An update

So, it's fast approaching 2 months now since I started the new thing and it's been a busy time. I've had to adjust to a quite a few new things, not least of which has been a longer and more involved commute. I'm actually mostly enjoying it too. While having to contend with busses isn't the best thing to be doing with my day, I do have a very fond spot for Edinburgh and it's nice to be in there most days of the week.

Part of the fallout from the new job has been that, in the last couple of weeks, I've thrown some more stuff up on PyPi. This comes about as part of a bit of a dog-fooding campaign we're on at the moment (you can read some background to this over on the company blog). While they have been, and will continue to be, mentioned on the Textualize blog, I thought I'd give a brief mention of them here on my own blog too given they are, essentially, personal projects.

gridinfo

This is one I'd like to tweak some more and improve on if possible. It is, in essence, a Python-coded terminal tool that does more or less the same as slstats.el. It started out as a rather silly quick hack, designed to do something different with rich-pixels.

Here's the finished version (as of the time of writing) being put through its paces:

Download from here, or install and play with it with a quick pipx install gridinfo.

unbored

The next experiment with Textual was to write a terminal-based client for the Bored-API. My initial plan for this was to just have a button or two that the user could mash on and they'd get an activity suggestion dropped into the middle of the terminal; but really that seemed a bit boring. Then I realised that it'd be a bit more silly and a bit more fun if I did it as a sort of TODO app. Bored? Run it up and use one of the activities you'd generated before. Don't like any of them? Ignore them and generate some more! Feeling bad that you've got such a backlog of reasons to not be bored? Delete a bunch!

And so on.

Here's a short video of it in action:

Download from here, or install and play with it with a quick pipx install unbored.

textual-qrcode

This one... this one I'm going to blame on the brain fog that followed flu and Covid jabs that happened the day before (and which are still kicking my arse 4 days later). Monday morning, at my desk, and I'm wondering what to next write to experiment with Textual, and I realised it would be interesting to write something that would show off that it's easy to make a third party widget library.

And... yeah, I don't know why, but I remembered qrencode.el and so textual-qrcode was born!

I think the most amusing part about this is that I did it in full knowledge that it would be useless; the idea being it would be a daft way of showing off how you could build a widget library as an add-on for Textual. But... more than one person actually ended up saying "yeah hold up there this could actually be handy!"

If you're one of those people... you'll find it here.

FivePyFive

While I was on a roll putting stuff up on PyPi, I also decided to tweak up my Textual-based 5x5 and throw that up too. This was my first app built with Textual, initially written before I'd even spoken to Will about the position here. At one point I even did a version in Lisp.

It's since gone on to become one of the example apps in Textual itself but I felt it deserved being made available to the world via an easy(ish) install. So, if you fancy trying to crack the puzzle in your terminal, just do a quick:

$ pipx install fivepyfive

and click away.

You can find it over here.

PISpy

Finally... for this week anyway, is a tool I've called PISpy. It's designed as a simple terminal client for looking up package information on PyPi. As of right now it's pretty straightforward, but I'd like to add more to it over time. Here's an example of it in action:

One small wrinkle with publishing it to PyPi was the fact that, once I'd chosen the name, I checked that it hadn't been used on PyPi (it hadn't) but when it came to publishing the package it got rejected because the name was too similar to another package! I don't know which, it wouldn't say, but that was a problem. So in the end the published name ended up having to be slightly different from the actual tool's name.

See over here for the package, and you can install it with a:

$ pipx install pispy-client

and then just run pispy in the terminal.

Conclusion

It's been a fun couple of weeks coming up with stuff to help exercise Textual, and there's more to come. Personally I've found the process really helpful in that it's help me learn more about the framework and also figure out my own approach to working with it. Each thing I've built so far has been a small step in evolution on from what I did in the previous thing. I doubt I've arrived at a plateau of understanding just yet.

Introduction

On Twitter, a few weeks back, @itsBexli asked me how I go about setting up Python for development on macOS. It's a great question and one that seems to crop up in various places, and since I first got into using macOS and then subsequently got back into coding lots in Python it's absolutely an issue I ran into.

With my previous employer, while I was the only developer, I wasn't the only person writing code and more than one other person had this issue so I eventually wrote up my approach to solving this problem. That document is on their internal GitLab, but I thought it worth me writing my personal macOS/Python "rules" up again, just in case they're useful to anyone else.

I am, of course, not the first person to tackle this, to document this, to write down a good approach to this. Before and after I settled on my approach I'd seen other people write about this. So... this post isn't here to try and replace those, it's simply to write down my own approach, so if anyone asks again I can point them here. I feel it's important to stress: this isn't the only way or thoughts on this issue, there are lots of others. Do go read them too and then settle on an approach that works for you.

