small adjustments

.github/workflows/deploy.yaml

@@ -24,8 +24,8 @@ jobs:
         uses: withastro/[email protected]
         with:
           path: ./ghpages-site/ # The root location of your Astro project inside the repository. (optional)
-          # node-version: 20 # The specific version of Node that should be used to build your site. Defaults to 18. (optional)
-          # package-manager: pnpm@latest # The Node package manager that should be used to install dependencies and build your site. Automatically detected based on your lockfile. (optional)
+          node-version: 22 # The specific version of Node that should be used to build your site. Defaults to 18. (optional)
+          package-manager: pnpm@latest # The Node package manager that should be used to install dependencies and build your site. Automatically detected based on your lockfile. (optional)
 
   deploy:
     needs: build

README.md

@@ -7,7 +7,7 @@
 [link-tests]: https://github.com/angelolab/tonic-vitessce/actions/workflows/test.yml
 [badge-docs]: https://img.shields.io/readthedocs/tonic-vitessce
 
-Vitessce Configs and Data Conversion for the dataset.
+Vitessce Configs and Data Conversion for the TONIC Publication.
 
 ## Getting started
 
@@ -18,7 +18,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 ## Installation
 
 You need to have Python 3.10 or newer installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) or [Rye](https://github.com/astral-sh/rye) if you prefer `.venvs`.
 
 There are several alternative options to install tonic-vitessce:
 

ghpages-site/README.md

@@ -1,7 +1,7 @@
 # Astro Starter Kit: Minimal
 
 ```sh
-npm create astro@latest -- --template minimal
+pnpm create astro@latest -- --template minimal
 ```
 
 [![Open in StackBlitz](https://developer.stackblitz.com/img/open_in_stackblitz.svg)](https://stackblitz.com/github/withastro/astro/tree/latest/examples/minimal)
@@ -33,14 +33,14 @@ Any static assets, like images, can be placed in the `public/` directory.
 
 All commands are run from the root of the project, from a terminal:
 
-| Command                   | Action                                           |
-| :------------------------ | :----------------------------------------------- |
-| `npm install`             | Installs dependencies                            |
-| `npm run dev`             | Starts local dev server at `localhost:4321`      |
-| `npm run build`           | Build your production site to `./dist/`          |
-| `npm run preview`         | Preview your build locally, before deploying     |
-| `npm run astro ...`       | Run CLI commands like `astro add`, `astro check` |
-| `npm run astro -- --help` | Get help using the Astro CLI                     |
+| Command                    | Action                                           |
+| :------------------------- | :----------------------------------------------- |
+| `pnpm install`             | Installs dependencies                            |
+| `pnpm run dev`             | Starts local dev server at `localhost:4321`      |
+| `pnpm run build`           | Build your production site to `./dist/`          |
+| `pnpm run preview`         | Preview your build locally, before deploying     |
+| `pnpm run astro ...`       | Run CLI commands like `astro add`, `astro check` |
+| `pnpm run astro -- --help` | Get help using the Astro CLI                     |
 
 ## 👀 Want to learn more?
 

src/tonic_vitessce/__init__.py

@@ -1,8 +1,8 @@
 from importlib.metadata import version
 
-from . import pl, pp, tl
+from . import tl
 from .core import NuclearTableColumns, SegmentationMasks, WholeCellTableColumns
 
-__all__ = ["pl", "pp", "tl", "NuclearTableColumns", "SegmentationMasks", "WholeCellTableColumns"]
+__all__ = ["tl", "NuclearTableColumns", "SegmentationMasks", "WholeCellTableColumns"]
 
 __version__ = version("tonic-vitessce")