Archive for the ‘markdown’ tag
Link problems : Markdown versus latex2wp.py
As John Baez (and hopefully others) noticed most links here on NeB are now screwed up.
For years I’ve used the Markdown syntax to include links in posts (that is something like [this is what you see](and here is the URL)). NeB used an older version ( Version 1.0.1k) of php Markdown to convert these to proper links (as I did have problems with the newer version).
Ever since the Return to LaTeX post, I’m trying to re-educate myself to write posts in LaTeX and convert them into wp-format using the Latex2WP python script.
Unfortunately this script doesn’t go together nicely with the Markdown-syntax, forcing me to go over the converted latex-file almost line by line fixing errors in order to be able to post. Not the time-saver I had in mind…
I hope to post a lot of new material once the semester finishes and therefore disabled the Markdown-plugin. This causes all links to remain in Markdown-format, which is a nuisance but, if you really want to follow the link it is still there for you to copy-paste. Depending on how exciting the christmas-break will be I’ll try to hard-code the links in some of the more popular posts.
If someone knows of an elegant solution, such as a micro-markdown wp-plugin only parsing links, please drop a comment.
UPDATE : I have downloaded the Markdown quicktags plugin. It replaces the standard HTML-editor of WordPress with a Markdown-editor. There is an option “Render” which transforms Markdown to HTML and then updating the post will save the HTML-version. This looks like a relative quick way to get my old post-links back. So far, I’ve rescued the posts of the last year, more later. Hopefully, this causes no overload in your RSS-aggregator…
Writing & Blogging
Terry Tao is reworking some of his better blogposts into a book, to be published by the AMS (here’s a preliminary version of the book “What’s New?”)
After some thought, I decided not to transcribe all of my posts from last year (there are 93 of them!), but instead to restrict attention to those articles which (a) have significant mathematical content, (b) are not announcements of material that will be published elsewhere, and (c) are not primarily based on a talk given by someone else. As it turns out, this still leaves about 33 articles from 2007, leading to a decent-sized book of a couple hundred pages in length.
If you have a blog and want to turn it into a LaTeX-book, there’s no need to transcribe or copy every single post, thanks to the WPTeX tool. Note that this is NOT a WP-plugin, but a (simple at that) php-program which turns all posts into a bookcontent.tex file. This file can then be edited further into a proper book.
Unfortunately, the present version chokes on LaTeXrender-code (which is easy enough to solve doing a global ‘find-and-replace’ of the tex-tags by dollar-signs) but worse, on Markdown-code… But then, someone fluent in php-regex will have no problems extending the libs/functions.php file (I hope…).
At the moment I’m considering turning the Mathieu-games-posts into a booklet. A possible title might be Mathieumatical Games. Rereading them (and other posts) I regret to be such an impatient blogger. Often I’m interested in something and start writing posts about it without knowing where or when I’ll land. This makes my posts a lot harder to get through than they might have been, if I would blog only after having digested the material myself… Typical recent examples are the tori-crypto-posts and the Bost-Connes algebra posts.
So, I still have a lot to learn from other bloggers I admire, such as Jennifer Ouellette who maintains the Coctail Party Physics blog. At the moment, Jennifer is resident blogger-journalist at the Kavli Institute where she is running a “Journal Club” workshop giving ideas on how to write better about science.
But the KITP is also committed to fostering scientific communication. That’s where I come in. Each Friday through April 26th, I’ll be presiding over a “Journal Club” meeting focusing on some aspect of communicating science.
Her most recent talk was entitled To Blog or Not to Blog? That is the Question and you can find the slides as well as a QuickTime movie of her talk. They even plan to set up a blog for the participants of the workshop. I will surely follow the rest of her course with keen interest!
NeB on Leopard and iPhone
If you have an iPhone or iPod Touch and point your Safari browser to this blog you can now view it in optimised format, thanks to the iWPhone WordPress Plugin and Theme. I’ve only changed the CSS slightly to have the same greeny look-and-feel of the current redoable theme.
Upgrading a WordPress-blog running under Tiger (Mac OS 10.4) to Leopard produces a few anxiety moments. All of the standard tools (Apache, PHP and MySQL) seem no longer to work as before. For those of you who do not want to waste too much time over it, I’ll walk through the process.
After upgrading to Leopard you want to check whether your blog is still alive, so you fire up Safari and will be greeted by the message that Safari cannot find your server. Sure enough you forgot to start the WebServer in SystemPreferences/Sharing/Web Sharing. Having fixed this you will see the default Apache-screen because Leopard put these default-files in your webserver-root directory (/Library/WebServer/Documents). In case you installed your blog under a user account you will get a message that you enter forbidden territory, see below for the solution to that problem. Having removed all those index.html files (making sure NOT to delete the index.php of your blog) a more serious problem presents itself : you see the text-version of index.php meaning that PHP isnt working. You check the /etc/httpd/httpd.conf file and it still contains all the changes you made to it to get PHP running under Tiger, so what is going on?
