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Merge pull request #21 from saezlab/feat/community-guidelines
Feat/community guidelines
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‎.github/ISSUE_TEMPLATE/a_bug_report.yaml‎

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name: 🪳 Bug Report
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description: Create a report to help us reproduce and fix the bug
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title: '[BUG]: '
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labels:
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- bug
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- triage
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body:
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- type: markdown
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attributes:
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value: >
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**Before submitting a bug, please make sure the issue hasn't been already addressed by [searching through](https://github.com/saezlab/ontograph/issues).**
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Please write your bug report in English to ensure it can be understood and addressed by the development team.
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#---------------- Installed From --------------
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- type: dropdown
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id: source
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attributes:
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label: Source
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description: OntoGraph has been installed from
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options:
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- conda
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- pip
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- uv
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- poetry
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- other (specify in text)
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validations:
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required: true
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- type: input
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id: source-other
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attributes:
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label: other source
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placeholder: e.g., from source
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#-------------- Python version --------------
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- type: input
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id: Python
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attributes:
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label: Python version
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placeholder: e.g., 3.10
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validations:
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required: true
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#-------------- OntoGraph version --------------
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- type: input
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id: OntoGraph-version
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attributes:
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label: OntoGraph version
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placeholder: e.g., OntoGraph v0.0.1
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validations:
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required: true
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#-------------- OS Platform and distribution --------------
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- type: input
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id: OS
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attributes:
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label: OS platform and distribution
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placeholder: e.g., Linux Ubuntu 16.04
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#-------------- Describe the Bug --------------
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- type: textarea
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attributes:
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label: Describe the bug
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description: |
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Please provide a clear and concise description of the bug.
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If applicable, include a minimal example that allows us to reproduce the error by running the code.
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It's crucial that the snippet is as short and focused as possible, so please remove any unnecessary code
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to help us debug efficiently. We will copy and paste your code, and we expect to see the same result as you did.
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Avoid using external data and make sure to include all relevant imports, etc. For example:
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```python
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# All necessary imports at the beginning
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from ontograph import ClientOntology
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# A succinct reproducing example trimmed down to the essential parts:
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go_client = ClientOntology()
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go_client.load() # Note: the bug is here!
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```
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If the code is too lengthy (though we hope it's not), feel free to place it in a public gist and share the link in the issue: https://gist.github.com.
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Instead of providing the expected results, please paste or describe the actual results you observe. If you encounter an error, include the error message along with the full traceback. It's helpful to wrap error messages in ```` ```triple quotes blocks``` ````.
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placeholder: |
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A clear and concise description of what the bug is.
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```python
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# Sample code to reproduce the problem
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```
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```
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The error message you got, with the full traceback.
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```
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validations:
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required: true
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#-------------- Relevant LOG Output --------------
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- type: textarea
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id: logs
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attributes:
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label: Relevant LOG output
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description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
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render: shell
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#-------------- Code of Conduct --------------
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- type: checkboxes
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id: terms
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attributes:
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label: Code of Conduct
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description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/saezlab/ontograph/blob/main/CODE_OF_CONDUCT.md).
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options:
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- label: I agree to follow this project's Code of Conduct
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required: true
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- type: markdown
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attributes:
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value: >
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Thank you for your contribution! 🎉 – Saezlab Organization - OmniPath team

‎.github/ISSUE_TEMPLATE/b_feature_request.yaml‎

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name: ✨ Feature Request
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description: Submit a proposal/request for a new OntoGraph feature
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title: '[FEAT]: '
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labels:
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- feature
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projects: [ontograph/1]
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body:
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- type: markdown
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attributes:
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value: >
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**Note:** Please write your bug report in English to ensure it can be understood and addressed by the development team.
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#-------------- Feature type --------------
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- type: dropdown
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id: feature-type
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attributes:
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label: Feature Type
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description: Please select what type of feature request you would like to propose.
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options:
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- Add new functionality to OntoGraph
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- Change existing functionality in OntoGraph
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- Remove existing functionality in OntoGraph
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multiple: false
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validations:
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required: true
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#-------------- Feature description and motivation --------------
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- type: textarea
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attributes:
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label: 🚀 The feature and motivation
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description: >
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Provide a clear and concise summary of the proposed feature, including the motivation behind it.
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If your request addresses a specific problem, describe it (e.g., "I'm working on X and need Y to be achievable").
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If this is connected to an existing GitHub issue, please include a link.
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placeholder: |
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**Feature description**
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As a user, I would like the ability to import a csv file from SwissLipids and create an ontology with this data.
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**Motivation**
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Enabling users to import CSV files from SwissLipids and automatically generate an ontology streamlines the integration
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of curated lipid data into the platform. This functionality reduces manual preprocessing, ensures data consistency,
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and accelerates research workflows, while supporting reproducibility and adherence to community standards.
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validations:
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required: true
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#-------------- Additional context --------------
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- type: textarea
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attributes:
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label: Additional context
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description: >
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Add any other context or screenshots about the feature request.
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#-------------- Code of Conduct --------------
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- type: checkboxes
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id: terms
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attributes:
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label: Code of Conduct
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description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/saezlab/ontograph/blob/main/CODE_OF_CONDUCT.md).
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options:
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- label: I agree to follow this project's Code of Conduct
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required: true
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- type: markdown
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attributes:
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value: >
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Thank you for your contribution! 🎉 – Saezlab Organization - OmniPath team