One other point to note, which may or may not make a difference (and may or may not affect how this changes with time): for the past few years I've been a heavy user of pipenv to manage my virtual environments. This is very likely to change from now on, but keep in mind that what follows was arrived at from the perspective of a pipenv user.

So... with that admin aside...

The Problem

When I first got back into writing Python it was on macOS and, really early on, I ran into all the usual issues: virtual environments breaking because they were based on the system Python and it got updated, virtual environments based on the Homebrew-installed Python and it got updated, etc... Simply put, an occasional, annoying, non-show-stopping breaking of my development environment which would distract me when I'd sat down to just hack on some code, not do system admin!

My Solution

For me, what's worked for me without a problem over the past few years, in short, is this:

1. NEVER use the system version of Python. Just don't.
2. NEVER use the Homebrew's own version of Python (I'm not even sure this is an issue any more; but it used to be).
3. NEVER use a version of Python installed with Homebrew (or, more to the point, never install Python with Homebrew).
4. Manage everything with pyenv; which I do install from Homebrew.

The Detail

As mentioned earlier, what I'm writing here assumes that virtual environments are being managed with pipenv (something I still do for personal projects, for now, but this may change soon). Your choices and mileage may vary, etc... This is what works well for me.

The "one time" items

These are the items that need initially installing into a new macOS machine:

Homebrew

Unless it comes from the Mac App Store, I try and install everything via Homebrew. It's really handy for keeping track of what I've got installed, for recreating a development environment in general, and for keeping things up to date.

pyenv

With Homebrew installed the next step for me is to install pyenv. Doing so is as easy as:

$ brew install pyenv

Once installed, if it's not done it for you, you may need to make some changes to your login profile. I'm a user of fish so I have these lines in my setup. Simply put: it asks pyenv to set up my environment so my calls to Python go via its setup.

Plenty of help on how to set up pyenv can be found in its README.

Once I've done this I tend to go on and install the Python versions I'm likely to need. For me this tends to be the most recent "active" stable versions (as of the time of writing, 3.7 through 3.10; although I need to now start throwing 3.11 into the mix too).

I use this command:

$ pyenv install --list

to see the available versions. If I want to see what's available for a specific version I'll pipe through grep:

$ pyenv install --list | fgrep "  3.9"

This is handy if I want to check what the very latest release of a specific version of Python is.

The "Global" Python

When I'm done with the above I then tend to use pyenv to set my "global" Python. This is the version I want to get when I run python and I'm not inside a virtual environment. Doing that is as simple as:

$ pyenv global 3.10.7

Of course, you'd swap the version for whatever works for you.

When Stuff Breaks

It seems more rare these days, but on occasion I've had it such that some update somewhere still causes my environment to break. Now though I find that all it takes is a quick:

$ pyenv rehash

and everything is good again.

Setting Up A Repo

With all of the stuff above being mostly a one-off (or at least something I do once when I set up a new machine -- which isn't often), the real "work" here is when I set up a fresh repository when I start a new project. Really it's no work at all. Again, as I've said before, I've tended to use pipenv for my own work, and still do for personal stuff (but do want to change that), mileage may vary here depending on tool.

When I start a new project I think about which Python version I want to be working with, I ensure I have the latest version of it installed with pyenv, and then ask pipenv to create a new virtual environment with that:

$ pipenv --python 3.10.7

When you do this, you should see pipenv pulling the version of Python from the pyenv directories:

$ pipenv --python 3.10.7
Creating a virtualenv for this project...
Pipfile: /Users/davep/temp/cool-project/Pipfile
Using /Users/davep/.pyenv/versions/3.10.7/bin/python3 (3.10.7) to create virtualenv...
⠙ Creating virtual environment...created virtual environment CPython3.10.7.final.0-64 in 795ms
  creator CPython3Posix(dest=/Users/davep/temp/cool-project/.venv, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/Users/davep/Library/Application Support/virtualenv)
    added seed packages: pip==22.2.2, setuptools==65.3.0, wheel==0.37.1
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator
✔ Successfully created virtual environment!
Virtualenv location: /Users/davep/temp/cool-project/.venv
Creating a Pipfile for this project...

The key thing here is seeing that pipenv is pulling Python from ~/.pyenv/versions/. If it isn't there's a good chance you have a Python earlier in your PATH than the pyenv one -- something you generally don't want. It will work, but it's more likely to break at some point in the future. That's the key thing I look for; if I see that I know things are going to be okay.

Conclusion

Since I adopted these personal rules and approaches (and really, calling them "rules" is kind of grand -- there's almost nothing to this) I've found I've had near-zero issues with the stability of my Python virtual environments (and what issues I have run into tend to be trivial and of my own doing).

