ersilia-os / ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.

🎉 Welcome to the Ersilia Model Hub 🌟

Table of Contents

1. Project Description
2. Quick start guide
3. Contribute
4. License and citation
5. About us

Project Description

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to 🦠 infectious and neglected disease research. Our mission is to offer an open-source, 🛠 low-code solution that provides seamless access to AI/ML models for 💊 drug discovery. Models housed in our hub come from two sources:

1. 📚 Published models from literature (with due third-party acknowledgement)
2. 🛠 Custom models developed by the Ersilia team or our valued contributors.

• Read more about the project in the Ersilia Book
• Browse available models in the Ersilia Model Hub

Quick Start Guide

Please check the package requirements in the Installation Guide. The next steps are a quickstart guide to installing Ersilia.

1. Create a conda environment and activate it

   conda create -n ersilia python=3.10
   conda activate ersilia

2. Clone this repository and install with pip

   git clone https://github.com/ersilia-os/ersilia.git
   cd ersilia
   pip install -e .

3. Once the Ersilia Model Hub is installed, you can use the CLI to run predictions. First, select a model from the Ersilia Model Hub and fetch it:

   ersilia fetch retrosynthetic-accessibility

4. Generate a few (5) example molecules, to be used as input. The example command will generate the adequate input for the model in use

   ersilia example retrosynthetic-accessibility -n 5 -f my_molecules.csv

5. Then, serve your model:

   ersilia serve retrosynthetic-accessibility

6. And run the model:

   ersilia run -i my_molecules.csv -o my_predictions.csv

7. Finally, close the service when you are done.

   ersilia close

8. If you no longer want to use the model, you can delete it.

   ersilia delete retrosynthetic-accessibility

Please see the Ersilia Book for more examples and detailed explanations.

Contribute

The Ersilia Model Hub is a Free, Open Source Software and we highly value new contributors. There are several ways in which you can contribute to the project:

• A good place to start is checking open issues.
• If you have identified a bug in the code, please open a new issue using the bug template.
• Share any feedback with the community using GitHub Discussions for the project
• Check our Contributing Guide for more details

The Ersilia Open Source Initiative adheres to the Contributor Covenant code of conduct.

Submit a New Model

If you want to incorporate a new model in the platform, open a new issue using the model request template or contact us using the following form.

After submitting your model request via an issue (suggested), a maintainer will review your request. If they /approve your request, a new model respository will be created for you to fork and use! There is a demo repository explaining the steps one-by-one.

License and Citation

This repository is open-sourced under the GPL-3 License. Please cite us if you use it!

About Us

The Ersilia Open Source Initiative is a Non Profit Organization (1192266) with the mission is to equip labs, universities and clinics in LMIC with AI/ML tools for infectious disease research.

Help us achieve our mission or volunteer with us!

ersilia's Issues

Outreachy Documentation Project: Dennis Onyeka / dchidindu5

Applicant: < @dchidindu5 >

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Add folder for Tutorials - Outreachy begginers

Hello,

Could you create an empty folder in the ersilia project with the name "tutorial" ?
This issue is great if you are a beginner who wants to test how the git fork, branch, and pull requests work. I recommend reading this tutorial first
Please note this issue will only be assigned to one applicant, ping me here if you want to contribute to this.

Improving the search engine in https://airtable.com/shrUcrUnd7jB9ChZV/tblZGe2a2XeBxrEHP

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Drug Discovery using Deep Learning Algorithms

Medicinal Literature

1. Collect Data from various open sources (learn more about the Isaura Data Store)
2. Perform EDA
3. Dimensionality Reduction algorithms (like PCA and t-SNE)
4. visualize the chemicals using matplotlib, plotly, dash
5. Combine two or more chemicals to form new drugs and make sense out of it (this will require domain expertise)

Models used

• CNN
• Softmax classifier
• GANs

Training
After a lot of epochs, the model should predict the correct drug with a good accuracy

Discussion
Please provide your valuable feedback and hopefully we might end up discovering a novel drug.
Thank You
-Kumari Surya Remanan

Installation steps of Ersilia Model for Windows operating system

I noticed that there are no installation steps for Ersilia Model on Windows and the steps would be coming soon.

