Dependencies built at the start of the pipeline

To enable easy/proper reproduction of results, all the high-level
dependencies are now built within the pipeline and installed in a fixed
directory that is added to the PATH of the Makefile. This includes GNU Bash
and GNU Make, which are then used to run the pipeline.

The `./configure' script will first build Bash and Make within itself, then
it will build

All the dependencies are also built to be static. So after they are built,
changing of the system's low-level libraries (like C library) won't change
the tarballs.

Currently the C library and C compiler aren't built within the pipeline,
but we'll hopefully add them to the build process also.

With this change, we now have full control of the shell and Make that will
be used in the pipeline, so we can safely remove some of the generalities
we had before.

7 files changed, 440 insertions, 87 deletions

diff --git a/reproduce/config/pipeline/LOCAL.mk.in b/reproduce/config/pipeline/LOCAL.mk.in
index 7a29344..02f8b11 100644
--- a/reproduce/config/pipeline/LOCAL.mk.in
+++ b/reproduce/config/pipeline/LOCAL.mk.in
@@ -22,17 +22,17 @@
 
 
 
-# Input data
-# ----------
+# (OPTIONAL) Dependencies directory
+# ---------------------------------
 #
-# This is where the input data (with the same file-name standard as the
-# online webpage) are stored. If this directory doesn't exist, or it
-# doesn't contain the files (with the correct file-name formats), it will
-# be created and the images will be downloaded. See
-# `reproduce/config/pipeline/web.mk', for the URLs containing the expected
-# inputs for each survey.
-SURVEY = reproduce/SURVEY
-
+# To ensure an identical build environment, the pipeline will use its own
+# build of the programs it needs. Therefore the tarball of the relevant
+# programs are necessary for this pipeline. If a tarball isn't present in
+# the specified directory, it will be downloaded by the pipeline. Therefore
+# an internet connection will be mandatory.
+#
+# Important note: Keep atleast one blank space before and after `='.
+DEPENDENCIES-DIR = /optional/path/to/directory/containing/tarballs
 
 
 
@@ -47,7 +47,9 @@ SURVEY = reproduce/SURVEY
 # intermediate/derivative files. Also to make synchronization and backups
 # more easy: the contents of the build directory do not need to be backed
 # up since they can be reproduced and they can be large.
-BDIR = reproduce/BDIR
+#
+# IMPORTANT NOTE: Keep atleast one blank space before and after `='.
+BDIR = /path/of/directory/for/building
 
 
 