As I said at the start: there are, of course, other approaches to this, but this is mine and works well for me. Do feel free to comment with your own, I'm always happy to learn about new ways!

As mentioned yesterday, I'm about to start working at Textualize, and building Open-source software is important to the company. Will -- the CEO -- is all about building in public. If you follow him on Twitter you'll notice that his Python coding adventure tweets actually outnumber is cooking tweets!

As someone who has long been a supporter of and fan of Free Software and Open-source software, and has made some small contributions along the way, I've also always made a point of building my own tools in public. In most cases they're things that are likely only helpful to me, but some are more generally useful. The point being though: it's all there in case it's helpfull to someone else.

Which means that, as much as possible, when I'm writing code, I write it as if it's going to be visible in public and someone else is going to be reading it. I try and make the code tidy. I try and comment it well. I try (but don't always manage for personal projects) to fully document it. The important thing here being that someone coming to the code fresh should be able to follow what's going on.

Against that background, and having just gone through the process of handing off almost 5 years of work to someone else as a left an employer, I got to thinking: we should always "build in public", even if it's in private.

When I started with my previous employer, and even to the day I left, I was the only software developer there. I worked with a team who wrote code, but being software developers wasn't what they did. Bioinformaticians and machine learning scientists have other things to be doing. But, as I wrote my code, I wrote every line assuming they, or some other developer down the line, would be reading it. Pretty much every line was written for an audience I couldn't see and didn't fully know. This, as mentioned above, meant trying to keep the code clean, ensuring it was commented in helpful ways, ensuring the documentation was helpful, and so on.

But it wasn't just about the code. Any non-trivial system will have more to it than code. We had an internal instance of GitLab and I tracked all of my work on there. So, as I planned and worked on new features, or went on bug hunts, I'd document the process in the issue tracker. As much as possible I'd be really verbose about the process. Often I wouldn't just open an issue, go work on it, and then mark it closed; as I worked through the issue I'd add comment after comment under it, documenting my thinking, problems, solutions, cite sources when looking something up, that sort of thing.

The whole process was an act in having a conversation with current or future team members if they ever needed to look; with future me (really, that helped more than once -- we all have those "that the hell was I thinking?" moments); with any developer(s) who took over from me in the future.

I did all this as if I was broadcasting it in public on Twitter or on GitHub, etc. It was in private, of course, but I approached it as if it was in public.

There were always three main reasons for this, I felt:

1. Accountability. At any moment someone who I worked with could review what I was doing and why I was doing it; it was an invitation to anyone curious enough to talk with me about what I was building and how I was building it.
2. Continuity of support for unplanned reasons. Life happens, sometimes you may, unplanned, never be available at work again. I never wanted to leave my employer in a position where picking up from such an event was a nightmare.
3. Continuity of support for planned reasons. It was possible, and it became inevitable, that I'd move on to something else. If that was to happen I wanted to be sure that whoever picked up after me would be able to do so without too much effort.

In the end item 3 seemed to really pay off. When it came time for me to hand over my work to someone else, as I left, the process was really smooth and trouble-free. I was able to point the developer at all the documentation and source code, at all the issues, and invite them to read through it all and then come back to me with questions. In terms of time actually spent talking about the main system I was handing over I'd say that 4 years of work was handed over with just a few hours of actual talking about it.

It remains to be seen if it really paid off, of course. If they get really stuck they do have an open invitation to ping me a question or two; I care enough about what I designed and built that I want it to carry on being useful for some time to come. But... I like to think that all of that building in public, in private, will ensure that this is an invitation that never needs to be called on. I like to think that, if something isn't clear, they'll be able to check the code, the documentation and the issue history and get to where they need to go.

Just over five years ago I got a message from my then employer to say I was going to be made redundant after 21 years working for them. After the 3 month notice period the final day came. Meanwhile, I found something new that looked terrifying but interesting. In the end it was less terrifying and way more interesting than I imagined it would be. It was fun too.

But... (there's always a but isn't there?)

In the four and change years I've been there the company got bought out, and then the result of that got bought up. As I've mentioned before I'm generally not a "big company" kind of person; in all my years I've found that I'm happier working in a smaller place. After a couple of buyouts my employer had gone from being 10s of people in size to 100s of people in size (and technically 10s of 1,000s of people in size depending on how you look at it).

This change in ownership and size meant the culture became... well, let's just say not as friendly as you tend to enjoy when it's a smaller group of folk. On top of that I was starting to notice that my efforts were making less of an impact as things got bigger, and I started to feel like my contributions weren't really relevant any more. There were some problematic things happening too: undermining of efforts, removal of responsibilities without consultation or communication, that sort of thing. Plus worse. There's little point in going into the detail, but it's fair to say that work wasn't as fun as it used to be.

