Lzip and Tar also built as basic dependencies

To ensure the easy unpacking and building of the programs, Lzip and Tar are
now also build during the initial setup phase.

Some minor corrections were also applied to make things cleaner and
smoother.

7 files changed, 125 insertions, 99 deletions

diff --git a/configure b/configure
index 8e15000..4810656 100755
--- a/configure
+++ b/configure
@@ -110,17 +110,19 @@ function absolute_dir() {
 #
 # Print some basic information so the user gets a feeling of what is going
 # on and is prepared on what will happen next.
-echo
-echo "-----------------------------------------"
-echo "Reproduction pipeline local configuration"
-echo "-----------------------------------------"
-echo
-echo "Local configuration includes things like top-level directories,"
-echo "or processing steps."
-echo
-echo "It is STRONGLY recommended to read the comments, and set the best "
-echo "values for your system (where necessary)."
-echo
+cat <<EOF
+
+-----------------------------------------
+Reproduction pipeline local configuration
+-----------------------------------------
+
+Local configuration includes things like top-level directories, or
+processing steps.
+
+It is STRONGLY recommended to read the comments, and set the best values
+for your system (where necessary).
+
+EOF
 
 
 
@@ -172,18 +174,25 @@ fi
 # calling `DOWNLOADER' within the Makefiles, and finish the command with
 # the web address.
 if [ $rewritepconfig = yes ]; then
-    if type wget > /dev/null; then
+    if type wget > /dev/null 2>/dev/null; then
         downloader="wget -O";
     else
-        echo "======="
-        echo "Warning"
-        echo "======="
-        echo "Couldn't find GNU Wget. It is used for downloading necessary "
-        echo "programs and data if they aren't already present in the specified "
-        echo "directories. Therefore the pipeline will crash if the necessary "
-        echo "files are not already present on the system."
-        echo "======="
-        echo
+        cat <<EOF
+
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+Couldn't find GNU Wget. It is used for downloading necessary programs and
+data if they aren't already present in the specified directories. Therefore
+the pipeline will crash if the necessary files are not already present on
+the system.
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+EOF
         downloader="no-downloader-found"
     fi;
 fi
diff --git a/paper.tex b/paper.tex
index 0e50b1d..04d6a7e 100644
--- a/paper.tex
+++ b/paper.tex
@@ -178,10 +178,11 @@ SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness
 
 The following free software tools were also critical component of this
 research (in alphabetical order): {\small CFITSIO} \cfitsioversion, CMake
-\cmakeversion, Git \gitversion, \gnu{Bash} \bashversion, \gnu{Coreutils}
-\coreutilsversion, \gnu{{\small AWK}} \gawkversion, \gnu{Grep}
-\grepversion, \gnu{Libtool} \libtoolversion, \gnu{Make} \makeversion,
-\gnu{Sed} \sedversion, \gnu{Scientific Library} ({\small GSL}) \gslversion,
+\cmakeversion, c{\small URL} \curlversion, Git \gitversion, \gnu{Bash}
+\bashversion, \gnu{Coreutils} \coreutilsversion, \gnu{{\small AWK}}
+\gawkversion, \gnu{Grep} \grepversion, \gnu{Libtool} \libtoolversion,
+\gnu{Make} \makeversion, \gnu{Sed} \sedversion, \gnu{Scientific Library}
+({\small GSL}) \gslversion, \gnu{Tar} \tarversion, Lzip \lzipversion,
     {\small GPL} Ghostscript \ghostscriptversion, Libgit2 \libgitwoversion,
     Libtiff \libtiffversion, {{\small WCSLIB}} \wcslibversion, and ZLib
     \zlibversion. We are very grateful to all their creators for freely
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index ad8dd2c..6d305cb 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -10,8 +10,10 @@ git-version         = 2.19.1
 gnuastro-version    = 0.7.60-4c9eb
 grep-version        = 3.1
 libtool-version     = 2.4.6
+lzip-version        = 1.20
 make-version        = 4.2.90
 sed-version         = 4.5
+tar-version         = 1.30
 
 # Libraries
 cfitsio-version     = 3.45
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index 33b682b..ed6e971 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -47,7 +47,11 @@ idir  = $(BDIR)/dependencies/installed
 ibdir = $(BDIR)/dependencies/installed/bin
 ildir = $(BDIR)/dependencies/installed/lib
 
-top-level-programs = bash make
+# As we build more programs, we want to use our own pipeline's built
+# programs, not the systems.
+PATH := $(ibdir):$(PATH)
+
+top-level-programs = bash
 all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 
 