Googling for something like ‘enabling PHP under Leopard’ you’ll discover that the configuration file used by the webserver is in a different location. It now resides at /private/etc/apache2/httpd.conf. You will have to remove the hash sign (#) at the beginning of line 114 so that it reads
LoadModule php5_module libexec/apache2/libphp5.so
Next, you have to create a php.ini file and change one line. The first thing is settled by the following Terminal-commands
cd /private/etc
sudo cp php.ini.default php.ini
and in the php.ini you have to modify line 305 so that it becomes (removing the latter part of the line)
error_reporting = E_ALL
Restarting the webserver enables PHP. If you need more details check out the article Enabling PHP and Apache in Leopard. However, you are not quite done yet. Your blog will now show the WordPress-page that something is wrong with your mysql-database. However, mysql seems to be running fine as you can check from the Terminal so PHP cannot find it.
To remedy this, you have to add the locations (after the = sign) in the follwing two lines of the php.ini file
mysql.default_socket = /private/tmp/mysql.sock
mysqli.default_socket = /private/tmp/mysql.sock
Restarting the webserver should resolve the problem. But then your blog can still choke on old PHP-code in one of the plugins you use. In my case I was using an ancient version of the PHP-Markdown plugin but after replacing it with the newest version NeB looked just like I left it with Tiger…
A final point : webpages stored in personal Sites-folders cannot be served by Apache2 and will produce a message that you have not enough privileges to view the page. To resolve this, type the following command from the Terminal
sudo cp /private/etc/httpd/users/*.conf /private/etc/Apache2/users
bookmarks tuesday cleanup
Geeky Mom : Why am I blogging?. Been there before. Sooner or later
all non-pseudonomenous bloggers are faced with the same dilemmas.
There’s really no answer or advice to give except : blog when you feel
like it, if not do something different, after all its just one of those
billion of blogs around.
Texmaker : another
LaTeX-frontend, possibly having a few extras such as : a structure-pane
including labels you gave to formulas, theorems etc. (click on them
brings you to them). Intend to use it now as I’m in another rewrite of
the never-ending-book..
Microformats : “Designed for
humans first and machines second, microformats are a set of simple, open
data formats built upon existing and widely adopted standards.” May
have another look.
Quicksilver : a recurring
link. At times when I feel learning key-strokes may save me a lot of
time I have (another) go at Quicksilver. Last week, Ive reinstalled this
blog more or less post by post and used keystrokes to send a line in the
SQL-file of the database dump of NEB as a clipping to Scrivener to
MultiMarkdown it further. I used the app Service Scrubber
to define my own key-strokes. Must have another go at Quicksilver soon.
Im sure it distinguishes ‚”power mac users” from the rest of
us.
List of GTDTools : a good list of GTD-software. I’m probably just
too chaotic for GTD to improve my workflow but somehow I cannot resist
trying some of these things out.
LifeDEV : One of those sites that tells
me I should take GTD more seriously
DoIt : One of
these GTD-tools. It is said to go well with Quicksilver, so maybe, one
day.
Think
: Here a little seemingly completely useless tool which works well (at
least for me). No, it does not make you think, but at least it helps you
while you are thinking (or doing anything a bit focussed). Install it
and enjoy! The principle is that it just blocks out all other open
windows (and there are keystrokes (yes, again) to get you quickly in
and out.) Besides, it looks great. It’s in my dock and this says it
all
Thinkature :
a brainstorming tool. Dont know why I did bookmark this. Perhaps one
day, a few years from now
a talk by Toby Stafford I came across by accident. Maybe there are other
interesting talks on the site?
idea! Give yourself badges for how well you do science (or talk/write
about science). Have to collect my badges soon. I’m sure this only
works for people with a scouting-history, but who
knows?
that may become useful. MacResearch.org is an open and independent
community for scientists using Mac OS X and related hardware in their
research. It is the mission of this site to cultivate a knowledgeable
and vibrant community of researchers to exchange ideas and information,
and collectively escalate the prominence of Apple technologies in the
scientific research community. They have some interesting articles
and tutorials on e.g. DevonThink and BibDesk etc. Worth to
revisit.
">Jennifer in love : well‚ should I say something about this?
probably best not.
Breakthrough CLI : another pamphlet in favor of the Command Line! A
must read for those who perfer GUIs to CLIs.
<
p>
site : Rod is working hard on CLI-20. Whenever he releases version
2.0, neverendingbooks will be among the first sites to run it. I still
love the idea.
">Why do I bother? : an n-category post I got briefly interested in,
but was somehow flooded by professional
math-philosophers
-reviewed.html">Newton Legacy Reviewed : just that, a first review
on the next bookmark.
Legacy : a free online book, a murder mystery with a physics touch.
Perhaps this is the best investment of time/energy : write a popular
science book rather than another paper. Read half way through it (sorry
but not the best prose Ive read so far), may continue but was held up
reading a (real) murder mystery Equinox featuring also Newton and
alchemy (must be in the air somehow), also not the best mystery read
so far
: no comment
(to be continued)
mathML and work ahead
It has
been a difficult design decision, but I’m going to replace the LaTeXRender WordPress
Plugin for mathML as the
default TeX-interface for NeverEndingBooks. I will keep LaTeXRender on
standby as I may have to use exotic packages or commands that iTeX does
not deliver, but for most math-related posts, MathML will do the job
nicely (as the n-category
cafe shows every day (or even more often)). Not that I stopped being
a dilettante but I’m going to do most of my writings (including
blog-posts) using Scrivener (more on this
another time) and Scrivener supports MultiMarkdown and allows exporting to LaTeX and XHTML (using MathML).