That felt like a good time to start to look around. If work makes you feel unhappy and you can look around... look around.

Thing is, I wasn't sure what to look for. I was in the comfortable position of, unlike last time, not needing to find something, so I could take my time at least. Over the course of the last year I've spoken to many different companies and organisations, some big (yes, I know, I said I don't like big places -- sometimes what's on offer deserves a fair hearing), some small, but none of them quite said "this feels like me". In some cases the whole thing didn't have the right vibe, in others the industry either didn't interest me, or felt uncomfortable given my personal values. In one particular case a place looked interesting until I checked the CTO's socials and OMG NO NO NO AVOID AVOID (that was a fun one).

Then I saw Will McGugan saying he was hiring to expand Textualize. This caught my interest right away for two good reasons.

I can't remember how long I've been following Will on Twitter; I likely stumbled on him as I got back into Python in 2018 and I also remember noting that he was a Python hacker just up the road from me. We'd vaguely chatted on Twitter, briefly, in that "Twitter acquaintance" way we all often do (I remember one brief exchange about fungus on The Meadows), and he'd seemed like a good sort. A small company run by a "good sort" kinda person felt like a damn good reason.

The second reason was Textual itself. I'd been watching Will develop it, in open, with great interest. I had (and still have) a plan to write a brand new CHUI-based (okay fine TUI-based as the kids like to say these days!) Norton Guide reader, all in Python, and Textual looked like the perfect framework to do the UI in. The chance to be involved with it sounded awesome.

Now, I said two reasons, but there's also a third I guess: Will's pitch for applying to Textualize felt so damn accessible! I'm on the older end of the age range of this industry; for much of my working life as a developer I've worked in isolation from other developers; while I first touched Python in the 90s, I've only been using it in anger since 2018 and still feel like I've got a lot to learn. Despite all these things, and more, saying "aye Dave this is beyond you" I felt comfortable dropping Will a line.

Which resulted in a chat.

Which resulted in some code tinkering and chatting.

Which resulted in...

Something new.

So, yeah, as of 2022-10-10 I'm on yet another new adventure. Time for me to really work on my Python coding as I work with Will and the rest of the team as part of Textualize.

Or, as I put it on Twitter a few days ago: I'm going to be a Python impostor syndrome speedrunner!

A little earlier this evening I got a new issue raised against boxquote.el. Apparently Emacs 29 (I'm running 28.1 as of the time of writing) is moaning about the likes of:

(setf (point) some-location-or-other)

and

(setf (buffer-string) "")

There's a whole background to why I've tended to code like that, that stems from enjoying Common Lisp, my days reading (and sometimes posting to) comp.lang.lisp, and I think some of the stuff Erik Naggum wrote back in the day. I won't get into it all now; I'm not sure I can even remember a lot of how I got there given how far back it was.

But...

Wanting to quickly get to the bottom of why the above was suddenly an issue, I dived into the NEWS file and found the following:

** Many seldom-used generalized variables have been made obsolete.
Emacs has a number of rather obscure generalized variables defined,
that, for instance, allowed you to say things like:

   (setf (point-min) 4)

These never caught on and have been made obsolete.  The form above,
for instance, is the same as saying

   (narrow-to-region 4 (point-max))

The following generalized variables have been made obsolete:
'buffer-file-name', 'buffer-local-value', 'buffer-modified-p',
'buffer-name', 'buffer-string', 'buffer-substring', 'current-buffer',
'current-column', 'current-global-map', 'current-input-mode',
'current-local-map', 'current-window-configuration',
'default-file-modes', 'documentation-property', 'frame-height',
'frame-visible-p', 'global-key-binding', 'local-key-binding', 'mark',
'mark-marker', 'marker-position', 'mouse-position', 'point',
'point-marker', 'point-max', 'point-min', 'read-mouse-position',
'screen-height', 'screen-width', 'selected-frame', 'selected-screen',
'selected-window', 'standard-case-table', 'syntax-table',
'visited-file-modtime', 'window-height', 'window-width', and
'x-get-secondary-selection'.

As suggested above... this is my thing, this is how I coded some Elisp stuff. Look through much of my Emacs Lisp code and you'll find me setfing stuff all over the place.

Apparently my style is "obscure". Actually, I'm kinda okay with that if I'm honest.

This is going to be a bit of a pain in the arse; I'm going to have to go through a whole bunch of code and make it "less obscure", at some point.

But...