@@ -76,9 +78,11 @@ MINMAPSIZE = 1000000000
 # Downloader program
 # ------------------
 #
-# The downloder program (and its output option name) that will be used if
-# any of the necessary datasets aren't already available on the
-# system. This is usually set at an early stage of the configuration system
+# The downloder program (and its output option name, for example `wget -O'
+# or `curl -o') that will be used if any of the necessary datasets aren't
+# already available on the system.
+#
+# This is usually set at an early stage of the configuration system
 # automatically before the file is opened for editing by the user. It is
 # thus recommended to not modify it manually.
 DOWNLOADER = @downloader@
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
new file mode 100644
index 0000000..3d9d8b3
--- /dev/null
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -0,0 +1,15 @@
+# Versions of the various dependnecies
+bash-version        = 4.4.18
+cfitsio-version     = 3450
+coreutils-version   = 8.30
+gawk-version        = 4.2.1
+ghostscript-version = 9.25
+gnuastro-version    = 0.7.58-e72a
+grep-version        = 3.1
+gsl-version         = 2.5
+libjpeg-version     = v9b
+libgit2-version     = 0.26.0
+libtool-version     = 2.4.6
+make-version        = 4.2.90
+sed-version         = 4.5
+wcslib-version      = 6.2
diff --git a/reproduce/src/make/Top-Makefile b/reproduce/src/make/Top-Makefile
new file mode 100644
index 0000000..5d94766
--- /dev/null
+++ b/reproduce/src/make/Top-Makefile
@@ -0,0 +1,108 @@
+# A ONE-LINE DESCRIPTION OF THE WHOLE PIPELINE
+#
+# Original author:
+#     Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Contributing author(s):
+#     Your name <your@email.address>
+# Copyright (C) 2018, Your Name.
+#
+# 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.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Ultimate target of this pipeline
+# --------------------------------
+#
+# The final paper (in PDF format) is the main target of this whole
+# reproduction pipeline. So as defined in the Make paradigm, we are
+# defining it here.
+#
+# Note that if you don't have LaTeX to build the PDF, or generally are just
+# interested in the processing, you can skip create the final PDF creation
+# with `pdf-build-final' of `reproduce/config/pipeline/pdf-build.mk'.
+all: paper.pdf
+
+
+
+
+
+# Include specific Makefiles
+# --------------------------
+#
+# 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. They are included in this top-level
+# Makefile through the command below.
+#
+# To further help in readability, it is best to avoid including Makefiles
+# within any other Makefile. So in short, it is best that the `foreach'
+# loop below contains all the `reproduce/src/make/*.mk' files.
+#
+# IMPORTANT NOTE: order matters in the inclusion of the processing
+# Makefiles. As the pipeline grows, some Makefiles will probably define
+# variables/dependencies that others need. Therefore unlike the
+# `reproduce/config/pipeline/*.mk' Makefiles which only define low-level
+# variables (not dependent on other variables and contain no rules), the
+# high-level processing Makefiles are included through the `foreach' loop
+# below by explicitly requesting them in a specific order here.
+include reproduce/config/pipeline/*.mk
+include $(foreach f, initialize                    \
+                     download                      \
+                     delete-me                     \
+                     paper                         \
+                   , reproduce/src/make/$(f).mk)
+
+
+
+
+
+# LaTeX macros for paper
+# ----------------------
+#
+# The final report's PDF (final target of this reproduction pipeline) takes
+# variable strings from the pipeline. Those variables are defined as LaTeX
+# macros in `tex/pipeline.tex'. This file is thus the interface between the
+# pipeline scripts and the final PDF.
+#
+# Each of the pipeline steps will save their macros into their own `.tex'
+# file in the `$(mtexdir)' directory. Those individual macros are the
+# pre-requisite to `tex/pipeline.txt'. `tex/pipeline.tex' is thus a
+# high-level output and is defined in this top-most Makefile (and not
+# `reproduce/src/make/paper.mk'). This enables a clear demonstration of the
+# top-level dependencies clearly.
+#
+# Note that if you don't want the final PDF and just want the processing
+# and file outputs, you can remove the value of the `pdf-build-final'
+# variable in `reproduce/config/pdf-build.mk'.
+tex/pipeline.tex: $(foreach f, initialize          \
+                               download            \
+                               delete-me           \
+                             , $(mtexdir)/$(f).tex)
+
+        # If no PDF is requested, then just exit here.
+ifeq ($(pdf-build-final),)
+	@echo
+	@echo
+	@echo "-----"
+	@echo "Everything is OK until this point, but not building PDF."
+	@echo "To do so, give a value to the 'pdf-build-final' variable."
+	@echo "It is defined in 'reproduce/config/pipeline/pdf-build.mk'."
+	@echo
+	@exit 1
+endif
+
+        # Merge all the TeX macros that are prepared for building the PDF.
+	@cat $(mtexdir)/*.tex > $@
diff --git a/reproduce/src/make/delete-me.mk b/reproduce/src/make/delete-me.mk
index de72873..67f0440 100644
--- a/reproduce/src/make/delete-me.mk
