R Annotation Vocabulary (Might Be) All You Need

Paper link: https://www.biorxiv.org/content/10.1101/2024.07.30.605924v1

Abstract:
>
Protein Language Models (pLMs) have revolutionized the computational modeling of protein systems, building numerical embeddings that are centered around structural features. To enhance the breadth of biochemically relevant properties available in protein embeddings, we engineered the Annotation Vocabulary, a transformer readable language of protein properties defined by structured ontologies. We trained Annotation Transformers (AT) from the ground up to recover masked protein property inputs without reference to amino acid sequences, building a new numerical feature space on protein descriptions alone. We leverage AT representations in various model architectures, for both protein representation and generation. To showcase the merit of Annotation Vocabulary integration, we performed 515 diverse downstream experiments. Using a novel loss function and only $3 in commercial compute, our premier representation model CAMP produces state-of-the-art embeddings for five out of 15 common datasets with competitive performance on the rest; highlighting the computational efficiency of latent space curation with Annotation Vocabulary. To standardize the comparison of de novo generated protein sequences, we suggest a new sequence alignment-based score that is more flexible and biologically relevant than traditional language modeling metrics. Our generative model, GSM, produces high alignment scores from annotation-only prompts with a BERT-like generation scheme. Of particular

/r/MachineLearning
https://redd.it/1egthqg

How many database rows can I have till Django starts to slow down?

How many rows can I have in my PostgreSQL database till Django starts to slow down? Each row has 9 columns. A single user can create as many as 1,000 rows.

/r/djangolearning
https://redd.it/1egpmcg

How to upload your Django project on github safely?

what things should i hide before i put the project on github?

/r/django
https://redd.it/1eh0dqc

Thursday Daily Thread: Python Careers, Courses, and Furthering Education!

# Weekly Thread: Professional Use, Jobs, and Education 🏢

Welcome to this week's discussion on Python in the professional world! This is your spot to talk about job hunting, career growth, and educational resources in Python. Please note, this thread is not for recruitment.

---

## How it Works:

1. Career Talk: Discuss using Python in your job, or the job market for Python roles.
2. Education Q&A: Ask or answer questions about Python courses, certifications, and educational resources.
3. Workplace Chat: Share your experiences, challenges, or success stories about using Python professionally.

---

## Guidelines:

- This thread is not for recruitment. For job postings, please see r/PythonJobs or the recruitment thread in the sidebar.
- Keep discussions relevant to Python in the professional and educational context.

---

## Example Topics:

1. Career Paths: What kinds of roles are out there for Python developers?
2. Certifications: Are Python certifications worth it?
3. Course Recommendations: Any good advanced Python courses to recommend?
4. Workplace Tools: What Python libraries are indispensable in your professional work?
5. Interview Tips: What types of Python questions are commonly asked in interviews?

---

Let's help each other grow in our careers and education. Happy discussing! 🌟

/r/Python
https://redd.it/1eh2h8o

Anyone know of any communities dedicated to software toys?

By "software toys" I mean silly little applications/scripts/whatever that serve no purpose other than to amuse, but don't quite meet the definition of a game.

For example, I once wrote a Python script that encoded text as mosaic of colored squares.

Or another time I wrote a non-interactive simulation of a crew of NPCS that explored a fictional ocean and posted their discoveries on Reddit.

Just silly, dumb things like that. It doesn't necessarily have to be strictly for Python but since that's what I normally code in I thought I'd ask here.

Anyone know of any communities dedicated to software like that?

/r/Python
https://redd.it/1eh7rlg

django-allauth 64.0.0 released: WebAuthn & Passkey support
https://allauth.org/news/2024/07/django-allauth-64.0.0-released/

/r/django
https://redd.it/1ehb6wb

Hosting Help

Hi, I have 3 sites pointing to 1 IP address hosted by Linode ubuntu. I did not have to do much when setting this up, all was auto filled by Linode when adding domain names.

I want to change my VPS from Linode to a new provider that supports only IPv4. The new service only gives me the vps, there is no interface like Linode where I can add domain names point to the VPS IP.

