the PDF with LaTeX, we'll comment the 'makepdf' LaTeX macro in the
+# paper. This will disable usage of TiKZ.
sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
paper.tex > $$dir/paper.tex
- # Copy ONLY the version-controlled files in 'reproduce' and
- # 'tex/src'. This is important because files like 'LOCAL.conf' (in
- # 'reproduce/software/config') should not be archived, they contain
- # information about the host computer and are irrelevant for
- # others. Also some project authors may have temporary files here
- # that are not under version control and thus shouldn't be archived
- # (although this is bad practice, but that is up to the user).
- #
- # To keep the sub-directory structure, we are packaging the files
- # with Tar, piping it, and unpacking it in the archive
- # directory. So afterwards we need to come back to the current
- # directory.
+# Copy ONLY the version-controlled files in 'reproduce' and
+# 'tex/src'. This is important because files like 'LOCAL.conf' (in
+# 'reproduce/software/config') should not be archived, they contain
+# information about the host computer and are irrelevant for
+# others. Also some project authors may have temporary files here
+# that are not under version control and thus shouldn't be archived
+# (although this is bad practice, but that is up to the user).
+#
+# To keep the sub-directory structure, we are packaging the files
+# with Tar, piping it, and unpacking it in the archive directory. So
+# afterwards we need to come back to the current directory.
tar -c -f - $$(git ls-files peer-review reproduce tex/src) \
| (cd $$dir ; tar -x -f -)
cd $(curdir)
- # Build the other two subdirectories of 'tex/' that we need in the
- # archive (in the actual project, these are symbolic links to the
- # build directory).
+# Build the other two subdirectories of 'tex/' that we need in the
+# archive (in the actual project, these are symbolic links to the
+# build directory).
mkdir $$dir/tex/tikz $$dir/tex/build
- # Copy the 'tex/build' directory into the archive (excluding the
- # temporary archive directory that we are now copying to). We will
- # be using Bash's extended globbing ('extglob') for excluding this
- # directory.
+# Copy the 'tex/build' directory into the archive (excluding the
+# temporary archive directory that we are now copying to). We will be
+# using Bash's extended globbing ('extglob') for excluding this
+# directory.
shopt -s extglob
cp -r tex/img $$dir/tex/img
cp tex/tikz/*.eps $$dir/tex/tikz
cp -r tex/build/!($(project-package-name)) $$dir/tex/build
- # Clean up the $(texdir)/build* directories in the archive (when
- # building in a group structure, there will be `build-user1',
- # `build-user2' and etc). These are just temporary LaTeX build
- # files and don't have any relevant/hand-written files in them.
+# Clean up the $(texdir)/build* directories in the archive (when
+# building in a group structure, there will be 'build-user1',
+# 'build-user2' and etc). These are just temporary LaTeX build files
+# and don't have any relevant/hand-written files in them.
rm -rf $$dir/tex/build/build*
- # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
- # PGFPlots was used to generate them), copy them too.
+# If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
+# PGFPlots was used to generate them), copy them too.
if ls tex/tikz/*.pdf &> /dev/null; then
cp tex/tikz/*.pdf $$dir/tex/tikz
fi
- # When submitting to places like arXiv, they will just run LaTeX
- # once and won't run `biber'. So we need to also keep the `.bbl'
- # file into the distributing tarball. However, BibLaTeX is
- # particularly sensitive to versioning (a `.bbl' file has to be
- # read by the same BibLaTeX version that created it). This is hard
- # to do with non-up-to-date places like arXiv. Therefore, we thus
- # just copy the whole of BibLaTeX's source (the version we are
- # using) into the top tarball directory. In this way, arXiv's LaTeX
- # engine will use the same BibLaTeX version to interpret the `.bbl'
- # file. TIP: you can use the same strategy for other LaTeX packages
- # that may cause problems on the arXiv server.
