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Infection

"You don't understand, do you? You're like my insanity. I want you to leave me alone and get out of my head forever, but at the same time, I know I'll never fully recover from what you're doing to my mind. Why can't you just get out of my mind?"

I sometimes feel like doing a Ryan Gosling: grow a huge beard, build a house, and mourn the death of painful love while looking suitably vulnerable to the women around me.

SequenceServer BLAST Frontend

Stretching my legs with some Ruby + Bioinformatics work on the excellent new open-source, Sinatra based web frontend to NCBI BLAST+ called SequenceServer (http://gihub.com/yannickwurm/sequenceserver).

I needed to get out of the stuffy C# room I've been in for months for a bit, but I'll be working on my testing framework again when I've cleaned out ma' brain.

My fork is at http://github.com/xiy/sequenceserver if you're an academic interested in using a nice clean interface to your local BLAST databases.

Stay classy, San Diago (which of course means "A Whale's Vagina")

"I thought I understood it, that I could grasp it. But I didn't, not really. Only the smudgeness of it; the pink-slippered, all-containered, semi-precious eagerness of it. I didn't realize it would sometimes be more than whole, that the wholeness was a rather luxurious idea. Because it's the halves that halve you in half. I didn't know, don't know, about the in-between bits; the gory bits of you, and the gory bits of me."

http://www.imdb.com/title/tt1758692/

Its not your fault

its all my fault

im not human at all

i have no heart

its not a fault

its not your fault

im not human at all i have no heart

pretty much.

Hallucination

Trying a new method to stop my epic migraine assault. Sleepeaze (sleeping pills) + Syndol (best headache pills around, and less addictive) + Mirtazipine (an anti-depressant that's good for migraine pain/prevention). I honestly thought I was being followed by a giant black rectangle, like the one from 2001 earlier. It's gone now. I think?

WARNING: May let you hear the echo inside the empty shell of your mind.

that’s the best revenge of all: happiness. nothing drives people crazier than seeing someone have a good fucking life.

Chuck Palahniuk

It's a strange feeling, knowing that you're heading into an abyss that you'll never come back out of. I'm okay with it though.

"You can't follow me. I'm going away."

#burial #massive-attack

I can't help falling in love with you.

Should: Func'y Testing

When it comes to testing anything, testing methods (or functions) is probably the test performed most. I know that most of the time, I want to know if the function I just wrote is going to do what I want it to do:

Will it return the correct value?

Will it return the correct type?

Will it throw an exception?

Will it throw anything else? (like a tantrum)

If it doesn't return anything, does it perform it's actions successfully?

These are a few of the things I constantly find myself testing, and I'm sure other people do too. After all, this is what Test-Driven Development (TDD) was created for. I have to admit, because of my previously-mentioned fussiness with current .NET testing frameworks and procedures, I've resorted to things like writing console apps to test output, creating obscure debugging classes to record information, and writing messy debug code that eventually just gets deleted.

Current testing procedure seems to follow along all the same lines. Create a class to hold test functions that test specific methods or parts of that class. Once you have all these functions set up, your usual next step would be to fill them with instances of your test class, a few parameters if any are needed, some test data and some assertions.

The problem here is the incredible amount of repetition. Clearly those who designed .NET testing frameworks had never heard of DRY (dont-repeat-yourself).

Now, what if all that could be done in one line? This is where Expectation Tests come in. I mentioned these in my previous post and went over their syntax, and I'm definitely still in the concept stages as I write this, but I've discovered that you can do just that:

this.Expects(Context.someFunction(), "should return true");

Note: here, this is a class that implements IShouldTest<T> where T is the class, or the "context". Within this test class, there is a property called Context which obviously points to your passed context, which is instantiated automatically on every test run. You don't have to do that yourself every time.

Now, this singular line hides a lot of workings behind the scenes, just like a good framework should, but it's also incredibly powerful. What we're saying here is that this test context expects the function Context.someFunction() to return true. In one fell swoop we've provided the code to test, the expected test parameters and made the test framework aware of the test. Easy peasy.

The concept behind it is pretty simple. Why should I have to specifically define every single element of my test, every single time? Why can't I just say "I want to test this, this is what it should do"?

This is all made possible due to the improvements in how delegates are used in .NET. I must admit, for a while I just didn't understand why you'd want to use a delegate, apart from async and event stuff, and the massive waste of time setting these things up was a huge put-off for me personally. Since Func<T> and it's cousin Action<T> turned up, you can now leave all the annoying delegate work to the framework. It performs all the necessary creation of delegate types for you, and the best thing about this is that it isn't doing anything more than it used to, so there's no performance hit.

Another reason why testing using Func<T> and it's friends is great is LINQ and Lambda. Have you ever wondered, 'how would my function react if i gave it this?':

this.Expects((hugeDictionary) => someSortingFunction(hugeDictionary), "should take < 1 minute");

Pretty cool, huh?

Shoulda, Woulda, Coulda

I hate Testing Frameworks. Actually, let me be specific…I hate .NET Testing Frameworks. They make me angry and sad; so I've decided that because I have nothing better to do, I'll write my own. But first, a little comparison...

VS2010 Testing Framework (MSTest?)

Microsoft’s built in testing system isn’t too bad. It's integration is done well, but it’s so bloody overly complicated and slow, and messy. Every test you perform dumps a shit-load of messy files everywhere on your filesystem and inside your solution folder. It then has the CHEEK to complain that you should delete some when it gets “full”?

Poor effort Bill (or is it Steve now?)

