From 3352a638ce812744d18cfeb83f62dc88a7456b44 Mon Sep 17 00:00:00 2001
From: "W. Trevor King"
Date: Thu, 15 Dec 2011 13:57:28 -0500
Subject: [PATCH] Move from physics.drexel.edu/~wking/unfolding-disasters to
blog.tremily.us.
Also assorted cleanups and sanitation work.
---
ikiwiki.setup | 20 +-
posts/Bugs.mdwn | 2 +-
posts/Comedi.mdwn | 2 +-
posts/Compose_key.mdwn | 2 +-
posts/DocBook_5.mdwn | 6 +-
posts/Emacs.mdwn | 1 -
posts/Email_interface_to_bugs_everywhere.mdwn | 2 +-
posts/FOAF/biblio.rdf.asc | 12 +-
posts/FOAF/foaf.rdf | 8 +-
posts/FOAF/foaf.rdf.asc | 12 +-
posts/Gentoo_Prefix_overlay/layman.xml | 8 +-
posts/Gentoo_overlay/layman.xml | 8 +-
.../Getting_numbers_from_journal_figures.mdwn | 18 +-
posts/Git/notes.org | 2 +-
posts/Giving_up_on_Gompertz_theory.mdwn | 6 +-
posts/Hooke-update-2.mdwn | 9 +-
posts/Hooke-update.mdwn | 14 +-
posts/Numpydoc_and_Sphinx_1.0.mdwn | 29 +--
posts/Parallel_computing.mdwn | 4 +-
...Reading_IGOR_binary_waves_from_Python.mdwn | 23 ++-
posts/SSI/footer.shtml | 2 +-
posts/SSI/header.shtml | 33 +--
posts/Stripchart.mdwn | 25 +--
posts/Subversion.mdwn | 24 ++-
posts/Thesis/Makefile | 2 +-
posts/Tove_overlay.mdwn | 7 +-
posts/Tove_overlay/layman.xml | 19 --
posts/Xmodmap/Makefile | 6 +-
posts/cookbook.mdwn | 2 +-
posts/dotfiles.mdwn | 2 +-
posts/git-php.mdwn | 8 +-
posts/mdwn_itex.mdwn_itex | 11 +-
posts/mdwn_itex/mdwn_itex-templates.patch | 19 --
posts/mdwn_itex/mdwn_itex.patch | 157 ---------------
posts/mdwn_itex/mdwn_itex.pm | 190 ------------------
posts/problempack.mdwn | 12 +-
posts/problempack/Makefile | 2 +-
posts/rel-vcs/chrome/content/about.xul | 6 +-
posts/rel-vcs/install.rdf | 2 +-
posts/send_pgp_mime.mdwn | 4 +-
sidebar.mdwn | 2 +-
templates/gitrepo.mdwn | 5 +-
42 files changed, 178 insertions(+), 550 deletions(-)
mode change 100644 => 100755 ikiwiki.setup
delete mode 100644 posts/Tove_overlay/layman.xml
delete mode 100644 posts/mdwn_itex/mdwn_itex-templates.patch
delete mode 100644 posts/mdwn_itex/mdwn_itex.patch
delete mode 100644 posts/mdwn_itex/mdwn_itex.pm
diff --git a/ikiwiki.setup b/ikiwiki.setup
old mode 100644
new mode 100755
index 3f728df..b81ff49
--- a/ikiwiki.setup
+++ b/ikiwiki.setup
@@ -19,11 +19,11 @@ use IkiWiki::Setup::Standard {
# where to build the wiki
destdir => 'html',
# base url to the wiki
- url => 'http://www.physics.drexel.edu/~wking/unfolding-disasters',
+ url => 'http://blog.tremily.us/',
# url to the ikiwiki.cgi
- #cgiurl => 'http://www.physics.drexel.edu/~wking/unfolding-disasters/ikiwiki.cgi',
+ #cgiurl => 'http://blog.tremily.us/cgi-bin/ikiwiki.cgi',
# filename of cgi wrapper to generate
- #cgi_wrapper => '/tmp/ikiwiki.build/ikiwiki.cgi',
+ #cgi_wrapper => 'html/cgi-bin/ikiwiki.cgi',
# mode for cgi_wrapper (can safely be made suid)
#cgi_wrappermode => '06755',
# rcs backend to use
@@ -127,9 +127,15 @@ use IkiWiki::Setup::Standard {
# mdwn_itex plugin
# path to the itex2MML binary
- #itex2mml => '/usr/local/bin/itex2MML',
- itex2mml => '/home/wking/bin/itex2MML --unicode-entities',
- # autonumber \[..\] equations?
+ #itex2mml => '/usr/bin/itex2MML',
+ itex2mml => '/home/wking/bin/itex2MML',
+ # Must return numeric character references (e.g. α) or UTF-8
+ # instead of MathML entities (e.g. α). If you're using the
+ # stock itex2MML, you might use a script like this:
+ # #!/bin/sh
+ # /usr/bin/itex2MML "${@}" | perl -e 'use MathML::Entities; print name2numbered($_) while(<>);'
+
+ # autonumber \[..\]x equations?
itex_num_equations => 1,
# recentchanges plugin
@@ -140,7 +146,7 @@ use IkiWiki::Setup::Standard {
# repolist plugin
# URIs of repositories containing the wiki's source
- repositories => [qw{http://www.physics.drexel.edu/~wking/code/git/blog.git}],
+ repositories => [qw{git://tremily.us/blog.git}],
# sidebar plugin
# show sidebar page on all pages?
diff --git a/posts/Bugs.mdwn b/posts/Bugs.mdwn
index 79712fd..aeb2e31 100644
--- a/posts/Bugs.mdwn
+++ b/posts/Bugs.mdwn
@@ -158,7 +158,7 @@ the changes at the time and my changes have bit-rotted since then.
I'm currently using using the `gitweb` distributed with [[Git]], which
is why I wasn't on the ball in getting the changes accepted upstream.