+# When submitting to places like arXiv, they will just run LaTeX once
+# and won't run 'biber'. So we need to also keep the '.bbl' file into
+# the distributing tarball. However, BibLaTeX is particularly
+# sensitive to versioning (a '.bbl' file has to be read by the same
+# BibLaTeX version that created it). This is hard to do with
+# non-up-to-date places like arXiv. Therefore, we thus just copy the
+# whole of BibLaTeX's source (the version we are using) into the top
+# tarball directory. In this way, arXiv's LaTeX engine will use the
+# same BibLaTeX version to interpret the '.bbl' 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 $$dir/
tltopdir=.local/texlive/maneage/texmf-dist/tex/latex
#find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
# | xargs -0 cp -t $$dir
- # Just in case the package users want to rebuild some of the
- # figures (manually un-comment the `makepdf' command we commented
- # above), correct the TikZ external directory, so the figures can
- # be rebuilt.
+# Just in case the package users want to rebuild some of the figures
+# (manually un-comment the 'makepdf' command we commented above),
+# correct the TikZ external directory, so the figures can be rebuilt.
pgfsettings="$$dir/tex/src/preamble-pgfplots.tex"
sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
mv $$pgfsettings.new $$pgfsettings
- # PROJECT SPECIFIC
- # ----------------
- # Put any project-specific distribution steps here.
+# PROJECT SPECIFIC
+# ----------------
+# Put any project-specific distribution steps here.
cd $$curdir
cp tex/build/build/appendix.bbl $$dir/
- # ----------------
+# ----------------
- # Clean temporary files that may have been created by text editors.
+# Clean temporary files that may have been created by text editors.
cd $(texdir)
find $(project-package-name) -name \*~ -delete
find $(project-package-name) -name \*.swp -delete
-# Package into `.tar.gz' or '.tar.lz'.
+# Package into '.tar.gz' or '.tar.lz'.
dist dist-lzip: $(project-package-contents)
curdir=$$(pwd)
cd $(texdir)
@@ -394,7 +408,7 @@ dist dist-lzip: $(project-package-contents)
cd $$curdir
mv $(texdir)/$(project-package-name).tar.$$suffix ./
-# Package into `.zip'.
+# Package into '.zip'.
dist-zip: $(project-package-contents)
curdir=$$(pwd)
cd $(texdir)
@@ -495,13 +509,13 @@ print-general-metadata = \
# This file will store some basic info about the project that is necessary
# for the final PDF. Since these are not version controlled, it must be
# calculated everytime the project is run. So even though this file
-# actually exists, it is also aded as a `.PHONY' target above.
+# actually exists, it is also aded as a '.PHONY' target above.
$(mtexdir)/initialize.tex: | $(mtexdir)
- # Version and title of project. About the starting '@': since these
- # commands are run every time with './project make', it is annoying
- # to print them on the standard output every time. With the '@',
- # make will not print the commands that it runs in this recipe.
+# Version and title of project. About the starting '@': since these
+# commands are run every time with './project make', it is annoying
+# to print them on the standard output every time. With the '@', make
+# will not print the commands that it runs in this recipe.
@d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}')
echo "\newcommand{\projectdate}{$$d}" > $@
echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
@@ -514,16 +528,15 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
v=$$(echo $(metadata-doi-zenodo) | sed -e's/\./ /g' | awk '{print $$NF}')
echo "\newcommand{\projectzenodoid}{$$v}" >> $@
- # Calculate the latest Maneage commit used to build this
- # project:
- # - The project may not have the 'maneage' branch (for example
- # after cloning from a fork that didn't include it!). In this
- # case, we'll print a descriptive warning, telling the user what
- # should be done (reporting the last merged commit and its date
- # is very useful for the future).
- # - The '--dirty' option (used in 'project-commit-hash') isn't
- # applicable to "commit-ishes" (direct quote from Git's error
- # message!).
+# Calculate the latest Maneage commit used to build this project:
+# - The project may not have the 'maneage' branch (for example
+# after cloning from a fork that didn't include it!). In this
+# case, we'll print a descriptive warning, telling the user what
+# should be done (reporting the last merged commit and its date
+# is very useful for the future).
+# - The '--dirty' option (used in 'project-commit-hash') isn't
+# applicable to "commit-ishes" (direct quote from Git's error
+# message!).
if git log maneage -1 &> /dev/null; then
c=$$(git merge-base HEAD maneage)
v=$$(git describe --always --long $$c)
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 00bd3b5..da2702c 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -1,6 +1,6 @@
# Build the final PDF paper/report.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -24,14 +24,14 @@
#
# To report the input settings and results, the final report's PDF (final
# target of this project) uses macros generated from various steps of the
-# project. All these macros are defined through `$(mtexdir)/project.tex'.