This isn't the part that had me thinking I must be getting old. Oh no. The NEWS file had another little surprise in store:

** The quickurl.el library is now obsolete.
Use 'abbrev', 'skeleton' or 'tempo' instead.

That.... that's me that is. Well, it's one of the me things. If you run about-emacs, dive into Authors, and search for my name, in any copy of GNU Emacs from the last decade or two, you'll find this:

Dave Pearson: wrote 5x5.el quickurl.el

quickurl.el was a package I wrote back in the late 1990s, back when I was a very heavy user of Usenet, and often found myself posting the same URLs in posts again and again; especially in comp.lang.clipper. As a fairly quick hack I wrote the code so that I could very quickly insert often-used URLs.

Some time later, I got an email from the FSF (I actually think it was from RMS -- but that's an mbox I've long ago lost -- or a backup of it might be in storage back in England, on a DVD), asking if I wanted to contribute it to Emacs proper. This seemed like an odd thing to add to Emacs but, sure, why the hell not?

And so I had my second contribution to a body of code I used a lot (the first being 5x5.el -- which itself was my first ever attempt at writing some non-trivial Elisp code).

So... yeah... here we are. I'm now old enough to have written some Emacs Lisp code, had it required by the FSF for inclusion in Emacs, had it live in there for something like two decades, and then become obselete!

A couple of days back (for vague values of "couple", of course), first of the month, having my morning coffee, I go and open my bank's mobile app to move a bit of money about and pay a couple of things. This happens every month. This is so routine I do it almost on autopilot.

Yeah, yeah, I know, it's banking, pay attention! But still... morning, coffee, routine.

I get to the final movement/payment and then notice something:

That.... that text! WTF? So then I look back at my payment history and notice that all but one payment hadn't gone through! O_o

This alone is fine. Stuff happens. Things fail. I'm okay with that. It's an inconvenience for sure but doubtless whatever the problem is will be fixed and I can make the payments again later. But...

That result. There's a tick. A GREEN tick. And a "Thank you". It's natural to see that image, know that it's always meant "shit worked" and just carry on.

In one of my systems at work there's a tool I wrote for checking a repository of code to make sure it conforms to a certain standard. When folk use it they get a night big, bold and bright green thumb-up above the text that says everything is cool. If there's a problem, any sort of problem at all, then the display is red and there's no jolly icon and it's obvious that things are different and you likely want to pay attention to the explanation of what isn't right.

This isn't news, of course. This isn't some revelation about UI design or anything. We know this stuff. I think what boggles my mind a little bit about this is that something as important -- and hopefully by this point as mature -- as a mobile banking app should get something as obvious as this right.

But here we are, with a nice friendly green icon showing a tick and a friendly big "Thank you" followed by smaller text going "aye shit didn't work pal".

Introduction

For well over a year now I've been recording my VR gameplay and uploading it to YouTube. Less as a "content creation" thing, more as a nice record of games I've played and, on occasion, as a little bit of help to others; in the past I've watched other folk play games I like to get ideas for approaches to them, and I've also received the odd comment now and again where my play-through has helped someone else.

A question I've had a couple of times is what I use to do the recording, so I thought I'd make an effort to write it all down here.

First up, a couple of things to note: I started recording PCVR around April 2021 and the initial setup was a bit trial-and-error and Google searching and blog reading. As such, not all of the details of how to set up will be here, and I may even miss off some stuff I changed and is worthy of note; at the same time I might mention stuff that's just an obvious default.

Consider this blog post as being a written version of one of my videos: it's for my own fun and benefit and might also help me in the future should I want to apply some of this again, and if it helps someone else that's a lovely bonus.

The Hardware

While it's not exactly the point of this post, I guess it's worth mentioning the hardware I use as of the time of writing. Given this is about PCVR, I of course have a PC which is running Windows. The machine information within Windows says it's a:

Intel(R) Core(TM) i5-10400F CPU @ 2.90GHz

Warning: I don't do hardware. I buy it from time to time, but hardware leaves me bored. It runs VR on a PC. This is fine.

The machine itself has 16 GB of memory, is running Windows 10 Home and has a GeForce RTX 3060 for handling the graphics.

The headset I'm using is a~~n Oculus~~ Meta Quest 2. I've had this since around November 2020, playing Quest-native games for the first few months, until I cracked and got the PC mentioned here to get into PCVR.

The headset is connected to the PC with a USB cable.

Finally, for recording voice, I use a USB lapel microphone with a really long cable.

It should be said that, yes, sometimes, I do get a little caught up in things with two cables hanging off me. If I could give one tip here it would be that running the microphone cable up your trousers and shirt makes life a ton easier. As a bonus I have the USB cable for the headset running around the headset's strap and connected to it at the back and then running down my back.

