Adam Ginsburg's blog

Articles by Adam (keflavich@gmail.com)

• Installing Snow Leopard

  I'm going to attempt to install snow leopard today. This post will serve as a record of the difficulties I run into. Things to install (and ensure they are 64-bit):

  • ipython
  • numpy
  • scipy
  • matplotlib
  • stsci-python
  • starlink
  • gfortran
  • latex
  • idl (check)

  Things that have happened:

  1. Had to restart again (twice) to install additional updates
  2. My bash command line looked funny - something about bash changed, but I don't know what. The fix was easy: commented out some code from http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html that I had been using to set the tab title
  3. My locate db broke. Needed repair: sudo /usr/libexec/locate.updatedb
  4. numpy svn failed to build: `` python setup.py buildRunning from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'F2PY Version 2_8111numpy/core/setup_common.py:86: MismatchCAPIWarning: API mismatch detected, the C API version numbers have to be updated. Current C api version is 4, with checksum 59750b518272c8987f02d66445afd3f1, but recorded checksum for C API version 4 in codegen_dir/cversions.txt is 3d8940bf7b0d2a4e25be4338c14c3c85. If functions were added in the C API, you have to update C_API_VERSION in numpy/core/setup_common.pyc. MismatchCAPIWarning)blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec']running buildrunning config_ccunifing config_cc, config, build_clib, build_ext, build commands --compiler optionsrunning config_fcunifing config_fc, config, build_clib, build_ext, build commands --fcompiler optionsrunning build_srcbuild_srcbuilding py_modules sourcesbuilding library "npymath" sourcescustomize NAGFCompilerFound executable /usr/local/bin/f95customize AbsoftFCompilerCould not locate executable f90Found executable /usr/bin/f77absoft: no Fortran 90 compiler foundabsoft: no Fortran 90 compiler foundcustomize IBMFCompilerCould not locate executable xlf90Could not locate executable xlfcustomize IntelFCompilerCould not locate executable ifortCould not locate executable ifccustomize GnuFCompilerFound executable /usr/local/bin/g77gnu: no Fortran 90 compiler foundgnu: no Fortran 90 compiler foundcustomize Gnu95FCompilerFound executable /usr/local/bin/gfortrancustomize Gnu95FCompilercustomize Gnu95FCompiler using configC compiler: gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypescompile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'gcc: _configtest.cgcc _configtest.o -o _configtestld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusfailure.removing: _configtest.c _configtest.oTraceback (most recent call last): File "setup.py", line 210, in setup_package() File "setup.py", line 203, in setup_package configuration=configuration ) File "/Users/adam/repos/numpy-svn/numpy/distutils/core.py", line 186, in setup return old_setup(new_attr) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 670, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program")RuntimeError: Broken toolchain: cannot link a simple C program`` **SOLUTION: Use the Mac OS X 10.6 python (/usr/bin/python). I will do this until I run into another problem. Numpy build successfully
  5. Build/install matplotlib - failed! Completely!
  6. Acquired gcc/gfortran from hpc
  7. Followed instructions from hyperjeff on fortran install...
  8. Get rid of numpy 1.2.1: `` mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/.not_numpy.bak``
  9. Try to install scipy. Fail on missing umfpack, follow hyperjeff's instructions (but make sure to edit the site.cfg in scipy, not just the one in numpy). Had to add the following code: sudo cp AMD/Lib/libamd.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp UMFPACK/Lib/libumfpack.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp AMD/Include/amd.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp UFconfig/UFconfig.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp UMFPACK/Include/*.h /System/Library/Frameworks/Python.framework/Versions/2.6/include
  10. Installed fftw from fftw.org with simple ./configure, make, sudo make install - no compiler opts as they killed the install
  11. Get SoundSource from rogueamoeba
  12. Updated istatmenus

---

• 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.

---

• keynote text boxes

---

• Last month's observations in L111

  Mapped sources: SH 2-156 [no high resolution observations; covered by 1.2m CO 1-0 survey] SH 2-157 Yancy CS 5-4, CO, 13CO 1-0, CS 2-1, HCN & SCUBA too.... IRAS 23151 (two pointings) Unmapped: BFS 18 = IRAS 23042+6000 = IRCO 859 Wu et al mapped this in CO 2-1 and detected no outflows. They used the NRAO 12m with a heterodyne array with very high T_sys ~700-1100K.

---

• latex: producing a bibliography and paper independently

  AG If you want citations to work, but you don't want your bibliography to show up, try the following: latex file.texbibtex file comment out \biblography{} line latex file.tex If you latex again, it will screw up. To make an independent bibliography, remove all text and replace all citep/citet/cite commands with \nocite{} in a different document. Remember to usepackage{natbib} etc. You may have to copy over the .bbl file.

---

• LaTeX: replace double quotes with tex quotes

  People often make the mistake of putting " in place of `` in LaTeX documents. To repair this, the only easy solution is something like: s/\(\s\)"/\1``/g in VIM or sed. I've seen alternate solutions posted but they're all too complicated. One recommendation was to switch to XeTeX, which sounds like overkill, and others all stated that a complicated perl script is required. The latter is technically true, but why isn't such a thing readily available? Any other ideas?

