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.

1 files changed, 254 insertions, 0 deletions

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)