+++ b/reproduce/src/make/delete-me.mk
@@ -63,10 +63,10 @@ $(mtexdir)/delete-me.tex: $(dm)
         # Here, we are first using AWK to find the minimum and maximum
         # values, then using it again to read each separately to use in the
         # macro definition.
-	mm=$$(awk 'BEGIN{min=99999; max=-min}                     \
-                   {if($$2>max) max=$$2; if($$2<min) min=$$2;}    \
-                   END{print min, max}' $(dm));                   \
-	v=$$(echo "$$mm" | awk '{printf "%.3f", $$1}');           \
-	echo "\newcommand{\deletememin}{$$v}"             >> $@;  \
-	v=$$(echo "$$mm" | awk '{printf "%.3f", $$2}');           \
+	mm=$$(awk 'BEGIN{min=99999; max=-min}
+	           {if($$2>max) max=$$2; if($$2<min) min=$$2;}
+	           END{print min, max}' $(dm));
+	v=$$(echo "$$mm" | awk '{printf "%.3f", $$1}');
+	echo "\newcommand{\deletememin}{$$v}"             >> $@;
+	v=$$(echo "$$mm" | awk '{printf "%.3f", $$2}');
 	echo "\newcommand{\deletememax}{$$v}"             >> $@
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
new file mode 100644
index 0000000..0fb5a34
--- /dev/null
+++ b/reproduce/src/make/dependencies.mk
@@ -0,0 +1,254 @@
+# Build the reproduction pipeline dependencies (programs and libraries).
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run by the initial `./configure' script. It is not
+# included into the reproduction pipe after that.
+#
+# This Makefile also builds GNU Bash and GNU Make. Therefore this is the
+# only Makefile in the reproduction pipeline where you MUST NOT assume that
+# GNU Bash or GNU Make are to be used.
+#
+# ------------------------------------------------------------------------
+#
+# Original author:
+#     Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Contributing author(s):
+#     Your name <your@email.address>
+# Copyright (C) 2018, Your Name.
+#
+# 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.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+# Top level environment
+include reproduce/config/pipeline/LOCAL.mk
+include reproduce/config/pipeline/dependency-versions.mk
+
+ddir  = $(BDIR)/dependencies
+tdir  = $(BDIR)/dependencies/tarballs
+idir  = $(BDIR)/dependencies/installed
+ibdir = $(BDIR)/dependencies/installed/bin
+ildir = $(BDIR)/dependencies/installed/lib
+
+# Define the top-level programs to build (installed in `.local/bin', so for
+# Coreutils, only one of its executables is enough).
+top-level-programs = ls gawk gs grep libtool sed astnoisechisel
+all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
+
+# This Makefile will be called to also build Bash locally. So when we don't
+# have it yet, we'll have to use the system's bash.
+ifeq ($(USE_LOCAL_BASH),yes)
+SHELL := $(ibdir)/bash
+else
+SHELL := /bin/sh
+endif
+
+# Other basic environment settings.
+.ONESHELL:
+.SHELLFLAGS      = -ec
+PATH            := $(ibdir):$(PATH)
+LDFLAGS         := -L$(ildir) $(LDFLAGS)
+CPPFLAGS        := -I$(idir)/include $(CPPFLAGS)
+LD_LIBRARY_PATH := $(ildir):$(LD_LIBRARY_PATH)
+
+
+
+
+
+# Tarballs
+# --------
+#
+# All the necessary tarballs are defined and prepared with this rule.
+tarballs = $(foreach t, bash-$(bash-version).tar.gz                 \
+	                cfitsio$(cfitsio-version).tar.gz            \
+                        coreutils-$(coreutils-version).tar.xz       \
+	                gawk-$(gawk-version).tar.gz                 \
+	                ghostscript-$(ghostscript-version).tar.gz   \
+	                gnuastro-$(gnuastro-version).tar.gz         \
+	                grep-$(grep-version).tar.xz                 \
+	                gsl-$(gsl-version).tar.gz                   \
+	                jpegsrc.$(libjpeg-version).tar.gz           \
+	                libtool-$(libtool-version).tar.gz           \
+                        libgit2-$(libgit2-version).tar.gz           \
+	                sed-$(sed-version).tar.xz                   \
+	                make-$(make-version).tar.gz                 \
+	                wcslib-$(wcslib-version).tar.bz2            \
+                      , $(tdir)/$(t) )
+$(tarballs): $(tdir)/%:
+	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
+	  cp $(DEPENDENCIES-DIR)/$* $@
+	else
+          # Remove all numbers, `-' and `.' from the tarball name so we can
+          # search more easily only with the program name.
+	  n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g'         \
+	               | awk '{print $$1}' )
+
+          # Set the top download link of the requested tarball.
+	  if   [ $$n = bash        ]; then w=http://ftp.gnu.org/gnu/bash
+	  elif [ $$n = cfitsio     ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = coreutils   ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = gawk        ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = ghostscript ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = gnuastro    ]; then w=http://akhlaghi.org
+	  elif [ $$n = grep        ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = gsl         ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = jpegsrc     ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = libtool     ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = libgit      ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = sed         ]; then w=WWWWWWWWWWWWWWWW
