serhii.net

Python dataclasses

• This module provides a decorator and functions for automatically adding generated special methods such as init() and repr() to user-defined classes. It

• dataclasses — Data Classes — Python 3.9.4 documentation

HuggingFace

“Token classification” includes but is not limited to NER: Hugging Face – The AI community building the future.. Really nice new correct phrase I’ll be using!

Installing (after tensorflow and/or pytorch):

pip install transformers

Caches by default in user folder but can be overridden:

export HF_HOME="/data/sh/experiments/bert/cache" 

The “hosted inference API” on the website is really cool! dslim/bert-base-NER · Hugging Face

Example of converting conll dataset to what BERT expects: Fine Tuning BERT for NER on CoNLL 2003 dataset with TF 2.0 | by Bhuvana Kundumani | Analytics Vidhya | Medium

The BERT model documentation shows the tokenizers etc etc etc. - BERT — transformers 4.5.0.dev0 documentation

• Training and fine-tuning — transformers 4.5.0.dev0 documentation - same model can be trained/imported from TF to pytorch and back! Wow!

• Documentation of a sample model: transformers/examples/research_projects/distillation at master · huggingface/transformers

  • It has examples of preparing data for finetuning
  • In general, HF’s examples are wonderful

• Another example of fine-tuning BERT in Pytorch for NER: transformers/examples/pytorch/token-classification at master · huggingface/transformers

  • Needs transformers installed from source (git/master): https://huggingface.co/transformers/installation.html#installing-from-source / pip install git+https://github.com/huggingface/transformers
  • Trained in 37 minutes, wrote everything to /tmp/test-ner/, checkpoints, eval data. Wow.
  • Command used was:

  CUDA_VISIBLE_DEVICES=1; python run_ner.py   --model_name_or_path bert-base-uncased   --dataset_name conll2003   --output_dir /tmp/test-ner   --do_train   --do_eval
  

  • I could train it on the Germaner (explore) dataset, it has no validation set and the script doesn’t support automagically splitting using CLI parameters (though the script supports a lot of other flags).

python datasets package

Here datasets is imported: transformers/requirements.txt at master · huggingface/transformers

TODO - what is this and where can I learn more? Is this HF specific? What else is there?

HuggingFace datasets

It has a really nice interface for searching datasets! Filter by task, language, etc.

German NER datasets: Hugging Face – The AI community building the future.

Some German NER models, sometimes based on bert: Hugging Face – The AI community building the future.

• I could try to reproduce them, for example this one using BERT-base-german-cased and finetuned on legal entity recognition: mrm8488/bert-base-german-finetuned-ler · Hugging Face

Huggingface converting between tf and pytorch

Converting Tensorflow Checkpoints — transformers 4.5.0.dev0 documentation

Is this real?

export BERT_BASE_DIR=/path/to/bert/uncased_L-12_H-768_A-12

transformers-cli convert --model_type bert \
  --tf_checkpoint $BERT_BASE_DIR/bert_model.ckpt \
  --config $BERT_BASE_DIR/bert_config.json \
  --pytorch_dump_output $BERT_BASE_DIR/pytorch_model.bin

Random / recipes / cooking

Tatar von geräuchertem Forellenfilet mit Avocado - Annemarie Wildeisens KOCHEN

Die Forellenfilets in kleine Würfelchen schneiden. Die Schalotte schälen und sehr fein hacken. Die Cherrytomaten je in 6 oder 8 Stücke schneiden. Alle diese Zutaten in eine kleine Schüssel geben und sorgfältig mit der Mayonnaise mischen.

Forelle + tomatos + mayonnaise is literally the only recipe I’ve liked with mayonnaise in it

Jira old issue view + qutebrowser config setting

To redirect an issue to the old view, add ?oldIssueView=true.

Added this to config.py:

config.bind('<Ctrl-J>', ':open {url}?oldIssueView=true')

Ubuntu screen apt-get

(18:03:38/10185) sudo apt install screen
# ...
Suggested packages:
  byobu | screenie | iselect
The following NEW packages will be installed:

… did I just get an advert for a competitor when installing screen? :) Since when does ubuntu do this and where can I read more about it?

Deutsch / German

“Meetingtourismus oder Papiergenerieren?” (heard at work)

Qutebrowser userscripts

It seems to run userscripts not in the virtualenv qutebrowser uses, but the standard system one? Installing packages in virtualenv didn’t work, but installing them globally did.

DVC

Moving/renaming a file/directory is easy: dvc move from to¹. Automatically updates the from.dvc files. Then .gitignore and the .dvc file have to be added and committed through git as usual.

Data organization / dataset structure link

This is interesting: Data Organization — documentation

In general: Best Practices for Scientific Data Management — documentation

This guide describes Axiom Data Science’s best practices for scientific data management. The intent of these practices is to improve the accessibility and usability of your data. These practices may be followed at any time during the preparation of your dataset, but are most useful when considered at the onset of project planning and implemented during data collection.

Also related: Organising your data | Research Data Management

Tree output only directories

tree -d does it.