Please, I would like to work with the developers to know how to install Ersilia on Windows and help write the steps.

I have already downloaded Miniconda, activated the Ersilia environment and installed Ersilia. I just need to collaborate with the developers for it to properly work on my system.

Thank you.

Enhancement of README.file

Is your feature request related to a problem? Please describe.
The readme file is absolutely stunning. When I was reading the file, it seems to be very simple, the alignments, bold fonts,etc. I would like to add my creativity.

Describe the solution you'd like
I will change the file look by adding some outstanding ideas on to it.
@GemmaTuron could you pls assign this to me

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Correct grammar in the Roadmap section in the ReadME file

Within the Road map section there is a need to correct grammar as part of the improvement to the read me file. cc: @GemmaTuron

Add "Back to top button" to the README file

Is your feature request related to a problem? Please describe.
Scrolling up and down is exhausting when exploring the readme file

Describe the solution you'd like
I want to incorporate a button to scroll back to the top page after every sub-section of the readme file
@GemmaTuron @miquelduranfrigola kindly assign this issue to me

code problems

@miquelduranfrigola @GemmaTuron I hope if there are more code problems that can tackles the contributors skills in python to improve
their skills .What do you think folks? we can do a discussion here

Add model search functionality in the CLI

Background

Ersilia models can be browsed on the web. Although we do not have a good interface now, this can be done through an Airtable base. There is no way to search/filter models using the CLI. As of now, the only thing that can be done is: ersilia catalog, which simply prints all models on a table.

Requested feature

We would like to have a search function in the ersilia CLI. For example: ersilia catalog search --text "antimicrobial" or ersilia catalog search --mode "pretrained"

Model request

Ersilia accepts the incorporation of third-party models and would not mind suggestions.

Model title
Suggest a title for your model. For example, 'Antimicrobial activity prediction'

Model features
Describe the features of the model. For example, "The Antimicrobial activit prediction model predicts antimicrobial activity in a specimen."

Use Case
Give a brief tutorial of how the model is used. Screenshots and/or videos can be included.

Benefit: What benefit can the model offer in the field of science?

Publication
Is there a link to a publication? (DOI, PMID, URL). If yes, include the link.

Code
Is code available? If so, please provide link to repository (GitHub, GitLab, BitBucket).

License
Please include a license for the model.

Add folder /documentation - Outreachy Applicants

Hello,

Could you create an empty folder in the ersilia project with the name /documentation ?
This issue is great if you are a beginner who wants to test how the git fork, branch, and pull requests work. I recommend reading this "tutorial" first
Please note this issue will only be assigned to one applicant, ping me here if you want to contribute to this.

Grammatical error in https://www.ersilia.io/ site

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Broken Links

Describe the bug
Some links are broken in the repository.

To Reproduce
Steps to reproduce the behavior:

1. Go to README.md
2. Click on 'Contributor Covenant' in the head section
3. Redirected to 404 page
4. See error

Expected behavior
This page should have rendered.

Screenshots

Desktop (please complete the following information):

• Linux, Ubantu, WIndows 10
• Chrome, safari, firefox
• Version [all]

Additional context
None

Track unused models and automatically delete them

Background

Most models in Ersilia require substantial disk usage. Deleting a model means removing all model files as well as the corresponding conda environment or docker container. A desirable feature would be to automatically remove models if they have not been used for e.g. a month.

Requested feature

Keep track of model last usage date, and delete it automatically if considered to be unused.

Improve catalog by including model size in "ersilia catalog" output

feature request : Improve catalog by including model size in "ersilia catalog" output. A Column displaying model size against each model would help the user to get an idea of the amount of time it will take to download, also the user would get to know how much space is required in the disk.
Problem : while working on the issue #8 , I had to test the deletion of models. for which I had to download a couple of models. I was looking the models that require the least space on disk so that the testing would take lesser time, but there was no mechanism of finding that out before running the fetch command.
Alternatives :

• A column of model size could be added to the "ersilia catalog" command's output
• An additional option could be added to the catalog command such as "ersilia catalog --size" that would print the catalog differently (including the size information)
• A webpage could open to display the catalog to include the model size (this idea was also mentioned in another issue)

set up conda environment

@miquelduranfrigola @GemmaTuron I want to address an issue not related to fixing a bug but something i encountered while trying to install ersilia CLI. As related to issue #36 i installed the Ubuntu because my system is windows 10 and downloaded all the packages needed but still it didnt work and it was due to my conda environment.