-[git-php]: http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=git-php.git;a=summary
+[git-php]: http://git.tremily.us/?p=git-php.git;a=summary
[PV]: http://people.proekspert.ee/peeter/git/git.php?p=git-php.git
[JDG]: http://github.com/josegonzalez/git-php
diff --git a/posts/Comedi.mdwn b/posts/Comedi.mdwn
index eddada9..a05e61b 100644
--- a/posts/Comedi.mdwn
+++ b/posts/Comedi.mdwn
@@ -23,7 +23,7 @@ and added them to my [[Gentoo overlay]].
[Comedi]: http://www.comedi.org/
[6052E]: http://sine.ni.com/nips/cds/view/p/lang/en/nid/2601
[external]: http://comedi.org/git?p=comedi/comedi.git;a=summary
-[kernel]: http://git.kernel.org/?p=linux/kernel/git/torvalds/linux-2.6.git;a=tree;f=drivers/staging/comedi
+[kernel]: http://git.kernel.org/?p=linux/kernel/git/torvalds/linux-2.6.git;a=tree;f=drivers/staging/comedi;hb=HEAD
[Debian]: http://packages.debian.org/sid/python-comedilib
[Ubuntu]: http://packages.ubuntu.com/natty/python-comedilib
[Gentoo]: http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-libs/comedilib/?hideattic=0
diff --git a/posts/Compose_key.mdwn b/posts/Compose_key.mdwn
index 0413487..0a614f1 100644
--- a/posts/Compose_key.mdwn
+++ b/posts/Compose_key.mdwn
@@ -100,7 +100,7 @@ an `~/.XCompose` file:
$ cat ~/.XCompose
include "%L"
- : "http://physics.drexel.edu/~wking" # Home page
+ : "http://tremily.us/" # Home page
Read `Compose(5)` for more information. You may need to log out and
log back in (or use the [[newgrp]] trick) for your new `~/.XCompose`
diff --git a/posts/DocBook_5.mdwn b/posts/DocBook_5.mdwn
index 0534c94..511d7e3 100644
--- a/posts/DocBook_5.mdwn
+++ b/posts/DocBook_5.mdwn
@@ -9,14 +9,14 @@ If you are interested in DocBook-based manpages, take a look at my
documentation. You can also try the [official BE
documentation][BE_doc], but that sometimes lags behind my version.
-[man]: http://www.physics.drexel.edu/~wking/code/git/git.php?tr=c9ce0b30672d653f46d0a2c269c468e8cffb9a97&tag=0a993be001ab5ff250fae4c5f20bab11f89e30cb&p=be.git&a=jump_to_tag&b=3b5c8d094c4f16257bdf1b4ba3edb6ca7351054c&n=be.1.xml
+[man]: http://git.tremily.us/?p=be.git;a=blob;f=be.1.xml;hb=HEAD
[BE]: http://bugseverywhere.org/
[DB]: http://www.docbook.org/
[xsltproc]: http://www.xmlsoft.org/XSLT/
-[doc]: http://www.physics.drexel.edu/~wking/code/be/doc/doc.html#man-page
-[install]: http://www.physics.drexel.edu/~wking/code/be/doc/install.html#dependencies
+[doc]: http://doc.be.tremily.us/doc.html#man-page
+[install]: http://doc.be.tremily.us/install.html#dependencies
[BE_doc]: http://docs.bugseverywhere.org/
diff --git a/posts/Emacs.mdwn b/posts/Emacs.mdwn
index b3285eb..6a8be75 100644
--- a/posts/Emacs.mdwn
+++ b/posts/Emacs.mdwn
@@ -1,4 +1,3 @@
-
[Emacs][] is the text exitor that does everything. Take a look at the
liki pages on [emacs in general][general], [unicode][], and
[org-mode][].
diff --git a/posts/Email_interface_to_bugs_everywhere.mdwn b/posts/Email_interface_to_bugs_everywhere.mdwn
index 350fa9c..4de9a8c 100644
--- a/posts/Email_interface_to_bugs_everywhere.mdwn
+++ b/posts/Email_interface_to_bugs_everywhere.mdwn
@@ -31,7 +31,7 @@ with other devs, so I don't have to bother with that ;).
Curious parties can branch my public repo:
- $ bzr branch http://www.physics.drexel.edu/~wking/code/bzr/be-email be.email
+ $ git clone http://www.physics.drexel.edu/~wking/code/bzr/be-email be.email
As a nice side effect of this little project, my [[send_pgp_mime] is
now much more elegant.
