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 " fidoneSave 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 endforendfunctionListing 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
Lunar Occultation Hi-Res measurements
The folks at the VLT have come up with a means of achieving extremely high resolution from the ground: Observe when the moon occults a source and how long the occultation takes. Sweet. This was applied in the galactic center first, of course: Observations of binaries in GC Additional observations in GC
Mac stuff cont'd
Trying to get Apache server to run, and it's just a pain. I frequently forget how to update the locate database because it's different on macs. Marcos' Mac Singularity has the instructions. In short: sudo /usr/libexec/locate.updatedb
Mac terminal stuff
xterm-color has some annoying features when SSHing to other compys, including 'top' not functioning properly. The error I receive: top: no termcap entry for a `xterm-color' terminal The solution: From MacOSXhints, in bash just add export TERM="vt100" to your .profile file.
macvim crash
well, it finally happened.... my reliable, trusty editor crashed. That should be impossible. I am ready to call it quits for the week....
Process: MacVim [650]Path: /Applications/Vim.app/Contents/MacOS/MacVimIdentifier: org.vim.MacVimVersion: 7.2 (49)Code Type: X86 (Native)Parent Process: Vim [649]Date/Time: 2010-02-25 13:12:43.001 -0700OS Version: Mac OS X 10.6.2 (10C540)Report Version: 6Interval Since Last Report: 871676 secCrashes Since Last Report: 26Per-App Interval Since Last Report: 938504 secPer-App Crashes Since Last Report: 1Anonymous UUID: 03159B9E-2257-4E38-8C4A-4D4DAF5641A7Exception Type: EXC_BAD_ACCESS (SIGSEGV)Exception Codes: 0x000000000000000d, 0x0000000000000000Crashed Thread: 0 Dispatch queue: com.apple.main-threadThread 0 Crashed: Dispatch queue: com.apple.main-thread0 com.apple.CoreFoundation 0x99119480 __CFSetCallback + 01 com.apple.CoreFoundation 0x990c78bc ___CFBasicHashFindBucket1 + 4442 com.apple.CoreFoundation 0x990cfaac CFBasicHashFindBucket + 2523 com.apple.CoreFoundation 0x990e8293 CFSetGetValue + 1314 com.apple.AppKit 0x961bae7e -[NSWindow _discardTrackingRect:] + 595 com.apple.AppKit 0x961badca -[NSView(NSInternal) _uninstallTrackingArea:] + 1236 com.apple.AppKit 0x960d2c32 -[NSView(NSInternal) _uninstallRemovedTrackingAreas] + 2937 com.apple.AppKit 0x960dac40 -[NSView(NSInternal) _updateTrackingAreas] + 6468 com.apple.CoreFoundation 0x990ea4e0 CFArrayApplyFunction + 2249 com.apple.AppKit 0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 134510 com.apple.CoreFoundation 0x990ea4e0 CFArrayApplyFunction + 22411 com.apple.AppKit 0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 134512 com.apple.CoreFoundation 0x990ea4e0 CFArrayApplyFunction + 22413 com.apple.AppKit 0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 134514 com.apple.AppKit 0x960da8db _handleInvalidCursorRectsNote + 39215 com.apple.CoreFoundation 0x99135892 __CFRunLoopDoObservers + 118616 com.apple.CoreFoundation 0x990f218d __CFRunLoopRun + 55717 com.apple.CoreFoundation 0x990f1864 CFRunLoopRunSpecific + 45218 com.apple.CoreFoundation 0x990f1691 CFRunLoopRunInMode + 9719 com.apple.HIToolbox 0x936f6f0c RunCurrentEventLoopInMode + 39220 com.apple.HIToolbox 0x936f6bff ReceiveNextEventCommon + 15821 com.apple.HIToolbox 0x936f6b48 BlockUntilNextEventMatchingListInMode + 8122 com.apple.AppKit 0x960b0ac5 _DPSNextEvent + 84723 com.apple.AppKit 0x960b0306 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 15624 com.apple.AppKit 0x9607249f -[NSApplication run] + 82125 com.apple.AppKit 0x9606a535 NSApplicationMain + 57426 org.vim.MacVim 0x0000238b _start + 20927 org.vim.MacVim 0x000022b9 start + 41Thread 1: Dispatch queue: com.apple.libdispatch-manager0 libSystem.B.dylib 0x98d0c0ea kevent + 101 libSystem.B.dylib 0x98d0c804 _dispatch_mgr_invoke + 2152 libSystem.B.dylib 0x98d0bcc3 _dispatch_queue_invoke + 1633 libSystem.B.dylib 0x98d0ba68 _dispatch_worker_thread2 + 2344 libSystem.B.dylib 0x98d0b4f1 _pthread_wqthread + 3905 libSystem.B.dylib 0x98d0b336 start_wqthread + 30Thread 2:0 libSystem.B.dylib 0x98ce58da mach_msg_trap + 101 libSystem.B.dylib 0x98ce6047 mach_msg + 682 com.apple.CoreFoundation 0x990f277f __CFRunLoopRun + 20793 com.apple.CoreFoundation 0x990f1864 CFRunLoopRunSpecific + 4524 com.apple.CoreFoundation 0x990f1691 CFRunLoopRunInMode + 975 com.apple.Foundation 0x91b24430 +[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 3296 com.apple.Foundation 0x91aeb8d8 -[NSThread main] + 457 com.apple.Foundation 0x91aeb888 __NSThread__main__ + 14998 libSystem.B.dylib 0x98d12fbd _pthread_start + 3459 libSystem.B.dylib 0x98d12e42 thread_start + 34Thread 3:0 libSystem.B.dylib 0x98d04856 select$DARWIN_EXTSN + 101 com.apple.CoreFoundation 0x99131ddd __CFSocketManager + 10852 libSystem.B.dylib 0x98d12fbd _pthread_start + 3453 libSystem.B.dylib 0x98d12e42 thread_start + 34Thread 4:0 libSystem.B.dylib 0x98d0b182 __workq_kernreturn + 101 libSystem.B.dylib 0x98d0b718 _pthread_wqthread + 9412 libSystem.B.dylib 0x98d0b336 start_wqthread + 30Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00515db0 ebx: 0x990c7711 ecx: 0x00516460 edx: 0xbfffcabc edi: 0x00001041 esi: 0x00504270 ebp: 0xbfffca38 esp: 0xbfffc99c ss: 0x0000001f efl: 0x00010246 eip: 0x99119480 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x97a20000
Major mac problems
The errors are, in short:
- Browser stops responding / starts returning "page not found" (indicating a failure of mDNSResponder)
- killing mDNSResponder sometimes brings browser back, but more often leads to a partial system freeze (some windows don't respond, can't switch between windows except by clicking)
- /var/log/system.log gets flooded with "too many files open" errors.
- somewhere in here the Dock fails
- killing Google Chrome and/or the Dock fails; the process never halts (even kill -9 + kill -s SIGCHLD)
- usually one or two crash reports pop up, at least one of which is for crash_reporter
- system.log stops getting flooded, but the browser and Dock never recover
The only message in system.log that gives me any hint about what might be happening is occasionally a freeze was resolved at the same time as this message: Jun 22 19:02:09 eta Quicksilver[93771]: Multiple Scans Attempted but it doesn't seem to change the situation if quicksilver is open or not. Google has nothing on this issue, either, except for the quicksilver source code, so evidently it has not caused problems for other people system.log was also being flooded with this message:
Jun 23 08:57:19 eta postfix/master[99954]: fatal: open /dev/null: Bad file descriptorJun 23 08:57:20 eta com.apple.launchd[1] (org.postfix.master[99954]): Exited with exit code: 1Jun 23 08:57:20 eta com.apple.launchd[1] (org.postfix.master): Throttling respawn: Will start in 9 seconds
so I disabled my postman:
Jun 23 08:57:27 eta sudo[99955]: adam : TTY=ttys006 ; PWD=/Users/adam/proposals/alma ; USER=root ; COMMAND=/bin/launchctl unload -w /System/Library/LaunchDaemons/org.postfix.master.plist
These errors:
Jun 23 09:06:40 eta Dock[99877]: kCGErrorIllegalArgument: CGSSetWindowTransformAtPlacement: Singular matrix [nan 0.000 0.000 nan]Jun 23 09:06:40 eta com.apple.Dock.agent[99877]: Thu Jun 23 09:06:40 eta.colorado.edu Dock[99877] : kCGErrorIllegalArgument: CGSSetWindowTransformAtPlacement: Singular matrix [nan 0.000 0.000 nan]
are correlated with opening Chrome windows and/or Chrome's crash_inspector
Jun 23 09:06:09 eta [0x0-0x69e69e].com.google.Chrome[99995]: [99995:24579:485131152128125:ERROR:shared_memory_posix.cc(164)] Creating shared memory in /var/folders/ni/ni+DtdqFGMeSMH13AvkNkU+++TI/-Tmp-/.com.google.chrome.sHcu6r failed: Too many open files in system
This is the problem that really gets me... I think it's crash_inspector's fault. But there's definitely more going on here than just Chrome. Trying to change default browsers (by opening Safari and opening Preferences) led to a partial Dock crash (?!) in which I can alt-tab but can't see the Dock. Not clear at all what's going on.... argh.