So if someone faced the same problem instead of using:
"conda create -n ersilia python=3.7"
please use:
"source ~/anaconda3/etc/profile.d/conda.sh"
Then activate the environment as per in Ersilia book. it worked and i hope it helps others.Thank you

Outreachy Code Project: <Maham Tariq , Github : https://github.com/mahamtariq58>

Applicant: https://github.com/mahamtariq58

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the Ersilia Model Hub, a FOSS platform offering pre-trained AI/ML models for research”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. This project requires knowledge of the Python programming language. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable.

---

Initial steps

• Record your application for the project in the Outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications.
• Comment under this issue explaining why you are interested in this project.

---

Installation of the Ersilia Model Hub

• Install the ersilia library.
• Add a screenshot under this issue showing that you are able to run one model (for example, the chemprop-antibiotic model)
• Fetch at least 3 models from the Ersilia Model Hub. You can find these models with the ersilia catalog command. Add a screenshot of the local catalog (ersilia catalog –local)

---

CLI

• Check if there are open issues related to the command line interface. Continue with the next tasks if they are open.
• Select one issue related to improving the CLI and request to be assigned to it.
• Link the #PR as a comment under this issue.
• Make any changes required in the PR and tick this box once it has been approved.
• Suggest at least one missing feature in the CLI (one sentence is enough, for example: “Add command to estimate memory usage of a particular model”).

---

Python library

• Add a screenshot showing that you are able to run predictions using ersilia as a Python library (find more information here). Ideally, use a Jupyter notebook.
• Create a simple Streamlit app using the ersilia Python library. The app can have an input and an output box, and perhaps a few models to select. Add a screenshot of the app as seen in your browser.
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Create a writing style guidelines for ersilia

What is your feature request?
A writing style guide that will have every document follow a standard style.

Is your feature request related to a problem?
Ersilia deals a with a lot of documentation, keeping that in mind it will be great if we introduce a writing style guideline. In that way we can maintain a standard format for every document. This will also help when we have new contributors in the future.

Set up an Issue Template for Model Requests

Create a template for an issue to request a model incorporation in the hub. Important questions to keep in mind are: name of the model, why is it for, license, where is the code living...
If someone else is working on this, you can create a new template or contribute your ideas to the existing one.

Make ersilia conda-installable

Background

Currently, Ersilia can be pip-installed. We have a GitHub Action to update ersilia on PyPi every time we do a new release. However, pip installation does not ensure that extra requirements (such as git-lfs) are installed. Perhaps having ersilia as a conda package would be desirable as well.

Requested feature

Make ersilia conda-installable and trigger a GitHub Action every to update the ersilia conda repository on every new release of the package.

Link Isaura to the AWS Registry of Open Data

Background

A few months ago, we created a small repository named isaura to manage calculated data. Storing calculations is very relevant, especially for computationally intensive models that have not been optimized for production by original authors. Isaura works mainly on HDF5 files, and our idea is to store these files in the AWS Registry of Open Data (ROD), eventually.

The current logic behind Isaura is that a local and a public file exist. The public file is typically large, and is downloaded (optionally) at fetching time. The local file contains only calculations performed by the user (i.e. those that were not available in the public file). Users have the option to contribute their calculations to the public file. We are currently tackling this issue with data version control DVC.

Discussion

We would like to open a discussion with the goal of identifying the best design of Isaura, and the best way to link it to the AWS ROD. Two urging questions we have are:

• Is it safe to allow users to contribute their precalculations? What risks may exists?
• Is it possible to keep the public file in the ROD and directly fetch precalculations from there?

We suggest that we start the discussion here and then we open more specific issues to tackle each point.

Outreachy Code Project: Abdelrahman Nawar

Applicant: Abdelrahman Nawar @Nawarrr

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the Ersilia Model Hub, a FOSS platform offering pre-trained AI/ML models for research”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. This project requires knowledge of the Python programming language. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable.

