serhii.net

• How to Read a Paper [pdf] | Hacker News (pdf)

  • I give all my doctoral students a copy of the following great paper (and I’ve used a variant of the check list at the end for years - avoids errors when working on multiple papers with multiple international teams in parallel) http://www-mech.eng.cam.ac.uk/mmd/ashby-paper-V6.pdf

I’ll write here the main points from each of the linked PDF, copyright belongs to the original authors ofc.

How to Write a Paper

How to Write a Paper
Mike Ashby
Engineering Department, University of Cambridge, Cambridge
6 rd Edition, April 2005

This brief manual gives guidance in writing a paper about your research. Most of the advice applies equally to your thesis or to writing a research proposal.

This is based on 2016 version of the paper, more are here: https://news.ycombinator.com/item?id=38446418#38449638 with the link to the 2016 version being https://web.archive.org/web/20220615001635/http://blizzard.cs.uwaterloo.ca/keshav/home/Papers/data/07/paper-reading.pdf

1. The design
   1. The market need - what is the purpose? Who will read it? How will it be used?
      1. Thesis / paper / research-proposal:
2. Concept

   1. When you can’t write, it is because you don’t know what you want to say. The first job is to structure your thinking.

   2. A3 paper where you draw things:
      1. 
      2. 

   3. Don’t yet think of style, neatness or anything else. Just add, at the appropriate place on the sheet, your thoughts.

3. Embodiement
   • the first draft
   • the PDF lists random bits about each sections, like abstract / introduction / …
   • Introduction:
     • What is the problem and why is it interesting?
     • Who are the main contributors?
     • What did they do?
     • What novel thing will you reveal?
   • Method
     • ‘just say what you did, succinctly’
   • Results
     • Same; also succinctly, without interpretation etc.
   • …
   • Appendices:
     • essential material that would interrupt the flow of the main text

• Grammar!
  • 
  • That VS which!
• Punctuation:
  • really interested and itemized
  • Dashes: “The dash sets off parenthetic material that results in a break in continuity in a sentence. [..] A dash can lead to an upshot, a final summary word or statement, and give emphasis:”
  • Parentheses—literally: putting-asides—embrace material of all sorts, and help structure scientific writing. But do not let them take over, clouding the meaning of the sentence with too many asides.
  • Italics: the best of the three ways (with bold and underline) to emphasize stuff in scientific writing.
  • Brackets are used to indicate editorial comments or words inserted as explanation: [continued on p. 62], [see footnote].
• Style
  • Be clear. Use simple language,familiar words, etc.
  • Design: Remember who you are writing for. Tell them what they want to know, not what they know already or do not want to know.
  • Define everything
  • Avoid cliches; avoid empty words

    • Avoid clichés (standard formalised phrases): they are corpses devoid of the vitality which makes meaning spring from the page

    • 
  • Do not overstate, over emphasise or apologise: не верь, не бойся не проси
  • Avoid being patronising, condescending or eccentric
  • Good first sentence:
    • Openings such as: It is widely accepted that X (your topic) is important … has the reader yawning before you’ve started.
• At the end it has examles of effective and ineffective writing
• At the very end it has this:

How to read a paper

How to Read a Paper
S. Keshav
David R. Cheriton School of Computer Science, University of Waterloo
Waterloo, ON, Canada
keshav@uwaterloo.ca

http://ccr.sigcomm.org/online/files/p83-keshavA.pdf

• Three passes of varying levels of thoroughness
• Literature survery:
  • also three steps:
    1. find recent papers in the area through google scholar etc.
    2. find top conferences
    3. look through their recent conference proceedings

I have a pytest of a function that uses python @lru_cache:

    cacheinfo = gbif_get_taxonomy_id.cache_info()
    assert cacheinfo.hits == 1
    assert cacheinfo.misses == 2

LRU cache gets preserved among test runs, breaking independence and making such bits fail.

Enter pytest-antilru · PyPI which resets the LRU cache between test runs. Installing it as a python package is all there’s to ite.

Needed argparse to accept yes/no decisions, should have been used inside a dockerfile that doesn’t have if/else logic, and all solutions except getting a parameter that accepts string like true/false seemed ugly.

