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Update template to v0.4.0 #16

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Update template to v0.4.0 #16

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4 changes: 2 additions & 2 deletions .cruft.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
"commit": "586b1652162ff7994b0070a034023d64289ae416",
"checkout": "v0.3.1",
"commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
"checkout": "v0.4.0",
"context": {
"cookiecutter": {
"project_name": "scCoral",
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4 changes: 2 additions & 2 deletions .github/workflows/test.yaml
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Expand Up @@ -26,9 +26,9 @@ jobs:
- os: ubuntu-latest
python: "3.10"
- os: ubuntu-latest
python: "3.11"
python: "3.12"
- os: ubuntu-latest
python: "3.11"
python: "3.12"
pip-flags: "--pre"
name: PRE-RELEASE DEPENDENCIES

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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -18,6 +18,7 @@ __pycache__/
/.pytest_cache/
/.cache/
/data/
/node_modules/

# docs
/docs/generated/
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5 changes: 5 additions & 0 deletions README.md
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Expand Up @@ -17,9 +17,14 @@

Increasing throughput in single-cell technologies enables researchers to create population-scale single-cell RNAseq datasets. An ongoing challenge in the analysis of this data is to link molecular features (i.e. single-cell gene expression) with patient-level covariates (e.g. disease severity, age, sex, ...). `sccoral` aims to find an interpretable link between subject/sample-level features and gene expression by embedding cellular metadata and gene expression in the same latent space of a variational autoencoder architecture {cite:p}`lopez2018`. By leveraging and improving the network architecture of linear scVI {cite:p}`svensson2020`, we aim to find a direct and interpretable link between embedded covariates and gene expression.

<<<<<<< ours
<!-- Please refer to the [documentation][link-docs]. In particular, the

- [API documentation][link-api]. -->
=======
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).
>>>>>>> theirs

### Installation

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10 changes: 5 additions & 5 deletions docs/conf.py
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@@ -1,5 +1,5 @@
# Configuration file for the Sphinx documentation builder.
#

# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
Expand Down Expand Up @@ -36,10 +36,10 @@

html_context = {
"display_github": True, # Integrate GitHub
"github_user": "lucas-diedrich", # Username
"github_repo": project_name, # Repo name
"github_version": "main", # Version
"conf_py_path": "/docs/", # Path in the checkout to the docs root
"github_user": "lucas-diedrich",
"github_repo": "https://github.com/lucas-diedrich/sccoral",
"github_version": "main",
"conf_py_path": "/docs/",
}

# -- General configuration ---------------------------------------------------
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2 changes: 1 addition & 1 deletion docs/contributing.md
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Expand Up @@ -51,7 +51,7 @@ and [prettier][prettier-editors].
## Writing tests

```{note}
Remember to first install the package with `pip install '-e[dev,test]'`
Remember to first install the package with `pip install -e '.[dev,test]'`
```

This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
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6 changes: 3 additions & 3 deletions pyproject.toml
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Expand Up @@ -7,7 +7,7 @@ name = "sccoral"
version = "0.0.1"
description = "Covariate informed scVI with linear decoder"
readme = "README.md"
requires-python = ">=3.9"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
{name = "Lucas Diedrich"},
Expand Down Expand Up @@ -37,7 +37,7 @@ doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4",
"sphinx-book-theme>=1.0.0",
"myst-nb",
"myst-nb>=1.1.0",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
Expand Down Expand Up @@ -102,7 +102,7 @@ ignore = [
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __magic__ methods are are often self-explanatory, allow missing docstrings
# __magic__ methods are often self-explanatory, allow missing docstrings
"D105",
# first line should end with a period [Bug: doesn't work with single-line docstrings]
"D400",
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