OBS Studio

The core software used is OBS Studio. This has got to be one of the best bits of free software I've ever used, in terms of interface and what it delivers.

Years back my son used to record and upload gameplay to YouTube and I can remember him having no end of issues using different recording software; some working with one game but not another, some other working with a different set of games, video and sync issues, etc... Lots of pain quite often. With OBS Studio the only issues I've ever had have been my own mistakes.

At this point I have to confess that when I set it up I didn't make a point of keeping a recording of what I changed -- I was experimenting and not expecting much to come of it. So what I note here are the things that feel like they're important, and only the things that relate to recording PCVR, not streaming it (that might end up being a different blog post).

That said, here are things I seem to remember as being key:

Output Settings

The items in the output pane in settings that I have and which might be important are:

• Output Mode: Simple
• Recording Quality: High Quality, Medium File Size
• Recording format: mkv
• Encoder: Hardware (NVENC)

I do remember the recording format being set to mkv as something that's really important. I think it's mp4 by default, or was when I first installed, and if your machine crashes or OBS were to crash or something, you could end up with footage that can't be used. Using mkv means you can still use the footage (as I understand it). It does mean that once you're finished you have to use the "remux" option under the File menu, but that's a small price to pay.

I can say that at least once I've had to hard-reboot my machine when a game and SteamVR and the like all got upset. I likely saved 45 minutes or more of footage thanks to mkv.

Video Settings

Nothing really special in here, I simply have both the base and output resolutions set to the desktop resolution. This might be something for me to tinker with in the future, but so far I've not run into any problems.

VR Capture

Now, of course, all of the above is great and fine and all but there's the issue of how you capture the VR gameplay. I approach this a couple of different ways. The first is I use the OpenVR Capture plugin for OBS. This makes capturing footage from SteamVR really easy. The only downside I found is that out of the box there's no default crop setting for using a Quest 2 (or I guess the Rift, as the Quest 2 sort of appears as a Rift to SteamVR games). As such I remember playing trial and error with that until I was happy I was getting as much footage as possible without having black bars and the like.

Something I also like about the OpenVR Capture plugin is you can say if you want to capture the left or right eye. Normally not that big a deal for some things, but if you're playing a shooter and want people to see exactly what your dominant eye is seeing, that matters.

Sadly, of course, not every game can be captured with that plugin. So far I've found that any game that can't be has its own mirror window on the desktop. In that case I use a Game Capture source and set it to capture that specific window. I could of course just get it to capture the focused window or something like that but I prefer to know that it's only grabbing what I want it to grab.

Conclusion

That's pretty much it I think. There's not a lot to it, although on occasion a lot can go wrong. Mostly it's a wonder any of it works. I mean, think about it, I have a computer with two screens strapped to my face, with two controllers in my hands talking to it; it's then connected via the Oculus Link to the Oculus Home; from which I start up SteamVR; and from the SteamVR home I start up the game and then "live" inside the game. It's a virtual world inside a virtual world inside a virtual world inside a real world; with lots of software along the way, all talking at once.

That is then being recorded.

Sometimes, on occasion, it takes a reboot or five to make it all work together.

Really, it's a wonder it ever works. ;-)

I'm back! Almost. More or less. In more ways than one. First off, as often happens with blogs (we've all been there right?), I've been away from blogging for a while. I've still been online, still been waffling away on twitter, and have also stumbled into fosstodon as well. Doubtless plenty of other things.

A big distraction for me, and one that is ongoing, is mucking about on YouTube. Since the last time I wrote anything on the blog I got myself a VR setup, and then a PCVR setup, and then finally fibre came to the village and I could stream, and... well, you can see how that would go.

So, in short, that's where I've been and that's what's been keeping me busy. Now that I'm paying some attention to blogging again (hopefully!) I imagine some of that will end up on here -- I'd quite like to write about VR and gaming amongst other things.

Now, I said I'd been away in more ways than one. Another way is explained by this post from back in 2019, where I said I was going to head over to Hashnode and carry on blogging there, obviously with an emphasis on development and just development.

That kept me busy for a while and worked out well, mostly. But... well, see above in part; I sort of ran out of steam when it came to purely-development topics. But I still wanted to write, a bit, and wanted to write about more than just development.

Also, something else was bothering me about being over on Hashnode. In the past year, in terms of what they promote themselves, especially blogs and posts they promote on their Twitter feed, they seem to have started to lean really hard into crypto and web3 and NFTs and all that stuff. This left me feeling like that was all a bit icky and it was time to put some distance between that platform and myself.

