Blogging in Markdown with Blogger and Markable (on a Mac)

In a recent post, I extolled the virtues of Markdown as well as the online Markable editor and the Markdown Service Tools available for Markdown to HTML conversion in Mac OSX. This got me to thinking whether I could use Markdown to speed up writing some of my blog posts.

For ease of controlling the layout and context - and potentially re-using text and HTML - I write all my blog posts in the Blogger HTML window rather than using the “Compose” tools. I’m not entirely sure why but I just tend to prefer the result. (Part of it, I think, is the purity of the underlying HTML - what that says about me, I’m not sure I want to know!)

I often email myself content and plain text notes to tidy up later (hence the massive pile of half-written draft posts that I have) but since (re)discovering Markdown, I have started making more notes in Markdown and wondered if I could harness that in my blog writing. Blogger does not have a dirext Markdown editor, sadly, but there does seem to be a pretty convenient solution for Mac users, at least.

1. Install Markdown Service Tools. Brett Terpstra’s Markdown Service Tools offer, among other things, the capability to direct copy Markdown onto the clipboard as HTML code or make the Markdown to HTML conversion in place.

2. Write your Markdown in Markable. Whilst not strictly necessary, writing the Markdown in the Markable editor will catch any problems with your Markdown as you go.

3. Convert your Markdown to HTML. Windows users might need to export the HTML and then open the file in a text editor to copy and paste into Blogger. On a Mac, with the Markdown Service Tool, it is a bit easier - although, sadly, not quite as easy as I had hoped. The Service to use is:

md - Convert - HTML to Clipboard

Unfortunately, this does not seem to be available for highlighted text in the Markable window. Instead, there is the need to first copy and paste the text to a regular text window. This is not so bad, as the regular Blogger window itself will do. You then need to use the conversion service and paste back into the Window. Alternatively, just use:

md - Convert - MultiMarkdown to HTML

This will convert the text in place. You can either use the Services menu item (or right-click), or you can setup a Markdown Service Shortcut to do it all with the keyboard.

4. Make sure that line breaks are used. One thing I noticed when converting the HTML is that it (sensibly) uses paragraph markers. If, like me, you use Blogger’s capacity to Press “Enter” for line breaks, you will need to change this. (The laziness and readibility this option enables are not needed when using Markdown anyway.)

5. Add pictures, tidy and post. With the main text, links and formatting in place, it is now a simple case of adding the pictures, tags etc., giving the post a quick preview (and tidy if necessary) and unleash it to the world. The added benefit, of course, is that you have an extra copy of your post saved in Markable in case anything goes wrong.

Disadvantages

As well as the line endings issue, there are a few disadvantages of doing things this way. One problem is that if you Preview a post and then spot an error, you have three obvious choices, none of which appeals:

1. Edit in the Blogger window, which is easy, but then have different Blogger and Markable versions of the text.
2. Edit in both Blogger and Markable.
3. Edit in Markable and then repeat the text copy and conversion process.

The latter is obviously the best if the changes are large but what if you have already added extra pictures and things?

One solution is to convert your HTML back to Markdown to continue editing.

md - Convert - HTML to Markdown

This has pros and cons. One pro and con is that the new Markdown does not necessarily look like the original. This can teach you new Markdown but might also confuse!

The picture placement and formatting also does not remain quite the same and may need re-jigging once the Markdown to HTML conversion is repeated. This only seems to be a problem for left/right-aligned images, though. It's also a fairly easy way to get images into Markable files, if that is your goal!

It may not be suitable for every post, and there is a good chance I will end up going for tweaking option 1 (abandoning the Markable version) in most cases, but it could prove a useful way to write posts with a lot of links and formatting. If nothing else, it's another good way to develop some Markdown skills.

Python in a Nutshell - free PDF available!

If you are a Python programmer, you might be interested to know that you can get a free PDF of Python in a Nutshell, 2nd Edition from IT ebBooks. It's a few year's old now but still has a lot of useful basic Python syntax. It doesn't cover Python 3, so if you are a newbie you might want to hunt down some specific advice about programming Python 3 compatible code in Python 2.7. (To be honest, I still haven't plucked up the courage to look at the Python 2 vs. Python 3 difference myself but it might be worth having a go at the Python 3 tutorial.)

