diff options
| -rw-r--r-- | .file-metadata | bin | 6413 -> 6492 bytes | |||
| -rw-r--r-- | reproduce/software/bibtex/galsim.tex | 27 | ||||
| -rw-r--r-- | reproduce/software/config/installation/checksums.mk | 9 | ||||
| -rw-r--r-- | reproduce/software/config/installation/versions.mk | 9 | ||||
| -rw-r--r-- | reproduce/software/make/python.mk | 112 |
5 files changed, 144 insertions, 13 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex 5735cf0..d8297e5 100644 --- a/.file-metadata +++ b/.file-metadata diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex new file mode 100644 index 0000000..abd70ff --- /dev/null +++ b/reproduce/software/bibtex/galsim.tex @@ -0,0 +1,27 @@ +%% Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% +%% Copying and distribution of this file, with or without modification, +%% are permitted in any medium without royalty provided the copyright +%% notice and this notice are preserved. This file is offered as-is, +%% without any warranty. + +@ARTICLE{galsim, + author = {{Rowe}, B.~T.~P. and {Jarvis}, M. and {Mandelbaum}, R. and + {Bernstein}, G.~M. and {Bosch}, J. and {Simet}, M. and {Meyers}, J.~E. and + {Kacprzak}, T. and {Nakajima}, R. and {Zuntz}, J. and {Miyatake}, H. and + {Dietrich}, J.~P. and {Armstrong}, R. and {Melchior}, P. and + {Gill}, M.~S.~S.}, + title = "{GALSIM: The modular galaxy image simulation toolkit}", + journal = {Astronomy and Computing}, + keywords = {Methods: data analysis, Techniques: image processing, Gravitational lensing, Cosmology: observations, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, 85-04}, + year = "2015", + month = "Apr", + volume = {10}, + pages = {121-150}, + doi = {10.1016/j.ascom.2015.02.002}, +archivePrefix = {arXiv}, + eprint = {1407.7676}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015A&C....10..121R}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.mk index 39c8a7f..d1b900d 100644 --- a/reproduce/software/config/installation/checksums.mk +++ b/reproduce/software/config/installation/checksums.mk @@ -141,19 +141,28 @@ chardet-checksum = 61a03b23447a2bfe52ceed4dd1b9afdb5784da1933a623776883ee9f297e3 cryptography-checksum = f14319e24d9dca52e74548cada5b78a6235f089ef875dbff4799e862f94da8b087f1b6e03e84dcef9fc7d7693c4a349c5f0cd54b8535806da777420ce8757d39 cycler-checksum = b7d2ba19861ffaf4dea0444bfe68b5a6264a022d7b3f02c9ff5e5859e3901de12a90f8dc7469e995e09c418515b3df55dbf05a0cfe5368d40790a2c878a74819 cython-checksum = bb8095b438a7d2567b8b831628fbb32c02299c866e41113da62fb5a5d4982dc0df947a9f723a82c52086806435d8f3518e78a803166149d476f81e042a12494e +eigency-checksum = 1e7cdfc43071da5edba30a0d32cd655442b516f15c166b049a195d151dec8c20a2177ad69bed3bba4788a668fa25a4c551ef4990717ff98d5b2f407bffb214c8 entrypoints-checksum = aa1274362d3a4b00266103319ca51aa266605b4999c89a9d0673eb61bfae9e646cb0ec6b86c95544493f6fe048385a2c7641d64adca8f45815546fb1e663c858 +esutil-checksum = c1cf8e7912b16dc675fdc7195ecc2bbffcd156c1257b2df45afdf09cc487c49f2e18a66cd5520ab30c77e60abb8ca802e327075bdd0f23eb634cc4f5a7e974f3 +flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e +future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030 +galsim-checksum = 11ecbfb9628cf85a4c25024c6f3a34bbdadf522f64e4e93e6428b545c65a48906a05eb7774d0faaacf52a48dddfd599bfc7cc7252ca854a18c3930f116533a3c h5py-checksum = 