So over the past couple of weeks, low-level and as a background task, I've been back-porting posts from over there back into this blog. Starting with this post all new blog content, be it about software development or anything else, will be on here. If I'm really sensible and don't get distracted by new shiny... this should be how it remains now.

Expect some changes over the next few weeks. While I'm aiming to stick with the core tech (Github pages, Markdown and Jekyll, Emacs to edit, etc), I'd like to tinker with the look and layout of the blog. The content will remain the same though.

So, yeah, anyway, if you're reading this... hey, it's good to be back. :-)

Introduction

This post will cover the most important content of a 2bit file: the actual sequence data itself. In the first post I wrote about the format of the file's header, and in the second post I wrote about the content of the file's index.

At this point that's enough information to know what's in the file and where to find it. In other words we know the list of sequences that live in the file, and we know where each one is positioned within the file. So, assuming we have our index in memory (ideally some sort of key/value store of sequences names and their offsets in the file), given the name of a sequence we can know where to go in the file to load up the data.

So the next obvious question is, what will we find when we get there? Actual sequence data is stored like this:

Breaking the above down:

N blocks

As mentioned in passing in the first post: technically it's necessary to encode 5 different characters for the bases in the sequences. As well as the usual T, C, A and G, there also needs to be an N, which means the base is unknown. Now, of course, you can't pack 5 states into two bits, so the 2bit file format solves this by having an array of block positions and sizes where any data in the actual DNA itself should be ignored and an N used in its place.

Mask blocks

This is where my ignorance of bioinformatics shows, and where it's made very obvious that I'm a software developer who likes to muck about with data and data structures, but who doesn't always understand why they're used. I'm actually not sure what purpose mask blocks serve in a 2bit file, but they do affect the output. If a base falls within a mask block the value that is output should be a lower-case letter, rather then upper-case.

The DNA data

So this is the fun bit, where the real data is stored. This should be viewed as a sequence of bytes, each of which contains 4 bases (except for the last byte, of course, which might contain 1, 2 or 3 depending on the size of the sequence).

Each byte should be viewed as an array of 2 bit values, with the values mapping like this:

So, given a byte whose value is 27, you're looking at the sequence TCAG. This is because 27 in binary is 00011011, which breaks down as:

How you pull that data out of the byte will depend on the language and what it makes available for bit-twiddling; those that don't have some form of bit field will probably provide the ability to bit shift and do a bitwise and (it's also likely that doing bitwise operations is better than using bit fields anyway). In the version I wrote in Emacs Lisp, it's simply a case of shifting the two bits I am interested in over to the right of the byte and then performing a bitwise and to get just its value. So, given an array called 2bit-bases whose content is this:

(defconst 2bit-bases ["T" "C" "A" "G"]
  "Vector of the bases.

Note that the positions of each base in the vector map to the 2bit decoding
for them.")

I use this bit of code to pull out the individual bases:

(aref 2bit-bases (logand (ash byte (- shift)) #b11))

Given code to unpack an individual byte, extracting all of the bases in a sequence then becomes the act of having two loops, the outer loop being over each byte in the file, the inner loop being over the positions within each individual byte.

In pseudo-code, assuming that start and end hold the base locations we're interested in and dna_pos is the location in the file where the DNA starts, the main loop for unpacking the data looks something like this:

# The bases.
bases = [ "T", "C", "A", "G" ]

# Calculate the first and last byte to pull data from.
start_byte = dna_pos + floor( start / 4 )
end_byte   = dna_pos + floor( ( end - 1 ) / 4 )

# Work out the starting position.
position = ( start_byte - dna_pos ) * 4

# Load up the bytes that contain the DNA.
buffer = read_n_bytes_from( start_byte, ( end_byte - start_byte ) + 1 )

# Get all the N blocks that intersect this sub-sequence.
n_blocks = relevant_n_blocks( start, end )

# Get all the mask blocks that interest this sub-sequence.
mask_blocks = relevant_mask_blocks( start, end )

# Start with an empty sequence.
sequence = ""

# Loop over every byte in the buffer.
for byte in buffer

  # Stepping down each pair of bits in the byte.
  for shift from 6 downto 0 by 2

    # If we're interested in this location.
    if ( position >= start ) and ( position < end )

      # If this position is in an N block, just collect an N.
      if within( position, n_blocks )
        sequence = sequence + "N"
      else

        # Not a N, so we should decode the base.
        base = bases[ ( byte >> shift ) & 0b11 ]

        # If we're in a mask block, go lower case.
        if within( position, mask_blocks )
          sequence = sequence + lower( base )
        else
          sequence = sequence + base
        end

      end

    end

    # Move along.
    position = position + 1

  end

end

Note that some of the detail is left out in the above, especially the business of loading up the relevant blocks; how that would be done will depend on language and the approach to writing the code. The Emacs Lisp code I've written has what I think is a fairly straightforward approach to it. There's a similar approach in the Common Lisp code I've written.