Marvellous Markdown

Another positive outcome of the recent Software Carpentry boot camp was the excuse and opportunity to get a bit more to grips with Markdown. This is really useful pseudocode that retains a high degree of human readability in plain text form, whilst being easily converted to HTML and other rich text formats. I'd already used it a bit for some of my content on the University of Southampton Computational Modelling Group website but I'd never fully realised its flexibility, value and potential until I started writing README files in it.

I won't try to explain Markdown itself here. The Wikipedia article is pretty informative if you want to know more. Instead, this a quick post to highlight/bookmark some useful Markdown tools that I've come across.

Markable

The first is the Markable website.

This is great if you just want to try your hand at a bit of Markdown and see what the HTML conversion would look like. Simply type your text in the online Markable editor and the HTML window will automatically update to reflect the changes! You can then copy the Markdown to the clipboard or export Markdown/HTML to a file.

If you see yourself using Markdown a lot, as I now do, you can register and take advantage of a whole bunch of other tools, such as (auto)saving content to work on later or exporting the Markdown (or HTML) directly into Dropbox.

Markdown Service Tools

Of course, if you are like me then saving to HTML code might not be enough for you. You might want to see the HTML code and/or copy it for use elsewhere. (I write all my blog posts in the HTML editor, for example.) On a Mac there is the tremendously useful Markdown Service Tools by Brett Terpstra that, among other things, includes tools for precisely this. Simply download the zip file, unpack and then copy the relevant *.workflow files to your OS X System Service folder:

~/Library/Services/

(Brett has a description of how to install Services here. You might have to make the Services/ folder first - I did.) This makes those services available via the Services menu item (or right-click → Services) across a range of Apple applications. My favourite so far is the "md - Convert - HTML to Clipboard" service, which converts highlighted Markdown text to HTML and copies it directly onto the clipboard. In combination with the Markable editor, I think this could be really useful.

Python-Markdown

It's worth quickly mentioning that there's a Markdown Python library, if for no other reason than that is appears in the Markable screen grab above! This can be used for easy conversions between formats, which might be handy for coding up batch conversions of *.md to HTML README files etc. I really need to save this one for another day as I am still getting to grips with it and working out how/where it can be useful for me.

Putting Archaeopteryx back on its perch?

Around this time last year, the sad news came out that South Korean textbook publishers were removing examples of evolution following pressure from Creationists. [Soo Bin Park (2012) South Korea surrenders to creationist demands. Nature 486:14.] One of the examples to be dropped was Archaeopteryx, on the grounds that it might not be an ancestral bird after all. I am not sure how they will respond to last week's news that recent research puts Archaeopteryx back in the bird lineage, as opposed to being "just another feathered dinosaur". (Just‽)

The study in question, A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds [Godefroit et al., Nature (2013) doi:10.1038/nature12168], describes a 170-million-year-old fossil (below). Twenty million years or so older than Archaeopteryx, Aurornis xui is touted as the earliest definite early bird. (Artist's reconstruction, above.) Furthermore, the traits it shared by the two seem to put Archaeopteryx fully back within the ancestral avian lineage.

The authors include one of my Southampton colleagues, Gareth Dyke, and you can hear him discuss the paper on the Nature Podcast at the Nature News article, New contender for first bird. You can also read a summary in the Science news of the week - Science 340:1024-1025, Earliest Birdie? [Pictures from the linked Nature and Science news items.]

Of course, whether or not Archaeopteryx is an ancestral bird or not, that does not alter the irrefutable fact that birds did evolve from dinosaurs. The real solution to the challenge by Creationists should not have been to take Archaeopteryx out of the textbook but to put more fossils into the textbook. Teach the actual "controversy", such as it is: from which dinosaurs did birds evolve?

Six useful things I have learnt at Software Carpentry boot camp

Monday and Tuesday this week, I attended a Software Carpentry boot camp at the University of Southampton. Topics covered included bash, shell scripting, Git and writing/testing reproducible code. The event was well-attended and whilst making an event like this relevant to everyone is obviously a challenge, they did a great job. I certainly learnt some useful tips even for the topics that I knew a fair bit about.

As well as the SWC presentations themselves, it was good to get tips from fellow programmers as well as "UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits)", which I brought along for some browsing. Here is half a dozen random things that I picked up over the two days...

