diff options
| -rw-r--r-- | .file-metadata | bin | 3993 -> 3927 bytes | |||
| -rw-r--r-- | paper.tex | 40 | ||||
| -rw-r--r-- | reproduce/config/pipeline/dependency-versions.mk | 1 | ||||
| -rw-r--r-- | reproduce/src/make/dependencies-python.mk | 63 | ||||
| -rw-r--r-- | reproduce/src/make/initialize.mk | 15 |
5 files changed, 71 insertions, 48 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex b56ff6c..5a4f942 100644 --- a/.file-metadata +++ b/.file-metadata @@ -202,23 +202,33 @@ SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P. The following free software tools were also critical component of this -research (in alphabetical order): Bzip2 \bziptwoversion, CFITSIO -\cfitsioversion, CMake \cmakeversion, cURL \curlversion, Discoteq flock -\flockversion, Git \gitversion, GNU Astronomy Utilities \gnuastroversion, -GNU AWK \gawkversion, GNU Bash \bashversion, GNU Coreutils -\coreutilsversion, GNU Diffutils \diffutilsversion, GNU Findutils -\findutilsversion, GNU Grep \grepversion, GNU Gzip \gzipversion, GNU -Libtool \libtoolversion, GNU Make \makeversion, GNU NCURSES -\ncursesversion, GNU Readline \readlineversion, GNU Sed \sedversion, GNU -Scientific Library (GSL) \gslversion, GNU Tar \tarversion, GNU Wget -\wgetversion, GNU Which \whichversion, Lzip \lzipversion, GPL Ghostscript -\ghostscriptversion, Libbsd \libbsdversion, Libgit2 \libgitwoversion, -Libjpeg \libjpegversion, Libtiff \libtiffversion, Metastore (forked) -\metastoreversion, OpenSSL \opensslversion, Pkg-config \pkgconfigversion, +research (in alphabetical order): ATLAS \atlasversion, Bzip2 +\bziptwoversion, CFITSIO \cfitsioversion, CMake \cmakeversion, cURL +\curlversion, Discoteq flock \flockversion, FreeType \freetypeversion, Git +\gitversion, GNU Astronomy Utilities \gnuastroversion, GNU AWK \gawkversion, +GNU Bash \bashversion, GNU Coreutils \coreutilsversion, GNU Diffutils +\diffutilsversion, GNU Findutils \findutilsversion, GNU Grep \grepversion, +GNU Gzip \gzipversion, GNU Libtool \libtoolversion, GNU Make \makeversion, +GNU NCURSES \ncursesversion, GNU Readline \readlineversion, GNU Sed +\sedversion, GNU Scientific Library (GSL) \gslversion, GNU Tar \tarversion, +GNU Wget \wgetversion, GNU Which \whichversion, Lapack \lapackversion, Lzip +\lzipversion, GPL Ghostscript \ghostscriptversion, Libbsd \libbsdversion, +Libgit2 \libgitwoversion, Libjpeg \libjpegversion, Libpng \libpngversion, +Libtiff \libtiffversion, Metastore (forked) \metastoreversion, OpenSSL +\opensslversion, Patchelf \patchelfversion, Pkg-config \pkgconfigversion, Unzip \unzipversion, WCSLIB \wcslibversion, XZ Utils \xzversion, Zip \zipversion, and ZLib \zlibversion. We use Python {\pythonversion} with the -following packages: Numpy {\numpyversion} and Astropy {\astropyversion} -\citep{astropy2013, astropy2018}. The final paper was produced with +following packages: Asn1crypto \asncryptoversion, Astroquery +\astroqueryversion, Astropy {\astropyversion} \citep{astropy2013, +astropy2018}, BeautifulSoup \beautifulsoupversion, Certifi \certifiversion, +Cffi \cffiversion, Chardet \chardetversion, Cryptography +\cryptographyversion, Cycler \cyclerversion, EntryPoints +\entrypointsversion, h5py \hpyversion, html5ib \htmlfivelibversion, idna +\idnaversion, Jeepney \jeepneyversion, Kiwisolver \kiwisolverversion, +keyring \keyringversion, Matplotlib \matplotlibversion, Numpy \numpyversion + + + The final paper was produced with \TeX{} Live \texliveversion, using the following packages: \TeX{} \textexversion, EC \texecversion, NewTX \texnewtxversion, Fontaxes \texfontaxesversion, Keyval, \texxkeyvalversion, Etoolbox diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk index 79ecdce..211ebbd 100644 --- a/reproduce/config/pipeline/dependency-versions.mk +++ b/reproduce/config/pipeline/dependency-versions.mk @@ -76,6 +76,7 @@ chardet-version = 3.0.4 cryptography-version = 2.6.1 cycler-version = 0.10.0 entrypoints-version = 0.3 +h5py-version = 2.9.0 html5lib-version = 1.0.1 idna-version = 2.8 jeepney-version = 0.4 diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk index e4c2324..54d3a56 100644 --- a/reproduce/src/make/dependencies-python.mk +++ b/reproduce/src/make/dependencies-python.mk @@ -116,6 +116,7 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ cryptography-$(cryptography-version).tar.gz \ cycler-$(cycler-version).tar.gz \ entrypoints-$(entrypoints-version).tar.gz \ + h5py-$(h5py-version).tar.gz \ html5lib-$(html5lib-version).tar.gz \ idna-$(idna-version).tar.gz \ jeepney-$(jeepney-version).tar.gz \ @@ -157,7 +158,10 @@ $(tarballs): $(tdir)/%: # because the tokenization above will produce `python' as the # first string. if [ $* = python-dateutil-$(python-dateutil-version).tar.gz ]; then - n=dateutil + n=dateutil + elif [ $* = h5py-$(h5py-version).tar.gz ]; then + n=h5py + # elif [ $* = strange-tarball5name-version.tar.gz ]; then # n=strange5-name else @@ -191,13 +195,14 @@ $(tarballs): $(tdir)/%: elif [ $$n = cryptography ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449 elif [ $$n = cycler ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488 elif [ $$n = entrypoints ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c + elif [ $$n = h5py ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec elif [ $$n = html ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f elif [ $$n = idna ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7 elif [ $$n = jeepney ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263 elif [ $$n = keyring ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2 elif [ $$n = kiwisolver ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864 elif [ $$n = matplotlib ]; then h=89/0c/653aec68e9cfb775c4fbae8f71011206e5e7fe4d60fcf01ea1a9d3bc957f - elif [ $$n = numpy ]; then h=2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c + elif [ $$n = numpy ]; then h=cf/8d/6345b4f32b37945fedc1e027e83970005fc9c699068d2f566b82826515f2 elif [ $$n = pip ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af elif [ $$n = pycparser ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a elif [ $$n = pyparsing ]; then h=b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc @@ -212,7 +217,7 @@ $(tarballs): $(tdir)/%: elif [ $$n = urllib ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1 elif [ $$n = virtualenv ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688 elif [ $$n = webencodings ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47 -# elif [ $$n = strange5-name ]; then h=XXXXX +# elif [ $$n = strange5-name ]; then h=XXXXX else echo; echo; echo; echo "'$$n' not recognized as a dependency name to download." @@ -310,7 +315,7 @@ $(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz \ # # All the necessary Python modules go here. $(ipydir)/asn1crypto: $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, asn1crypto-$(asn1crypto-version)) $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \ @@ -323,6 +328,7 @@ $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \ $(call pybuild, tar xf, $<, astroquery-$(astroquery-version)) $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \ + $(ipydir)/h5py \ $(ipydir)/numpy $(call pybuild, tar xf, $<, astropy-$(astropy-version)) @@ -331,80 +337,83 @@ $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.g $(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version)) $(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, certifi-$(certifi-version)) $(ipydir)/cffi: $(tdir)/cffi-$(cffi-version).tar.gz \ - $(ipydir)/pycparser \ - $(ilidir)/libffi + $(ilidir)/libffi \ + $(ipydir)/pycparser $(call pybuild, tar xf, $<, cffi-$(cffi-version)) $(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, chardet-$(chardet-version)) $(ipydir)/cryptography: $(tdir)/cryptography-$(cryptography-version).tar.gz \ - $(ipydir)/cffi \ - $(ipydir)/asn1crypto + $(ipydir)/asn1crypto \ + $(ipydir)/cffi $(call pybuild, tar xf, $<, cryptography-$(cryptography-version)) $(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \ - $(ipydir)/six + $(ipydir)/six $(call pybuild, tar xf, $<, cycler-$(cycler-version)) $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version)) +$(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \ + $(ipydir)/setuptools + $(call pybuild, tar xf, $<, h5py-$(h5py-version)) + $(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz \ $(ipydir)/six \ $(ipydir)/webencodings $(call pybuild, tar xf, $<, html5lib-$(html5lib-version)) $(ipydir)/idna: $(tdir)/idna-$(idna-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, idna-$(idna-version)) $(ipydir)/jeepney: $(tdir)/jeepney-$(jeepney-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, jeepney-$(jeepney-version)) $(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz \ - $(ipydir)/setuptools_scm \ + $(ipydir)/entrypoints \ $(ipydir)/secretstorage \ - $(ipydir)/entrypoints + $(ipydir)/setuptools_scm $(call pybuild, tar