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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: "[Bug]"
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labels: ''
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assignees: ''
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---
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## Description
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A clear and concise description of what the bug is.
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## Reproducing the issue
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Steps to reproduce the behavior.
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## Expected behavior
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A clear and concise description of what you expected to happen.
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## System
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- OS: [e.g. Linux]
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- Python version [e.g. 3.9.7]
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<details>
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<summary>Dependencies versions</summary>
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<br>
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Paste here what 'pip list' gives you.
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</details>

‎.github/ISSUE_TEMPLATE/custom.md‎

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---
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name: Custom issue template
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about: Describe this issue template's purpose here.
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title: ''
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labels: ''
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assignees: ''
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---
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‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: "[Feature]"
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/workflows/ci.yml‎

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name: ci
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on:
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push:
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tags:
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- v*
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v3
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- name: Set up python
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id: setup-python
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uses: actions/setup-python@v4
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with:
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python-version: 3.9
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#----------------------------------------------
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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uses: snok/install-poetry@v1
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#----------------------------------------------
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# load cached venv if cache exists
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#----------------------------------------------
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/cache@v3
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with:
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path: .venv
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key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
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#----------------------------------------------
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# install dependencies if cache does not exist
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#----------------------------------------------
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install
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#----------------------------------------------
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# run test suite
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#----------------------------------------------
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- name: Tests
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run: poetry run pytest
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- name: Deploy doc
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run: poetry run mkdocs gh-deploy --force

‎README.md‎

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# SpatialData to Xenium Explorer
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Converting any [`SpatialData`](https://github.com/scverse/spatialdata) object into files that can be open by the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer).
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> *Xenium Explorer* is a registered trademark of 10x Genomics
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## Installation
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This package is currently in development. You can test it out, but you may experience some issues.
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`pip install git+https://github.com/quentinblampey/spatialdata_xenium_explorer.git`
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```sh
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pip install spatialdata_xenium_explorer
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```
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## Usage
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You can use our [CLI](TODO) or [API](TODO), see examples below. It will create up to 6 files, among which a file called `experiment.xenium`. Double-click on this file to open it on the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer/downloads) (make sure you have the latest version of the software).
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### CLI
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```sh
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spatialdata_xenium_explorer write /path/to/sdata.zarr
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```
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### API
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```python
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import spatialdata
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import spatialdata_xenium_explorer
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spatialdata_xenium_explorer.write("/path/to/directory", sdata, image_key, shapes_key, points_key, gene_column)
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```
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For more details about the arguments, see the [function docstrings](https://github.com/quentinblampey/spatialdata_xenium_explorer/blob/master/spatialdata_xenium_explorer/converter.py#L29).
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This will create up to 6 files, among which a file called `experiment.xenium`. Double-click on this file to open it on the [Xenium Explorer](https://www.10xgenomics.com/support/software/xenium-explorer/downloads) (make sure you have the latest version of the software).
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## Future improvements and contributions
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Contributions are welcome. Some of the most urgent features to be added:
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- Support all types of images (not just `MultiscaleSpatialImage`)
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- Better user experience (less arguments)
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- Write `.tif` image without loading the spatial image in memory
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- Write transcripts without computing the whole coordinates
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This package is still in early development. Contributions are welcome (new issues, pull requests, ...).

‎docs/README.md‎

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# `spatialdata_xenium_explorer` documentation
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The documentation is generated by [Mkdocs material](https://squidfunk.github.io/mkdocs-material/) and deployed when pushing a new tag on Github.
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## Serve locally
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Clone the repository, and install all the dependencies:
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```
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poetry install --all-extras
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```
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Then, run:
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```sh
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mkdocs serve
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```
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You can also update the CLI docs (if you install `typer-cli`) with the following command line:
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```sh
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typer spatialdata_xenium_explorer.main utils docs --output tmpfile --name spatialdata_xenium_explorer && sed '1,2d; s/## /### /g; s/Usage:/!!! note '\"'Usage'\"'/g' tmpfile >> docs/cli.md && rm tmpfile
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```

‎docs/api.md‎

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::: spatialdata_xenium_explorer.write
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_image
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_cell_categories
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_transcripts
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_gene_counts
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_polygons
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.write_metadata
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.int_cell_id
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.str_cell_id
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.align
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options:
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show_root_heading: true
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::: spatialdata_xenium_explorer.save_column_csv
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options:
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show_root_heading: true

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