diff options
| -rw-r--r-- | .file-metadata | bin | 5439 -> 6236 bytes | |||
| -rwxr-xr-x | configure | 1 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 6 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 8 | ||||
| -rw-r--r-- | reproduce/software/bibtex/tides.tex | 19 | ||||
| -rw-r--r-- | reproduce/software/config/installation/texlive.mk | 2 | ||||
| -rw-r--r-- | reproduce/software/config/installation/versions.mk | 1 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 5 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 221 |
9 files changed, 157 insertions, 106 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex f688e62..ae36840 100644 --- a/.file-metadata +++ b/.file-metadata @@ -1140,6 +1140,7 @@ function prepare_name_version() { # Put them all in one paragraph. .local/bin/cat $@ \ | .local/bin/sort \ + | sed 's/_/\\_/' \ | .local/bin/awk 'NF>0 { \ c++; \ if(c==1) \ diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index fe7b5ea..d176489 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -103,8 +103,13 @@ curdir := $(shell echo $$(pwd)) # itself and doesn't use the local system's default tools. With these # environment variables, we are setting it to prefer the software we have # build here. +# +# `TEXINPUTS': we have to remove all possible user-specified directories to +# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'), +# we are also going to overwrite `TEXINPUTS' just before `pdflatex'. .ONESHELL: .SHELLFLAGS = -ec +export TEXINPUTS := export CCACHE_DISABLE := 1 export PATH := $(installdir)/bin export LD_LIBRARY_PATH := $(installdir)/lib @@ -115,7 +120,6 @@ export CPPFLAGS := -I$(installdir)/include - # Python enviroment # ----------------- # diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 34d88a4..c17028a 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -98,10 +98,10 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # We'll run LaTeX first to generate the `.bcf' file (necessary # for `biber') and then run `biber' to generate the `.bbl' file. - p=$$(pwd); - export TEXINPUTS=$$p:$$TEXINPUTS; + p=$$(pwd) + export TEXINPUTS=$$p: cd $(texbdir); - pdflatex -shell-escape -halt-on-error $$p/paper.tex; + pdflatex -shell-escape -halt-on-error $$p/paper.tex biber paper fi @@ -126,7 +126,7 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # Go into the top TeX build directory and make the paper. p=$$(pwd) - export TEXINPUTS=$$p:$$TEXINPUTS + export TEXINPUTS=$$p: cd $(texbdir) pdflatex -shell-escape -halt-on-error $$p/paper.tex diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex new file mode 100644 index 0000000..f902da0 --- /dev/null +++ b/reproduce/software/bibtex/tides.tex @@ -0,0 +1,19 @@ +%% 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{tides, + author = {{Abad}, A. and {Barrio}, R. and {Belsa}, F. and {Rodriguez}, M}, + title = "{Algorithm 924: TIDES, a Taylor Series Integrator for Differential EquationS}", + journal = {ACM TOMS}, + year = 2012, + month = nov, + volume = 39, + eid = {5}, + pages = {5:1}, + doi = {10.1145/2382585.2382590}, + keywords = {Taylor series method, automatic differentiation, high precision, numerical integration of ODEs, variational equations}, +} diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive.mk index d68f94e..f0c7755 100644 --- a/reproduce/software/config/installation/texlive.mk +++ b/reproduce/software/config/installation/texlive.mk @@ -19,4 +19,4 @@ texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xcolor \ setspace caption footmisc datetime fmtcount titlesec \ preprint ulem biblatex biber logreq pgf pgfplots fp \ - courier tex-gyre txfonts times csquotes + courier tex-gyre txfonts times csquotes kastrup diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk index 3bc95fc..61f7879 100644 --- a/reproduce/software/config/installation/versions.mk +++ b/reproduce/software/config/installation/versions.mk @@ -99,6 +99,7 @@ scons-version = 3.0.5 sextractor-version = 2.25.0 swarp-version = 2.38.0 swig-version = 3.0.12 +tides-version = 2.0 yaml-version = 0.2.2 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index e22879b..f0083d6 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -844,8 +844,11 @@ $(ibidir)/libiconv: $(tdir)/libiconv-$(libiconv-version).tar.gz \ $(ibidir)/git: $(tdir)/git-$(git-version).tar.xz \ $(ibidir)/libiconv \ $(ibidir)/curl # Coreutils, so Git is built after it. + if [ x$(on_mac_os) = xyes ]; then \ + export LDFLAGS="$$LDFLAGS -lcharset"; \ + fi; \ $(call gbuild, $<, git-$(git-version), static, \ - --without-tcltk --with-shell=$(ibdir)/bash \ + --without-tcltk --with-shell=$(ibdir)/bash \ --with-iconv=$(idir), V=1) \ && echo "Git $(git-version)" > $@ diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index daad4f9..90fc060 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -135,6 +135,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz \ sextractor-$(sextractor-version).tar.lz \ swarp-$(swarp-version).tar.gz \ swig-$(swig-version).tar.gz \ + tides-$(tides-version).tar.gz \ tiff-$(libtiff-version).tar.gz \ wcslib-$(wcslib-version).tar.bz2 \ yaml-$(yaml-version).tar.gz \ @@ -202,6 +203,7 @@ $(tarballs): $(tdir)/%: | $(lockdir) elif [ $$n = sextractor ]; then w=http://akhlaghi.org/src elif [ $$n = swarp ]; then w=https://www.astromatic.net/download/swarp elif [ $$n = swig ]; then w=https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) + elif [ $$n = tides ]; then w=http://akhlaghi.org/src elif [ $$n = tiff ]; then w=https://download.osgeo.org/libtiff elif [ $$n = wcslib ]; then w=ftp://ftp.atnf.csiro.au/pub/software/wcslib elif [ $$n = yaml ]; then w=pyyaml.org/download/libyaml @@ -234,6 +236,11 @@ $(tarballs): $(tdir)/%: | $(lockdir) + + + + + # Libraries # --------- # @@ -242,105 +249,6 @@ $(tarballs): $(tdir)/%: | $(lockdir) # libraries. Therefore, we can't use the easy `.a' suffix for static # libraries as targets and there are different conventions for shared # library names. -$(ibidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \ - $(ibidir)/curl - - # CFITSIO hard-codes '@rpath' inside the shared library on - # Mac systems. So we need to change it to our library - # installation path. It doesn't affect GNU/Linux, so we'll - # just do it in any case to keep things clean. - topdir=$(pwd); cd $(ddir); tar xf $< - customtar=cfitsio-$(cfitsio-version)-custom.tar.gz - cd cfitsio-$(cfitsio-version) - sed configure -e's|@rpath|$(ildir)|g' > configure_tmp - mv configure_tmp configure - chmod +x configure - cd .. - tar cf $$customtar cfitsio-$(cfitsio-version) - cd $$topdir - - # Continue the standard build on the customized tarball. - $(call gbuild, $$customtar, cfitsio-$(cfitsio-version), , \ - --enable-sse2 --enable-reentrant \ - --with-bzip2=$(idir), , make shared) \ - && rm $$customtar \ - && echo "CFITSIO $(cfitsio-version)" > $@ - -$(ibidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz \ - $(ibidir)/freetype \ - $(ibidir)/libpng \ - $(ibidir)/pixman - $(call gbuild, $<, cairo-$(cairo-version), static, \ - --with-x=no) \ - && echo "Cairo $(cairo-version)" > $@ - -$(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz - $(call gbuild, $<, gsl-$(gsl-version), static) \ - && echo "GNU Scientific Library $(gsl-version)" > $@ - -$(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz - # In order to build single and double precission libraries of - # `fftw', installation of `fftw' is done twice. First time is to - # build single precission float libraries and second time is for - # building the default double precission float libraries - $(call gbuild, $<, fftw-$(fftw-version), static, \ - --enable-shared enable-threads \ - --enable-single --enable-type-prefix) \ - && $(call gbuild, $<, fftw-$(fftw-version), static, \ - --enable-shared --enable-threads \ - --enable-type-prefix) \ - && cp $(dtexdir)/fftw.tex $(ictdir)/ \ - && echo "FFTW $(fftw-version) \citep{fftw}" > $@ - -# Freetype is necessary to install matplotlib -$(ibidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \ - $(ibidir)/libpng - $(call gbuild, $<, freetype-$(freetype-version), static) \ - && echo "FreeType $(freetype-version)" > $@ - -$(ibidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz \ - $(ibidir)/openmpi - export CC=mpicc; \ - export FC=mpif90; \ - $(call gbuild, $<, hdf5-$(hdf5-version), static, \ - --enable-parallel \ - --enable-fortran, -j$(numthreads) V=1) \ - && echo "HDF5 library $(hdf5-version)" > $@ - -$(ibidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz - $(call gbuild, $<, jpeg-9b, static) \ - && echo "Libjpeg $(libjpeg-version)" > $@ - -$(ibidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz - $(call gbuild, $<, libpng-$(libpng-version), static) \ - && echo "Libpng $(libpng-version)" > $@ - -$(ibidir)/libxml2: $(tdir)/libxml2-$(libxml2-version).tar.gz - # The libxml2 tarball also contains Python bindings which are built and - # installed to a system directory by default. If you don't need the Python - # bindings, the easiest solution is to compile without Python support: - # ./configure --without-python - # If you really need the Python bindings, try the - # --with-python-install-dir=DIR option - $(call gbuild, $<, libxml2-$(libxml2-version), static, \ - --without-python) \ - && echo "Libxml2 $(libxml2-version)" > $@ - -$(ibidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz - $(call gbuild, $<, pixman-$(pixman-version), static) \ - && echo "Pixman $(pixman-version)" > $@ - -$(ibidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \ - $(ibidir)/libjpeg - $(call gbuild, $<, tiff-$(libtiff-version), static, \ - --disable-webp --disable-zstd) \ - && echo "Libtiff $(libtiff-version)" > $@ - -$(ibidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz - $(call gbuild, $<, openmpi-$(openmpi-version), static, , \ - -j$(numthreads) V=1) \ - && echo "Open MPI $(openmpi-version)" > $@ - $(ibidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \ $(tdir)/lapack-$(lapack-version).tar.gz @@ -421,6 +329,96 @@ $(ibidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \ echo "ATLAS $(atlas-version)" > $@; \ fi +$(ibidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \ + $(ibidir)/curl + + # CFITSIO hard-codes '@rpath' inside the shared library on + # Mac systems. So we need to change it to our library + # installation path. It doesn't affect GNU/Linux, so we'll + # just do it in any case to keep things clean. + topdir=$(pwd); cd $(ddir); tar xf $< + customtar=cfitsio-$(cfitsio-version)-custom.tar.gz + cd cfitsio-$(cfitsio-version) + sed configure -e's|@rpath|$(ildir)|g' > configure_tmp + mv configure_tmp configure + chmod +x configure + cd .. + tar cf $$customtar cfitsio-$(cfitsio-version) + cd $$topdir + + # Continue the standard build on the customized tarball. + $(call gbuild, $$customtar, cfitsio-$(cfitsio-version), , \ + --enable-sse2 --enable-reentrant \ + --with-bzip2=$(idir), , make shared) \ + && rm $$customtar \ + && echo "CFITSIO $(cfitsio-version)" > $@ + +$(ibidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz \ + $(ibidir)/freetype \ + $(ibidir)/libpng \ + $(ibidir)/pixman + $(call gbuild, $<, cairo-$(cairo-version), static, \ + --with-x=no) \ + && echo "Cairo $(cairo-version)" > $@ + +$(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz + # In order to build single and double precission libraries of + # `fftw', installation of `fftw' is done twice. First time is to + # build single precission float libraries and second time is for + # building