diff --git a/posts/FOAF/biblio.rdf.asc b/posts/FOAF/biblio.rdf.asc
index 3f39dcb..b4420ba 100644
--- a/posts/FOAF/biblio.rdf.asc
+++ b/posts/FOAF/biblio.rdf.asc
@@ -1,7 +1,11 @@
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.11 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
-iEYEABECAAYFAk2nWZQACgkQ/Cm9zfFfW+heCQCgnEgIRw4RSjI9mTYN3MWQR3Se
-GR4AoJZMepIJBCVsl11sS+D0pL0/nnTD
-=4aHg
+iQEcBAABAgAGBQJO4TiuAAoJEPe7CdOcrcTZs0YH/35bxO8bEZfMU+8ir//OXo4R
+pS/rjjDMfp3NO8aA83qkM4c6ufLAyCktFxs/zDH28q6R0+eOo07IWWUpocGQA1vv
+qNHqkKmKH2vTi+4emUIEwkbJBSdfEZdf9zoOl6Sbl2qlatu4Hwn7Tnh8D58dYjt7
+Y9bvZB0AIuerWFffD4cm22a0uUSvaCDXiiZJtibh4B1yrLmBm1whS+00pUEhMkXu
+uYj88kwYVtcdcH5AGocxYMhfMEkT5WN36P0LuLVJ5+7BpdRXwPtjJWS6huTSNYZB
+YDNV14aedYtRowPia0qYjM7lKS3YLTfj66opZzlX3on6pij21HC/KS95bcpgTzs=
+=ND2N
-----END PGP SIGNATURE-----
diff --git a/posts/FOAF/foaf.rdf b/posts/FOAF/foaf.rdf
index 640ac03..dc26443 100644
--- a/posts/FOAF/foaf.rdf
+++ b/posts/FOAF/foaf.rdf
@@ -13,9 +13,9 @@
031d265f390b454d9b62554ab6ae12978f473f53
-
-
-
+
+
+
@@ -23,7 +23,7 @@
F15F5BE8
-
+
diff --git a/posts/FOAF/foaf.rdf.asc b/posts/FOAF/foaf.rdf.asc
index d99ba40..524b86a 100644
--- a/posts/FOAF/foaf.rdf.asc
+++ b/posts/FOAF/foaf.rdf.asc
@@ -1,7 +1,11 @@
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.11 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
-iEYEABECAAYFAk2nW1wACgkQ/Cm9zfFfW+hhKACffzrs5NCiOqcMQPsguGxnCHnn
-qV4An2vMNlrIC5xjs6anse318f/95l3s
-=gz71
+iQEcBAABAgAGBQJO4TiuAAoJEPe7CdOcrcTZmm0H/idVFFzvdG6KWtDW8A/j0Rot
+M9Bn14+39NhnzkO7S0CCk3tl6BbzbjEHVup+HyvdSHph+8DQXhVazcDeR8mr6pkV
+wwjleprWIkyKIHZBPc2oAGO/PyQk1uyTNBN1TXA70j9y7PJ0/ybJrAvW8BevDpUB
+IM8xv5+h0F1Av/joLctZHcEMPZZISVpa/RlyF5aylmfwdCby4GGaBDKknD4I3gLw
+wGwims5UCwtrKX9k2LIUdv2NHtG9Vvj5UXs8SyVlX0sJLQUhDrY0xzJQ4YRI//fw
+9Dtmu3uapgVGk1mxOhWE6dHVg0IMKvfhmcLOtGx1PqY4U/A9HTI6b55N9/4SR7Q=
+=CilW
-----END PGP SIGNATURE-----
diff --git a/posts/Gentoo_Prefix_overlay/layman.xml b/posts/Gentoo_Prefix_overlay/layman.xml
index 35e10a4..87c7e6e 100644
--- a/posts/Gentoo_Prefix_overlay/layman.xml
+++ b/posts/Gentoo_Prefix_overlay/layman.xml
@@ -5,19 +5,19 @@
wtkW. Trevor King's prefix overlay
- http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/Gentoo_Prefix_overlay/
+ http://blog.tremily.us/posts/Gentoo_Prefix_overlay/
wking@drexel.edu
- http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=wtk-prefix-overlay.git;a=atom
+ http://git.tremily.us?p=wtk-prefix-overlay.git;a=atom
- http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=wtk-overlay.git;a=rss
+ http://git.tremily.us?p=wtk-prefix-overlay.git;a=rss
diff --git a/posts/Gentoo_overlay/layman.xml b/posts/Gentoo_overlay/layman.xml
index c8886ee..f3d858d 100644
--- a/posts/Gentoo_overlay/layman.xml
+++ b/posts/Gentoo_overlay/layman.xml
@@ -5,19 +5,19 @@
wtkW. Trevor King's overlay
- http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/Gentoo_overlay/
+ http://blog.tremily.us/posts/Gentoo_overlay/
wking@drexel.edu
- http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=wtk-overlay.git;a=atom
+ http://git.tremily.us/?p=wtk-overlay.git;a=atom
- http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=wtk-overlay.git;a=rss
+ http://git.tremily.us/?p=wtk-overlay.git;a=rss
diff --git a/posts/Getting_numbers_from_journal_figures.mdwn b/posts/Getting_numbers_from_journal_figures.mdwn
index df47874..2e7a8fd 100644
--- a/posts/Getting_numbers_from_journal_figures.mdwn
+++ b/posts/Getting_numbers_from_journal_figures.mdwn
@@ -8,17 +8,17 @@ out of graphs and whatnot that show up in journal articles.
$ scale_click.sh 0 10 5 20 fig-000.pixels > fig-000.data
Just use your first four clicks in
-[clickloc.tk](http://www.physics.drexel.edu/~wking/code/tcl-tk/clickloc.tk)
-to mark out the x and y minimum and maximum values. Then use
-[scale_click.sh](http://www.physics.drexel.edu/~wking/code/bash/scale_click.sh)
-to convert the pixel values to the units listed in the figure. In my
-example, the x axis ran from 0 to 10 units, and the y axis ran from 5
-to 20 units. Supports log-scaled axes too.
+[[clickloc.tk|clickloc/clickloc.tk]] to mark out the x and y minimum
+and maximum values. Then use
+[[scale_click.sh|clicloc/scale_click.sh]] to convert the pixel values
+to the units listed in the figure. In my example, the x axis ran from
+0 to 10 units, and the y axis ran from 5 to 20 units. Supports
+log-scaled axes too.
Having gotten some numbers, my sawtooth simulator matches up fairly
-well to [Schlierf & Rief's
-results](http://www.biophysj.org/cgi/content/abstract/90/4/L33) on
-both models. Hooray! ;).
+well to [Schlierf & Rief's results][SR] on both models. Hooray! ;).
+
+[SR]: http://www.biophysj.org/cgi/content/abstract/90/4/L33
[[!tag tags/linux]]
[[!tag tags/programming]]
diff --git a/posts/Git/notes.org b/posts/Git/notes.org
index 82ff927..6ec07a4 100644
--- a/posts/Git/notes.org
+++ b/posts/Git/notes.org
@@ -420,7 +420,7 @@ to =.git/config=, after which you can push with
: devel$ git push public master
Note that you may need to copy =.git/description= over by hand. I
-wrote up a [[http://www.physics.drexel.edu/~wking/code/index.shtml#git-publish][git-publish]] script to automate this.
+wrote up a [[http://blog.tremily.us/posts/Git/git-publish.py][git-publish]] script to automate this.
** Gitting comedi, using Git as a frontend for CVS
From [[http://issaris.blogspot.com/2005/11/cvs-to-git-and-back.html][Takis blog]]
diff --git a/posts/Giving_up_on_Gompertz_theory.mdwn b/posts/Giving_up_on_Gompertz_theory.mdwn
index 49d28f0..d8aa037 100644
--- a/posts/Giving_up_on_Gompertz_theory.mdwn
+++ b/posts/Giving_up_on_Gompertz_theory.mdwn
@@ -7,11 +7,11 @@ On to find out about analytic solutions to Kramers' unfolding rates.