+# project. All these macros are defined through '$(mtexdir)/project.tex'.
#
-# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# '$(mtexdir)/project.tex' is actually just a combination of separate files
# that keep the LaTeX macros related to each workhorse Makefile (in
-# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
-# `$(mtexdir)/verify.tex' which will check them before starting to build
+# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# '$(mtexdir)/verify.tex' which will check them before starting to build
# the paper. The only workhorse Makefile that doesn't need to produce LaTeX
-# macros is this Makefile (`reproduce/src/make/paper.mk').
+# macros is this Makefile ('reproduce/src/make/paper.mk').
#
# This file is thus the interface between the analysis/processing steps and
# the final PDF: when we get to this point, all the processing has been
@@ -39,38 +39,38 @@
#
# Note that if you don't want the final PDF and just want the processing
# and file outputs, you can give any value other than 'yes' to
-# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
$(mtexdir)/project.tex: $(mtexdir)/verify.tex
- # If no PDF is requested, or if LaTeX isn't available, don't
- # continue to building the final PDF. Otherwise, merge all the TeX
- # macros into one for building the PDF.
+# If no PDF is requested, or if LaTeX isn't available, don't continue
+# to building the final PDF. Otherwise, merge all the TeX macros into
+# one for building the PDF.
@if [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" = xyes ]; then
- # Put a LaTeX input command for all the necessary macro files.
- # 'hardware-parameters.tex' is created in 'configure.sh'.
+# Put a LaTeX input command for all the necessary macro files.
+# 'hardware-parameters.tex' is created in 'configure.sh'.
projecttex=$(mtexdir)/project.tex
rm -f $$projecttex
for t in $(subst paper,,$(makesrc)) hardware-parameters; do
echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
done
- # Possibly print the appendix in the final PDF.
+# Possibly print the appendix in the final PDF.
if [ x"$(separatesupplement)" = x1 ]; then
echo "\newcommand{\separatesupplement}{}" >> $$projecttex
fi
- # Possibly highlight the '\new' parts of the text.
+# Possibly highlight the '\new' parts of the text.
if [ x"$(highlightnew)" = x1 ]; then
echo "\newcommand{\highlightnew}{}" >> $$projecttex
fi
- # Possibly show the text within '\tonote'.
+# Possibly show the text within '\tonote'.
if [ x"$(highlightnotes)" = x1 ]; then
echo "\newcommand{\highlightnotes}{}" >> $$projecttex
fi
- # The paper shouldn't be built.
+# The paper shouldn't be built.
else
echo
echo "-----"
@@ -101,76 +101,76 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
# The bibliography
# ----------------
#
-# We need to run the `bibtex' program on the output of LaTeX to generate
+# We need to run the 'bibtex' program on the output of LaTeX to generate
# the necessary bibliography before making the final paper. So we'll first
-# have one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# have one run of LaTeX (similar to the 'paper.pdf' recipe), then 'bibtex'.
#
-# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
-# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
-# recipe and the `paper.pdf' recipe. But if `tex/src/references.bib' hasn't
+# NOTE: '$(mtexdir)/project.tex' is an order-only-prerequisite for
+# 'paper.bbl'. This is because we need to run LaTeX in both the 'paper.bbl'
+# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
# been modified, we don't want to re-build the bibliography, only the final
# PDF.
bbls = $(foreach t,$(subst .pdf,,$(top-pdfs)),$(texbdir)/$(t).bbl)
$(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
$(mtexdir)/dependencies-bib.tex | $(mtexdir)/project.tex
- # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+# If '$(mtexdir)/project.tex' is empty, don't build PDF.
@macros=$$(cat $(mtexdir)/project.tex)
if [ x"$$macros" != x ]; then
- # Unfortunately I can't get bibtex to look into a special
- # directory for the references, so we'll copy it into the LaTeX
- # building directory.
