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@@ -39,19 +39,26 @@ jobs: | |
| git tag -a "v${{ steps.version.outputs.VERSION }}" -m "v${{ steps.version.outputs.VERSION }}" | ||
| # Tagging happens implicitly; no need to push explicitly | ||
| - name: Update version in CITATION.cff | ||
| - name: Update version and release date in CITATION.cff | ||
| id: update-citation | ||
| env: | ||
| VERSION: ${{ steps.version.outputs.VERSION }} | ||
| run: | | ||
| RELEASE_DATE: ${{ github.run_started_at }} # This captures the timestamp when the workflow run was triggered/started | ||
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| run: | | ||
| pip install PyYAML | ||
| python -c " | ||
| import os | ||
| import yaml | ||
| release_date = os.environ['RELEASE_DATE'].split('T')[0] | ||
| with open('CITATION.cff', 'r') as file: | ||
| content = file.read() | ||
| citation = yaml.safe_load(content) | ||
| citation = yaml.safe_load(file) | ||
| citation['version'] = os.environ['VERSION'] | ||
| citation['date-released'] = release_date | ||
| with open('CITATION.cff', 'w') as file: | ||
| yaml.dump(citation, file, default_flow_style=False, sort_keys=False) | ||
| " | ||
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@@ -72,7 +79,7 @@ jobs: | |
| with: | ||
| author_name: "ersilia-bot" | ||
| author_email: "[email protected]" | ||
| message: "update version [skip ci]" | ||
| message: "update version and release date [skip ci]" | ||
| repository: "ersilia-os/${{ github.event.repository.name }}" | ||
| github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| amend: true | ||
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| @@ -0,0 +1,118 @@ | ||
| # 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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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| import pytest | ||
| from ersilia.utils.identifiers.compound import CompoundIdentifier | ||
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| @pytest.fixture | ||
| def compound_identifier(): | ||
| return CompoundIdentifier() | ||
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| @pytest.mark.parametrize("header", ["smiles", "input", "SMILES", "INPUT"]) | ||
| def test_is_input_header_positive(compound_identifier, header): | ||
| """Test that valid input headers return True.""" | ||
| assert compound_identifier.is_input_header(header) is True |