---

Initial steps

• Record your application for the project in the Outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications.
• Comment under this issue explaining why you are interested in this project.

---

Installation of the Ersilia Model Hub

• Install the ersilia library.
• Add a screenshot under this issue showing that you are able to run one model (for example, the chemprop-antibiotic model)
• Fetch at least 3 models from the Ersilia Model Hub. You can find these models with the ersilia catalog command. Add a screenshot of the local catalog (ersilia catalog –local)

---

CLI

• Check if there are open issues related to the command line interface. Continue with the next tasks if they are open.
• Select one issue related to improving the CLI and request to be assigned to it.
• Link the #PR as a comment under this issue.
• Make any changes required in the PR and tick this box once it has been approved.
• Suggest at least one missing feature in the CLI (one sentence is enough, for example: “Add command to estimate memory usage of a particular model”).

---

Python library

• Add a screenshot showing that you are able to run predictions using ersilia as a Python library (find more information here). Ideally, use a Jupyter notebook.
• Create a simple Streamlit app using the ersilia Python library. The app can have an input and an output box, and perhaps a few models to select. Add a screenshot of the app as seen in your browser.
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Better model catalog display

Background

Currently, users can list the catalog of all available ersilia models with the command ersilia catalog. They have the option to list only models that are available on their local computer with ersilia catalog --local.
The current output of these commands is a table printed on the terminal using the tabulate python library.

Requested features

We would like to have a better output, although it is not clear to us what would be the best option. Options we've considered are:

1. Open a browser tab and display models there.
2. Continue with tabulate (or similar) and add a multi-page view.

Guidelines for onboarding of new contributors

Is your feature request related to a problem? Please describe.
As a contributor for quite sometime now, I can tell from my experience the initial experience can be stressful. On the other hand, a lot of new contributors are sometimes shy to open up about their issues and problems to the project maintainers, or discuss about in the public communication channels.

Describe the solution you'd like
In this situation, it will be great if we could introduce a readme file, specifically designed for the new contributors with all the relevant links or resources. This makes the process of contribution easy and smooth for new onboarding contributors and also encourages more future contributions.

Add progress bar when fetching a model

Background

The fetch command downloads a model from a GitHub repository corresponding to the identifier of the model, for example, eos4e40. In verbose mode (ersilia -v fetch eos4e40), the logging is displayed on the terminal. However, if verbose mode is not used, (ersilia fetch eos4e40) the user does not have a sense of the progress in downloading and setting up the model on the local computer.

Requested feature

Add a progress bar or percentage to the fetch command. Progress should ideally capture:

1. Downloading all files from the model repository. A challenge is that large files are stored as part of Git LFS, which may make it more difficult to estimate the size of the repository.
2. Time needed to perform the packing functions, in particular, creating conda environments or docker containers.

Outreachy Documentation Project: <Chineme C.>

Applicant: <@MsChineme>

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

For Third-party Model incorporation into the Hub

Ersilia accepts the incorporation of third-party models and would not mind suggestions.

Model title
Suggest a title for your model. For example, 'Antimicrobial activity prediction'

Model features
Describe the features of the model. For example, "The Antimicrobial activit prediction model predicts antimicrobial activity in a specimen."

Use Case
Give a brief tutorial of how the model is used. Screenshots and/or videos can be included.

Publication
Is there a link to a publication? (DOI, PMID, URL). If yes, include the link.

Code
Is code available? If so, please provide link to repository (GitHub, GitLab, BitBucket)

License
Please include a license for the model.

Bug report for the Ersilia model

Describe the bug
A clear and concise description of what the bug is. Example can be a calculation error or a missing command.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

issue #57 -1. In 'our strategy' section at the content of the foster in-country research there should be working on instead of working in infectious and neglected diseases. 2. Can I know what are we planning to include in the volunteer part in the footer section to know if I can contribute or help in any way if possible.

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context
Add any other context about the problem here.