1. Useful grep flags. I've used grep to pull out matches from text files a fair amount and was familiar with a few of the flags that I use a lot:

-i = case-insensitive search
-v = inverse search
-A n = return n lines after match
-B n = return n lines before match

I learnt a few more useful ones, though:

-w = match whole words only
-n = show line numbers
--color = highlight matches in colour
-r = search subdirectories (recursive)

2. Useful ls flags. ls is another must-have part of the UNIX users toolkit. There were still a few useful flags with which I was unfamiliar and am likely to use in future, though:

-G = colour-code directory contents
-F = appends / to directories
-R = recursive ls including subdirectory contents
-1 = one entry per line
-a = show all files including hidden files

Along with my old favourites, of course:

-l = "long" mode (more info)
-r = reverse sort
-t = sort by time
-S = sort by size
-h = user-friendly file sizes

3. Catching the standard error and standard output. I've seen this a few times but for some reason this was the first time it really sunk in. Most UNIX users will be familiar with redirecting the standard output from a command into a file using > file (or >> to append). Catching the standard error is less obvious/common. This can be done using 2> to catch the stderr alone, or &> to catch both stdout and stderr at the same time. If you want to redirect them both into different files, do something like this:

[cmd] 2> error.txt > stdout.txt

The stdout will slip by the first redirect and then get caught by the second. Of course, you can have those the other way round if you wish!

4. Navigating the terminal. This one actually came from "UNIX and Perl to the Rescue" but I discovered it at the boot camp:

Ctrl+a = move to start of line
Ctrl+e = move to end of line
Ctrl+w = delete previous word
Ctrl+l = clear screen (clear works too)
Ctrl+r = search through previous commands one letter at a time (this was an SWC revelation)

Using Ctrl+a and Ctrl+e seems to work in a number of other Mac editors too - including this blogger HTML window! If you are a Mac user, just make sure that you don't use cmd+w by mistake - this will close the current terminal window with much wailing and gnashing of teeth!

5. Reversing Python strings. In the past, I have reversed a python string by converting into a list, using the list.reverse() method and then string.join() to convert it back. But there is a better way!

string[::-1]

I've used string slicing loads before but never realised that you could add a step to this syntax as with the range() method! (string[::-1] translates as string[start=end:end=start:step=-1].) Now I am wondering where else in my code I can use this knowledge!

6. Changing the command prompt to $. Sometimes, the command prompt is too long (or the terminal window too narrow) so that almost every command wraps around in an annoying fashion. To replace with a simple $ character, just type:

PS1="\s"
PS1="\$ "


I must admit that I do not (yet) really understand exactly what this does and how it works but it does! (And if you now get lost as to where you are, just remember that pwd gives you the full path to the working directory.

There were more but I think that's enough for now! If this is the sort of thing that floats your boat, you can find useful stuff like this plus a whole bunch of lessons at the Software Carpentry website:

If you get the chance to attend a boot camp yourself, my advice is: do!

Warhammer Quest for iOS is here (if a bit buggy)

I posted a while back about about the Warhammer Quest iPad App, which is now out. I've had it a couple of days (despite only getting the email today!) and early indications are good. It's quite old school but that's actually part of the appeal, and it doesn't look too old school.

The game is a little buggy (and not just because of the giant bats, rats and spiders) but the occasional crash is not a problem as it saves progress after every turn with iCloud so a quick restart sorts it out. Gameplay might be a little repetitive, with fairly standard fare of visiting settlements, picking up quests and using the spoils to upgrade the skills and equipment of your party of warriors. It's good, though, and the quests are short enough to make it ideal for a quick go now and again without (necessarily) being sucked in for hours - ideal for a mobile device.

As with Hunters 2, Rodeo Games have made a good-looking game with a simple but effective combat system. Well worth the £2.99, I think. The iPad is the perfect medium for turn-based tactical games and I look forward to more of its ilk from the genre. (Particularly X-Com!)

McGuigan Estate Shiraz

Tonight was a steak night, which called for a hearty red wine. With the forthcoming move Down Under, an Aussie number seemed appropriate.

I'm not sure how much it's drunk in Australia itself but the McGuigan Estate Shiraz is on offer at Sainsburys at the moment and has a couple of IWSC trophies to its name. I can see why - it's full-bodied, robust and packed full of flavour.

It pairs well with a juicy steak but easily has enough flavour to hold its own for some quality quaffing in its own right. One more reason to look forward to the move later this year!