Update: I figured out how to use the [NIST reference][] while writing
my [[sawsim]] paper, listing the mean and standard deviation of the
-Gumbel distribution. So many names... Anyway, the `pysawsim` tests
-now use the [improved guessing procedure][].
+Gumbel distribution. So many names⦠Anyway, the `pysawsim` tests
+now use the [improved guessing procedure][guess].
[NIST reference]: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366g.htm
-[improved guessing procedure]: http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=sawsim.git;a=blob;f=pysawsim/test/bell_rate.py;hb=837c425eaeccae280cc7f7784d03dfcfcb03678c#l106
+[guess]: http://git.tremily.us/?p=sawsim.git;a=blob;f=pysawsim/test/bell_rate.py;hb=837c425eaeccae280cc7f7784d03dfcfcb03678c#l106
[[!tag tags/sawsim]]
[[!tag tags/theory]]
diff --git a/posts/Hooke-update-2.mdwn b/posts/Hooke-update-2.mdwn
index 0cbfef0..b99fee8 100644
--- a/posts/Hooke-update-2.mdwn
+++ b/posts/Hooke-update-2.mdwn
@@ -1,8 +1,7 @@
In [[an earlier post|Hooke-update]], I reported seeing `surface
distance (m) (m)` columns in my playlist files, but had been unable to
reproduce them. Today, after [fixing bugs with Curve
-copying](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/59390d466f0d),
-I did reproduce them with:
+copying][copy-bug], I did reproduce them with:
$ ./bin/hk.py
-c 'load_playlist test/data/vclamp_picoforce/playlist'
@@ -26,8 +25,10 @@ curves.
I'll update this post once I've tracked down the culprit.
-Update:
-[fixed](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/230d4483c9da).
+Update: [fixed][].
+
+[copy-bug]: http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/59390d466f0d
+[fixed]: http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/230d4483c9da
[[!tag tags/hooke]]
[[!tag tags/programming]]
diff --git a/posts/Hooke-update.mdwn b/posts/Hooke-update.mdwn
index fd00a01..66f356c 100644
--- a/posts/Hooke-update.mdwn
+++ b/posts/Hooke-update.mdwn
@@ -1,5 +1,5 @@
-Minor tweaks to Hooke's [command
-stacks](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/8c0882dfbaf5). I can now execute the GUI alternative of
+Minor tweaks to Hooke's [command stacks][stacks]. I can now execute
+the GUI alternative of
./bin/hk.py
-c 'new_playlist'
@@ -20,9 +20,7 @@ Issues resolved today:
Update:
-After [fixing up a few more
-bugs](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/7ba2243a9b45),
-I successfully ran:
+After [fixing up a few more bugs][bugs], I successfully ran:
./bin/hk.py
-c 'new_playlist'
@@ -50,10 +48,14 @@ It did, however turn up a couple of outstanding issues:
- lots of useless `!!python/unicode 'retract'` tags. If the strings
are all in ASCII, I don't really care if they are loaded as unicode
or string objects.
- ([fixed](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/302413fafa96))
+ ([fixed][])
- `surface distance (m) (m)` column. Obviously someone is adding
units twice. I need to figure out who it is ;).
([[Reproduced|Hooke-update-2]])
+[stacks]: http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/8c0882dfbaf5
+[bugs]: http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/7ba2243a9b45
+[fixed]: http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/rev/302413fafa96
+
[[!tag tags/hooke]]
[[!tag tags/programming]]
diff --git a/posts/Numpydoc_and_Sphinx_1.0.mdwn b/posts/Numpydoc_and_Sphinx_1.0.mdwn
index ce0aaeb..f137d4e 100644
--- a/posts/Numpydoc_and_Sphinx_1.0.mdwn
+++ b/posts/Numpydoc_and_Sphinx_1.0.mdwn
@@ -1,20 +1,25 @@
I finally got around to upgrading the environment on the server that
-autogenerates my [Hooke
-documentation](http://www.physics.drexel.edu/~wking/rsrch/hooke/).
+autogenerates my [Hooke documentation][doc].
+
The new setup is:
-- [Python](http://www.python.org/) 2.7 (previously Python 2.5)
-- [Sphinx]() 1.0.3 (previously Sphinx 0.6.5)
-- [Numpydoc](http://pypi.python.org/pypi/numpydoc/0.3.1) from the
- current [git source](http://projects.scipy.org/numpy/browse_git)
- (previously 0.3.1, see [numpy ticket
- 1489](http://projects.scipy.org/numpy/ticket/1489))
-- [SCons](http://www.scons.org/) 2.0.1.r5134 (unchanged)
+- [[Python]] 2.7 (previously Python 2.5)
+- [[Sphinx]] 1.0.3 (previously Sphinx 0.6.5)
+- [Numpydoc][] from the current [git source][git] (previously 0.3.1,
+ see [numpy ticket 1489][1489])
+- [SCons][] 2.0.1.r5134 (unchanged)
The main effect of the change is that the [hooke module
-documentation](http://www.physics.drexel.edu/~wking/rsrch/hooke/hooke/hooke.html)
-is now generated in its entirety, while the previous implementation
-only generated documentation for Python 2.5-compatible submodules.
+documentation][mod] is now generated in its entirety, while the
+previous implementation only generated documentation for Python
+2.5-compatible submodules.
+
+[doc]: http://doc.hooke.tremily.us/
+[Numpydoc]: http://pypi.python.org/pypi/numpydoc/
+[git]: http://projects.scipy.org/numpy/browse_git
+[1489]: http://projects.scipy.org/numpy/ticket/1489
+[SCons]: http://www.scons.org/
+[mod]: http://doc.hooke.tremily.us/hooke.html
[[!tag tags/hooke]]
[[!tag tags/programming]]
diff --git a/posts/Parallel_computing.mdwn b/posts/Parallel_computing.mdwn
index 4cb770f..1be54c5 100644
--- a/posts/Parallel_computing.mdwn
+++ b/posts/Parallel_computing.mdwn
@@ -23,9 +23,9 @@ Differences from my course website project:
computing class, there are fewer graphics than there are in an
intro-physics class, so the extra power of LaTeX is not as useful.
