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* Create DEVELOPMENT.md Added the getting started and Ersilia Artifacts session * Update DEVELOPMENT.md * Add creating a PR section * Add review changes to DEVELOPMENT.md --------- Co-authored-by: Dhanshree Arora <[email protected]>
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# Development | ||
This file highlight the installation process of getting started with Ersilia, Ersilia Artifacts and Creating a Pull Request. | ||
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## Getting Started | ||
Ersilia can be run either on local computer or with the use of GitHub codespaces. Ersilia is designed to run on **Linux or Linux-like environments** namely: MacOS, Windows Sub-system for Linux (WSL) and at present is not supported on Windows systems. | ||
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- ### Installation of Ersilia on local computer | ||
To get started with Ersilia installation, there are few dependencies that needs to be installed before proceeding to installation of Ersilia. Please, check the package requirement in the [Installation Guide](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/installation) | ||
1. Once the required dependencies has been installed, open a terminal and set up a Conda environment. | ||
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``` | ||
# create a conda environment | ||
conda create -n ersilia python=3.10 | ||
# activate the environment | ||
conda activate ersilia | ||
``` | ||
2. Clone the repository and run to install the Ersilia Python package. | ||
``` | ||
# clone from github | ||
git clone https://github.com/ersilia-os/ersilia.git | ||
cd ersilia | ||
# install with pip (use -e for developer mode) | ||
pip install -e .[test] | ||
``` | ||
**The -e (editable) for developer mode ensures that whenever a user change the code, they don't need to reinstall ersilia for those changes to take effect.** | ||
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3. To test that the CLI works, explore this command | ||
``` | ||
# output to see command options for ersilia | ||
ersilia --help | ||
``` | ||
4. Once ersilia is recognized in the CLI, test any model of your choice. | ||
- First, you can check the list of available model in ersilia's catalog | ||
``` | ||
#see ersilia's model catalog | ||
ersilia catalog | ||
``` | ||
- Next, you can run the model | ||
``` | ||
ersilia -v fetch eos2ta5 #fetch a model | ||
ersilia serve eos2ta5 #serve a model | ||
ersilia -v api run -i "CCCC" #run a model | ||
``` | ||
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Note: The usage -v (verbose) flag is of utmost importance for developers as it provides detailed logs which helps to debug and troubleshoot issues. | ||
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- ### Using GitHub Codespaces | ||
If difficulties are encountered while setting up Ersilia locally, another cloud-based development environment which suppoort linux is a great alternative. | ||
GitHub codespaces allows you to run and develop Ersilia directly from your browser. | ||
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To use Github Codespaces: | ||
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**1. Fork and Clone the Repository** | ||
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- Navigate [Ersilia repository](https://github.com/ersilia-os/ersilia) on GitHub. | ||
- Click on the **Fork** button in the top right corner to create a fork. | ||
- Go to the forked repository, Click on the <> **Code**. | ||
- Click **Create codespace**. | ||
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A pop up page "Setting up your codespace" is displayed on the screen. After a while, the codespace is created in a browser-based version using the built-in Visual studio code interface | ||
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**2. Setting Up GitHub Codespaces Environment** | ||
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- Once you open the codespaces environment, ersilia has been installed and ready for usage. To double check, you can verify by running this command `ersilia --version`. This | ||
will display the version of ersilia installed. | ||
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**3. Run Ersilia Model** | ||
- Directly from the code space terminal, you can fetch, serve and run Ersilia model. | ||
To run a model with verbose output: | ||
`ersilia -v run eos2ta5` | ||
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## Ersilia Artifacts | ||
After successful installation of ersilia in the user's local computer, the system creates an EOS directory in the user's `$HOME` path. This directory stores ersilia artifacts that the local computer uses when doing any operation (model execution) in Ersilia. | ||
Folders found in the `$HOME` directory includes: | ||
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**Folders** | ||
- dest/: stores output generated when running a model. | ||
- isaura/: cache model prediction which stores them in the local computer | ||
- repository/: main directory to cache models files and datasets. This prevent redundant download by storing previously fetched model | ||
- sessions/: Tracks user session | ||
- tmp/: stores temporary file during model execution. | ||
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## Creating a Pull Request | ||
To get started, please read and follow our [Code of Conduct](https://github.com/ersilia-os/ersilia/blob/master/CODE_OF_CONDUCT.md). | ||
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Before submitting a pull request, please ensure your code has been tested. After making any changes, **run the test suites** to test the code properly. | ||
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To do this, use this command to run the test with -v (verbose) output: `pytest -v` | ||
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**1. Via GitHub Codespaces Environment** | ||
- In the codespace terminal, create a new branch | ||
``` | ||
git checkout -b your-branch-name | ||
``` | ||
- Make all necessary changes and commit them | ||
``` | ||
git add . | ||
git commit -m "Description of changes made" | ||
``` | ||
- Push changes to GitHub | ||
``` | ||
git push origin your-branch-name | ||
``` | ||
- Click on **Create pull request** in the prompt that will be shown | ||
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**2. Via GitHub Desktop** | ||
- Fork the repository | ||
- Create a new branch and name it. | ||
- Commit your changes | ||
- Navigate the repository,Click on **Compare & pull request** | ||
- Set the main branch to **master** (name of ersilia repository main branch) and set the compare branch to your-branch-name | ||
- Fill out the title section and give a brief description of any changes made | ||
- Click **Create Pull Request** | ||
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