@@ -61,56 +65,62 @@ all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 # is not recognized by some versions of Make (even older GNU Makes). So
 # we'll have to make sure the recipe doesn't break into multiple shell
 # calls (so we can preserve the variables).
-tarballs = $(foreach t, bash-$(bash-version).tar.gz                       \
-	                make-$(make-version).tar.gz                       \
+tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
+                        lzip-$(lzip-version).tar.gz                         \
+	                make-$(make-version).tar.gz                         \
+	                tar-$(tar-version).tar.gz                           \
                       , $(tdir)/$(t) )
 $(tarballs): $(tdir)/%:
-	if [ -f $(DEPENDENCIES-DIR)/$* ]; then                            \
-	  cp $(DEPENDENCIES-DIR)/$* $@;                                   \
-	else                                                              \
-	  n=$$(echo $* | sed -e's/[0-9\-]/ /g'                            \
-	                     -e's/\./ /g'                                 \
-	               | awk '{print $$1}' );                             \
-	                                                                  \
-	  mergenames=1;                                                   \
-	  if   [ $$n = bash        ]; then w=http://ftp.gnu.org/gnu/bash; \
-	  elif [ $$n = make        ]; then w=http://akhlaghi.org/src;     \
-	  else                                                            \
-	    echo; echo; echo;                                             \
-	    echo "'$$n' not recognized as a dependency name to download." \
-	    echo; echo; echo;                                             \
-	    exit 1;                                                       \
-	  fi;                                                             \
-	                                                                  \
-	  if [ $$mergenames = 1 ]; then  tarballurl=$$w/"$*";             \
-	  else                           tarballurl=$$w;                  \
-	  fi;                                                             \
-	  echo "Downloading $$tarballurl";                                \
-	  $(DOWNLOADER) $@ $$tarballurl;                                  \
+	if [ -f $(DEPENDENCIES-DIR)/$* ]; then                              \
+	  cp $(DEPENDENCIES-DIR)/$* $@;                                     \
+	else                                                                \
+	  n=$$(echo $* | sed -e's/[0-9\-]/ /g'                              \
+	                     -e's/\./ /g'                                   \
+	               | awk '{print $$1}' );                               \
+	                                                                    \
+	  mergenames=1;                                                     \
+	  if   [ $$n = bash ]; then w=http://ftp.gnu.org/gnu/bash;          \
+	  elif [ $$n = lzip ]; then w=http://download.savannah.gnu.org/releases/lzip; \
+	  elif [ $$n = make ]; then w=http://akhlaghi.org/src;              \
+	  elif [ $$n = tar  ]; then w=http://ftp.gnu.org/gnu/tar;           \
+	  else                                                              \
+	    echo; echo; echo;                                               \
+	    echo "'$$n' not a dependency name (for downloading)."           \
+	    echo; echo; echo;                                               \
+	    exit 1;                                                         \
+	  fi;                                                               \
+	                                                                    \
+	  if [ $$mergenames = 1 ]; then  tarballurl=$$w/"$*";               \
+	  else                           tarballurl=$$w;                    \
+	  fi;                                                               \
+	  echo "Downloading $$tarballurl";                                  \
+	  $(DOWNLOADER) $@ $$tarballurl;                                    \
 	fi
 
 
 
 
 
-# GNU Bash
-# --------
-#
-# Everything is standard and we can make it statically.
-$(ibdir)/bash: $(tdir)/bash-$(bash-version).tar.gz
-	$(call gbuild,$(subst $(tdir),,$<), bash-$(bash-version), static)
-
-
-
+# Basic programs (sorted alphabetically), see prerequisites for which one
+# will be built first.
+$(ibdir)/bash: $(tdir)/bash-$(bash-version).tar.gz \
+	       $(ibdir)/make
+	$(call gbuild,$(subst $(tdir)/,,$<), bash-$(bash-version), static)
 
+$(ibdir)/lzip: $(tdir)/lzip-$(lzip-version).tar.gz
+	$(call gbuild,$(subst $(tdir)/,,$<), lzip-$(lzip-version), static)
 