-[MV]: http://www.physics.drexel.edu/directory/faculty/homepage/?lname=Valli%C3%A8res&fname=Michel
+[MV]: http://www.drexel.edu/physics/contact/facultyDirectory/Vallieres%20Michel/
[phys405]: http://www.physics.drexel.edu/~valliere/PHYS405/
-[f10]: http://www.physics.drexel.edu/~wking/courses/phys405_f10/
+[f10]: http://course.tremily.us/2010-fall/phys405/
[[!tag tags/code]]
[[!tag tags/web]]
diff --git a/posts/Reading_IGOR_binary_waves_from_Python.mdwn b/posts/Reading_IGOR_binary_waves_from_Python.mdwn
index 64cdae2..643936f 100644
--- a/posts/Reading_IGOR_binary_waves_from_Python.mdwn
+++ b/posts/Reading_IGOR_binary_waves_from_Python.mdwn
@@ -1,17 +1,18 @@
[[!meta title="Reading IGOR binary waves from Python"]]
[[!meta date="2010-06-04 18:48:46"]]
+
I finally got around to translating some IBW readers from C to Python.
-And so, I present (drumroll :)
-[igorbinarywave.py](http://www.physics.drexel.edu/~wking/code/hg/hgwebdir.cgi/hooke/file/tip/hooke/driver/igorbinarywave.py).
-Python because it's easy to drop it into my other Python projects (in
-this case, [Hooke](http://code.google.com/p/hooke/)). It's also easy
-to get a hold of all that useful metadata in a hurry. No writing
-ability yet, but I don't know why you'd want to move data that
-direction anyway ;).
+And so, I present (drumroll :) [igorbinarywave.py][] Python because
+it's easy to drop it into my other Python projects (in this case,
+[[Hooke]). It's also easy to get a hold of all that useful metadata
+in a hurry. No writing ability yet, but I don't know why you'd want
+to move data that direction anyway ;).
+
+Thanks to the folks at [WaveMetrics][] for publishing some good
+[documentation][], even if it's in a goofy format.
-Thanks to the folks at [WaveMetrics](http://www.wavemetrics.com/) for
-publishing some good
-[documentation](ftp://ftp.wavemetrics.net/IgorPro/Technical_Notes/TN003.zip),
-even if it's in a goofy format.
+[igorbinarywave.py]: http://git.tremily.us/?p=hooke.git;a=blob;f=hooke/driver/igorbinarywave.py;hb=HEAD
+[WaveMetrics]: http://www.wavemetrics.com/
+[documentation]: ftp://ftp.wavemetrics.net/IgorPro/Technical_Notes/TN003.zip
[[!tag tags/programming]]
diff --git a/posts/SSI/footer.shtml b/posts/SSI/footer.shtml
index 7cac68a..a5f5a4a 100644
--- a/posts/SSI/footer.shtml
+++ b/posts/SSI/footer.shtml
@@ -9,7 +9,7 @@
diff --git a/posts/Stripchart.mdwn b/posts/Stripchart.mdwn
index ada479b..f732373 100644
--- a/posts/Stripchart.mdwn
+++ b/posts/Stripchart.mdwn
@@ -1,17 +1,18 @@
[[!meta title="Stripchart"]]
[[!meta date="2008-07-08 17:03:08"]]
-I was trying to troubleshoot the feedback loop on our NanoScope today, and
-when I went to fire up my [Comedi](http://www.comedi.org/)-driven stripcharts
-monitoring some lines in the DB-25 cable connecting the [[MultiMode]] to the
-Nanoscope, I got a bunch of wierd errors (errnos 11 and 29). I tracked them
-down to some of the Xlib function calls in my stripchart code (yes, I wrote my
-own
-[stripchart](http://www.physics.drexel.edu/~wking/rsrch/code/index.shtml#stripchart)
-code, so sue me), which I don't understand, since I can't find any reference to
-Xlib functions setting errnos.
+[[!template id=gitrepo repo=stripchart]]
-Anyhow, I've patched up my source to gleefully ignore any Xlib errno settings,
-and things seem to be back up and running now. Feel free to give my stripchart
-code a whirl, since I quite enjoy it :p.
+I was trying to troubleshoot the feedback loop on our NanoScope today,
+and when I went to fire up my [[Comedi]]-driven stripcharts monitoring
+some lines in the DB-25 cable connecting the [[MultiMode]] to the
+Nanoscope, I got a bunch of weird errors (errnos 11 and 29). I
+tracked them down to some of the Xlib function calls in my stripchart
+code (yes, I wrote my own stripchart code, so sue me), which I don't
+understand, since I can't find any reference to Xlib functions setting
+errnos.
+
+Anyhow, I've patched up my source to gleefully ignore any Xlib errno
+settings, and things seem to be back up and running now. Feel free to
+give my stripchart code a whirl, since I quite enjoy it :p.
[[!tag tags/programming]]
diff --git a/posts/Subversion.mdwn b/posts/Subversion.mdwn
index 77042e5..5454042 100644
--- a/posts/Subversion.mdwn
+++ b/posts/Subversion.mdwn
@@ -1,18 +1,20 @@
[[!meta title="Subversion"]]
[[!meta date="2008-07-16 19:42:55"]]
-I finally broke down and learned how to serve
-[subversion](http://subversion.tigris.org/)
-repositories. You're welcome to poke around `svn://abax.physics.drexel.edu`
-to see if there is anything interesting.
-I'll probably dump all my code in there, so don't worry if version numbers
-seem to be spiralling out of control :p. I'll try to keep an updated
-[index page](http://www.physics.drexel.edu/~wking/svn) explaining what
-everything does.
+I finally broke down and learned how to serve [subversion][]
+repositories. You're welcome to poke around
+`svn://abax.physics.drexel.edu` to see if there is anything
+interesting.