And that's pretty much it. There are a few other details that differ depending on how this is approached, the language used, and other considerations; one body of 2bit reader code that I've written attempts to optimise how it does things as much as possible because it's capable of reading the data locally or via ranged HTTP GETs from a web server; the Common Lisp version I wrote still needs some work because I was having fun getting back into Common Lisp; the Emacs Lisp version needs to try and keep data as small as possible because it's working with buffers, not direct file access.

Having got to know the format of 2bit files a fair bit, I'm adding this to my list of "fun to do a version of" problems when getting to know a new language, or even dabbling in a language I know.

As mentioned in the first post, once you've read in the header data for a 2bit file, the next step is to read the index. This is an index into all the different sequences held in the file. Reading the index itself is fairly straightforward.

The index comes right after the header -- so it starts on the 17th byte of the file. Each entry in the index contains three items of information:

So, in some sort of pseudo-code, you'd read in the index as follows:

index = dict()
for seq = 1 to seq_count // seq_count comes from the header
  name_len = (int) read_bytes( 1 )
  name     = (string) read_bytes( name_len )
  offset   = (int) read_bytes( 4 )
  index[ name ] = offset
end

Note, as mentioned in the first post, the index will need to be byte-swapped if the file is in an endian form other than the machine you're running your code on. How you'd go about this will, of course, vary from language to language, but the main idea is always going to be the same.

There's a fairly striking downside to this approach though: reading data can often be an expensive (in terms of time) operation -- this is especially true if the data is coming in from a remote machine, perhaps even one that's being accessed over the Internet. As such, it's best if you can make as few "trips" to the file as possible.

With this in mind, the best thing to do is to read the whole index into memory in one go and then process it from there -- the idea being that that's just one trip to the data source. The problem here, however, is that there's nothing in the header or the index that tells you how large the index actually is. What you can do though is work on the worst case scenario (assuming memory will allow). The worst case is fairly easy to handle: it's going to be 1 byte for the name length, plus 255 bytes for the name (the longest possible name), plus 4 bytes for the offset; multiply all that by the number of sequences in the index and you have the worst-case buffer size.

When reading this data in you might also want to ensure you're not going to run off the end of the file (perhaps the names are all quite small and so are the sequences).

Recently I've been working on a package for Emacs that can read data from 2bit files, so here's the core code for reading in the index:

(defun 2bit--read-index (source)
  "Read the sequence index from SOURCE.

As a side effect `2bit-data-pos' of SOURCE will move."
  (cl-loop
   ;; The index will be a hash of sequence names, with the values being the
   ;; offsets within the file.
   with index = (make-hash-table :test #'equal)
   ;; We could read each name/value pair one by one, but because we're doing
   ;; this within Emacs, which means making a temp buffer for every read,
   ;; that could get pretty expensive pretty fast. So instead we'll read the
   ;; index data in in one go. However, there is no easy-to-calculate size
   ;; for the index. The best we can do is calculate the worst case size. So
   ;; let's do that. The worst case size is the maximum size of the name of
   ;; a sequence (255), plus the size of the byte that tells us the name
   ;; (1), plus the size of the word that is the offset in the file (4).
   with buffer = (2bit--read source (* (2bit-data-sequence-count source) (+ 255 1 4)))
   ;; For every sequence in the file...
   for n from 1 to (2bit-data-sequence-count source)
   ;; Calculate the position within the buffer for this loop around. Note
   ;; that the skip is the last position plus 1 for the size byte plus the
   ;; size plus the length of the offset word.
   for pos = 0 then (+ pos 1 size 4)
   ;; Get the length of the name of the sequence.
   for size = (aref buffer pos)
   ;; Pull out the name itself.
   for name = (substring buffer (1+ pos) (+ pos 1 size))
   ;; Pull out the offset.
   for offset = (2bit--word-from-bytes source (substring buffer (+ pos 1 size) (+ pos 1 size 4)))
   ;; Collect the offset into the hash.
   do (setf (gethash name index) offset)
   ;; Once we're all done.... return the index.
   finally return index))

This code does what I mention above: it grabs enough data into a buffer in one go that I'll have the whole index in memory to pull apart, and then I work with the in-memory copy. The index is added to a hashing dictionary. Note that, in this case, I don't actually do the test for running off the end of the file because at the heart of the file reading code is insert-file-contents-literally and it doesn't error if you request too much.

With that done you'll have a list of all the sequences in the file. The next part, which will come in the next post, is the properly tricky part: the decoding of the sequence data itself.