NUnit

As far as I’ve ever been able to tell, this is simply a big, even more bloated version of the above. Some of the testing functionality is simpler and easier to understand, and it does have more assertions…that’s where the good things end. Like a lot of software, it’s probably the most used? Weird that.

xUnit

Made by the same blokes as the above, but apparently it’s better and easier to use. I went over their comparison table they’ve got up on their Codeplex site….yeah, no. If anything, it’s a massive excercise in how to complicate a piece of supposedly useful software even further. I mean…test methods are called “Facts”? Not only that, the method to actually get testing is beyond annoying.

Getting there…but not quite.

Should...

I’m tired. I like ruby, I like libraries like “shoulda” and “cucumber”. You just want to test whether that function does what you want it to; does it fulfil the requirements? Does it do what you expected it to do? I got tired of fumbling around the above libraries. I wanted a simple, easy to use, easy to understand testing framework so that I could test Nucleo quickly and effectively, so I created “Should”. At least that’s what It’s called at the moment.

Creating a test involves (at the moment) two things:

A ShouldTestContext<T> object. Think of it as the manager for all your tests. The generic type parameter <T> is the object you want to perform tests on, or the “context”.

One or more Expectation objects. An expectation test is exactly that; it tests an expectation of something else.

Once you’ve set up all your expectation tests, you make a call to the ShouldTestContext<T>.RealiseExpectations() method and shazzam, it tests away!

Expectation Test Syntax

I wanted to make writing the actual tests as easy as possible; plain english if i could. Turns out I could:

Expectation ex = new Expectation(() = { return true; }, "should return true");

Here, I’ve created a new expectation test and fed it a lambda expression as a delegate that simply returns true (for demo purposes) and my expectation (logically) is that it “should return true”. Using a simple parser, an Expectation is then created by analysing the logic of the expectation string. The parser determines the type of test by what kind of type is passed to it (method, property, field etc.) and then runs a test against the object based on the given expectation. The kind of tests you can run are all your usual suspects, and I may add a few more in the future. Here are some examples of some expectation test strings:

"should contain 'Hello'" (test a collection, array or string) "shouldalways return true" (test a constant) "shouldnot have length > 10" (test a property or field)

The important thing to note is that, underlying all of this is the same basic usage of assertions. It’s the way in which those assertions are performed which is the cool thing. I am also making it completely programmatic too, so if you want to write your tests in the standard way, you still can, and they’ll still be beautiful:

Should.BeEqual(1, 1); Should.ReturnTrue(() => { return true; }); Etc. etc. - more to come..

#.net #c-sharp #testing #test-driven-development #nunit #xunit #msbuild

Addiction

Codeine is like an argumentative bitch of a girlfriend that loves you one moment and makes you feel incredible, and then turns on you the next, leaving you in a shaky mess. Still, I managed to create some epic addiction tunes while I was gone.

Sky job news

So I had a terrifying and surreal telephone interview with the guys from Sky on Monday afternoon. Scary, but it sounded like it went well and they were happy. I was told I'd be contacted within 2-3 weeks, so I was a little surprised this afternoon when I got a call from them asking me if I could go to one of their graduate assessment centres as soon as possible. Interesting, to say the least. Especially as I missed the first call and the person calling was subjected to my Monty Python voicemail message. That's gonna take some explaining haha.

Fingers (and toes) crossed.

Jobs!

So I currently have two jobs on the go, very busy, but soon I'll share some nice little examples of what I'm doing:

CUDA Programmer in the Virus Genomics Group at the Sanger Insitute (AWESOME)

Associate Software Engineer at Sky (BSkyB) (AMAZING)

Life Economics, sure.

Life Economics

Many things have changed for me since my last post on here. I've never been good at keeping up posting on blogs and things but I think I probably have good reason to these days, so here goes:

1. My dad nearly died from a brain bleed in March. He's recovering now, slowly.

2. My girlfriend of six years decided she was bored and left me. It was bound to happen sooner or later, and I just didn't love her anymore, so...It's not so bad.

3. I've finished my degree in Computer Science after three long, hard years. I didn't think I'd even get past the first year when I started it. I'm a smart guy but I didn't think by the end of it that I'd be programming np-Hard algorithms for fun..

4. I've started working on a lot of projects I've been dying to work on for those three years:

- A dedicated programming environment for CUDA in Windows.

- CUDA-C#/C versions of a few of my favourite algorithms: k-means, ktJET (for the ATLAS project at CERN/LHC), various DNA repeat masking/finding algorithms, including my own (see below).

- My own typesetting language based on what I learnt this year in my Compilers and Code Generation course. The hardest education I've ever had, but I learnt a lot, so I'm creating a typesetting language that will be much more accessible than LaTeX.

- My own mono-spaced programming font - I'm tired of searching for the right one for all my different programming environments I bounce around in.

- Finishing off my final-year project program, Nucleo. I plan on fully implementing my algorithm in both serial, parallel and CUDA-C#.

- A CUDA algorithm for finding repeats that uses matrix scoring.

So there we go, lots to keep me occupied until I manage to find a job. Speaking of jobs, I applied to Centrica for a summer internship (fingers crossed), and I should be working for Pluralsight on an HTML5 version of their player some time soon.

Life is mad, eh?

Breaking my brain trying to figure out how to read in massive genbank sequence files efficiently in C#. These links might help you too.

http://www.shrinkrays.net/code-snippets/csharp/fast-text-file-reading-in-csharp.aspx

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