Dependency BibTeX entries included only when necessary

Until now, there was a single `tex/src/references.tex' file that housed the
BibTex entries for everything (software and non-software).

Since we have started to include the BibTeX entry for more software, it
will be hard to manage the large (sometime unused) BibTeX entries of the
software in the middle of the non-software related citations in the text of
the paper.

Therefore, with this commit, a `tex/dependencies' directory has been made
which has a separate BibTeX entry file for each software that needs
one. After the software is built, this file is copied to the new
`.local/version-info/cite' directory. At the end, the configure script will
concatenate all the files in this directory into one file which will later
be used with `tex/src/references.tex' by BibLaTeX.

This greatly simplifies managing of citations. Allowing us to focus on the
software-building and paper-writing citations separately/cleanly (and thus
be more efficient in both).

2 files changed, 15 insertions, 9 deletions

diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index 11c6b1f..7ccf6b3 100644
--- a/reproduce/src/make/dependencies-python.mk
+++ b/reproduce/src/make/dependencies-python.mk
@@ -295,10 +295,8 @@ $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
                    $(ipydir)/h5py                            \
                    $(ipydir)/numpy                           \
                    $(ipydir)/scipy
-        # Since we have two citations in Astropy (with the `,' character
-        # which can be confused in Make), its easier to just re-write the
-        # full version after the build.
 	$(call pybuild, tar xf, $<, astropy-$(astropy-version)) \
+	&& cp $(dtexdir)/astropy.tex $(ictdir)/                 \
 	&& echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
 $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
@@ -336,6 +334,7 @@ $(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \
 $(ipydir)/cython: $(tdir)/cython-$(cython-version).tar.gz \
                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, Cython-$(cython-version)) \
+	&& cp $(dtexdir)/cython.tex $(ictdir)/                \
 	&& echo "Cython $(cython-version) \citep{cython2011}" > $@
 
 $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
@@ -389,7 +388,8 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
                       $(ipydir)/numpy                                   \
                       $(ipydir)/pyparsing                               \
                       $(ipydir)/python-dateutil
-	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version))       \
+	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) \
+	&& cp $(dtexdir)/matplotlib.tex $(ictdir)/                    \
 	&& echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
 # Currently mpi4py doesn't build because of some conflict with OpenMPI:
@@ -404,7 +404,8 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
 $(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz    \
                   $(ipydir)/setuptools                       \
                   $(ilidir)/openmpi
-	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version))    \
+	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version)) \
+	&& cp $(dtexdir)/mpi4py.tex $(ictdir)/                \
 	&& echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
 $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
@@ -420,6 +421,7 @@ $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
 	conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \
 	$(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf,            \
 	                Numpy $(numpy-version))                              \
+	&& cp $(dtexdir)/numpy.tex $(ictdir)/                                \
 	&& echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
 $(ibidir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
@@ -465,7 +467,8 @@ $(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
 	  export LDFLAGS="$(LDFLAGS) -shared";                               \
 	fi;                                                                  \
 	conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \
-	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf)           \
+	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf)           \
+	&& cp $(dtexdir)/scipy.tex $(ictdir)/                                \
 	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
 
 $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index ae1daa7..67ce490 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -37,6 +37,7 @@ include reproduce/config/pipeline/dependency-versions.mk
 
 lockdir = $(BDIR)/locks
 ddir    = $(BDIR)/dependencies
+dtexdir = $(shell pwd)/tex/dependencies
 tdir    = $(BDIR)/dependencies/tarballs
 idir    = $(BDIR)/dependencies/installed
 ibdir   = $(BDIR)/dependencies/installed/bin
@@ -44,6 +45,7 @@ ildir   = $(BDIR)/dependencies/installed/lib
 ibidir  = $(BDIR)/dependencies/installed/version-info/bin
 ilidir  = $(BDIR)/dependencies/installed/version-info/lib
 itidir  = $(BDIR)/dependencies/installed/version-info/tex
+ictdir  = $(BDIR)/dependencies/installed/version-info/cite
 ipydir  = $(BDIR)/dependencies/installed/version-info/python
 
 # Define the top-level programs to build (installed in `.local/bin').
@@ -604,9 +606,10 @@ $(ibidir)/gnuastro: $(tdir)/gnuastro-$(gnuastro-version).tar.lz \
 ifeq ($(static_build),yes)
 	staticopts="--enable-static=yes --enable-shared=no";
 endif
-	$(call gbuild, $<, gnuastro-$(gnuastro-version), static,     \
-	               $$staticopts, -j$(numthreads),                \
-	               make check -j$(numthreads))                   \
+	$(call gbuild, $<, gnuastro-$(gnuastro-version), static, \
+	               $$staticopts, -j$(numthreads),            \
+	               make check -j$(numthreads))               \
+	&& cp $(dtexdir)/gnuastro.tex $(ictdir)/                 \
 	&& echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
 $(ibidir)/unzip: $(tdir)/unzip-$(unzip-version).tar.gz