---

• LaTeX: VIM + Skim

  macvim-skim-install.sh is my install script for using MacVim.app with Skim.app. The agpy wiki page has instructions that are probably more clear; I don't really like the colorscheme / layout of this blog. You can use synctex to make an editor and viewer work together, but it is far from easy and far harder than it should be. Forward-search is pretty easy, but the latex-suite \ls only works intermittently and is not easily customizable. I had to do the following: For VIM->Skim.app (Skim.app is necessary for any of this to work), add these commands to .vimrc:

  " Activate skimmap ,v :w<CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>map ,p :w<CR>:silent !pdflatex -synctex=1 --interaction=nonstopmode %:p <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>map ,m :w<CR>:silent !make <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>" Reactivate VIMmap ,r :w<CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR>:silent !osascript -e "tell application \"MacVim\" to activate" <CR><CR>map ,t :w<CR>:silent !pdflatex -synctex=1 --interaction=nonstopmode %:p <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR>:silent !osascript -e "tell application \"MacVim\" to activate" <CR><CR>
  

  The ,m command will reload the file and put your cursor where the text is. ,t will return VIM to the front afterwards. Going the other way (reverse-search / inverse-search) was MUCH more challenging. The code that does this is on agpy. Reproduced here for posterity (I hope to update the agpy version to deal with tabs). [A few hours later, I HAVE replaced the code. Below are the old applescript version, then the new, vim-based version #!/bin/bashfile="$1"line="$2"[ "${file:0:1}" == "/" ] || file="${PWD}/$file"# Use Applescript to activate VIM, find file, and load it# the 'delay' command is needed to prevent command/control/shift from sticking when this# is activated (e.g., from Skim, where the command is command-shift-click)## key code 53 is "escape" to escape to command mode in VIMexec osascript \-e "delay 0.2" \-e "tell application \"MacVim\" to activate" \-e "tell application \"System Events\"" \-e "  tell process \"MacVim\"" \-e "    key code 53 "\-e "    keystroke \":set hidden\" & return " \-e "    keystroke \":if bufexists(bufname('$file'))\" & return " \-e "    keystroke \":exe \\\":buffer \\\" . bufnr(bufname('$file'))\"  & return " \-e "    keystroke \":else \" & return " \-e "    keystroke \":echo \\\"Could not load file\\\" \" & return " \-e "    keystroke \":endif\" & return " \-e "    keystroke \":$line\" & return " \-e "  end tell" \-e "end tell" New code: download link A

  #!/bin/bash# Install directions:# Put this file somewhere in your path and make it executable# To set up in Skim, go to Preferences:Sync# Change Preset: to Custom# Change Command: to macvim-load-line# Change Arguments: to "%file" %linefile="$1"line="$2"debug="$3"echo file: $fileecho line: $lineecho debug: $debugfor server in `mvim --serverlist` do    foundfile=`mvim --servername $server --remote-expr "WhichTab('$file')"`    if [[ $foundfile > 0 ]]    then        mvim --servername $server --remote-expr "foreground()"         if [[ $debug ]] ; then echo mvim --servername $server --remote-send ":exec \"tabnext $foundfile\" "; fi        mvim --servername $server --remote-send ":exec \"tabnext $foundfile\" "        if [[ $debug ]] ; then echo mvim --servername $server --remote-send ":$line "; fi        mvim --servername $server --remote-send ":$line "    fidone
  

  Save that as an executable in your default path (e.g., /usr/local/bin/macvim-load-line) and open Skim.app, go to Preferences:Sync and make the command look like this:

  

  You need to have mvim on your path. mvim comes with MacVim.app, but is NOT installed by default. Install it by doing something like: `` cp /Users/adam/Downloads/MacVim-7_3-53/mvim /usr/local/bin/mvim `` You'll also need to install WhichTab.vim in your ~/.vim/plugins/ directory. It's available here (download link B). Here's the source:

  function! WhichTab(filename)    " Try to determine whether file is open in any tab.      " Return number of tab it's open in    let buffername = bufname(a:filename)    if buffername == ""        return 0    endif    let buffernumber = bufnr(buffername)    " tabdo will loop through pages and leave you on the last one;    " this is to make sure we don't leave the current page    let currenttab = tabpagenr()    let tab_arr = []    tabdo let tab_arr += tabpagebuflist()    " return to current page    exec "tabnext ".currenttab    " Start checking tab numbers for matches    let i = 0    for tnum in tab_arr        let i += 1        echo "tnum: ".tnum." buff: ".buffernumber." i: ".i        if tnum == buffernumber            return i        endif    endforendfunctionfunction! WhichWindow(filename)    " Try to determine whether the file is open in any GVIM *window*    let serverlist = split(serverlist(),"\n")    "let currentserver = ????    for server in serverlist        let remotetabnum = remote_expr(server,             \"WhichTab('".a:filename."')")        if remotetabnum != 0            return server        endif    endforendfunction
  

---

• Listing variables (e.g IDL help) in Python

  Again, IDL has the simple 'help' command to tell you all variables in your namespace. Python has the same thing, but the namespace tends to be cluttered with imported functions. The commands who, who_ls, and whos are meant for interactive use. They are a hell of a lot more useful than var, locals, globals, and dir. examples: whos floatwhos ndarraywho modulefloat_vars = %who_ls floatgrep('x',float_vars) I'm afraid I don't know how to make the last two lines into a one-liner, as would be desirable.

---

• Logarithmic Colormap / Other Colormap in Matplotlib

  This is kind of a pain to find out: from matplotlib.colors import LogNormim = imshow(.... cmap=... , norm=LogNorm(vmin=clevs[0], vmax=clevs[-1])) `` It also works for contours, and can be particularly useful if you only want to display contours at a few levels, but you want the colormap to start at a different point. e.g.: ``contour(xx,levels=[2,3,4,5,6,7,8,9,10],norm=matplotlib.colors.Normalize(vmin=0,vmax=10)) will start at light blue instead of dark blue in the default colormap

---

• login shell

  to change your default login shell, use chsh

---

« Page 9 / 19 »