The standard linux --do-thing and --no-do-thing were also impossible to do within Docker, if I want to use an env. variable etc., unless I literally set them to --do-thing which is a mess for many reasons.

I had 40 tabs open because apparently this is not a solved problem, and all ideas I had felt ugly.

How do I convert strings to bools in a good way? (bool alone is not an option because bool('False') etc.)

Basic if value=="true" would work, but maybe let’s support other things as a bonus because why not.

My first thought was to see what YAML does, but then I found the deprecated in 3.12 distutils.util.strtobool: 9. API Reference — Python 3.9.17 documentation

It converts y,yes,t,true,on,1 / n,no,f,false,off,0 into boolean True/False.

The code, the only reason it’s a separate function (and not a lambda inside the type= parameter) was because I wanted a custom ValueError and to add the warning for deprecation, as if Python would let me forget. An one-liner was absolutely possible here as well.

def _str_to_bool(x: str):
    """Converts value to a boolean.

    Currently uses (the rules from) distutils.util.strtobool:
        (https://docs.python.org/3.9/distutils/apiref.html#distutils.util.strtobool)
        True values are y, yes, t, true, on and 1
        False values are n, no, f, false, off and 0
        ValueError otherwise.

    ! distutils.util.strtobool is deprecated in python 3.12
        TODO solve it differently by then

    Args:
        value (str): value
    """
    try:
        res = bool(strtobool(str(x).strip()))
    except ValueError as e:
        logger.error(
            f"Invalid str-to-bool value '{x}'. Valid values are: y,yes,t,true,on,1 / n,no,f,false,off,0."
        )
        raise e
    return res

# inside argparse
    parser.add_argument(
        "--skip-cert-check",
        help="Whether to skip a cert check (%(default)s)",
        type=_str_to_bool,
        default=SKIP_CERT_CHECK,
    )

This allows:

• sane human-readable default values specified elsewhere
• use inside Dockerfiles and Rancher configmaps etc. where you just set it to a plaintext value
• no if/else bits for --no-do-thing flags

distutils is deprecated in 3.12 though :(

YAML is known for it’s bool handling: Boolean Language-Independent Type for YAML™ Version 1.1.

Regexp:

y|Y|yes|Yes|YES|n|N|no|No|NO
|true|True|TRUE|false|False|FALSE
|on|On|ON|off|Off|OFF`

I don’t like it and think it creates more issues than it solves, e.g. the “Norway problem” (211020-1304 YAML Norway issues), but for CLI I think that’s okay enough.

Using Kubernetes envFrom for environment variables describes how to get env variables from config map or secret, copying here:

#####################  
### deployment.yml
#####################  
# Use envFrom to load Secrets and ConfigMaps into environment variables

apiVersion: apps/v1beta2
kind: Deployment
metadata:
  name: mans-not-hot
  labels:
    app: mans-not-hot
spec:
  replicas: 1
  selector:
    matchLabels:
      app: mans-not-hot
  template:
    metadata:
      labels:
        app: mans-not-hot
    spec:
      containers:
        - name: app
          image: gcr.io/mans-not-hot/app:bed1f9d4
          imagePullPolicy: Always
          ports:
            - containerPort: 80
          envFrom:
          - configMapRef:
              name: env-configmap
          - secretRef:
              name: env-secrets
#####################  
### env-configmap.yml
#####################  
# Use config map for not-secret configuration data

apiVersion: v1
kind: ConfigMap
metadata:
  name: env-configmap
data:
  APP_NAME: Mans Not Hot
  APP_ENV: production
  
#####################  
### env-secrets.yml
#####################  
# Use secrets for things which are actually secret like API keys, credentials, etc
# Base64 encode the values stored in a Kubernetes Secret: $ pbpaste | base64 | pbcopy
# The --decode flag is convenient: $ pbpaste | base64 --decode

apiVersion: v1
kind: Secret
metadata:
  name: env-secrets
type: Opaque
data:
  DB_PASSWORD: cDZbUGVXeU5e0ZW
  REDIS_PASSWORD: AAZbUGVXeU5e0ZB
@caiquecastro

This is neater than what I used before, listing literally all of them:

spec:
  containers:
    - name: name
      image: image
      env:
        - name: BUCKET_NAME
          valueFrom:
            configMapKeyRef:
              name: some-config
              key: BUCKET_NAME

Wanted to do coloring and remembered about Krita and the tutorial about flat coloring (Flat Coloring — Krita Manual 5.2.0 documentation) mentioned the Colorize Mask and it’s awesome!

