Development.md

Development Notes

Getting Started

You will need Pixi to build this project.

pixi run dev-install

The service is written using FastAPI and runs inside of Uvicorn. You can start a dev server quickly with this command:

Then run the development server:

pixi run dev-launch

On a remote system, you may need SSL certs (e.g. for loading into Neuroglancer), which can be added like this (assuming your certificate is found at /opt/certs/cert.key and /opt/certs/cert.crt):

pixi run dev-launch-remote

For production deployments, please refer to the main README file.

Testing

To run the unit tests and produce a code coverage report:

pixi run test

These tests are automatically run whenever changes are merged to the main branch.

Release

First, increment the version in pyproject.toml and push it to GitHub. Create a Release there and then publish it to PyPI as follows.

To create a Python source package (.tar.gz) and the binary package (.whl) in the dist/ directory, do:

pixi run pypi-build

To upload the package to the PyPI, you'll need one of the project owners to add you as a collaborator. After setting up your access token, do:

pixi run pypi-upload

Building the Docker container

Run the Docker build and push to GHCR, replacing <version> with your version number:

cd docker/
export VERSION=<version>
docker buildx build --platform linux/amd64,linux/arm64 --build-arg GIT_TAG=$VERSION -t ghcr.io/janeliascicomp/x2s3:$VERSION -t ghcr.io/janeliascicomp/x2s3:latest --push .

If you are using Podman, you can do something like this:

cd docker/
export VERSION=<version>
export IMAGE="ghcr.io/janeliascicomp/x2s3"
podman build --jobs=2 --platform=linux/amd64,linux/arm64 \
      --manifest "$IMAGE:$VERSION" --tag "$IMAGE:latest" .

Push the images to GHCR:

podman manifest push --all "$IMAGE:$VERSION" "docker://$IMAGE:$VERSION"
podman manifest push --all "$IMAGE:latest" "docker://$IMAGE:latest"