+# Unfortunately I can't get bibtex to look into a special directory
+# for the references, so we'll copy it into the LaTeX building
+# directory.
p=$$(pwd)
if ! [ -L $(texbdir)/references.bib ]; then
ln -sf $$p/tex/src/references.tex $(texbdir)/references.bib
fi
- # Copy the improved IEEE bst file into the build directory.
- # The improved bst file provides ArXiv clickable URLs and
- # if available, open-access URLs based on the DOIs, with
- # closed-access URLs as a fallback, via https://oadoi.org .
+# Copy the improved IEEE bst file into the build directory. The
+# improved bst file provides ArXiv clickable URLs and if available,
+# open-access URLs based on the DOIs, with closed-access URLs as a
+# fallback, via https://oadoi.org .
ln -sf $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)/
- # We'll run LaTeX first to generate the `.bcf' file (necessary
- # for `biber') and then run `biber' to generate the `.bbl' file.
+# We'll run LaTeX first to generate the '.bcf' file (necessary for
+# 'bibtex') and then run 'bibtex' to generate the '.bbl' file.
export TEXINPUTS=$$p:
cd $(texbdir);
- # Delete any possibly existing target (a '.bbl' file) to avoid
- # complications with LaTeX being run before the command that
- # generates it. Otherwise users will have to manually delete
- # it. It will be built anyway once this rule is done.
+# Delete any possibly existing target (a '.bbl' file) to avoid
+# complications with LaTeX being run before the command that
+# generates it. Otherwise users will have to manually delete it. It
+# will be built anyway once this rule is done.
rm -f $@
- # Put a link to the main LaTeX source that we want to build.
+# Put a link to the main LaTeX source that we want to build.
if [ $* = paper ]; then sdir="$$p"
else sdir="$$p"/tex/src
fi
ln -sf "$$sdir"/$*.tex ./
- # The pdflatex option '-shell-escape' is "normally disallowed for
- # security reasons" according to the `info pdflatex' manual, but
- # is enabled here in order to allow the use of PGFPlots. If you
- # do not use PGFPlots, then you can remove the `-shell-escape'
- # option for better security. See
- # https://savannah.nongnu.org/task/?15694 for details.
+# The pdflatex option '-shell-escape' is "normally disallowed for
+# security reasons" according to the 'info pdflatex' manual, but is
+# enabled here in order to allow the use of PGFPlots. If you do not
+# use PGFPlots, then you should remove the '-shell-escape' option
+# for better security. See https://savannah.nongnu.org/task/?15694
+# for details.
latex -shell-escape -halt-on-error $*.tex
- # When we are building the main paper and the appendices are to
- # be built within the main paper's PDF, we need two
- # bibliographies: one for the main body, and one for the
- # appendix. For this, we use 'multibib'. Multibib creates a
- # separate '.aux' file for each bibliography.
+# When we are building the main paper and the appendices are to be
+# built within the main paper's PDF, we need two bibliographies:
+# one for the main body, and one for the appendix. For this, we use
+# 'multibib'. Multibib creates a separate '.aux' file for each
+# bibliography.
bibtex $*
if [ x"$(separatesupplement)" != x1 ]; then
bibtex appendix
fi
- # Hack: tidy up eprint+doi style that didn't work in .bst file.
- # TODO (better): read Part 4 of
- # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
- # and fix the .bst style properly.
+# Hack: tidy up eprint+doi style that didn't work in .bst file.
+# TODO (better): read Part 4 of
+# http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf and
+# fix the .bst style properly.
cp -pv $*.bbl $*-tmp.bbl \
&& sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
| tr -d '\n' \
@@ -188,7 +188,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
| sed -e 's/EOLINE/\n/g' > appendix.bbl
fi
- # Paper-specific hacks for reducing very-long author lists.
+# Paper-specific hacks for reducing very-long author lists.
cp -pv $*.bbl $*-tmp.bbl \
&& sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
| tr -d '\n' \
@@ -196,7 +196,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
| sed -e 's;, V\..Khodiyar[^{]*Whyte; et al.\\/;' \
| sed -e 's/EOLINE/\n/g' > $*.bbl
- # The pre-final run of LaTeX after 'paper.bbl' was created.