-# GNU Make
-# --------
-#
 # 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)/make: $(tdir)/make-$(make-version).tar.gz \
+               $(ibdir)/tar
+	$(call gbuild,$(subst $(tdir)/,,$<), make-$(make-version), , , ,)
+
+# When built statically, tar gives a segmentation fault on unpacking
+# Bash. So we'll build it dynamically.
+$(ibdir)/tar: $(tdir)/tar-$(tar-version).tar.gz \
+              $(ibdir)/lzip
+	$(call gbuild,$(subst $(tdir)/,,$<), tar-$(tar-version))
diff --git a/reproduce/src/make/dependencies-build-rules.mk b/reproduce/src/make/dependencies-build-rules.mk
index a4d25aa..b53bc52 100644
--- a/reproduce/src/make/dependencies-build-rules.mk
+++ b/reproduce/src/make/dependencies-build-rules.mk
@@ -71,7 +71,7 @@ cbuild = if [ $(3)x = staticx ]; then                                   \
 	   opts="-DBUILD_SHARED_LIBS=OFF";                              \
 	 fi;                                                            \
 	 cd $(ddir) && rm -rf $(2) && tar xf $(tdir)/$(1) && cd $(2) && \
-	 rm -rf my-build && mkdir my-build && cd my-build && opts="" && \
+	 rm -rf my-build && mkdir my-build && cd my-build &&            \
 	 cmake .. $$opts $(4) &&                                        \
 	 cmake --build . &&                                             \
 	 cmake .. -DCMAKE_INSTALL_PREFIX=$(idir) &&                     \
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index 6da554c..45ceadc 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -151,46 +151,42 @@ $(tarballs): $(tdir)/%:
 
 # Libraries
 # ---------
-$(ildir)/libcfitsio.a: $(tdir)/cfitsio-$(cfitsio-version).tar.gz         \
-                       $(ildir)/libcurl.a                               \
+$(ildir)/libcfitsio.a: $(tdir)/cfitsio-$(cfitsio-version).tar.gz           \
+                       $(ildir)/libcurl.a                                  \
                        $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), cfitsio, static,            \
+	$(call gbuild,$(subst $(tdir)/,,$<), cfitsio, static,              \
                       --enable-sse2 --enable-reentrant)
 
-$(ildir)/libcurl.a: $(tdir)/curl-$(curl-version).tar.gz \
-                    $(ildir)/libz.a                     \
-                    $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), curl-$(curl-version), static, \
-                      --without-brotli)
 
-$(ildir)/libgit2.a: $(tdir)/libgit2-$(libgit2-version).tar.gz             \
-                    $(ildir)/libcurl.a                                    \
+$(ildir)/libgit2.a: $(tdir)/libgit2-$(libgit2-version).tar.gz              \
+                    $(ildir)/libcurl.a                                     \
                     $(ibdir)/cmake
-	$(call cbuild,$(subst $(tdir),,$<), libgit2-$(libgit2-version),   \
-	              static, -DUSE_SSH=OFF -DUSE_OPENSSL=OFF             \
-                      -DBUILD_CLAR=OFF -DTHREADSAFE=ON, )
+	$(call cbuild,$(subst $(tdir)/,,$<), libgit2-$(libgit2-version),   \
+	              static, -DUSE_SSH=OFF -DUSE_OPENSSL=OFF              \
+	              -DBUILD_CLAR=OFF -DTHREADSAFE=ON)
 
-$(ildir)/libgsl.a: $(tdir)/gsl-$(gsl-version).tar.gz \
+$(ildir)/libgsl.a: $(tdir)/gsl-$(gsl-version).tar.gz                       \
                    $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), gsl-$(gsl-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), gsl-$(gsl-version), static)
 
 $(ildir)/libjpeg.a: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
-	$(call gbuild,$(subst $(tdir),,$<), jpeg-9b, static)
+	$(call gbuild,$(subst $(tdir)/,,$<), jpeg-9b, static)
 
-$(ildir)/libtiff.a: $(tdir)/tiff-$(libtiff-version).tar.gz \
+$(ildir)/libtiff.a: $(tdir)/tiff-$(libtiff-version).tar.gz                 \
                    $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), tiff-$(libtiff-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), tiff-$(libtiff-version),      \
+	              static)
 
-$(ildir)/libwcs.a: $(tdir)/wcslib-$(wcslib-version).tar.bz2 \
+$(ildir)/libwcs.a: $(tdir)/wcslib-$(wcslib-version).tar.bz2                \
 	           $(ildir)/libcfitsio.a
-	$(call gbuild,$(subst $(tdir),,$<), wcslib-$(wcslib-version),     \
-                      static, LIBS="-pthread -lcurl -lm" --without-pgplot \
+	$(call gbuild,$(subst $(tdir)/,,$<), wcslib-$(wcslib-version),     \
+                      static, LIBS="-pthread -lcurl -lm" --without-pgplot  \
                          --disable-fortran)
 
 # Zlib's `./configure' doesn't use Autoconf's configure script, it just
 # accepts a direct `--static' option.
 $(ildir)/libz.a: $(tdir)/zlib-$(zlib-version).tar.gz
-	$(call gbuild,$(subst $(tdir),,$<), zlib-$(zlib-version), , \
+	$(call gbuild,$(subst $(tdir)/,,$<), zlib-$(zlib-version), ,       \
                       --static)
 