‎.github/ISSUE_TEMPLATE/c_documentation.yaml‎

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name: 📔 Documentation Improvement
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description: Report wrong or missing documentation
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title: '[DOC]: '
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labels:
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- docs
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- triage
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projects: [ontograph/1]
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body:
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#---------------- Location of the documentation --------------
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- type: textarea
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id: location
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attributes:
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label: Location of the documentation
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description: >
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Please provide the location of the documentation, e.g. "catalog.load_catalog()" or the
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URL of the documentation, e.g.
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"https://saezlab.github.io/ontograph/reference/source/ontograph/client-catalog/"
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placeholder: https://saezlab.github.io/ontograph/reference/source/ontograph/client-catalog/
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validations:
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required: true
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#---------------- Problem Description --------------
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- type: textarea
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id: problem
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attributes:
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label: Documentation problem
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description: >
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Please provide a description of what documentation you believe needs to be fixed/improved
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validations:
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required: true
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#---------------- Suggested Fix --------------
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- type: textarea
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id: suggested-fix
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attributes:
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label: Suggested fix for documentation
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description: >
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Please explain the suggested fix and **why** it's better than the existing documentation
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validations:
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required: true
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#-------------- Code of Conduct --------------
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- type: checkboxes
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id: terms
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attributes:
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label: Code of Conduct
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description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/saezlab/ontograph/blob/main/CODE_OF_CONDUCT.md).
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options:
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- label: I agree to follow this project's Code of Conduct
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required: true
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- type: markdown
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attributes:
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value: >
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Thank you for your contribution! 🎉 – Saezlab Organization - OmniPath team

‎.github/PULL_REQUEST_TEMPLATE.md‎

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# Pull Request
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> When to use: Use this default template for most changes (features, small fixes, refactors, docs). If your change is a bug fix, performance optimization, maintenance/chore, or a breaking change, consider using one of the specialized templates under `.github/PULL_REQUEST_TEMPLATE/`.
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Thank you for contributing to OntoGraph! Please fill out the sections below to help us review efficiently.
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## Summary
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- Link to issue(s): Closes #<issue-number> (or) Related to #<issue-number>
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- Brief description of the change:
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## Type of change
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Select one or more:
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- [ ] Bug fix (non-breaking change that fixes an issue)
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- [ ] Feature (non-breaking change that adds functionality)
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- [ ] Documentation update
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- [ ] Refactor/maintenance (no functional change)
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- [ ] Performance improvement
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- [ ] CI/CD or tooling
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- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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## Changes
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- High-level list of changes (modules, major functions/classes touched)
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- Any data files or schema changes
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- Any API changes (inputs/outputs, public interfaces)
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## Screenshots or demos (optional)
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If relevant, include images, terminal outputs, or notebook snippets.
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## Checklist
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- Code quality & style
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- [ ] Follows project style and conventions
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- [ ] Pre-commit hooks run locally
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```bash
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pre-commit run -a
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```
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- Tests
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- [ ] Unit tests added/updated
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- [ ] All tests pass locally (`pytest`)
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- [ ] Includes edge cases (empty/null, invalid input, large inputs)
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- Documentation
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- [ ] User docs updated (MkDocs in `docs/` as needed)
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- [ ] README updated if behavior or usage changed
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- [ ] Docstrings and comments added where helpful
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- Reliability
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- [ ] No secrets or credentials in code or history
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- [ ] Backwards compatibility considered; migration notes added if breaking
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- [ ] Performance implications considered (time/memory), benchmarks if relevant
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- Project hygiene
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- [ ] Linked issues referenced with `Closes #...` or `Related to #...`
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- [ ] Changelog entry prepared (see `CHANGELOG.md`)
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- [ ] Labels applied (bug, enhancement, docs, etc.)
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- Community standards
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- [ ] I have read and agree to the [Code of Conduct](../CODE_OF_CONDUCT.md)
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## Test plan
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Describe how you tested the changes. Include commands, datasets, and expected outcomes. If applicable, reference tests in `tests/`:
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```bash
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# Example (adjust as needed)
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pytest -q
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```
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## Breaking changes (if any)
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- Describe what breaks and how users should migrate.
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- Provide a migration example or script if possible.
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## Additional context
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- Risks, trade-offs, or follow-up tasks
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- Dependencies or environment changes
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- Related PRs

‎.github/PULL_REQUEST_TEMPLATE/breaking_change.md‎

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# Breaking Change Pull Request
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> When to use: Changes that break backwards compatibility; requires a migration guide and communication plan.
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## Summary
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- Closes #<issue-number>
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- Scope and rationale for breaking change
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## Deprecation & Migration
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- Deprecation path and timeline
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- Migration guide and examples
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- Scripts or tools to assist migration
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## API / Data impacts
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- Public API changes
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- Data/schema changes
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## Versioning & Communication
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- Version bump strategy
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- Communication plan (release notes, docs)
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## Tests
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- [ ] Updated tests for new behavior
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- [ ] Migration tests where possible
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- [ ] All tests pass locally (`pytest -q`)
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## Documentation
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- [ ] Docs updated (MkDocs) and README
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- [ ] Clear migration instructions visible to users
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## Checklist
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- [ ] Backwards compatibility noted as broken (explicit)
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- [ ] Changelog entry prepared (see `CHANGELOG.md`)
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- [ ] Risk assessment and rollback plan
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- [ ] Labels set (breaking-change)
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- [ ] I agree to the [Code of Conduct](../../CODE_OF_CONDUCT.md)
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## Additional notes
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- Known limitations and follow-ups

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