+# The pre-final run of LaTeX after 'paper.bbl' was created.
latex -shell-escape -halt-on-error $*.tex
fi
@@ -207,36 +207,36 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
# The final paper
# ---------------
#
-# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# Run LaTeX in the '$(texbdir)' directory so all the intermediate and
# auxiliary files stay there and keep the top directory clean. To be able
# to run everything cleanly from there, it is necessary to add the current
-# directory (top project directory) to the `TEXINPUTS' environment
+# directory (top project directory) to the 'TEXINPUTS' environment
# variable.
$(top-pdfs): %.pdf: $(mtexdir)/project.tex paper.tex \
tex/src/appendix-*.tex $(texbdir)/%.bbl
- # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+# If '$(mtexdir)/project.tex' is empty, don't build the PDF.
@macros=$$(cat $(mtexdir)/project.tex)
if [ x"$$macros" != x ]; then
- # Go into the top TeX build directory and make the paper.
+# Go into the top TeX build directory and make the paper.
p=$$(pwd)
export TEXINPUTS=$$p:
cd $(texbdir)
- # See above for a warning and brief discussion on the the
- # pdflatex option `-shell-escape'.
+# See above for a warning and brief discussion on the the pdflatex
+# option '-shell-escape'.
latex -shell-escape -halt-on-error $*.tex
- # Convert the DVI to PostScript, and the PostScript to PDF. The
- # `-dNOSAFER' option to GhostScript allows transparencies in the
- # conversion from PostScript to PDF, see
- # https://www.ghostscript.com/doc/current/Language.htm#Transparency
+# Convert the DVI to PostScript, and the PostScript to PDF. The
+# '-dNOSAFER' option to GhostScript allows transparencies in the
+# conversion from PostScript to PDF, see
+# https://www.ghostscript.com/doc/current/Language.htm#Transparency
dvips $*.dvi
ps2pdf $*.ps
- # Come back to the top project directory and copy the built PDF
- # file here.
+# Come back to the top project directory and copy the built PDF
+# file here.
cd "$$p"
cp $(texbdir)/$*.pdf $@
fi
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index d0b61d9..ecb6842 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
-# Basic preparations, called by `./project prepare'.
+# Basic preparations, called by './project prepare'.
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
@@ -21,30 +21,29 @@
# Final-target
#
-# Without this file, `./project make' won't work.
+# Without this file, './project make' won't work.
prepare-dep = $(subst prepare, ,$(makesrc))
$(bsdir)/preparation-done.mk: \
$(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
- # If you need to add preparations define targets above to do the
- # preparations, then set the value below to `yes'. Recall that just
- # like `./project make', before loading this file, `./project
- # prepare' loads loads `initialize.mk' and `download.mk', so you
- # can safely assume everything that is defined there in the
- # preparation phase also.
- #
- # TIP: the targets can actually be automatically generated
- # Makefiles that are used by `./project make'. They can include
- # variables, or automatically generated rules. Just make sure that
- # those Makefiles aren't written in the source directory. Even
- # though they are Makefiles, they are automatically built, so they
- # don't belong in the source. `$(prepdir)' has been defined for
- # this purpose (see `initialize.mk'), we recommend that you put all
- # automatically generated Makefiles under this directory. In the
- # `make' phase, `initialize.mk' will automatically load all the
- # `*.mk' files. If you need to load your generated
- # configuration-makefiles before automatically generated Makefiles
- # containing rules, you can use some naming convension like
- # `conf-*.mk' and `rule-*.mk', or you can put them in
- # subdirectories.
+# If you need to add preparations define targets above to do the
+# preparations, then set the value below to 'yes'. Recall that just
+# like './project make', before loading this file, './project
+# prepare' loads loads 'initialize.mk' and 'download.mk', so you can
+# safely assume everything that is defined there in the preparation
+# phase also.
+#
+# TIP: the targets can actually be automatically generated Makefiles
+# that are used by './project make'. They can include variables, or
+# automatically generated rules. Just make sure that those Makefiles
+# aren't written in the source directory. Even though they are
+# Makefiles, they are automatically built, so they don't belong in
+# the source. '$(prepdir)' has been defined for this purpose (see
+# 'initialize.mk'), we recommend that you put all automatically
+# generated Makefiles under this directory. In the 'make' phase,
+# 'initialize.mk' will automatically load all the '*.mk' files. If
+# you need to load your generated configuration-makefiles before
+# automatically generated Makefiles containing rules, you can use
+# some naming convension like 'conf-*.mk' and 'rule-*.mk', or you can
+# put them in subdirectories.