 
@@ -199,37 +195,43 @@ $(ildir)/libz.a: $(tdir)/zlib-$(zlib-version).tar.gz
 
 # Programs
 # --------
-$(ibdir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz \
+$(ibdir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz                        \
                 $(ibdir)/ls
-	$(call cbuild,$(subst $(tdir),,$<), cmake-$(cmake-version))
+	$(call cbuild,$(subst $(tdir)/,,$<), cmake-$(cmake-version))
+
+$(ibdir)/curl: $(tdir)/curl-$(curl-version).tar.gz                           \
+               $(ildir)/libz.a                                               \
+               $(ibdir)/ls
+	$(call gbuild,$(subst $(tdir)/,,$<), curl-$(curl-version), static,   \
+                      --without-brotli)
 
 $(ibdir)/ls: $(tdir)/coreutils-$(coreutils-version).tar.xz
-	$(call gbuild,$(subst $(tdir),,$<), coreutils-$(coreutils-version), \
+	$(call gbuild,$(subst $(tdir)/,,$<), coreutils-$(coreutils-version), \
                       static)
 
 $(ibdir)/gawk: $(tdir)/gawk-$(gawk-version).tar.gz \
                $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), gawk-$(gawk-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), gawk-$(gawk-version), static)
 
 $(ibdir)/sed: $(tdir)/sed-$(sed-version).tar.xz \
               $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), sed-$(sed-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), sed-$(sed-version), static)
 
 $(ibdir)/grep: $(tdir)/grep-$(grep-version).tar.xz \
                $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), grep-$(grep-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), grep-$(grep-version), static)
 
 $(ibdir)/libtool: $(tdir)/libtool-$(libtool-version).tar.gz \
                   $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), libtool-$(libtool-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), libtool-$(libtool-version), static)
 
 $(ibdir)/gs: $(tdir)/ghostscript-$(ghostscript-version).tar.gz \
              $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), ghostscript-$(ghostscript-version))
+	$(call gbuild,$(subst $(tdir)/,,$<), ghostscript-$(ghostscript-version))
 
 $(ibdir)/git: $(tdir)/git-$(git-version).tar.xz \
              $(ibdir)/ls
-	$(call gbuild,$(subst $(tdir),,$<), git-$(git-version), static)
+	$(call gbuild,$(subst $(tdir)/,,$<), git-$(git-version), static)
 
 $(ibdir)/astnoisechisel: $(tdir)/gnuastro-$(gnuastro-version).tar.lz \
                          $(ildir)/libgsl.a                           \
@@ -240,5 +242,5 @@ $(ibdir)/astnoisechisel: $(tdir)/gnuastro-$(gnuastro-version).tar.lz \
                          $(ildir)/libtiff.a                          \
                          $(ildir)/libgit2.a                          \
 
-	$(call gbuild,$(subst $(tdir),,$<), gnuastro-$(gnuastro-version), \
+	$(call gbuild,$(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 d0f69a3..1acec9f 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -191,8 +191,9 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
         # Versions of programs (same order as 'dependency-versions.mk').
 	$(call pvcheck, bash, $(bash-version), GNU Bash, bashversion)
 	$(call pvcheck, cmake, $(cmake-version), CMake, cmakeversion)
+	$(call pvcheck, curl, $(curl-version), cURL, curlversion)
 	$(call pvcheck, ls, $(coreutils-version), GNU Coreutils,       \
-                         coreutilsversion)
+	                coreutilsversion)
 	$(call pvcheck, awk, $(gawk-version), GNU AWK, gawkversion)
 	$(call pvcheck, gs, $(ghostscript-version), GPL Ghostscript,   \
 	                    ghostscriptversion)
@@ -202,12 +203,13 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	$(call pvcheck, grep, $(grep-version), GNU Grep, grepversion)
 	$(call pvcheck, libtool, $(libtool-version), GNU Libtool,      \
 	                libtoolversion)
+	$(call pvcheck, lzip, $(lzip-version), Lzip, lzipversion)
 	$(call pvcheck, make, $(make-version), GNU Make, makeversion)
 	$(call pvcheck, sed, $(sed-version), GNU SED, sedversion)
+	$(call pvcheck, tar, $(tar-version), GNU Tar, tarversion)
 
         # Versions of libraries.
 	$(call lvcheck, fitsio.h, $(cfitsio-version), CFITSIO, cfitsioversion)
-        ########## Curl library not yet checked.
 	$(call lvcheck, gsl/gsl_version.h, $(gsl-version),  \
 	                GNU Scientific Library (GSL), gslversion)
         ########## libjpeg not  yet checked.