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-rw-r--r--.file-metadatabin4780 -> 4780 bytes
-rw-r--r--reproduce/config/pipeline/dependency-versions.mk1
-rw-r--r--reproduce/src/make/dependencies-basic.mk13
-rw-r--r--reproduce/src/make/dependencies-python.mk29
-rw-r--r--tex/src/references.tex115
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
Binary files differ
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},
+}
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