@echo "include-prepare-results = no" > $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 27c1b5b..7755174 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -1,6 +1,6 @@
# Top-level Makefile (first to be loaded).
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -20,7 +20,7 @@
# Load the local configuration (created after running
-# `./project configure').
+# './project configure').
include reproduce/software/config/LOCAL.conf
@@ -30,7 +30,7 @@ include reproduce/software/config/LOCAL.conf
# Ultimate target of this project
# -------------------------------
#
-# The final paper/report (`paper.pdf') is the main target of this
+# The final paper/report ('paper.pdf') is the main target of this
# project. As defined in the Make paradigm, it must be the first target
# that Make encounters (immediately after loading the local configuration
# settings, necessary for a group building scenario mentioned next).
@@ -50,8 +50,8 @@ include reproduce/software/config/LOCAL.conf
#
# Controlling this requires two variables that are available at this stage:
#
-# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-# - `maneage_group_name': value to the `--group' option.
+# - 'GROUP-NAME': from 'LOCAL.conf' (which was built by './project configure').
+# - 'maneage_group_name': value to the '--group' option.
#
# The analysis is only done when both have the same group name. Note that
# when the project isn't being built for a group, both variables will be an
@@ -63,7 +63,7 @@ include reproduce/software/config/LOCAL.conf
#
# If you are just interested in the processing and don't want to build the
# PDF, you can skip the creation of the final PDF by giving a value of
-# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'yes' to 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
ifeq ($(separatesupplement),0)
top-pdfs = paper.pdf
else
@@ -92,13 +92,13 @@ endif
# To keep things clean, managable and readable, each set of operations
# is (and must be) classified (modularized) by context into separate
# Makefiles: the more the better. These modular steps are then
-# included in this top-level Makefile through the `include' command of
+# included in this top-level Makefile through the 'include' command of
# the next step. Each Makefile should also produce a LaTeX macro file
# with the same fixed name (used to keep all the parameters and
# relevant outputs of the steps in it for the final paper).
#
# In the rare case that no special LaTeX macros are necessary in a
-# workhorse Makefile, you can simply make an empty file with `touch
+# workhorse Makefile, you can simply make an empty file with 'touch
# $@'. This will not add any lines to the final combined LaTeX macros
# file, but will create the file that is a prerequisite to the final
# paper generation.
@@ -112,7 +112,7 @@ endif
# IMPORTANT NOTE: order matters in the inclusion of the processing
# Makefiles. As the project grows, some Makefiles will define
# variables/dependencies that later Makefiles need. Therefore we are using
-# a `foreach' loop in the next step to explicitly request loading them in
+# a 'foreach' loop in the next step to explicitly request loading them in
# the same order that they are defined here (we aren't just using a
# wild-card like the configuration Makefiles).
makesrc = initialize \
@@ -136,7 +136,7 @@ makesrc = initialize \
# contain rules to actually do this project's processing.
#
# But before that, we need to identify the phase for the Makefiles that are
-# run both in `./project prepare' and `./project make'.
+# run both in './project prepare' and './project make'.
project-phase = make
include reproduce/analysis/config/*.conf
include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index fb5700e..3950bf1 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -1,10 +1,10 @@
# Do basic preparations to optimize the project's running.
#
-# NOTE: This file is very similar to `top-make.mk', so the large comments
+# NOTE: This file is very similar to 'top-make.mk', so the large comments
# are not included here. Please see that file for thorough comments on each
# step.
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
@@ -24,7 +24,7 @@
# Load the local configuration (created after running
-# `./project configure').
+# './project configure').
include reproduce/software/config/LOCAL.conf
@@ -34,7 +34,7 @@ include reproduce/software/config/LOCAL.conf
# Ultimate target of this project
# -------------------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
ifeq (x$(maneage_group_name),x$(GROUP-NAME))
all: $(BDIR)/software/preparation-done.mk
@echo "Project preparation is complete.";
@@ -57,12 +57,12 @@ endif
# Define source Makefiles
# -----------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
#
-# To ensure that `prepare' and `make' have the same basic definitions and
-# environment and that all `downloads' are managed in one place, both
-# `./project prepare' and `./project make' will first read `initialize.mk'
-# and `downloads.mk'.