Could anyone provide guidance on how to setup my domains to point to my new vps IP?

my domains are with with 2x godaddy, 1x namecheap.

/r/flask
https://redd.it/1ehga1n

Django Compose - Head start on development

Hello Everyone, 👋

I am excited to share with you, Django Compose 🚀

https://preview.redd.it/yo8y7518vufd1.png?width=3456&format=png&auto=webp&s=4c55579a1a33c74c22b9cda008c2bc890577e452

Django Compose shortens the time needed to create a full fledged Django project.

Build at the speed of no-code. Export to code and customise. Build fast not from scratch.

With few steps, you have 10x productivity which allows you focus on what matters (your business logic).

Create project: Describe your Django application or use our template.

Map your fields: Describe and Map your project's model schema (Entity Relations).

Configure what you want: Select technologies, features and dependencies you want.

Get your code: That's it. Your codebase is ready, with specified apps, models, views, templates, urls and much more configured for you, API and WEB 🪄.

Live now ✨

https://djangocompose.com

/r/django
https://redd.it/1eh8ndc

ImportError in VS Code

/r/djangolearning
https://redd.it/1ehd1e0

The trouble with all

https://www.gauge.sh/blog/the-trouble-with-all

I wrote a blog post discussing the issues that __all__ in Python has - particularly it's lack of ability to enforce public APIs despite letting you define them. It led to a fun exploration of importlib and me writing my first import hook! Code here - https://github.com/gauge-sh/hook/blob/main/hook.py

Curious to hear folks thoughts on this problem, especially as compared to other languages! How do you enforce interfaces on your Python modules?

/r/Python
https://redd.it/1ehjy9g

ENVKEY Shutting Down - Alternatives for secrets / keys?

Hey all, ENVKEY just announced they're shutting down. What is everyone using for secrets / keys?

Here is the email from ENVKEY:

>Today I have some difficult news to share. After nearly 7 years of working on EnvKey, I’ve decided to begin winding down the company. In order to give all customers and users plenty of time to transition away, EnvKey will wind down over the next 6 months. EnvKey Cloud will shut down on February 1st, 2025 and then the EnvKey company will be dissolved.

>This has been a stressful and emotional decision for me, but unfortunately I’ve had to accept that continuing to run EnvKey is no longer financially sustainable for myself and my family, and therefore it’s time to move on.

>I understand that this may come as a surprise and a disappointment. I’m deeply honored by the trust that hundreds of organizations and thousands of users have placed in EnvKey over the years, and I regret giving you extra work to do in transitioning away.

>I hope that the gradual wind down period will help to soften any negative impact. Additionally, I've been in touch with the CEO of Infisical, another secrets management platform that is also open source, end-to-end encrypted, and similar in its spirit and

/r/Python
https://redd.it/1ehny2x

Real-time chat application with Django + Firebase Cloud Messaging.

I need to create a real-time chat application where users can send messages, videos, pictures, voice messages, etc.

There will be one-to-one chats or group chats for users.

Now my question is about the tech stack, basically up until now I have been writing DRF API and I am thinking of using Django channels with FCM for push notifications and I wanted to know if this is a good idea or if I should do something else.

Also, I have heard about Firebase's real-time database and wanted to ask if I can use it instead of Django channels.

I am a beginner and a bit lost so please any recommendation or suggestion will be appreciated.

/r/django
https://redd.it/1ehnjqn

New interesting funeral brochure and donation website with django htmx my second project will django

https://anytribute.com

Hi this is my second project with Django
Can you check it up and give me your feedback. It’s free to use.

Stack
Django
Bootstrap
Htmx
Hyperscript
Django widgets tweeks
Djago all auth


/r/django
https://redd.it/1ehqomc

Friday Daily Thread: r/Python Meta and Free-Talk Fridays

# Weekly Thread: Meta Discussions and Free Talk Friday 🎙️

Welcome to Free Talk Friday on /r/Python! This is the place to discuss the r/Python community (meta discussions), Python news, projects, or anything else Python-related!