-Update: I took down the SVN server and switched to Git. Much nicer
-:). The code index page is now
-[here](http://www.physics.drexel.edu/~wking/code).
+I'll probably dump all my code in there, so don't worry if version
+numbers seem to be spiralling out of control :p. I'll try to keep an
+updated index page explaining what everything does.
+
+Update: I took down the SVN server and switched to [[Git]]. Much
+nicer :). The code index page is now [here][index].
+
+[Subversion]: http://subversion.tigris.org/
+[index]: http://git.tremily.us/
[[!tag tags/linux]]
[[!tag tags/programming]]
diff --git a/posts/Thesis/Makefile b/posts/Thesis/Makefile
index 582260f..e689f7b 100644
--- a/posts/Thesis/Makefile
+++ b/posts/Thesis/Makefile
@@ -1,4 +1,4 @@
-REPO = http://www.physics.drexel.edu/~wking/code/git/thesis.git
+REPO = git://tremily.us/thesis.git
PACKAGE = thesis
.PHONY : all checkout clean
diff --git a/posts/Tove_overlay.mdwn b/posts/Tove_overlay.mdwn
index 7d5ebb5..d403d09 100644
--- a/posts/Tove_overlay.mdwn
+++ b/posts/Tove_overlay.mdwn
@@ -5,14 +5,14 @@ this blog before pushing commits to the live server. Gentoo's ikiwiki
ebuild ([bug 144453][]) is in Torsten Veller's overlay, so I forked
his overlay and bumped the Ikiwiki version number. I've emailed
Torsten with a merge request, but haven't heard back yet. Anyhow, add
-this [[layman.xml]] to your `/etc/layman/layman.cfg` `overlays` listing
+this `layman.xml` to your `/etc/layman/layman.cfg` `overlays` listing
and run:
- layman -a tove-wtk
+ # layman -a tove-wtk
Then:
- emerge -av ikiwiki
+ # emerge -av ikiwiki
and you're off!
@@ -20,7 +20,6 @@ Update: Torsten just [pushed the ikiwiki ebuild into Portage][pushed].
There is no longer any need to mess around with layman if you want to
install ikiwiki.
-
[ikiwiki]: http://ikiwiki.info/
[bug 144453]: http://bugs.gentoo.org/show_bug.cgi?id=144453
[pushed]: http://bugs.gentoo.org/show_bug.cgi?id=144453#c34
diff --git a/posts/Tove_overlay/layman.xml b/posts/Tove_overlay/layman.xml
deleted file mode 100644
index 60920da..0000000
--- a/posts/Tove_overlay/layman.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-
-
-
- tove
- Torsten Veller's Overlay
-
- Torsten Veller <tove@gentoo.org>
-
-
-
-
- tove-wtk
- Torsten Veller's Overlay (WTK branch)
-
- W. Trevor King <wking@drexel.edu>
-
-
-
-
diff --git a/posts/Xmodmap/Makefile b/posts/Xmodmap/Makefile
index de35624..e70bd00 100644
--- a/posts/Xmodmap/Makefile
+++ b/posts/Xmodmap/Makefile
@@ -1,5 +1,5 @@
-REPO = http://www.physics.drexel.edu/~wking/code/git/dotfiles.git/
-PACKAGE = dotfiles
+REPO = git://tremily.us/dotfiles-public.git
+PACKAGE = dotfiles-public
.PHONY : all checkout clean
@@ -15,7 +15,7 @@ checkout : $(PACKAGE)
(cd $(PACKAGE) && git pull && git reset --hard HEAD)
_Xmodmap : checkout
- cp $(PACKAGE:%=%/$@) $@
+ cp $(PACKAGE:%=%/src/$(@:_%=.%)) $@
unicode_sampler : _Xmodmap gen_sampler.py
./gen_sampler.py $< > $@
diff --git a/posts/cookbook.mdwn b/posts/cookbook.mdwn
index 4c828fa..cd8dd8f 100644
--- a/posts/cookbook.mdwn
+++ b/posts/cookbook.mdwn
@@ -13,7 +13,7 @@ See the [README][] for details.
[Django]: https://www.djangoproject.com/
[Grappelli]: https://github.com/sehmaschine/django-grappelli
[django-taggit]: https://github.com/alex/django-taggit
-[README]: http://www.physics.drexel.edu/~wking/code/git/gitweb.cgi?p=cookbook.git;a=blob;f=README;hb=HEAD
+[README]: http://git.tremily.us/?p=cookbook.git;a=blob;f=README;hb=HEAD
[[!tag tags/code]]
[[!tag tags/linux]]
diff --git a/posts/dotfiles.mdwn b/posts/dotfiles.mdwn
index 0080c17..6112241 100644
--- a/posts/dotfiles.mdwn
+++ b/posts/dotfiles.mdwn
@@ -18,7 +18,7 @@ Python][dotfilemanager] by Sean Hammond.
[SK]: http://repository.steve.org.uk/cgi-bin/hgwebdir.cgi/dotfiles/file/tip?file/tip/
[blog post]: http://blog.steve.org.uk/didn_t_i_kill_you_already_.html
-[README]: http://physics.drexel.edu/~wking/code/git/gitweb.cgi?p=dotfiles-framework.git;a=blob;f=README;hb=HEAD
+[README]: http://git.tremily.us/p=dotfiles-framework.git;a=blob;f=README;hb=HEAD
[dotfile-manager]: http://blog.steve.org.uk/poppa_s_got_a_brand_new_bang_.html
[dotfilemanager]: https://github.com/seanh/dotfilemanager
diff --git a/posts/git-php.mdwn b/posts/git-php.mdwn
index ca09b76..3f61da3 100644
--- a/posts/git-php.mdwn
+++ b/posts/git-php.mdwn
@@ -3,9 +3,11 @@
[[!template id=gitrepo repo=git-php]]
[Peeter Vois's][PV] [git-php][] is a nice PHP script which you can
-drop in to make your public [[Git]] repo's browsable. [Take a
-look][look]!
+drop in to make your public [[Git]] repo's browsable.