+	  elif [ $$n = make        ]; then w=http://akhlaghi.org
+	  elif [ $$n = wcslib      ]; then w=WWWWWWWWWWWWWWWW
+	  else
+	    echo; echo; echo;
+	    echo "'$$n' not recognized as a dependency name to download."
+	    echo; echo; echo;
+	    exit 1
+	  fi
+
+          # Download the requested tarball.
+	  $(DOWNLOADER) $@ $$w/$*
+	fi
+
+
+
+
+
+# Customized build
+# ----------------
+#
+# Programs that need some customization on their build.
+# For CFITSIO we'll need to intervene manually to remove the check on
+# libcurl (which can be real trouble in this controlled environment).
+$(ildir)/libcfitsio.a: $(ibdir)/ls                              \
+                          $(tdir)/cfitsio$(cfitsio-version).tar.gz
+        # Same as before
+	cd $(ddir)
+	tar xf $(tdir)/cfitsio$(cfitsio-version).tar.gz
+	cd cfitsio
+
+        # Remove the part that checks for the CURL library, so it assumes
+        # that the CURL library wasn't found.
+	awk 'NR<4785 || NR>4847' configure > new_configure
+	mv new_configure configure
+	chmod +x configure
+
+        # Do the standard configuring and building
+	./configure CFLAGS=--static --disable-shared --prefix=$(idir)
+	make; make install;
+	cd ..; rm -rf cfitsio
+
+
+# Why not shared: Gnuastro's configure can't link with it in static mode.
+$(ildir)/libgit2.a: $(tdir)/libgit2-$(libgit2-version).tar.gz
+	cd $(ddir)
+	tar xf $(tdir)/libgit2-$(libgit2-version).tar.gz
+	cd libgit2-$(libgit2-version)
+	mkdir build
+	cd build
+	export CFLAGS="--static $$CFLAGS"
+	cmake .. -DUSE_SSH=OFF -DUSE_OPENSSL=OFF -DBUILD_SHARED_LIBS=OFF \
+                 -DBUILD_CLAR=OFF -DTHREADSAFE=ON
+	cmake --build .
+	cmake .. -DCMAKE_INSTALL_PREFIX=$(idir)
+	cmake --build . --target install
+	cd ../..
+	rm -rf libgit2-$(libgit2-version)
+
+
+
+
+
+# GNU Build system programs
+# -------------------------
+#
+# Programs that use the basic GNU build system.
+gbuild = cd $(ddir); tar xf $(tdir)/$(1); cd $(2);               \
+         if [ $(3)x = staticx ]; then                            \
+         opts="CFLAGS=--static --disable-shared";                \
+         fi;                                                     \
+         ./configure $$opts $(4) --prefix=$(idir); make $(5);    \
+         check="$(6)"; if [ x"$$check" != x ]; then $$check; fi; \
+         make install; cd ..; rm -rf $(2)
+
+$(ibdir)/bash: $(tdir)/bash-$(bash-version).tar.gz
+	$(call gbuild,$(subst $(tdir),,$<), bash-$(bash-version), static)
+
+
+# Unfortunately GNU Make needs dynamic linking in two instances: when
+# loading objects (dynamically linked libraries), or when using the
+# `getpwnam' function (for tilde expansion). The first can be disabled with
+# `--disable-load', but unfortunately I don't know any way to fix the
+# second. So, we'll have to build it dynamically for now.
+$(ibdir)/make: $(tdir)/make-$(make-version).tar.gz
+	$(call gbuild,$(subst $(tdir),,$<), make-$(make-version))
+
+
+$(ibdir)/ls: $(tdir)/coreutils-$(coreutils-version).tar.xz
+	$(call gbuild,$(subst $(tdir),,$<), coreutils-$(coreutils-version), \
+                      static)
+
+
+$(ibdir)/gawk: $(tdir)/gawk-$(gawk-version).tar.gz \
+               $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), gawk-$(gawk-version), static)
+
+
+$(ibdir)/sed: $(tdir)/sed-$(sed-version).tar.xz \
+              $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), sed-$(sed-version), static)
+
+
+$(ibdir)/grep: $(tdir)/grep-$(grep-version).tar.xz \
+               $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), grep-$(grep-version), static)
+
+
+$(ibdir)/libtool: $(tdir)/libtool-$(libtool-version).tar.gz \
+                  $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), libtool-$(libtool-version), static)
+
+
+$(ildir)/libgsl.a: $(tdir)/gsl-$(gsl-version).tar.gz \
+                   $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), gsl-$(gsl-version), static)
+
+
+$(ildir)/libwcs.a: $(tdir)/wcslib-$(wcslib-version).tar.bz2 \
+	           $(ildir)/libcfitsio.a
+	$(call gbuild,$(subst $(tdir),,$<), wcslib-$(wcslib-version), , \
+                      LIBS="-pthread -lcurl -lm" --without-pgplot       \
+                         --disable-fortran)
+
+
+$(ibdir)/gs: $(tdir)/ghostscript-$(ghostscript-version).tar.gz \
+             $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir),,$<), ghostscript-$(ghostscript-version))
+
+
+$(ildir)/libjpeg.a: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
+	$(call gbuild,$(subst $(tdir),,$<), jpeg-9b, static)
+
+
+$(ibdir)/astnoisechisel: $(tdir)/gnuastro-$(gnuastro-version).tar.gz \
+                         $(ildir)/libgsl.a                           \
+                         $(ildir)/libcfitsio.a                       \
+                         $(ildir)/libwcs.a                           \
+                         $(ibdir)/gs                                 \
+                         $(ildir)/libjpeg.a                          \
+                         $(ildir)/libgit2.a                          \
+
+	$(call gbuild,$(subst $(tdir),,$<), gnuastro-$(gnuastro-version), \
+                      static, , -j8, make check -j8)
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index f615e22..165db78 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -47,36 +47,24 @@ pconfdir    = reproduce/config/pipeline
 