73b1f59e3e2b3eceebf7b97e49bd8f5199afafd7ef29917af05ff8415c2f2129a5c59db9658944370c9bcf8fc04ab26948ee27fc6fd948a22d19cace1ce8c853 html5lib-checksum = 35939b4450893864da04e735ee5e0addacf1dd34bae6a6909c76572abf6bfded446a78a713dfde91c1485ba45867d7abeb6a45cf0545c16ea968707be7de5dd2 idna-checksum = 8ca5cfe6350c51250bafdac7c6e4ddd54c4a5d6bf7acbcef896760a759868c8e9df1fdf550121d8512fa3eb316dcf031ec6058e03b4f66eadee21b63e2187d33 jeepney-checksum = 43083994a7c6af84a5a68d3ff8f6dc4d9129ce9fa55517838fb62d9f62bb78bdf52067649d0b95d08d689b7d7475cb9b2a956662e265a776ad42dcf4ccc0ab63 keyring-checksum = 3863f2cd89131d7e927e55691b4eb4b7c2599af189525293d0948aef5215efbbbd74d45db3cd4885ba5b18a79f0fa0b0edc3783a020a6702f6a6fb7ed86b2cf2 kiwisolver-checksum = 80ed3d7429a2ed4944aa09766bebac2709a3a0e0a184ff414f04bf3c7ec3034ea7d0f70dff319922b870dedaf13d64fc87eff86a82e720ec93a2510885ad738d +lsstdesccoord-checksum = a66b8b702cd8122f0c8aee05abe0fc0c6299f8bdb99b151f54bd7ad7430d6bc9f843f7294a7f08f3ce9f8606ea0ced0796a63b79cc8a53ae73068b691e2e6871 matplotlib-checksum = d44729028b91523c7ed2659e7ce7e9c2022ff322c3804e1ca16c9f64038f21d63ebf74a4da4239605cfb9c65729bf519360ac7f2a25dc70daa6fdcfa9c610c31 mpi4py-checksum = 0a18332fd45e8e80b8dab0761fbaa30444a0d55776af7a2333be17ade827e92d04ac5bb8619ce26937142f344f75de0e5ef6dcb7502f33389716aa9482ddf5ab mpmath-checksum = 58c69a801f65d73cc0eeb0d2c79277ed638568c656e7213d06ab4709c218aac908b2752377139010bed0e91bbfff01d129c60835ff0a928ba1185aded6de7c0a numpy-checksum = 3f7691de2b3c5423b9bf55f51ba961bf9931b13c59da80f406a1b50fcf1aa4174db948eb7e450c851c98eb7406f8b7da373df48fb07b0e577638360affad40ee pip-checksum = c6e13da3a57462371d32982c80575c5181592f5c6a8e70d60ec879e689442f4ad468e7aef97eb58c9da50a5a770385aa35e701eefd713a8e9fafeb12e11d956b +pybind11-checksum = 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ec7da86203572582f883a4686acf8a732a2de4f396d809057eb51b2c60dbca5623a7fa90c2c0618c281a2282c60841739bd837731a51cc876f4ff369297f2f81 diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk index 54e1f2e..20e6632 100644 --- a/reproduce/software/config/installation/versions.mk +++ b/reproduce/software/config/installation/versions.mk @@ -136,19 +136,28 @@ chardet-version = 3.0.4 cryptography-version = 2.6.1 cycler-version = 0.10.0 cython-version = 0.29.6 +eigency-version = 1.77 entrypoints-version = 0.3 +esutil-version = 0.6.4 +flake8-version = 3.7.8 +future-version = 0.18.1 +galsim-version = 2.2.1 h5py-version = 2.9.0 html5lib-version = 1.0.1 idna-version = 2.8 jeepney-version = 0.4 keyring-version = 18.0.0 kiwisolver-version = 1.0.1 +lsstdesccoord-version = 1.2.0 matplotlib-version = 3.1.1 mpi4py-version = 3.0.2 mpmath-version = 1.1.0 numpy-version = 1.17.2 pip-version = 19.0.2 +pycodestyle-version = 2.5.0 pycparser-version = 2.19 +pyflakes-version = 2.1.1 +pybind11-version = 2.4.3 pyparsing-version = 2.3.1 pypkgconfig-version = 1.5.1 python-dateutil-version = 2.8.0 diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 9cf99e5..b7cbc9b 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -44,6 +44,10 @@ export MPI_PYTHON_SITEARCH := export MPI_PYTHON2_SITEARCH := export MPI_PYTHON3_SITEARCH := +# Python-specific installation directories. +python-major-version = $(shell echo $(python-version) | awk 'BEGIN{FS="."} \ + {printf "%d.