Outreachy Documentation Project: Maxwell Kambona https://github.com/camus60

Applicant: Maxwell Kambona https://github.com/camus60

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Fix typo in the Readme file

The Readme file contains a typo in the word acknowledgement and there is a need to be fixed. cc: @GemmaTuron

Create a contributing guidelines for the project

Is your feature request related to a problem? Please describe.
From a beginner's perspective, the first thing someone looks for is the contribution guidelines. In order to understand how to make a pull request, check related formats and to look for beginner friendly issues.

Describe the solution you'd like
A readme file about contribution guidelines will be a great addition to make the project more user friendly and will also help in improving participation in the project.

Describe alternatives you've considered

Additional context

The Installation guide for intalling ersilia model did not specify the Conda Environment that should be used

While reading through the conda documentation, I found out that the Conda environment is made up of two versions (miniconda and anaconda).
Both are recommended but with different features and functionalities.

I'm suggesting that both versions should be outlined in the "Ersilia Installation Guide" so that users can make their choices.

Code documentation

Background

Our high-level documentation is being built using a GitBook. In addition, we have the automatically generated documentation (package index) as created by Sphinx. This low-level documentation can be seen here.

Help needed

We currently lack docstrings for most of the classes in ersilia, which results in poor code documentation. We are seeking advice on how to write code documentation efficiently, as well as contributors who would be able to help us in the writing.
Please comment under this issue with good resources on how to write documentation

Outreachy Documentation Project: <Sayantani Saha/sayantani11>

Applicant: <@sayantani11>

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Tutorial inspiration

We are working to develop simple tutorials for the Ersilia Model Hub.
Ca you comment below suggestion one example of a good tutorial from another FOSS project we could get inspiration from?

This is a required step to tackle Issue #17

Create a mock tutorial slide

Create one or two slides with a schema of how to use the Ersilia Model Hub and upload them in the folder /tutorials
Feel free to use any tools you want, we recommend checking carbon for snippets of code, and also reading our brand guidelines here.
You can start working on this project even if other applicants are working on it as well, feel free to make your own design.

To answer this issue, please first go to issue #16 and comment there. Also note this is a medium-sized issue, and requires some technical expertise. To create a tutorial, you probably need to install and run the Hub.

Be creative and have fun!

Outreachy Documentation Project: Lowe Yvana

Applicant: @loweyvana

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points

• Comment under this issue with a link to the blogpost (a google docs for example)

• Incorporate feedback from the mentor

• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience

• Comment under this issue with a link to the blogpost (a google docs for example)

• Incorporate feedback from the mentor

• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue

• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

New Suggestion
There is so much to write about when it comes to NTDs, If you permit me, I would like to suggest we write several blog posts about the different aspects of NTDs and add them as links to this main blog post. In that way, we could cover the whole topic and our audience would have enough stuff to read about. Let me know what you think, please.

Feedback from mentor @miquelduranfrigola
Miquel Duran (Ersilia) il y a 2 jours
As for the series of blogposts idea, this is quite interesting. I think we could frame it within the context of the Ersilia Model Hub, for example: "What models should we prioritize, based on the current status of drug discovery/development for NTDs?

Issue forms

Creating Issue Templates using the Issue forms and replacing the markdown files with YAML files.

The issue form looks like this:---

Also, the Outreachy Documentation template is not generated correctly, I also want to update that using yaml.

Outreachy Documentation Project: Ifeoluwa Favour Ojumoro

Applicant: @ifeoluwafavour

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Show Installation and Run of the Ersilia Model Hub - Outreachy

This issue is for Outreachy Applicants interested in contributing to the Project "Improve the Ersilia Model Hub, a FOSS platform offering pre trained AI/ML models for research"

Before tackling any coding issue, comment here with:

• Your name
• System (OS, Windows., Linux) and version
• Your background in Python (required skill for this project)
• A snapshot of your CLI showing that you have successfully run a model

This is required before we accept any pull request for the issues labelled with the tag "code"

Outreachy Documentation Project: <Busirat Azeez/busiratazeez>

Applicant:

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

---

Initial steps:

• Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications
• Comment under this issue explaining why are you interested in this project

---

GitHub documentation:

• Create a README file with the name <README_yourname.md> under the /documentation folder
• Link the #PR in a comment under this issue
• Incorporate feedback from the mentor

