Outreachy Code Project: <Fortune Max>

[fortune-max]

Applicant:

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.

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Initial steps

• [x] Record your application for the project in the Outreachy website referencing this issue. Please make sure to select the right project on the website.
• [x] Join the Slack channel to follow public communications.

• [x] Comment under this issue explaining why you are interested in this project.

  Installation of the Ersilia Model Hub

• [x] Install the ersilia library.
• [x] Add a screenshot under this issue showing that you are able to run one model (for example, the chemprop-antibiotic model)

• [x] 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

[fortune-max]

I am not sure if it's a common enough issue but on Mac it seems you have to install hdf5 library perhaps using homebrew as the python dependency (hf5py) requires the library to be present locally first.

Followed the installation instructions here: https://ersilia.gitbook.io/ersilia-book/quick-start/installation

To fix run: brew install hdf5@1.8

Then on ARM chip Macs: ln -s /opt/homebrew/opt/hdf5@1.8/lib/libhdf5.10.dylib /usr/local/lib/libhdf5.dylib

On Intel chip Macs: ln -s /usr/local/opt/hdf@1.8/lib/libhdf5.10.dylib /usr/local/lib/libhdf5.dylib

[fortune-max]

Another Mac specific issue I encountered while setting up.

The .bashrc file is read when starting up ersilia.

As my default shell is zsh, no .bashrc file exists. This causes ersilia/default.py/bashrc_cli_snippet function call to fail (line 119).

It is not immediately obvious this is the cause from the error thrown.

Running touch ~/.bashrc fixed this locally for me.

[fortune-max]

Running ersilia fetch molecular-weight kept failing for me until I ran conda create -n eosbase-bentoml-0.11.0-py37

and activated environment conda activate eosbase-bentoml-0.11.0-py37

Kept throwing a source environment not found File "/Users/fortune/code/ersilia/ersilia/utils/conda.py", line 297, in clone raise Exception("{0} source environment does not exist".format(src_env)) Exception: eosbase-bentoml-0.11.0-py37 source environment does not exist

[fortune-max]

For Apple Silicon, the h5py dependency doesn't work with pip install as it has to be built from source and the headers and shared library files are not present.

Before running pip install -e . , make sure to install hdf5 with brew

brew install hdf5@1.8

Add the necessary flags to your session to allow local compilation of h5py:

export LDFLAGS="-L/opt/homebrew/opt/hdf5@1.8/lib" export CPPFLAGS="-I/opt/homebrew/opt/hdf5@1.8/include"

Make the shared library accessible to compiler

ln -s /opt/homebrew/opt/hdf5@1.8/lib/libhdf5.10.dylib /usr/local/lib/libhdf5.dylib

Then finally install erisilia dependencies

pip install -e .

FOR INTEL MACs: Replace all /opt/homebrew/ with /usr/local/

[fortune-max]

Screenshot of a model in use to determine molecular weight of aspirin.

[fortune-max]

Local catalog of installed models.

[GemmaTuron]

Hi @fortune-max

Thanks for checking the set up and installation of Ersilia. Please, could you report those problems in the form of a bug tracker opening a new issue for each one of them?

[fortune-max]

Sure, I'll be glad to help make the setup process go smoother for people sharing a similar environment as I am.

[fortune-max]

Hi @GemmaTuron

Is there a reason the dependencies are being installed using pip instead of with conda install?

Using conda install --file requirements.txt instead of pip install -e . is preferable to me and actually works around the h5py dependency compilation installation issue I faced.

See https://ersilia.gitbook.io/ersilia-book/quick-start/installation

[fortune-max]

I have attempted to install ersilia's dependencies using conda. Unfortunately a number of them are unavailable from conda's repo alone. I think the best way would be to have the instructions say

conda install h5py

Then

pip install -e .

to get around the issue for Mac users. I will detail more of my findings in the issue I open.

[GemmaTuron]

Hi @fortune-max

Thanks for the suggestions we will look into them as soon as possible. Unfortunately we won't be able to provide feedback before the application deadline so please go ahead and make your application listing these contributions so far.

Thanks!

[fortune-max]

Sure Gemma,

Glad to have helped. Will add to contributions now.