Imported recent corrections, no conflicts

Some recent corrections that were done by Raul are now merged into the
pipeline. There weren't any conflicts.

5 files changed, 143 insertions, 15 deletions

diff --git a/.file-metadata b/.file-metadata
index 115bae6..0607790 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index 3b43aae..91d1265 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -29,6 +29,7 @@ coreutils-version          = 8.30
 curl-version               = 7.63.0
 diffutils-version          = 3.7
 fftw-version               = 3.3.8
+file-version               = 5.36
 findutils-version          = 4.6.0.199-e3fc
 flock-version              = 0.2.3
 freetype-version           = 2.9
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index bedbc38..9e277f7 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -67,7 +67,7 @@ export CPPFLAGS          := -I$(idir)/include $(CPPFLAGS)
 export LD_LIBRARY_PATH   := $(ildir):$(LD_LIBRARY_PATH)
 
 # Define the programs that don't depend on any other.
-top-level-programs = low-level-links wget gcc
+top-level-programs = low-level-links wget gcc file
 all: $(foreach p, $(top-level-programs), $(ibidir)/$(p))
 
 
@@ -104,6 +104,7 @@ tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
                         cert.pem                                            \
                         coreutils-$(coreutils-version).tar.xz               \
                         diffutils-$(diffutils-version).tar.xz               \
+                        file-$(file-version).tar.gz                         \
                         findutils-$(findutils-version).tar.lz               \
                         gawk-$(gawk-version).tar.lz                         \
                         gcc-$(gcc-version).tar.xz                           \
@@ -144,6 +145,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  elif [ $$n = cert      ]; then w=http://akhlaghi.org/src;         \
 	  elif [ $$n = coreutils ]; then w=http://ftp.gnu.org/gnu/coreutils;\
 	  elif [ $$n = diffutils ]; then w=http://ftp.gnu.org/gnu/diffutils;\
+	  elif [ $$n = file      ]; then w=ftp://ftp.astron.com/pub/file;   \
 	  elif [ $$n = findutils ]; then w=http://akhlaghi.org/src;         \
 	  elif [ $$n = gawk      ]; then w=http://ftp.gnu.org/gnu/gawk;     \
 	  elif [ $$n = gcc       ]; then w=http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version); \
@@ -769,6 +771,12 @@ $(ibidir)/binutils: $(tdir)/binutils-$(binutils-version).tar.lz
 	$(call gbuild, $<, binutils-$(binutils-version), static) \
 	&& echo "GNU Binutils $(binutils-version)" > $@
 
+# `file' is not a prerequisite of GCC. However, since it is low level, it is
+# set as a prerequisite of GCC to have it installed.
+$(ibidir)/file: $(tdir)/file-$(file-version).tar.gz
+	$(call gbuild, $<, file-$(file-version), static) \
+	&& echo "File $(file-version)" > $@
+
 $(ilidir)/isl: $(tdir)/isl-$(isl-version).tar.bz2 \
                $(ilidir)/gmp
 	$(call gbuild, $<, isl-$(isl-version), static)  \
@@ -801,9 +809,10 @@ gcc-prerequisites = $(tdir)/gcc-$(gcc-version).tar.xz \
 endif
 $(ibidir)/gcc: $(gcc-prerequisites)   \
                $(ibidir)/sed          \
+               $(ibidir)/bash         \
+               $(ibidir)/file         \
                $(ibidir)/gawk         \
                $(ibidir)/grep         \
-               $(ibidir)/bash         \
                $(ibidir)/which        \
                $(ibidir)/glibtool     \
                $(ibidir)/findutils    \
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index 5b12757..11c6b1f 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:
 #
@@ -404,21 +404,23 @@ $(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               \
                  $(ilidir)/openblas                 \
-                 $(ilidir)/fftw
+                 $(ilidir)/fftw                     \
+                 $(ibidir)/unzip
 	if [ x$(on_mac_os) = xyes ]; then                                    \
 	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle";     \
 	else                                                                 \
 	  export LDFLAGS="$(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
@@ -463,8 +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{scipy2007,scipy2011}" > $@
 
 $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
                          $(ipydir)/cryptography                                \
@@ -473,7 +475,8 @@ $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
 	                SecretStorage $(secretstorage-version))
 
 $(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
-                      $(ibidir)/python3
+                      $(ibidir)/python3                            \
+                      $(ibidir)/unzip
 	$(call pybuild, unzip, $<, setuptools-$(setuptools-version), ,\
 	                Setuptools $(setuptools-version))
 
diff --git a/tex/src/references.tex b/tex/src/references.tex
index a0f606f..641089e 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -129,6 +129,7 @@ archivePrefix = "arXiv",
 
 
 
+
 @ARTICLE{astropy2013,
    author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud}, E.~J. and
 	{Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and
@@ -158,3 +159,117 @@ 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 = {CiSE},
+     year = 2011,
+    month = mar,
+   volume = 13,
+   number = 2,
+    pages = {31},
+      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},
+      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{scipy2011,
+author={K. J. {Millman} and M. {Aivazis}},
+journal={CiSE},
+title={Python for Scientists and Engineers},
+year={2011},
+volume={13},
+number={2},
+pages={9},
+keywords={Special issues and sections;Computer languages;Programming;Scientific computing;Numerical models;Programming languages;Python;Scientific computing;interactive research;Python libraries;Python tools},
+doi={10.1109/MCSE.2011.36},
+ISSN={1521-9615},
+month={March},
+}
+
+
+
+
+
+@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 = {CiSE},
+archivePrefix = "arXiv",
+   eprint = {1102.1523},
+ primaryClass = "cs.MS",
+     year = 2011,
+    month = mar,
+   volume = 13,
+   number = 2,
+    pages = {22},
+      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   = {CiSE},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90},
+  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
+}
+
+
+
+
+
+@ARTICLE{scipy2007,
+author={T. E. {Oliphant}},
+journal={CiSE},
+title={Python for Scientific Computing},
+year={2007},
+volume={9},
+number={3},
+pages={10},
+keywords={high level languages;Python;scientific computing;steering language;scientific codes;high-level language;Scientific computing;High level languages;Libraries;Writing;Application software;Embedded software;Software standards;Standards development;Internet;Prototypes;Python;computer languages;scientific programming;scientific computing},
+doi={10.1109/MCSE.2007.58},
+ISSN={1521-9615},
+month={May},
+}