 
 
-# Sanity check
-# ------------
+# High level environment
+# ----------------------
 #
-# We need to make sure that the `./configure' command has already been
-# run. The output of `./configure' is the `$(pconfdir)/LOCAL.mk' file and
-# this is the non-time-stamp prerequisite of $(BDIR), see below.
+# We want the full recipe to be executed in one call to the shell. Also we
+# want Make to run the specific version of Bash that we have installed
+# during `./configure' time.
 #
-# There is one problem however: if the user hasn't run `./configure' yet,
-# then `BDIR' isn't defined (will just evaluate to blank space). Therefore
-# it won't appear in the prerequisites and the pipeline will try to build
-# the other directories in the top root directory (`/'). To solve this
-# problem, when `BDIR' isn't defined, we'll define it with a place-holder
-# name (only so it won't evaluate to blank space). Note that this
-# directory will never be built.
-ifeq ($(BDIR),)
-configure-run = no
-BDIR = reproduce/BDIR
-else
-configure-run = yes
-endif
-$(pconfdir)/LOCAL.mk:
-	@echo
-	@echo "================================================================"
-	@echo "For the pipeline's local settings, please run this command first"
-	@echo "(P.S. this local configuration is only necessary one time)"
-	@echo
-	@echo "    $$ ./configure"
-	@echo "================================================================"
-	@echo
-	@exit 1
+# Regarding the directories, this pipeline 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.
+.ONESHELL:
+.SHELLFLAGS      = -ec
+SHELL           := .local/bin/bash
+PATH            := .local/bin:$(PATH)
+LDFLAGS         := -L.local/lib $(LDFLAGS)
+CPPFLAGS        := -I.local/include $(CPPFLAGS)
+LD_LIBRARY_PATH := .local/lib:$(LD_LIBRARY_PATH)
 