the default double precission float libraries + $(call gbuild, $<, fftw-$(fftw-version), static, \ + --enable-shared enable-threads \ + --enable-single --enable-type-prefix) \ + && $(call gbuild, $<, fftw-$(fftw-version), static, \ + --enable-shared --enable-threads \ + --enable-type-prefix) \ + && cp $(dtexdir)/fftw.tex $(ictdir)/ \ + && echo "FFTW $(fftw-version) \citep{fftw}" > $@ + +# Freetype is necessary to install matplotlib +$(ibidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \ + $(ibidir)/libpng + $(call gbuild, $<, freetype-$(freetype-version), static) \ + && echo "FreeType $(freetype-version)" > $@ + +$(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz + $(call gbuild, $<, gsl-$(gsl-version), static) \ + && echo "GNU Scientific Library $(gsl-version)" > $@ + +$(ibidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz \ + $(ibidir)/openmpi + export CC=mpicc; \ + export FC=mpif90; \ + $(call gbuild, $<, hdf5-$(hdf5-version), static, \ + --enable-parallel \ + --enable-fortran, -j$(numthreads) V=1) \ + && echo "HDF5 library $(hdf5-version)" > $@ + +$(ibidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz + $(call gbuild, $<, jpeg-9b, static) \ + && echo "Libjpeg $(libjpeg-version)" > $@ + +$(ibidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz + $(call gbuild, $<, libpng-$(libpng-version), static) \ + && echo "Libpng $(libpng-version)" > $@ + +$(ibidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \ + $(ibidir)/libjpeg + $(call gbuild, $<, tiff-$(libtiff-version), static, \ + --disable-webp --disable-zstd) \ + && echo "Libtiff $(libtiff-version)" > $@ + +$(ibidir)/libxml2: $(tdir)/libxml2-$(libxml2-version).tar.gz + # The libxml2 tarball also contains Python bindings which are built and + # installed to a system directory by default. If you don't need the Python + # bindings, the easiest solution is to compile without Python support: + # ./configure --without-python + # If you really need the Python bindings, try the + # --with-python-install-dir=DIR option + $(call gbuild, $<, libxml2-$(libxml2-version), static, \ + --without-python) \ + && echo "Libxml2 $(libxml2-version)" > $@ + $(ibidir)/openblas: $(tdir)/openblas-$(openblas-version).tar.gz if [ x$(on_mac_os) = xyes ]; then \ export CC=clang; \ @@ -434,12 +432,29 @@ $(ibidir)/openblas: $(tdir)/openblas-$(openblas-version).tar.gz && rm -rf OpenBLAS-$(openblas-version) \ && echo "OpenBLAS $(openblas-version)" > $@ +$(ibidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz + $(call gbuild, $<, openmpi-$(openmpi-version), static, , \ + -j$(numthreads) V=1) \ + && echo "Open MPI $(openmpi-version)" > $@ + +$(ibidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz + $(call gbuild, $<, pixman-$(pixman-version), static) \ + && echo "Pixman $(pixman-version)" > $@ + +$(ibidir)/tides: $(tdir)/tides-$(tides-version).tar.gz + $(call gbuild, $<, tides-$(tides-version), static,\ + --with-gmp=$(idir) --with-mpfr=$(idir)) \ + && cp $(dtexdir)/tides.tex $(ictdir)/ \ + && echo "TIDES $(tides-version) \citep{tides}" > $@ + $(ibidir)/yaml: $(tdir)/yaml-$(yaml-version).tar.gz $(call gbuild, $<, yaml-$(yaml-version), static) \ && echo "LibYAML $(yaml-version)" > $@ + + # Libraries with special attention on Mac OS # ------------------------------------------ # @@ -496,6 +511,11 @@ $(ibidir)/wcslib: $(tdir)/wcslib-$(wcslib-version).tar.bz2 \ + + + + + # Programs # -------- # @@ -533,6 +553,9 @@ $(ibidir)/astrometrynet: $(tdir)/astrometry.net-$(astrometrynet-version).tar.gz && cp $(dtexdir)/astrometrynet.tex $(ictdir)/ \ && echo "Astrometry.net $(astrometrynet-version) \citep{astrometrynet}" > $@ + + + # cdsclient is a set of software written in c to interact with astronomical # database servers. It is a dependency of `scamp' to be able to download # reference catalogues. |