xf, $<, keyring-$(keyring-version)) $(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz \ $(ipydir)/setuptools $(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version)) - $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \ $(ipydir)/cycler \ $(ilidir)/freetype \ + $(ipydir)/kiwisolver \ $(ipydir)/numpy \ $(ipydir)/pyparsing \ - $(ipydir)/python-dateutil \ - $(ipydir)/kiwisolver + $(ipydir)/python-dateutil $(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \ - $(ibdir)/python3 + $(ipydir)/setuptools export LDFLAGS="$$LDFLAGS -shared"; \ conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \ $(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf) $(ibdir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pip-$(pip-version)) $(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pycparser-$(pycparser-version)) $(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version)) $(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz \ @@ -440,17 +449,17 @@ $(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.g $(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version)) $(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, six-$(six-version)) $(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version)) $(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, urllib3-$(urllib3-version)) $(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, webencodings-$(webencodings-version)) diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk index 545fcc1..66e7c77 100644 --- a/reproduce/src/make/initialize.mk +++ b/reproduce/src/make/initialize.mk @@ -369,10 +369,6 @@ $(mtexdir)/initialize.tex: | $(mtexdir) echo "\newcommand{\\grepversion}{$(grep-version)}" >> $@ echo "\newcommand{\\gzipversion}{$(gzip-version)}" >> $@ echo "\newcommand{\\islversion}{$(isl-version)}" >> $@ - echo "\newcommand{\\libbsdversion}{$(libbsd-version)}" >> $@ - echo "\newcommand{\\libffiversion}{$(libffi-version)}" >> $@ - echo "\newcommand{\\libpngversion}{$(libpng-version)}" >> $@ - echo "\newcommand{\\libtoolversion}{$(libtool-version)}" >> $@ echo "\newcommand{\\lzipversion}{$(lzip-version)}" >> $@ echo "\newcommand{\\makeversion}{$(make-version)}" >> $@ echo "\newcommand{\\metastoreversion}{$(metastore-version)}" >> $@ @@ -394,12 +390,18 @@ $(mtexdir)/initialize.tex: | $(mtexdir) echo "\newcommand{\\zipversion}{$(zip-version)}" >> $@ # Libraries. + echo "\newcommand{\\atlasversion}{$(cfitsio-version)}" >> $@ echo "\newcommand{\\cfitsioversion}{$(cfitsio-version)}" >> $@ echo "\newcommand{\\curlversion}{$(curl-version)}" >> $@ echo "\newcommand{\\gslversion}{$(gsl-version)}" >> $@ + echo "\newcommand{\\lapack}{$(lapack-version)}" >> $@ + echo "\newcommand{\\libbsdversion}{$(libbsd-version)}" >> $@ + echo "\newcommand{\\libffiversion}{$(libffi-version)}" >> $@ echo "\newcommand{\\libgittwoversion}{$(libgit2-version)}" >> $@ echo "\newcommand{\\libjpegversion}{$(libjpeg-version)}" >> $@ + echo "\newcommand{\\libpngversion}{$(libpng-version)}" >> $@ echo "\newcommand{\\libtiffversion}{$(libtiff-version)}" >> $@ + echo "\newcommand{\\libtoolversion}{$(libtool-version)}" >> $@ echo "\newcommand{\\wcslibversion}{$(wcslib-version)}" >> $@ echo "\newcommand{\\zlibversion}{$(zlib-version)}" >> $@ @@ -414,8 +416,9 @@ $(mtexdir)/initialize.tex: | $(mtexdir) echo "\newcommand{\\cryptographyversion}{$(cryptography-version)}" >> $@ echo "\newcommand{\\cyclerversion}{$(cycler-version)}" >> $@ echo "\newcommand{\\entrypointsversion}{$(entrypoints-version)}" >> $@ + echo "\newcommand{\\hpyversion}{$(h5py-version)}" >> $@ echo "\newcommand{\\htmlfivelibversion}{$(html5lib-version)}" >> $@ - echo "\newcommand{\\indaversion}{$(idna-version)}" >> $@ + echo "\newcommand{\\idaversion}{$(idna-version)}" >> $@ echo "\newcommand{\\jeepneyversion}{$(jeepney-version)}" >> $@ echo "\newcommand{\\kiwisolverversion}{$(kiwisolver-version)}" >> $@ echo "\newcommand{\\keyringversion}{$(keyring-version)}" >> $@ @@ -433,7 +436,7 @@ $(mtexdir)/initialize.tex: | $(mtexdir) echo "\newcommand{\\sixversion}{$(six-version)}" >> $@ echo "\newcommand{\\soupsieveversion}{$(soupsieve-version)}" >> $@ echo "\newcommand{\\urllibthreeversion}{$(urllib3-version)}" >> $@ - echo "\newcommand{\\virtualenvversion}{$(virtualenv-version)}" >> $@ +# echo "\newcommand{\\virtualenvversion}{$(virtualenv-version)}" >> $@ echo "\newcommand{\\webencodingsversion}{$(webencodings-version)}" >> $@ # TeX package versions |