+# To ensure that 'prepare' and 'make' have the same basic definitions and
+# environment and that all 'downloads' are managed in one place, both
+# './project prepare' and './project make' will first read 'initialize.mk'
+# and 'downloads.mk'.
makesrc = initialize \
download \
prepare
@@ -74,7 +74,7 @@ makesrc = initialize \
# Include all analysis Makefiles
# ------------------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
project-phase = prepare
include reproduce/analysis/config/*.conf
include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 6503172..ac91089 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -1,6 +1,6 @@
# Verify the project outputs before building the paper.
#
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -94,7 +94,7 @@ verify-txt-no-comments-no-space = \
# (generated in various stages of the analysis.
#
# Since each analysis step's data files are already prerequisites of their
-# respective TeX macro file, its enough for `verify.tex' to depend on the
+# respective TeX macro file, its enough for 'verify.tex' to depend on the
# final TeX macro.
#
# USEFUL TIP: during the early phases of your research (when you are
@@ -103,41 +103,41 @@ verify-txt-no-comments-no-space = \
#
# Here is a description of the variables defined here.
#
-# verify-dep: The major step dependencies of `verify.tex', this includes
+# verify-dep: The major step dependencies of 'verify.tex', this includes
# all the steps that must be finished before it.
#
# verify-changes: The files whose contents are important. This is
-# essentially the same as `verify-dep', but it has removed
-# the `initialize' step (which is information about the
+# essentially the same as 'verify-dep', but it has removed
+# the 'initialize' step (which is information about the
# pipeline, not the results).
verify-dep = $(subst verify,,$(subst paper,,$(makesrc)))
verify-check = $(subst initialize,,$(verify-dep))
$(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
- # Make sure that verification is actually requested, the '@' at the
- # start of the recipe is added so Make doesn't print the commands
- # on the standard output because this recipe is run on every call
- # to the project and can be annoying (get mixed in the middle of
- # the analysis outputs or the LaTeX outputs).
+# Make sure that verification is actually requested, the '@' at the
+# start of the recipe is added so Make doesn't print the commands on
+# the standard output because this recipe is run on every call to the
+# project and can be annoying (get mixed in the middle of the
+# analysis outputs or the LaTeX outputs).
@if [ x"$(verify-outputs)" = xyes ]; then
- # Make sure the temporary output doesn't exist (because we want
- # to append to it). We are making a temporary output target so if
- # there is a crash in the middle, Make will not continue. If we
- # write in the final target progressively, the file will exist,
- # and its date will be more recent than all prerequisites, so
- # next time the project is run, Make will continue and ignore the
- # rest of the checks.
+# Make sure the temporary output doesn't exist (because we want to
+# append to it). We are making a temporary output target so if
+# there is a crash in the middle, Make will not continue. If we
+# write in the final target progressively, the file will exist, and
+# its date will be more recent than all prerequisites, so next time
+# the project is run, Make will continue and ignore the rest of the
+# checks.
rm -f $@.tmp
- # Verify the figure datasets.
+# Verify the figure datasets.
$(call verify-txt-no-comments-leading-space, \
$(a2mk20f1c), 76fc5b13495c4d8e8e6f8d440304cf69)
- # Verify TeX macros (the values that go into the PDF text).
+# Verify TeX macros (the values that go into the PDF text).
for m in $(verify-check); do
file=$(mtexdir)/$$m.tex
- if [ $$m == download ]; then s=64da83ee3bfaa236849927cdc001f5d3
+ if [ $$m == download ]; then s=5d0ab54ca95366d1aab12196966dd3b6
elif [ $$m == format ]; then s=e04d95a539b5540c940bf48994d8d45f
elif [ $$m == demo-plot ]; then s=48bffe6cf8db790c63a33302d20db77f
else echo; echo "'$$m' not recognized."; exit 1
@@ -145,7 +145,7 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
$(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
done
- # Move temporary file to final target.
+# Move temporary file to final target.
mv $@.tmp $@
else
echo "% Verification was DISABLED!" > $@