usetex failure in latex documents

When I use matplotlib's internal tex (rcParams['text.useTex']=False), the postscript files generated cause errors that look like this when you try to ps2pdf them:


ps2pdf h2co_pilot.ps
Error: /rangecheck in --get--
Operand stack:
--dict:20/25(ro)(L)-- --nostringval-- 71
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1862 1 3 %oparray_pop 1861 1 3 %oparray_pop 1845 1 3 %oparray_pop 1739 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- %finish_show --nostringval-- --nostringval-- 9 6 0 --nostringval-- (pdf_text_enum_t) %op_show_continue --nostringval--
Dictionary stack:
--dict:1147/1684(ro)(G)-- --dict:0/20(G)-- --dict:70/200(L)-- --dict:116/300(L)-- --dict:44/200(L)-- --dict:25/42(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 791626
GPL Ghostscript 8.64: Unrecoverable error, exit code 1
make: *** [h2co_pilot.pdf] Error 1


They will not open in MacOS's Preview.app either.

Solution: Make figures with rcParams['text.useTex'] = True

RATRAN on Mac OS X

Mac OS X doesn't like the defaults built in to RATRAN. It died unhappily with errors like:

ld_classic: can't locate file for: -lcrt0.o
and
ld: warning: in /usr/local/lib//libcfitsio.a, file is not of required architecture


In order to get it to run, I had to do the following:

1. Install CFITSIO with CFLAGS="-arch x86_64 -arch i386 -g -O2" to /usr/local/lib
   
2. Edit the sky/Makefile OPT variable (line 23) to read:
   OPT = -I. -O2 -fno-automatic -arch x86_64
   

Also, you need to set up system variables:

export RATRAN=/path/to/Ratran 
export RATRANRUN=/path/to/Ratran/run 

Gildas CLASS

It's absurdly difficult to find help on GILDAS Class, probably because you can't google "class" and most people probably don't label every piece of code with "GILDAS class".

Anyway, here are some scripts that I refer back to often:

file in August2009BGPS.dat
file out August2009fits.dat multiple
on error "file out August2009fits.dat"
say "READ IN FILES"
define character sourcelist*10[300]
accept sourcelist /column observed_sources.txt
on error "continue"
get 1001
set window -100 160
set mask -400 -100 160 400
set mode x -400 400
set align velocity
for i 1 to 161
say "Working on SOURCE "'i'
find /source 'sourcelist[i]' /telescope "CSO 4GHZ IF1" /offset 0 0 /quality 5
average
on error "@avplot2 'sourcelist[i]' 'i'; next"
base 3
line 0
min
plot
vis
write i
! on error "continue"
next


and


file in araya-2004.cls
find
define character filename*20
for i 1 to 20
say "Working on source "'i'
get next
let filename "araya-2004_"'i'".fits"
say "fits write "'filename'" /mode spectrum"
fits write 'filename' /mode spectrum
next

!file in araya-2002.cls
!find
!define character filename*20
!for i 1 to 42
! say "Working on source "'i'
! get i
! let filename "araya-2002_"'i'".fits"
! say "fits write "'filename'" /mode spectrum"
! fits write 'filename' /mode spectrum
!next


IRAF append/prepend/replace

IRAF has special syntax to append/replace, so you can do something like:
imarith *.fits - dark.fits ds_//*.fits
...though I can't remember right now how to do replacement etc.

command line & escape key

Problem: in both the bash command line and ipython, if I hit escape twice, I can never again do history-search-backwards (i.e. when you type part of a command and type "up" and reverse-search through your command history). Any idea how to fix this?

Rebuilding python from scratch again

I got scipy working a week or two ago, but doing so killed matplotib's tkagg. So, I switched to the MacOSX backend, which worked ok until I realized that the interactive (connect) features of macosx failed miserably. This led me to try to get matplotlib working.... which broke with those awful "symbol not found" errors in ft2font.so and _path.so, which I've determined all have to do with linking to the wrong library files.

The most worrisome part of this process was discovering that a full Time Machine recovery of /usr and /Library/Frameworks and /Library/Python did *not* restore python - it stayed dead with IDENTICAL errors. So there are probably additional layers of hidden links.

The process below is based on hyperjeff's blog post but differs substantially based on Sam Skillman's recommendations and the very big issue I ran into that my /usr/local files appeared to be corrupted. After this install, my path no longer includes /usr/local/bin and /sw has been moved to /_sw... hopefully one of these days I'll be ballsy enough to delete it.