%d\n", $$1, $$2}') + @@ -68,7 +72,12 @@ pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ cryptography-$(cryptography-version).tar.gz \ cycler-$(cycler-version).tar.gz \ cython-$(cython-version).tar.gz \ + eigency-$(eigency-version).tar.gz \ + esutil-$(esutil-version).tar.gz \ entrypoints-$(entrypoints-version).tar.gz \ + flake8-$(flake8-version).tar.gz \ + future-$(future-version).tar.gz \ + galsim-$(galsim-version).tar.gz \ h5py-$(h5py-version).tar.gz \ html5lib-$(html5lib-version).tar.gz \ idna-$(idna-version).tar.gz \ @@ -76,13 +85,17 @@ pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ kiwisolver-$(kiwisolver-version).tar.gz \ keyring-$(keyring-version).tar.gz \ libffi-$(libffi-version).tar.gz \ + lsstdesccoord-$(lsstdesccoord-version).tar.gz \ matplotlib-$(matplotlib-version).tar.gz \ mpi4py-$(mpi4py-version).tar.gz \ mpmath-$(mpmath-version).tar.gz \ numpy-$(numpy-version).zip \ pkgconfig-$(pypkgconfig-version).tar.gz \ pip-$(pip-version).tar.gz \ + pybind11-$(pybind11-version).tar.gz \ + pycodestyle-$(pycodestyle-version).tar.gz \ pycparser-$(pycparser-version).tar.gz \ + pyflakes-$(pyflakes-version).tar.gz \ python-$(python-version).tar.gz \ python-dateutil-$(python-dateutil-version).tar.gz \ pyparsing-$(pyparsing-version).tar.gz \ @@ -131,21 +144,31 @@ $(pytarballs): $(tdir)/%: # that have non-standard filenames (differing from our archived # tarball names) are treated first, then the standard ones. mergenames=1 - if [ $$n = cython ]; then + if [ $$n = cython ]; then mergenames=0 c=$(cython-checksum) hash=36/da/fcb979fc8cb486a67a013d6aefefbb95a3e19e67e49dff8a35e014046c5e h=$(pytopurl)/$$hash/Cython-$(cython-version).tar.gz - elif [ $$n = python ]; then + elif [ $$n = galsim ]; then + mergenames=0 + c=$(galsim-checksum) + hash=8f/3b/bbc7cff7590d3624d528564f08745f071e316c67fce154ad38210833c103 + h=$(pytopurl)/$$hash/GalSim-$(galsim-version).tar.gz + elif [ $$n = lsstdesccoord ]; then + mergenames=0 + c=$(lsstdesccoord-checksum) + hash=9d/39/ad17697571c9aed36d20ed9ae0a135e3a734fb7f15a8605f92bf27c3b02c + h=$(pytopurl)/$$hash/LSSTDESC.Coord-$(lsstdesccoord-version).tar.gz + elif [ $$n = python ]; then mergenames=0 c=$(python-checksum) h=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz - elif [ $$n = pyyaml ]; then + elif [ $$n = pyyaml ]; then mergenames=0 c=$(pyyaml-checksum) hash=9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d h=$(pytopurl)/$$hash/PyYAML-$(pyyaml-version).tar.gz - elif [ $$n = libffi ]; then + elif [ $$n = libffi ]; then mergenames=0 c=$(libffi-checksum) h=ftp://sourceware.org/pub/libffi/libffi-$(libffi-version).tar.gz @@ -163,7 +186,11 @@ $(pytarballs): $(tdir)/%: elif [ $$n = chardet ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d; c=$(chardet-checksum) elif [ $$n = cryptography ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449; c=$(cryptography-checksum) elif [ $$n = cycler ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488; c=$(cycler-checksum) + elif [ $$n = eigency ]; then h=fb/6e/bc4359fbfb0bb0b588ec328251b0d0836bdd7c0a4c568959ea06df023e18; c=$(eigency-checksum) elif [ $$n = entrypoints ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c; c=$(entrypoints-checksum) + elif [ $$n = esutil ]; then h=5b/91/77e38282fd3d47b55e351544ab179eb209b309a8d2d40f8cdb6241beda00; c=$(esutil-checksum) + elif [ $$n = flake ]; then h=8d/a7/99222c9200af533c1ecb1120d99adbd1c033b57296ac5cb39d121db007a8; c=$(flake8-checksum) + elif [ $$n = future ]; then