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Wrap lightning's train as an ST method #40

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merged 6 commits into from
Apr 25, 2024
Merged

Wrap lightning's train as an ST method #40

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1ce19e2
add train method to starling class, injecting defaults
cklamann Apr 1, 2024
6b3544e
return AnnData object from result method
cklamann Apr 1, 2024
b8a0869
remove redundant type descriptions in docstrings
cklamann Apr 1, 2024
055e2c6
update second tutorial link in README
cklamann Apr 4, 2024
48d90f5
remove notebook output
cklamann Apr 4, 2024
5f79c5b
only check for size column if model_cell_size is True
cklamann Apr 4, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -35,6 +35,6 @@ RUN python3 -m venv $VIRTUAL_ENV && \

USER $USERNAME

COPY . .
COPY --chown=${USER_UID}:${USER_GID} . .

RUN poetry install --with docs,dev
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -11,7 +11,7 @@ It outputs:

A **preprint** describing the method and introducing a novel benchmarking workflow is available: [Lee et al. (2024) _Segmentation error aware clustering for highly multiplexed imaging_](https://www.biorxiv.org/content/10.1101/2024.02.29.582827v1)

A **tutorial** outlining basic usage is available [here](https://github.com/camlab-bioml/starling/blob/main/docs/source/tutorial/getting-started.ipynb).
A **tutorial** outlining basic usage is available [here][tutorial].

![Model](https://github.com/camlab-bioml/starling/raw/main/starling-schematic600x.png)

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2 changes: 2 additions & 0 deletions docs/source/conf.py
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Expand Up @@ -21,6 +21,8 @@

nb_execution_timeout = -1

autodoc_typehints = "description"

html_theme = "sphinx_rtd_theme"
html_static_path = ["_static"]
html_css_files = [
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