I could never have pulled this off in such a short time without Jacques Distler
more or less on constant stand-by (thanks Jacques!). Looking at the
times his emails were send I have no idea in which time zone he lives
(let alone sleeps…). So, here a walk-through the changes :
As
I’m on WP 2.0.5 I’ll start with Frederick’ post. He tells me I have to install first the itex2MML binary as
explained by
Jacques but I find that there is more recent
material and therefore download the most recent imath2MML-package
and follow the readme. There is a Mac OSX binary but it’s not clear
for what processor (PPC/Intel/Binary) but a quick mail to Jacques learns
me that it’s PPC which is fine by me but on the spot he puts a
universal binary online, so whatever your Mac is you can just download
the binary, copy it to /usr/local/bin and make sure its chmodded
755.
Back to Frederick’s post, download and install the plugin itexToMML.php in the usual way
(fortunately I spot just in time that I have to change one line saying
where my itex2MML binary is (in Frederick’s file it is NOT the default
location)). You can verify whether the plugin and itex2MML do what they
are supposed to do by typing a LaTeX-command in a post and save it. The
output will not produce the desired formula but have a look at the
source file and see whether there is some mathML code in it. If so,
fine! If not, go back and check everything.
If this works, it is
“merely” a problem of getting your mathML served. Frederick suggests
to unpack wordpress_mathML.zip in the wp-includes directory (but you
better make sure you have made a copy of the original class.php and
functions-formatting.php files. In the end I decided against this
approach (that is, to replace only the functions-formatting.php but NOT
the class.php file). If you have two or more themes you want to
maintain, it is probably better to change the headers (because this is
what we have to do to get mathML served) only in those themes which are
XML-sound. In my case, the Command Line Interface theme most certainly is NOT!!!).
Go to your
theme-files and look for the header.php (or similar) file and replace
the default header by the code in the addendum to
this post within php-tags. If you can go to your blog-page then you
are in good shape and things should work well (apart possibly from
layout considerations, see below). Of course, in my case i was greeted
by ” XML “yellow screen of death” (as Jacques calls
it) and I was convinced I did something wrong, so I tried out several
useless things for a couple of hours before it dawned on me that the
reason might just be that my blog-files were not valid XHTML (and the
new headers are very demanding on serving only well-form XHTML). I had
to modify all changes I made to sidebars etc. as well as rewrite parts
of my first posts (I used to take a rather liberal view on writing
blog-posts, writing a mixture between Markdown and improvised HTML and
in the process was very lax about closing IMG-tags and the likes).
But after some time and numerous corrections to the files I got the
main-page up and running (and even had the mathML served as a readable
formula) apart from the fact that I barely recognized my own site.
I printed out source files of the page with and without changed
headers and couldn’t find a difference. So, it had to do with the
CSS-style files, but why on earth would the new headers be picky about
CSS? But as a last resort, after narrowing the search down to one
CSS-line, I asked Jacques whether he had an idea what went on. His reply
will be remembered for quite some time :
A fascinating
question. The answer is that it *is* following the CSS directive, but
in XHTML, ‘body’ is not what you think it is. ‘body’ is just big enough
to contain its content. It does not fill the viewport. ‘html’ fills the
viewport. The solution (a solution) is described inhttp://golem.ph.utexas.edu/~distler/blog/archives/000203.html
Many hours later, I still haven’t got a clue what
this is all about, but I blindly followed the hint and surely all
problems vanished. In short, another day wasted in front of a
computer-screen.
At the moment I’m back to old headers and
will not be writing mathML for some time as I have the vast job ahead to
validate all my previous posts to XHTML-standards (if not you would see
more yellows screens of death than anything else. So, here’s the
strategy I’ll be taking in the weeks ahead (I’ll sleep on it tonight
so if any of you think there is a better way, reply quickly)
- rewrite each and every post in proper MultiMarkdown using iTeX for
the most common math and only resorting to LaTeXRender for exotic things
(such as Sudoku, Chess, Dvonn) and run these posts through Markdown
(to get basic HTML and all links in place). - download these
files to the WP-database (so that in the CLI-interface you will be able
to follow all links, but will read all iTeX as TeX-commands (as the
command line intended after all). - in the process change all
broken links to the default permalink-structure (with index.php?p=231 or
so).
Clearly, this is a work that will take a couple of
weeks but it may be fun to reread these old posts and possibly add new
information about the subjects. When I’m making these changes, I’ll
use the new headers so if you are using a smart browser look out for the
yellow screens. When they happen, either use a dumb browser (such as
Safari) or go into CLI-interface mode where everything should still
work. I plan to start with the oldest posts as this seems more fun to
me.