h=3f/bf/57733d44afd0cf67580658507bd11d3ec629612d5e0e432beb4b8f6fbb04; c=$(future-checksum) elif [ $$n = h5py ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec; c=$(h5py-checksum) elif [ $$n = html ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f; c=$(html5lib-checksum) elif [ $$n = idna ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7; c=$(idna-checksum) @@ -176,7 +203,10 @@ $(pytarballs): $(tdir)/%: elif [ $$n = numpy ]; then h=ac/36/325b27ef698684c38b1fe2e546e2e7ef9cecd7037bcdb35c87efec4356af; c=$(numpy-checksum) elif [ $$n = pip ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af; c=$(pip-checksum) elif [ $$n = pkgconfig ]; then h=6e/a9/ff67ef67217dfdf2aca847685fe789f82b931a6957a3deac861297585db6; c=$(pypkgconfig-checksum) + elif [ $$n = pybind ]; then h=aa/91/deb6743e79e22ab01502296570b39b8404f10cc507a6692d612a7fee8d51; c=$(pybind11-checksum) + elif [ $$n = pycodestyle ]; then h=1c/d1/41294da5915f4cae7f4b388cea6c2cd0d6cd53039788635f6875dfe8c72f; c=$(pycodestyle-checksum) elif [ $$n = pycparser ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a; c=$(pycparser-checksum) + elif [ $$n = pyflakes ]; then h=52/64/87303747635c2988fcaef18af54bfdec925b6ea3b80bcd28aaca5ba41c9e; c=$(pyflakes-checksum) elif [ $$n = pyparsing ]; then h=b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc; c=$(pyparsing-checksum) elif [ $$n = dateutil ]; then h=ad/99/5b2e99737edeb28c71bcbec5b5dda19d0d9ef3ca3e92e3e925e7c0bb364c; c=$(python-dateutil-checksum) elif [ $$n = requests ]; then h=52/2c/514e4ac25da2b08ca5a464c50463682126385c4272c18193876e91f4bc38; c=$(requests-checksum) @@ -267,11 +297,9 @@ $(ibidir)/python: $(tdir)/python-$(python-version).tar.gz \ --without-ensurepip \ --with-system-ffi \ --enable-shared) \ - && v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \ - {printf "%d.%d\n", $$1, $$2}') \ - && ln -sf $(ildir)/python$$v $(ildir)/python \ - && ln -sf $(ibdir)/python$$v $(ibdir)/python \ - && ln -sf $(iidir)/python$$v"m" $(iidir)/python$$v \ + && ln -sf $(ildir)/python$(python-major-version) $(ildir)/python \ + && ln -sf $(ibdir)/python$(python-major-version) $(ibdir)/python \ + && ln -sf $(iidir)/python$(python-major-version)m $(iidir)/python(python-major-version) \ && rm -rf $(ipydir) \ && mkdir $(ipydir) \ && echo "Python $(python-version)" > $@ @@ -291,6 +319,7 @@ $(ibidir)/python: $(tdir)/python-$(python-version).tar.gz \ # 3) Unpacked directory name after unpacking the tarball # 4) site.cfg file (optional) # 5) Official software name.(for paper). +# 6) Manual step after installation. pybuild = cd $(ddir); rm -rf $(3); \ if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \ cd $(3); \ @@ -299,8 +328,11 @@ pybuild = cd $(ddir); rm -rf $(3); \ -e 's|@INCDIR[@]|'"$(idir)/include"'|' \ $(4) > site.cfg; \ fi; \ - python setup.py build \ + if [ x"$(6)" = x ]; then after="echo no after"; \ + else after="$(6)"; fi \ + && python setup.py build \ && python setup.py install \ + && $$after \ && cd .. \ && rm -rf $(3) \ && echo "$(5)" > $@ @@ -374,11 +406,42 @@ $(ipydir)/cython: $(tdir)/cython-$(cython-version).tar.gz \ && cp $(dtexdir)/cython.tex $(ictdir)/ \ && echo "Cython $(cython-version) \citep{cython2011}" > $@ +$(ipydir)/esutil: $(tdir)/esutil-$(esutil-version).tar.gz \ + $(ipydir)/numpy + $(call pybuild, tar xf, $<, esutil-$(esutil-version), ,\ + esutil $(esutil-version)) + +$(ipydir)/eigency: $(tdir)/eigency-$(eigency-version).tar.gz \ + $(ibidir)/eigen + $(call pybuild, tar xf, $<, eigency-$(eigency-version), ,\ + eigency $(eigency-version)) + $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \ $(ipydir)/setuptools $(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version), ,\ EntryPoints $(entrypoints-version)) +$(ipydir)/flake8: $(tdir)/flake8-$(flake8-version).tar.gz \ + $(ipydir)/pycodestyle \ + $(ipydir)/pyflakes + $(call pybuild, tar xf, $<, flake8-$(flake8-version), ,\ + Flake8 $(flake8-version)) + +$(ipydir)/future: $(tdir)/future-$(future-version).tar.gz \ + $(ipydir)/setuptools + $(call pybuild, tar xf, $<, future-$(future-version), ,\ + Future $(future-version)) + +$(ipydir)/galsim: $(tdir)/galsim-$(galsim-version).tar.gz \ + $(ipydir)/lsstdesccoord \ + $(ipydir)/pybind11 \ + $(ipydir)/astropy \ + $(ipydir)/eigency \ + $(ipydir)/future + $(call pybuild, tar xf, $<, GalSim-$(galsim-version), ,) \ + && cp $(dtexdir)/galsim.tex $(ictdir)/ \ + && echo "Galsim $(galsim-version) \citep{galsim}" > $@ + $(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \ $(ipydir)/pypkgconfig \ $(ipydir)/setuptools \ @@ -420,6 +483,11 @@ $(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz \ $(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version), ,\ Kiwisolver $(kiwisolver-version)) +$(ipydir)/lsstdesccoord: $(tdir)/lsstdesccoord-$(lsstdesccoord-version).tar.gz \ + $(ipydir)/setuptools + $(call pybuild, tar xf, $<, LSSTDESC.Coord-$(lsstdesccoord-version), ,\ + LSSTDESC.Coord $(lsstdesccoord-version)) + $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \ $(ipydir)/python-dateutil \ $(ibidir)/ghostscript \ @@ -466,21 +534,39 @@ $(ibidir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \ $(call pybuild, tar xf, $<, pip-$(pip-version), ,\ PiP $(pip-version)) -$(ipydir)/pypkgconfig: $(tdir)/pkgconfig-$(pypkgconfig-version).tar.gz \ +$(ipydir)/pycodestyle: $(tdir)/pycodestyle-$(pycodestyle-version).tar.gz \ $(ipydir)/setuptools - $(call pybuild, tar xf, $<, pkgconfig-$(pypkgconfig-version), , - pkgconfig $(pypkgconfig-version)) + $(call pybuild, tar xf, $<, pycodestyle-$(pycodestyle-version), ,\ + pycodestyle $(pycodestyle-version)) + +$(ipydir)/pybind11: $(tdir)/pybind11-$(pybind11-version).tar.gz \ + $(ipydir)/setuptools \ + $(ibidir)/boost \ + $(ibidir)/eigen + $(call pybuild, tar xf, $<, pybind11-$(pybind11-version), ,\ + pybind11 $(pybind11-version), + cp -r include/pybind11 $(iidir)/python$(python-major-version)m/) $(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \ $(ipydir)/setuptools $(call pybuild, tar xf, $<, pycparser-$(pycparser-version), ,\ pycparser $(pycparser-version)) +$(ipydir)/pyflakes: $(tdir)/pyflakes-$(pyflakes-version).tar.gz \ + $(ipydir)/setuptools + $(call pybuild, tar xf, $<, pyflakes-$(pyflakes-version), ,\ + pyflakes $(pyflakes-version)) + $(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \ $(ipydir)/setuptools $(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version), ,\ PyParsing $(pyparsing-version)) +$(ipydir)/pypkgconfig: $(tdir)/pkgconfig-$(pypkgconfig-version).tar.gz \ + $(ipydir)/setuptools + $(call pybuild, tar xf, $<, pkgconfig-$(pypkgconfig-version), , + pkgconfig $(pypkgconfig-version)) + $(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz \ $(ipydir)/setuptools_scm \ $(ipydir)/six |