Needed to actually understand it, and even had to watch a video tutorial (Tutorial: Coloring with “Colorize-mask” in Krita - YouTube) but it was so worth it!

It’s basically a bucket fill tool on steroids, and even might be reason enough to move away from Inkscape for some of these tasks!

Cleaned lineart:

Mask (red is transparent):

Result:

Result with random brushes moon texture below it:

Interesting bits:

• any unfilled areas will be filled, that is - if there’s an area that should be left alone it has to be explicitly marked as transparent or any color. This was the most confusing to me at first
• The colorize mask layer should be Multiply, but if there’s anything else below it it’ll be a mess - sometimes it should just be converted to a paint layer w/ the correct settings to see what it will look like in the end
• if you want to remove all instances of a specific color and use color select by color tool for that - it WILL be a mess because borders, and the color mask tool has already a button to remove a color, USE IT.

Heard the expression “roter Faden”, googled it, and it’s actually interesting and relevant.

In a scientific context, it’s the main topic / leitmotiv / … of the text. You ask a question, and all parts of the text should work together to answer it, relating to it in a clear way.

Excellent (PDF) link on this exact topic in scientific writing & an itemized list of ways to make it clear: https://www.uni-osnabrueck.de/fileadmin/documents/public/1_universitaet/1.3_organisation/sprachenzentrum/schreibwerkstatt/Roter_Faden_Endversion.pdf

TODO hypothetically save it from link rot somewhere

Also:

• untermauern: underpin
  • durch ein Grafik XXX_(Akk.)_ untermauern

wolph/python-progressbar: Progressbar 2 - A progress bar for Python 2 and Python 3 - “pip install progressbar2” really cool flexible progressbar.

Also: progressbar.widgets — Progress Bar 4.3b.0 documentation:

Examples of markers:
	 - Smooth: ` ▏▎▍▌▋▊▉█` (default)
	 - Bar: ` ▁▂▃▄▅▆▇█`
	 - Snake: ` ▖▌▛█`
	 - Fade in: ` ░▒▓█`
	 - Dots: ` ⡀⡄⡆⡇⣇⣧⣷⣿`
	 - Growing circles: ` .oO`

You can export your own papers as single file and the entire Internet tells you how. But if you’re NOT the author, this is a workaround I found:

• Add the papers to your library
• Export them all from your library!

Github: simonw/llm: Access large language models from the command-line

Originally seen here: Patrick McKenzie on X: “You might not know about @simonw’s command line ’llm’ tool. Here let me demo it. git log | head -n 200 | llm -s “Of the most recent 5 commits, which is probably the most important? I use ‘Minor’ and similar commit messages to mark unimportant commits.” https://t.co/jtxV6ULwKc” / X

The example from the tweet:

git log | head -n 200 | llm -s "Of the most recent 5 commits, which is probably the most important? I use 'Minor' and similar commit messages to mark unimportant commits."

llm on pypy

I’ll restart https://serhii.net/links later, and this will be the first bit I’ll add there:

Sad clown paradox - Wikipedia

TL;DR comedians are associated with depression/anxiety:

Humour has been shown to develop from a young age, fostered by parental behaviour. A parent’s immature nature can lead to additional responsibilities forced onto children, which can evoke issues of self-worth and a need for acceptance. The constant search for approval may cause mental health issues such as anxiety or depression […] Laughter can evolve as a medium for self-preservation, detaching the individual from any adversity faced allowing for perceived control over uncomfortable situations.

Sad clown paradox is characterised by a cyclothymic temperament, which encourages the creation of light-hearted humour in a professional setting, despite inner turmoil.