+
+Update: I've migrated from `git-php` to `gitweb` (which is distributed
+with Git). [Take a look][look]!
[PV]: http://people.proekspert.ee/peeter/
[git-php]: http://people.proekspert.ee/peeter/git/git.php?p=git-php.git
-[look]: http://www.physics.drexel.edu/~wking/code/git/git.php
+[look]: http://git.tremily.us/
diff --git a/posts/mdwn_itex.mdwn_itex b/posts/mdwn_itex.mdwn_itex
index 99db83c..45c1f99 100644
--- a/posts/mdwn_itex.mdwn_itex
+++ b/posts/mdwn_itex.mdwn_itex
@@ -6,11 +6,10 @@ get the plugin working with ikiwiki, so I'm recording the steps I took
here in case other ikiwiki users find this useful.
* Install [itex2MML][]
-* [Install][install_plugin] my updated [[mdwn_itex.pm|mdwn_itex.pm]]
- plugin ([[mdwn_itex.patch|mdwn_itex.patch]] against Jason's
- version).
+* [Install][install_plugin] my updated `mdwn_itex.pm` plugin
+ (`mdwn_itex.patch` against Jason's version).
* Patch your ikiwiki [templates][] to use a `DOCTYPE` supporting
- MathML ([[mdwn_itex-templates.patch|mdwn_itex-templates.patch]]).
+ MathML (`mdwn_itex-templates.patch`).
* Add config options along the lines of:
# plugins to add to the default configuration
@@ -49,8 +48,8 @@ The `htmlscrubber` and `htmltidy` plugins must be disabled because
otherwise they [strip][scrubber_strip] [out][tidy_strip] the MathML
markup.
-Update: current versions of my patched files can be found in my
-ikiwiki git branch.
+Update: current versions of my patched files can be found in the
+`mdwn_itex` branch of my ikiwiki git repository.
[plugin]: http://jblevins.org/git/ikiwiki/plugins.git/plain/mdwn_itex.pm
[itex2MML]: http://golem.ph.utexas.edu/~distler/blog/itex2MML.html
diff --git a/posts/mdwn_itex/mdwn_itex-templates.patch b/posts/mdwn_itex/mdwn_itex-templates.patch
deleted file mode 100644
index 65a12c6..0000000
--- a/posts/mdwn_itex/mdwn_itex-templates.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-diff -ru /usr/share/ikiwiki/templates/page.tmpl .ikiwiki/templates/page.tmpl
---- /usr/share/ikiwiki/templates/page.tmpl 2010-09-30 08:58:51.000000000 -0400
-+++ .ikiwiki/templates/page.tmpl 2010-09-30 09:10:02.000000000 -0400
-@@ -1,8 +1,12 @@
-
-
--
--
-+
-+
-+
-
-
-
diff --git a/posts/mdwn_itex/mdwn_itex.patch b/posts/mdwn_itex/mdwn_itex.patch
deleted file mode 100644
index 1c68aa5..0000000
--- a/posts/mdwn_itex/mdwn_itex.patch
+++ /dev/null
@@ -1,157 +0,0 @@
-diff -u a/mdwn_itex.pm b/mdwn_itex.pm
---- a/mdwn_itex.pm 2010-09-29 17:30:37.000000000 -0400
-+++ b/mdwn_itex.pm 2010-09-29 23:59:59.713046023 -0400
-@@ -2,66 +2,70 @@
- #
- # itex to MathML plugin for IkiWiki. Based on the itex MovableType
- # plugin by Jacques Distler.
--#
--# Jason Blevins
--# Chapel Hill, March 16, 2008
-
- package IkiWiki::Plugin::mdwn_itex;
-
- use warnings;
- use strict;
--use IkiWiki 2.00;
-+use IkiWiki 3.00;
-
- use File::Temp qw(tempfile);
-
--my $markdown_sub;
--my %itex_pages;
--
- sub import {
-- hook(type => "getopt", id => "mdwn_itex", call => \&getopt);
-- hook(type => "htmlize", id => "mdwn", call => \&htmlize);
-- hook(type => "preprocess", id => "itex", call => \&preprocess_itex);
--}
--
--sub getopt () {
-- eval q{use Getopt::Long};
-- error($@) if $@;
-- Getopt::Long::Configure('pass_through');
-- GetOptions(
-- # Location of the itex2mml binary
-- "itex2mml=s" => \$config{itex2mml},
-- # Enable or disable numbering of \[..\] equations
-- "itex_num_equations!" => \$config{num_equations},
-- # Process all pages by default or require [[!itex ]] directive?
-- "itex_default!" => \$config{itex_default},
-- );
--
-- # Default settings
-- $config{itex2mml} = '/usr/local/bin/itex2MML' unless defined $config{itex2mml};
-- $config{itex_num_equations} = 1 unless defined $config{itex_num_equations};
-- $config{itex_default} = 0 unless defined $config{itex_default};
--}
--
--sub preprocess_itex (@) {
-- my %params = @_;
-- if (defined $params{disable}) {
-- $itex_pages{$params{page}} = 0;
-- } else {
-- $itex_pages{$params{page}} = 1;
-+ # register the plugin
-+ hook(type => "getsetup", id => "mdwn_itex", call => \&getsetup);
-+ hook(type => "checkconfig", id => "mdwn_itex", call => \&checkconfig);
-+ hook(type => "preprocess", id => "itex", call => \&preprocess);
-+ hook(type => "htmlize", id => "mdwn_itex", call => \&htmlize,
-+ longname => "Markdown + itex");
-+}
-+
-+sub getsetup () {
-+ # declare plugin options etc. for the setup file
-+ return
-+ plugin => {
-+ description => "itex to MathML conversion followed by Markdown formatting",
-+ safe => 1,
-+ rebuild => 1,
-+ section => "format",
-+ },
-+ itex2mml => {
-+ type => "string",
-+ example => '/usr/local/bin/itex2MML',
-+ description => "path to the itex2MML binary",
-+ safe => 0, # path
-+ rebuild => 0,
-+ },
-+ itex_num_equations => {
-+ type => "boolean",
-+ example => 1,
-+ description => "autonumber \[..\] equations?",
-+ safe => 1,
-+ rebuild => 1,
-+ },
-+}
-+
-+sub checkconfig () {
-+ # setup default settings
-+ if (! exists $config{itex2mml}) {
-+ $config{itex2mml} = '/usr/local/bin/itex2MML';
-+ }
-+ if (! exists $config{itex_num_equations}) {
-+ $config{itex_num_equations} = 1;
-+ }
-+ if (! exists $config{itex_default}) {
-+ $config{itex_default} = 0;
- }
-- return '';
- }
-
--# Taken from mdwn plugin and modified to call itex2MML.
