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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2019-04-12 15:51:26 +0100
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2019-04-12 15:51:26 +0100
commit41c444a1a0fcff2aaa5c9b0dd2fc1e6b3aaf6de1 (patch)
treef18889a878d752562246218c0f8e89a61fdedf2b
parentb177c7e99cdf605fd826d4f0f2026251e42ce164 (diff)
parent1442a5ebe5f9ca66f25c0f0a585c6ac4083101d8 (diff)
Imported recent corrections, no conflicts
Some recent corrections that were done by Raul are now merged into the pipeline. There weren't any conflicts.
-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},
+}