Git paths from root of repo

Root of repo: git rev-parse --show-prefix ²

--git-dir returns the location of the .git folder, and --show-toplevel returns the absolute location of the git root.

Patterns / phrases / Random

• “It’s not a solution, but it’s an approach” - heard at work, VF

vim delete all lines not matching pattern

I’ll memorize the g/... syntax someday.

:g!/pattern/d

I can just look for the pattern as usual with /pattern and tweak it live, then do

:g!//d

and it will atke the last used pattern.

Pizza sauce recipes

I should try doing something more interesting with the passata di pomodoro!

Options:

• Barbecue Pizza Sauce Recipe | Serious Eats
• Thick & Rich Homemade Pizza Sauce Recipe - Budget Bytes (can be frozen)
• Pizza sauce recipe | BBC Good Food

In general all seem to require both tomato puree and chopped tomatoes; and olive oil + garlic + oregano/basil + (brown) sugar seems to cover 90% of cases.

Deutsch

die Kaffeesatzleserei - reading in coffee beans (heard at work)

screen attaching screens without full name

I shouldn’t forget that screen -R screenname can be replaced by screen -R s if it’s the only screen with such a name. Not sure if better or worse than tab completion, likely worse because it’s surprising, but quite nice to use.

Logoff i3 with a CLI

i3-msg exit¹ does the magic.

Blocking ips with ipset

• ipset - ArchWiki

ipset -N myset nethash  # create myset
ipset add myset 27.8.0.0/13 
iptables -I INPUT -m set --match-set myset src -j DROP # create temporary iptables thing

# making it persistent

ipset save > /etc/ipset.conf

# then enable ipset services

# Listing stuff
ipset -L

# Deleting set
ipset destroy myset

iptables basics

If you can’t destroy an ipset set because it’s being used by kernel:

iptables -L --line-numbers returns this:

Chain INPUT (policy DROP)
num  target     prot opt source               destination
1    DROP       all  --  anywhere             anywhere             match-set myset src
...

Then to delete number 1:

iptables -D INPUT 1

Generally blocking countries

GitHub - mkorthof/ipset-country: Block countries using iptables + ipset + ipdeny.com can do both a whitelist and a blacklist.

Data Scientist roadmap/curriculum

Article with a very interesting graph: Becoming a Data Scientist - Curriculum via Metromap – Pragmatic Perspectives

{:height=“500px”}

German / Deutsch

• “Die Prioritäten sind ein bißchen volatil geworden”
• “Sammle von XY Team ein bißchen Stimmung”

German

der Tonus - heard at work in context of

JQ producing nice comma-separated json

Option to return objects as a list of objects (separated by a comma) · Issue #124 · stedolan/jq: TL;DR use jq "[foo]" instead of jq "foo".

Yunohost full app information / data / install paths

yunohost app info -f appname returns the A LOT of info about the appname, including installation paths.

Qutebrowser userscripts folder location / Writing informative error messages

… can be located in ~/.config/qutebrowser/userscripts, not just in ~/.local ..! When tried to run one it didn’t find it helpfully outputted all the paths it looks for them - which is great and I’ll steal this. If a file is not found you know the person will probably need this, especially if they are many.

GNU Stow for dotfiles management

One of the cooler solutions I’ve seen: Managing dotfiles with GNU stow - Alex Pearce (There seems to be a canonical page¹ I found first, but I like the other one more)

TL;DR create a directory for the dotfiles, with each folder containing dotfiles mirroring the usual dotfiles’ locations in the system; Then from inside the main dotfiles directory do stow vim bash whatever and it’ll magically put it in the right place in the home directory.

This works because

Stow assumes that the contents of the

you specify should live one directory above where the stow command is run, so having our .dotfiles directory at ~/.dotfiles means using stow to manage our dotfiles just works. ²

This is awesome because:

• No manual symlinking
• Dotfiles directory can be easily backed up with git or whatever

The same article²’s sample github repo: dotfiles/neovim at master · alexpearce/dotfiles

Cool dotfile ideas

The stow linked github repo’s dotfiles are actually fascinating: alexpearce/dotfiles: My dotfiles.

dotfiles/.gitconfig at master · alexpearce/dotfiles:

# Clone git repos with URLs like "gh:alexpearce/dotfiles"
[url "https://github.com/"]
  insteadOf = "gh:"
[url "git@github.com:"]
  pushInsteadOf = "gh:"
# Clone CERN GitLab repos with URLs like "gl:lhcb/Hlt"
[url "ssh://git@gitlab.cern.ch:7999/"]
  insteadOf = "gl:"

Git config aliases

Applying the above to my own configs in ~/.gitconfig.

Assuming the ssh port is 1234 ~/.gitconfig is like

[url "ssh://git@myserver:1234/"]
  insteadOf = "gh:"

and then in the per-repo settings something similar to

[remote "bitbucket"]
	url = gh:myusername/myproject.git

Cloning it is now easy:

git clone gh:myusername/myproject

Neat!

Jekyll syntax highlighting supported languages

List of supported languages and lexers · rouge-ruby/rouge Wiki Quite a lot! Will try the generic conf for the .gitconfig above.