Sanity checks added, local settings now in LOCAL.mk.in

The choice of whether or not to make a PDF is now also a local system
issue, not a general pipeline issue. So it has been put in the new
`LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local
settings (things that when changed should not be version-controlled) should
be defined in this file.

A sanity check was added to find if `./configure' has been run before
`make' or not (using the `LOCAL.mk' file which is an output of the
configuration step). If `LOCAL.mk' doesn't exist, an error will be printed
informing the user that `./configure' needs to be run first.

The configure script also provides more clear and hopefully better
information on its purpose and what must be done.

Since `make clean', it is executed even when `./configure' hasn't been run,
it will only delete the build directory and its contents when local
configuration has been done.

A `distclean' target was also added which will first "clean" the pipeline,
then delete the `LOCAL.mk.in' file.

To allow rules like `make' to be run even if `BDIR' isn't defined
(`./configure' hasn't been run yet), a fake `BDIR' is defined in such
cases.

4 files changed, 80 insertions, 29 deletions

diff --git a/reproduce/config/pipeline/DIRECTORIES.mk.in b/reproduce/config/pipeline/LOCAL.mk.in
index 9ebd67b..e5a9f96 100644
--- a/reproduce/config/pipeline/DIRECTORIES.mk.in
+++ b/reproduce/config/pipeline/LOCAL.mk.in
@@ -22,8 +22,8 @@
 
 
 
-# Input data directories
-# ----------------------
+# Input data
+# ----------
 #
 # 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
@@ -48,3 +48,22 @@ SURVEY = reproduce/SURVEY
 # 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
+
+
+
+
+
+# Make the final PDF?
+# -------------------
+#
+# During the testing a pipeline, it is usually not necessary to build
+# the PDF file (which makes a lot of output lines on the command-line
+# and can make it hard to find the commands and possible errors (and
+# their outputs). Also, in some cases, only the produced results may
+# be of interest and not the final PDF, so LaTeX (and its necessary
+# packages) may not be installed.
+#
+# If this variable is given any string, a PDF will be made with
+# LaTeX. Otherwise, a notice will just printed that for now, no PDF
+# will be created.
+BUILD-FINAL-PDF = yes
diff --git a/reproduce/config/pipeline/pdf.mk b/reproduce/config/pipeline/pdf.mk
deleted file mode 100644
index 51ab933..0000000
--- a/reproduce/config/pipeline/pdf.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# Make the final PDF?
-# -------------------
-#
-# During the testing a pipeline, it is usually not necessary to build
-# the PDF file (which makes a lot of output lines on the command-line
-# and can make it hard to find the commands and possible errors (and
-# their outputs). Also, in some cases, only the produced results may
-# be of interest and not the final PDF, so LaTeX (and its necessary
-# packages) may not be installed.
-#
-# If this variable is given any string, a PDF will be made with
-# LaTeX. Otherwise, a notice will just printed that for now, no PDF
-# will be created.
-pdf-compile = yes
diff --git a/reproduce/config/pipeline/web.mk b/reproduce/config/pipeline/web.mk
index f80b886..5af11a7 100644
--- a/reproduce/config/pipeline/web.mk
+++ b/reproduce/config/pipeline/web.mk
@@ -1,6 +1,6 @@
 # Web server(s) hosting the input data for this pipeline.
 #
 # This is the web page containing the files that must be located in the
-# `SURVEY' directory of `reproduce/config/pipeline/DIRECTORIES.mk' on the
-# local system.
+# `SURVEY' directory of `reproduce/config/pipeline/LOCAL.mk' on the local
+# system.
 web-survey = https://some.webpage.com/example/server
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 1478881..927c292 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -33,24 +33,67 @@
 # parallel. Also, some programs may not be thread-safe, therefore it will
 # be necessary to put a lock on them. This pipeline uses the `flock'
 # program to achieve this.
-texdir = $(BDIR)/tex
-lockdir = $(BDIR)/locks
-bdirsym = reproduce/build
-mtexdir = $(texdir)/macros
-pconfdir = reproduce/config/pipeline
+texdir      = $(BDIR)/tex
+srcdir      = reproduce/src
+lockdir     = $(BDIR)/locks
+bdirsym     = reproduce/build
+mtexdir     = $(texdir)/macros
+gconfdir    = reproduce/config/gnuastro
+pconfdir    = reproduce/config/pipeline
+
+
+
+
+
+# Sanity check
+# ------------
+#
+# We need to make sure that the `./configure' command has already been
+# run. The output of `./configure' is the `$(pconfdir)/LOCAL.mk' file and
+# this is the non-time-stamp prerequisite of $(BDIR), see below.
+#
+# There is one problem however: if the user hasn't run `./configure' yet,
+# then `BDIR' isn't defined (will just evaluate to blank space). Therefore
+# it won't appear in the prerequisites and the pipeline will try to build
+# the other directories in the top root directory (`/'). To solve this
+# problem, when `BDIR' isn't defined, we'll define it with a place-holder
+# name ((only so it won't evaluate to blank space). Note that this
+# directory will never be built.
+ifeq ($(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
 
 
 
 
 
 # Make the high-level level directories
-# ------------------------------
+# -------------------------------------
 #
 # These are just the top-level directories for all the separate steps. The
 # directories (or possible sub-directories) for individual steps will be
 # defined and added within their own Makefiles.
-$(BDIR):; mkdir $@;
+#
+# IMPORTANT NOTE for $(BDIR)'s dependency: it only depends on the existance
+# (not the time-stamp) of `$(pconfdir)/LOCAL.mk'. So the user can make any
+# changes within that file and if they don't affect the pipeline. For
+# example a change of the top $(BDIR) name, while the contents are the same
+# as before.
 $(mtexdir): | $(texdir); mkdir $@
+$(BDIR): | $(pconfdir)/LOCAL.mk; mkdir $@
 $(texdir) $(lockdir): | $(BDIR); mkdir $@
 
 
@@ -65,11 +108,14 @@ $(texdir) $(lockdir): | $(BDIR); mkdir $@
 # 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.
-.PHONY: all clean clean-mmap $(mtexdir)/initialize.tex
+.PHONY: all clean distclean clean-mmap $(mtexdir)/initialize.tex
+distclean: clean; rm -f $(pconfdir)/LOCAL.mk
 clean-mmap:; rm -f reproduce/config/gnuastro/mmap*
 clean:
-	rm -rf $(BDIR) $(bdirsym) *.pdf *.log *.out *.aux *.auxlock \
-               reproduce/config/gnuastro/mmap*
+ifeq ($(configure-run),yes)
+	rm -rf $(BDIR)
+endif
+	rm -f $(bdirsym) $(gconfdir)/mmap* *.pdf *.log *.out *.aux *.auxlock
 
 
 
@@ -93,7 +139,7 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\gnuastroversion}{$$v}" >> $@
 
         # Location of the build directory (for LaTeX inputs).
-	echo "\newcommand{\bdir}{$(BDIR)}"        >> $@
+	@echo "\newcommand{\bdir}{$(BDIR)}"       >> $@