1. Install python 2.6.4
   
   1. Needed a clean terminal with no flags set at all. Don't know why - all I had set were a bunch of -arch x86_64 flags.
      
export LD_LIBRARY_PATH="/usr/local/lib:/usr/X11/lib"
./configure --enable-framework=/Library/Frameworks MACOSX_DEPLOYMENT_TARGET=10.6
make -j 17
sudo make install

      
   2. Reset PYTHONPATH to blank
      
   3. alias clearflags='export CFLAGS=""; export CCFLAGS=""; export CXXFLAGS=""; export LDFLAGS=""; export FFLAGS="";' to make sure
      
   
   
2. Install FFTW
   
cd ~/tmp
curl -O http://www.fftw.org/fftw-3.2.2.tar.gz
tar xf fftw-3.2.2.tar.gz
cd fftw-3.2.2
clearflags
./configure CC="gcc -arch x86_64" CXX="g++ -arch x86_64" CPP="gcc -E" CXXCPP="g++ -E"
make -j 17
sudo make install

   
3. Install UMFPACK
   
cd ~/tmp
curl -O http://www.cise.ufl.edu/research/sparse/umfpack/current/UMFPACK.tar.gz
curl -O http://www.cise.ufl.edu/research/sparse/UFconfig/current/UFconfig.tar.gz
curl -O http://www.cise.ufl.edu/research/sparse/amd/current/AMD.tar.gz
tar xf AMD.tar.gz
tar xf UFconfig.tar.gz
tar xf UMFPACK.tar.gz
sed -ibck 's/F77 = f77/F77 = gfortran/' UFconfig/UFconfig.mk
sed -ibck '299,303s/# //' UFconfig/UFconfig.mk
cp UFconfig/UFconfig.h AMD/Include/
cp UFconfig/UFconfig.h UMFPACK/Include/
cd UMFPACK
make -j 17
make hb
make clean

   
4. Install numpy
   
   1. Set environment variables
      
export MACOSX_DEPLOYMENT_TARGET=10.6
export CFLAGS="-arch x86_64"
export FFLAGS="-m64"
export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch x86_64"
export PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/"
echo "[amd]
library_dirs = /Users/adam/tmp/AMD/Lib
include_dirs = /Users/adam/tmp/AMD/Include
amd_libs = amd

[umfpack]
library_dirs = /Users/adam/tmp/UMFPACK/Lib
include_dirs = /Users/adam/tmp/UMFPACK/Include
umfpack_libs = umfpack" > site.cfg

      
   2. Setup & Install
      
python setup.py build --fcompiler=gnu95
sudo python setup.py install

      
   3. Test: python -c "import numpy"
      
   
   
5. Install scipy. The important thing is to use g++-4.2 because g++-4.5 doesn't accept the -arch flag. Also, get rid of /sw if it's on your computer at all.
   
sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyX
cd ~/repos/scipy-0.7.1
python setup.py clean
rm -rf build
clearflags
FFLAGS="-m64" CFLAGS="-arch x86_64 -I/usr/local/include/freetype2 -I/usr/X11/include -L/usr/X11/lib" LDFLAGS="-Wall -undefined dynamic_lookup -bundle -lpng -arch x86_64" CXX="/usr/bin/g++-4.2" CC="/usr/bin/gcc-4.2" python setup.py build
python setup.py install

   Test the install:
   
python -c "import scipy, scipy.fftpack, scipy.interpolate"

   
6. 1. Install matplotlib. MAKE SURE /usr/bin/texbin is in front of /usr/local/bin and /sw/bin so that dvipng comes from MacTEX. I also ended up having to remove /usr/local/bin from my path completely
      
sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyX
cd ~/repos/matplotlib-svn
python setup.py clean
rm -rf build
clearflags

      
   2. Do hyperjeff's recommended edits except don't use /usr/local because it's f'd:
      make.osx:
      
MACOSX_DEPLOYMENT_TARGET=10.6
PREFIX=/usr
PYTHON=/Library/Frameworks/Python.framework/Versions/Current/bin/python

## You shouldn't need to configure past this point (and yet…)

PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig"
CFLAGS="-arch i386 -arch x86_64 -I${PREFIX}/include -I${PREFIX}/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk"
LDFLAGS="-arch i386 -arch x86_64 -L${PREFIX}/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk"
FFLAGS="-arch i386 -arch x86_64"

      setup.cfg:
      
wxagg = False

      
   3. Do the install (different from hyperjeff b/c I don't want root)
      sudo make -f make.osx fetch deps
make -f mpl_build mpl_install
python setup.py install

      
   
   
7. Install setuptools
   
8. easy_install ipython
   
9. install everything else pythonically
   

apache/php/mysql on snow leopard

This post helped me out