Acknowledged Scipy-related packages: Cython, Matplotlib, Numpy and Scipy

Until now, name and version of all Python packages were indicated in the
final paper, but not the main paper of them (if it exists).

With this commit, some Python packages (Cython, Matplotlib, Numpy and
Scipy) are now properly acknoledged by citating the source paper.
`mpi4py' is also cited although this package is not yet included into
the pipeline.

3 files changed, 97 insertions, 11 deletions

diff --git a/.file-metadata b/.file-metadata
index d1dea6f..a1e8ad4 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index a6634ff..221fad2 100644
--- a/reproduce/src/make/dependencies-python.mk
+++ b/reproduce/src/make/dependencies-python.mk
@@ -254,7 +254,7 @@ $(ibidir)/python3: $(tdir)/python-$(python-version).tar.gz \
 #   3) Unpacked directory name after unpacking the tarball
 #   4) site.cfg file (optional)
 #   5) Official software name.(for paper).
-pybuild = cd $(ddir); rm -rf $(3);                                \
+pybuild = cd $(ddir); rm -rf $(3);                            \
 	 if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \
 	 cd $(3);                                                 \
 	 if [ "x$(strip $(4))" != x ]; then                       \
@@ -335,8 +335,8 @@ $(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), ,\
-	                Cython $(cython-version))
+	$(call pybuild, tar xf, $<, Cython-$(cython-version)) \
+	&& echo "Cython $(cython-version) \citep{cython2011}" > $@
 
 $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
                        $(ipydir)/setuptools
@@ -389,8 +389,8 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
                       $(ipydir)/numpy                                   \
                       $(ipydir)/pyparsing                               \
                       $(ipydir)/python-dateutil
-	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version), ,\
-	                Matplotlib $(matplotlib-version))
+	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version))       \
+	&& echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
 # Currently mpi4py doesn't build because of some conflict with OpenMPI:
 #
@@ -404,8 +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), ,\
-	                mpi4py $(mpi4py-version))
+	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version))    \
+	&& echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
 $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
                  $(ipydir)/setuptools               \
@@ -418,8 +418,9 @@ $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
 	  export LDFLAGS="$(LDFLAGS) -shared";                               \
 	fi;                                                                  \
 	conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \
-	$(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf, \
-	                Numpy $(numpy-version))
+	$(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf,            \
+	                Numpy $(numpy-version))                              \
+	&& echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
 $(ibidir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
                 $(ipydir)/setuptools
@@ -464,8 +465,8 @@ $(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,\
-	                Scipy $(scipy-version))
+	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf)           \
+	&& echo "Scipy $(scipy-version) \citep{scipy2001}" > $@
 
 $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
                          $(ipydir)/cryptography                                \
diff --git a/tex/src/references.tex b/tex/src/references.tex
index c1c4084..47015bb 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -158,3 +158,88 @@ archivePrefix = "arXiv",
    adsurl = {http://adsabs.harvard.edu/abs/2013A\%26A...558A..33A},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+
+
+
+
+@ARTICLE{cython2011,
+   author = {{Behnel}, S. and {Bradshaw}, R. and {Citro}, C. and {Dalcin}, L. and
+	{Seljebotn}, D.~S. and {Smith}, K.},
+    title = "{Cython: The Best of Both Worlds}",
+  journal = {Computing in Science and Engineering},
+     year = 2011,
+    month = mar,
+   volume = 13,
+   number = 2,
+    pages = {31-39},
+      doi = {10.1109/MCSE.2010.118},
+   adsurl = {http://adsabs.harvard.edu/abs/2011CSE....13b..31B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
+@ARTICLE{mpi4py2011,
+   author = {{Dalcin}, L.~D. and {Paz}, R.~R. and {Kler}, P.~A. and {Cosimo}, A.
+	},
+    title = "{Parallel distributed computing using Python}",
+  journal = {Advances in Water Resources},
+     year = 2011,
+    month = sep,
+   volume = 34,
+    pages = {1124-1139},
+      doi = {10.1016/j.advwatres.2011.04.013},
+   adsurl = {http://adsabs.harvard.edu/abs/2011AdWR...34.1124D},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+@ARTICLE{numpy2011,
+   author = {{van der Walt}, S. and {Colbert}, S.~C. and {Varoquaux}, G.},
+    title = "{The NumPy Array: A Structure for Efficient Numerical Computation}",
+  journal = {Computing in Science and Engineering},
+archivePrefix = "arXiv",
+   eprint = {1102.1523},
+ primaryClass = "cs.MS",
+     year = 2011,
+    month = mar,
+   volume = 13,
+   number = 2,
+    pages = {22-30},
+      doi = {10.1109/MCSE.2011.37},
+   adsurl = {http://adsabs.harvard.edu/abs/2011CSE....13b..22V},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+@Article{matplotlib2007,
+  Author    = {Hunter, J. D.},
+  Title     = {Matplotlib: A 2D graphics environment},
+  Journal   = {Computing In Science \& Engineering},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90--95},
+  abstract  = {Matplotlib is a 2D graphics package used for Python
+  for application development, interactive scripting, and
+  publication-quality image generation across user
+  interfaces and operating systems.},
+  publisher = {IEEE COMPUTER SOC},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = 2007
+}
+
+
+
+
+@Misc{scipy2001,
+  author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
+  title =     {{SciPy}: Open source scientific tools for {Python}},
+  year =      {2001--},
+  url = "http://www.scipy.org/"
+}