---

Writing dissemination material

• Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• Comment under this issue with a link to the blogpost (a google docs for example)
• Incorporate feedback from the mentor
• Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue
• Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

---

Technical skills (required for the tutorial only)

• Install the Ersilia Model Hub
• Test one model
• Add a screenshot under this issue showing the model running in your computer
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Graphic material

• Read the Ersilia Brand Guidelines
• Read “Why Ersilia?”
• Create one image / slide to explain Ersilia’s mission and vision
• Link to the image/slide as a comment under this issue
• Incorporate feedback from the mentor
• Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• Link the #PR in this issue
• Incorporate feedback from the mentor

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Test issue

Outreachy Code Project: Name: Anamika Yadav

Applicant: https://github.com/anamika-yadav99

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the Ersilia Model Hub, a FOSS platform offering pre-trained AI/ML models for research”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. This project requires knowledge of the Python programming language. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable.

---

Initial steps

• Record your application for the project in the Outreachy website referencing this issue. Please make sure to select the right project on the website.
• Join the Slack channel to follow public communications.
• Comment under this issue explaining why you are interested in this project.

---

Installation of the Ersilia Model Hub

• Install the ersilia library.
• Add a screenshot under this issue showing that you are able to run one model (for example, the chemprop-antibiotic model)
• Fetch at least 3 models from the Ersilia Model Hub. You can find these models with the ersilia catalog command. Add a screenshot of the local catalog (ersilia catalog –local)

---

CLI

• Check if there are open issues related to the command line interface. Continue with the next tasks if they are open.
• Select one issue related to improving the CLI and request to be assigned to it.
• Link the #PR as a comment under this issue.
• Make any changes required in the PR and tick this box once it has been approved.
• Suggest at least one missing feature in the CLI (one sentence is enough, for example: “Add command to estimate memory usage of a particular model”).

---

Python library

• Add a screenshot showing that you are able to run predictions using ersilia as a Python library (find more information here). Ideally, use a Jupyter notebook.
• Create a simple Streamlit app using the ersilia Python library. The app can have an input and an output box, and perhaps a few models to select. Add a screenshot of the app as seen in your browser.
• Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

---

Scientific content

• Check the models available in the Hub
• Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• Add your card as a comment to this issue
• Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

---

Other

If you have interest in working on related topics, or have new suggestions, please do the following

• Add a comment in this issue with your new idea, tagging the mentor
• Get feedback from the mentor and act accordingly
• Link in the comments any other PR you have contributed to.

---

Community

• Look up two other projects and comment on their issues with feedback on one of their tasks
• If you have feedback from your peers, answer it in this issue.

---

Final application

• I have answered all comments from mentors and contributors
• All PR or issues assigned to me are complete
• I have submitted my final application to the project

Outreachy Documentation Project: <Simran1604>

What is your feature request?
There are some spelling and grammatical errors in the readme.md file which can be resolved and also there is as of now no information or links to direct the new commers to the contribution guidelines in the readme file. Including that information can be quite helpful.

Is your feature request related to a problem?
As I landed on the repository and went through the readme.md file, I searched for some information or direction to contributing in this codebase in the file but couldn't get it. Someone who is new to the repository will find it easier to navigate to that information from the readme page than looking for the new_contributors.md and contributing.md file in the repository.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Write a more standard README file

We want to write a better README file, including better installation instructions and a better description of the package features. Are there any guidelines to a good README file?

How Ersilla Model Hub will help in future for mankind. It is not mentioned anywhere.

What is your feature request?
A clear concise descritprion of what you want to happen.

Is your feature request related to a problem?
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Feature request

What is your feature request ?, Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Calculate disk usage of a model

Background

When a model is downloaded with the fetch command, the corresponding GitHub repository is cloned, including Git LFS files. As of now, there is no way to know the size of the downloaded files before cloning. In addition, a conda environment or a docker container is created after download. We do not have a way of estimating the size of such environments/containers. Therefore, we are unable to inform the user about the size of the model they are about to fetch.

Requested feature

We would like to calculate total disk usage of a model before fetching it. This includes:

• Size of files from GitHub (including Git LFS)
• Size of conda environment or docker container