From 64ed282c9dd0c39c695cbb2bae534049a42f724e Mon Sep 17 00:00:00 2001 From: Sricharan Reddy Varra Date: Fri, 19 Jul 2024 11:59:05 -0700 Subject: [PATCH] small adjustments --- .github/workflows/deploy.yaml | 4 +- README.md | 4 +- ghpages-site/README.md | 18 ++++----- src/tonic_vitessce/__init__.py | 4 +- src/tonic_vitessce/pl/__init__.py | 1 - src/tonic_vitessce/pl/basic.py | 63 ------------------------------- src/tonic_vitessce/pp/__init__.py | 1 - src/tonic_vitessce/pp/basic.py | 17 --------- 8 files changed, 15 insertions(+), 97 deletions(-) delete mode 100644 src/tonic_vitessce/pl/__init__.py delete mode 100644 src/tonic_vitessce/pl/basic.py delete mode 100644 src/tonic_vitessce/pp/__init__.py delete mode 100644 src/tonic_vitessce/pp/basic.py diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 6826663..a7cefa4 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -24,8 +24,8 @@ jobs: uses: withastro/action@v2.0.1 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 diff --git a/README.md b/README.md index 1870318..3532711 100644 --- a/README.md +++ b/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: diff --git a/ghpages-site/README.md b/ghpages-site/README.md index e34a99b..fec7d6a 100644 --- a/ghpages-site/README.md +++ b/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? diff --git a/src/tonic_vitessce/__init__.py b/src/tonic_vitessce/__init__.py index 7fb003a..32a473b 100644 --- a/src/tonic_vitessce/__init__.py +++ b/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") diff --git a/src/tonic_vitessce/pl/__init__.py b/src/tonic_vitessce/pl/__init__.py deleted file mode 100644 index c2315dd..0000000 --- a/src/tonic_vitessce/pl/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .basic import BasicClass, basic_plot diff --git a/src/tonic_vitessce/pl/basic.py b/src/tonic_vitessce/pl/basic.py deleted file mode 100644 index ed390ef..0000000 --- a/src/tonic_vitessce/pl/basic.py +++ /dev/null @@ -1,63 +0,0 @@ -from anndata import AnnData - - -def basic_plot(adata: AnnData) -> int: - """Generate a basic plot for an AnnData object. - - Parameters - ---------- - adata - The AnnData object to preprocess. - - Returns - ------- - Some integer value. - """ - print("Import matplotlib and implement a plotting function here.") - return 0 - - -class BasicClass: - """A basic class. - - Parameters - ---------- - adata - The AnnData object to preprocess. - """ - - my_attribute: str = "Some attribute." - my_other_attribute: int = 0 - - def __init__(self, adata: AnnData): - print("Implement a class here.") - - def my_method(self, param: int) -> int: - """A basic method. - - Parameters - ---------- - param - A parameter. - - Returns - ------- - Some integer value. - """ - print("Implement a method here.") - return 0 - - def my_other_method(self, param: str) -> str: - """Another basic method. - - Parameters - ---------- - param - A parameter. - - Returns - ------- - Some integer value. - """ - print("Implement a method here.") - return "" diff --git a/src/tonic_vitessce/pp/__init__.py b/src/tonic_vitessce/pp/__init__.py deleted file mode 100644 index 5e7e293..0000000 --- a/src/tonic_vitessce/pp/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .basic import basic_preproc diff --git a/src/tonic_vitessce/pp/basic.py b/src/tonic_vitessce/pp/basic.py deleted file mode 100644 index 5db1ec0..0000000 --- a/src/tonic_vitessce/pp/basic.py +++ /dev/null @@ -1,17 +0,0 @@ -from anndata import AnnData - - -def basic_preproc(adata: AnnData) -> int: - """Run a basic preprocessing on the AnnData object. - - Parameters - ---------- - adata - The AnnData object to preprocess. - - Returns - ------- - Some integer value. - """ - print("Implement a preprocessing function here.") - return 0