## How it Works:

1. Open Mic: Share your thoughts, questions, or anything you'd like related to Python or the community.
2. Community Pulse: Discuss what you feel is working well or what could be improved in the /r/python community.
3. News & Updates: Keep up-to-date with the latest in Python and share any news you find interesting.

## Guidelines:

All topics should be related to Python or the /r/python community.
Be respectful and follow Reddit's Code of Conduct.

## Example Topics:

1. New Python Release: What do you think about the new features in Python 3.11?
2. Community Events: Any Python meetups or webinars coming up?
3. Learning Resources: Found a great Python tutorial? Share it here!
4. Job Market: How has Python impacted your career?
5. Hot Takes: Got a controversial Python opinion? Let's hear it!
6. Community Ideas: Something you'd like to see us do? tell us.

Let's keep the conversation going. Happy discussing! 🌟

/r/Python
https://redd.it/1ehvu5t

Jeremy Howard has announced FastHTML, Dynamic modern html pages using python!
https://fastht.ml

/r/flask
https://redd.it/1ei1dw1

Best practice for including a ton of error checking in a functional api view?

Hi, I'm doing an integration which involves taking data from service A, parsing it, sending it to service B, then returning a response back to service A. Service A has given a list of error codes that it expects when my server detects specific issues, so I've implemented them, but found that the code I wrote is quite lengthy to read.

I have implemented permission classes for things like this before, like detecting an api key or something, but the problem here is that the error checks vary per endpoint slightly, so I'd be writing at best a permission class per endpoint. I suppose I could try to create a permission class which checks for any similar errors, but it would still not solve the issue of having a bunch of error checking sprinkled into the views. Creating a separate file that contains functions that check for the errors is possible, but I just want to get a sense of best practice here. There are 5 endpoints, and each have similar if/else blocks for error checking per service A's requirements.

Here is an example of the if/else block for the error checks that service A wants, any suggestions on refactoring

/r/django
https://redd.it/1ei316o

Picked up an old project again and upgraded to the latest dependencies. Now I receive this error: "The current Flask app is not registered with this 'SQLAlchemy' instance." and I cant wrap my head around it.

Hey folks, I picked up an old project of mine, upgraded the versions in my requiement file and I receive this odd error for something that must have worked years ago.

I'd like to explain what's going on by guiding you through one request that triggers it, but should work.
I's a request to see if the username that's used to sign-up already exists.

Requirements:

Flask==3.0.3
flasklogin==0.6.3
Flask-Migrate==4.0.7
flasksqlalchemy==3.1.1
requests==2.32.3
Werkzeug==3.0.3
dnspython==2.3.0
email-validator==1.3.1
urllib3==1.26.14


My app.py (simplified)

from flask import Flask, rendertemplate, makeresponse, sendfromdirectory, jsonify, request
from flasksqlalchemy import SQLAlchemy
from sqlalchemy import text
from flaskmigrate import Migrate

app.secretkey = b'supersecret'

app.config['SQLALCHEMYDATABASEURI'] = 'mysql+pymysql://dbuser:password@mariadb/kinda?charset=utf8mb4'

app.config['SQLALCHEMYTRACKMODIFICATIONS'] = False
app.config['SECURITYDEFAULTREMEMBERME'] = True


db = SQLAlchemy(app)

# Initialize Flask-Migrate


/r/flask
https://redd.it/1ei6p69

help to deploy python api


I am building a fullstack application using MERN, there are some features in it which requires AI/ML, so I've integrated python with this project. I can deploy the Node.js on vercel, but don't know how do I deply the python, as vercel doesn't allows python deployment. please suggest me some good platforms, should be free, to deploy python.

thank you

/r/flask
https://redd.it/1ehmqwy

Django devs from Colombia, are you there ?

Hi guys what are you up to these days in Colombia, how is the django scene moving ? I'd love to connect with fellow django devs currently in Colombia 👋

/r/django
https://redd.it/1ei570j

Best Approach to Styling Django Forms

I am always struggling to style Django forms(field, label, field/form errors), how are you guys dealing with this? What will you propose as the best approach(or library)?

/r/django
https://redd.it/1eiazvx