 
 
@@ -103,52 +91,32 @@ $(pconfdir)/LOCAL.mk:
 # are looking for in this pipeline.
 .SUFFIXES:
 $(tikzdir): | $(texbdir); mkdir $@
-$(BDIR): | $(pconfdir)/LOCAL.mk; mkdir $@
 $(texdir) $(lockdir): | $(BDIR); mkdir $@
 $(mtexdir) $(texbdir): | $(texdir); mkdir $@
 
 
 
 
-# Symbolic link to build directory
-# --------------------------------
-#
-# Besides $(BDIR), we are also making a symbolic link to it for easy
-# access. Recall that it is recommended that the actual build directory be
-# in a completely separate part of the file system (a place that may easily
-# be completely deleted).
-#
-# Note that $(BDIR) might not be an absolute path and this will complicate
-# the symbolic link creation. To be generic, we'll first call `readlink' to
-# make sure we have an absolute address, then we'll make a symbolic link to
-# that.
-reproduce/build: | $(BDIR)
-	absbdir=$$(readlink -f $(BDIR));                        \
-	ln -s $$absbdir $@
-
-
-
-
 
 # High-level Makefile management
 # ------------------------------
 #
 # About `.PHONY': these are targets that must be built even if a file with
-# their name exists. Most don't correspond to a file, but those that do are
-# included here ensure that the file is always built in every run: for
-# example the pipeline versions may change within two separate runs, so we
-# want it to be rebuilt every time.
+# their name exists.
+#
+# 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 pipeline version which may change between two separate runs, even
+# when no file actually differs.
 .PHONY: all clean distclean clean-mmap $(mtexdir)/initialize.tex
-distclean: clean; rm -f $(pconfdir)/LOCAL.mk
 # --------- Delete for no Gnuastro ---------
 clean-mmap:; rm -f reproduce/config/gnuastro/mmap*
 # ------------------------------------------
 clean: clean-mmap
-ifeq ($(configure-run),yes)
 	rm -rf $(BDIR)
-endif
 	rm -f reproduce/build *.pdf *.log *.out *.aux *.auxlock
-
+distclean: clean
+	rm -f Makefile $(pconfdir)/LOCAL.mk .gnuastro
 
 
 
@@ -163,12 +131,12 @@ endif
 $(mtexdir)/initialize.tex: | $(mtexdir)
 
         # Version of the pipeline.
-	@v=$$(git describe --dirty --always);                      \
+	@v=$$(git describe --dirty --always);
 	echo "\newcommand{\pipelineversion}{$$v}"  > $@
 
 # --------- Delete for no Gnuastro ---------
         # Version of Gnuastro.
-	@v=$$(astnoisechisel --version | awk 'NR==1{print $$NF}'); \
+	@v=$$(astnoisechisel --version | awk 'NR==1{print $$NF}');
 	echo "\newcommand{\gnuastroversion}{$$v}" >> $@
 # ------------------------------------------
 
diff --git a/reproduce/src/make/paper.mk b/reproduce/src/make/paper.mk
index 844f157..79d7722 100644
--- a/reproduce/src/make/paper.mk
+++ b/reproduce/src/make/paper.mk
@@ -40,10 +40,10 @@ $(texbdir)/paper.bbl: tex/references.tex                         \
 
         # We'll run LaTeX first to generate the `.bcf' file (necessary for
         # `biber') and then run `biber' to generate the `.bbl' file.
-	p=$$(pwd);                                               \
-	export TEXINPUTS=$$p:$$TEXINPUTS;                        \
-	cd $(texbdir);                                           \
-        pdflatex -shell-escape -halt-on-error $$p/paper.tex;     \
+	p=$$(pwd);
+	export TEXINPUTS=$$p:$$TEXINPUTS;
+	cd $(texbdir);
+	pdflatex -shell-escape -halt-on-error $$p/paper.tex;
 	biber paper
 
 
@@ -61,9 +61,13 @@ $(texbdir)/paper.bbl: tex/references.tex                         \
 paper.pdf: tex/pipeline.tex paper.tex $(texbdir)/paper.bbl       \
 	   | $(tikzdir) $(texbdir)
 
-        # Make the report.
-	p=$$(pwd);                                               \
-	export TEXINPUTS=$$p:$$TEXINPUTS;                        \
-	cd $(texbdir);                                           \
-        pdflatex -shell-escape -halt-on-error $$p/paper.tex
+        # Go into the top TeX build directory and make the paper.
+	p=$$(pwd)
+	export TEXINPUTS=$$p:$$TEXINPUTS
+	cd $(texbdir)
+	pdflatex -shell-escape -halt-on-error $$p/paper.tex
+
+        # Come back to the top pipeline directory and copy the built PDF
+        # file here.
+	cd $$p
 	cp $(texbdir)/$@ $@