- sub htmlize (@) {
-+ # convert the page contents to XHTML.
- my %params=@_;
-+
- my $content = $params{content};
- my $page = $params{page};
-
-- # Default settings
-- $itex_pages{$page} = $config{itex_default} unless defined $itex_pages{$page};
--
-- $params{content} = itex_filter($content) if $itex_pages{$page};
-+ $params{content} = itex_filter($content);
-
- return IkiWiki::Plugin::mdwn::htmlize(%params);
- }
-@@ -77,6 +81,7 @@
-
- my ($Reader, $outfile) = tempfile( UNLINK => 1 );
- my ($Writer, $infile) = tempfile( UNLINK => 1 );
-+ binmode $Writer, ":utf8";
- print $Writer "$content";
- system("$config{itex2mml} < $infile > $outfile");
- my @out = <$Reader>;
-@@ -136,6 +141,9 @@
-
- =head1 AUTHORS
-
-+W. Trevor King ,
-+updates to IkiWiki v3.00
-+
- Jason Blevins ,
- itex Blosxom plugin
-
-@@ -144,6 +152,12 @@
-
- =head1 SEE ALSO
-
-+W. Trevor King's blog entry for this plugin:
-+http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/mdwn_itex/
-+
-+Jason Blevins' ikiwiki plugin:
-+http://jblevins.org/git/ikiwiki/plugins.git/plain/mdwn_itex.pm
-+
- ikiwiki Homepage:
- http://ikiwiki.info/
-
-@@ -155,6 +169,8 @@
-
- =head1 LICENSE
-
-+Copyright (C) 2010 W. Trevor King
-+
- Copyright (C) 2008 Jason Blevins
-
- Copyright (C) 2003-2007 Jacques Distler
diff --git a/posts/mdwn_itex/mdwn_itex.pm b/posts/mdwn_itex/mdwn_itex.pm
deleted file mode 100644
index 2d3072f..0000000
--- a/posts/mdwn_itex/mdwn_itex.pm
+++ /dev/null
@@ -1,190 +0,0 @@
-#!/usr/bin/perl
-#
-# itex to MathML plugin for IkiWiki. Based on the itex MovableType
-# plugin by Jacques Distler.
-
-package IkiWiki::Plugin::mdwn_itex;
-
-use warnings;
-use strict;
-use IkiWiki 3.00;
-
-use File::Temp qw(tempfile);
-
-sub import {
- # register the plugin
- hook(type => "getsetup", id => "mdwn_itex", call => \&getsetup);
- hook(type => "checkconfig", id => "mdwn_itex", call => \&checkconfig);
- hook(type => "preprocess", id => "itex", call => \&preprocess);
- hook(type => "htmlize", id => "mdwn_itex", call => \&htmlize,
- longname => "Markdown + itex");
-}
-
-sub getsetup () {
- # declare plugin options etc. for the setup file
- return
- plugin => {
- description => "itex to MathML conversion followed by Markdown formatting",
- safe => 1,
- rebuild => 1,
- section => "format",
- },
- itex2mml => {
- type => "string",
- example => '/usr/local/bin/itex2MML',
- description => "path to the itex2MML binary",
- safe => 0, # path
- rebuild => 0,
- },
- itex_num_equations => {
- type => "boolean",
- example => 1,
- description => "autonumber \[..\] equations?",
- safe => 1,
- rebuild => 1,
- },
-}
-
-sub checkconfig () {
- # setup default settings
- if (! exists $config{itex2mml}) {
- $config{itex2mml} = '/usr/local/bin/itex2MML';
- }
- if (! exists $config{itex_num_equations}) {
- $config{itex_num_equations} = 1;
- }
- if (! exists $config{itex_default}) {
- $config{itex_default} = 0;
- }
-}
-
-sub htmlize (@) {
- # convert the page contents to XHTML.
- my %params=@_;
-
- my $content = $params{content};
- my $page = $params{page};
-
- $params{content} = itex_filter($content);
-
- return IkiWiki::Plugin::mdwn::htmlize(%params);
-}
-
-sub itex_filter {
- my $content = shift;
-
- # Remove carriage returns. itex2MML expects Unix-style lines.
- $content =~ s/\r//g;
-
- # Process equation references
- $content = number_equations($content) if $config{itex_num_equations};
-
- my ($Reader, $outfile) = tempfile( UNLINK => 1 );
- my ($Writer, $infile) = tempfile( UNLINK => 1 );
- binmode $Writer, ":utf8";
- print $Writer "$content";
- system("$config{itex2mml} < $infile > $outfile");
- my @out = <$Reader>;
- close $Reader;
- close $Writer;
- eval { unlink ($infile, $outfile); };
- return join('', @out);
-}
-
-sub number_equations {
- my $body = shift;
-
- my $prefix = "eq";
- my $cls = "numberedEq";
-
- my %eqnumber;
- my $eqno=1;
-
- # add equation numbers to \[...\]
- # - introduce a wrapper-
and a with the equation number
- while ($body =~ s/\\\[(.*?)\\\]/\n\n
\($eqno\)<\/span>\$\$$1\$\$<\/div>\n\n/s)
- {
- $eqno++;
- }
-
- # assemble equation labels into a hash
- # - remove the \label{} command, collapse surrounding whitespace
- # - add an ID to the wrapper-
. prefix it to give a fighting chance
- # for the ID to be unique
- # - hash key is the equation label, value is the equation number
- while ($body =~ s/