From ab9c43382f300ff9ee239a79114ee939bcb80e40 Mon Sep 17 00:00:00 2001
From: scverse-bot <None>
Date: Tue, 21 May 2024 13:45:54 +0000
Subject: [PATCH] Update template to v0.4.0
---
.cruft.json | 4 ++--
.github/workflows/test.yaml | 6 +++---
.gitignore | 1 +
README.md | 2 +-
docs/conf.py | 10 +++++-----
docs/contributing.md | 2 +-
pyproject.toml | 4 ++--
pyproject.toml.rej | 10 ++++++++++
8 files changed, 25 insertions(+), 14 deletions(-)
create mode 100644 pyproject.toml.rej
diff --git a/.cruft.json b/.cruft.json
index eb6cb97..0bcc061 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -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": "ehrdata",
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index c5b152b..2bfe232 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -24,11 +24,11 @@ jobs:
matrix:
include:
- os: ubuntu-latest
- python: "3.9"
+ 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
diff --git a/.gitignore b/.gitignore
index dcdc618..eeec7e2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,7 @@ __pycache__/
/.pytest_cache/
/.cache/
/data/
+/node_modules/
# docs
/docs/generated/
diff --git a/README.md b/README.md
index 710e8e6..0cc1a4c 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
## Installation
-You need to have Python 3.9 or newer installed on your system. If you don't have
+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).
There are several alternative options to install ehrdata:
diff --git a/docs/conf.py b/docs/conf.py
index 44990aa..a857bb6 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -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
@@ -36,10 +36,10 @@
html_context = {
"display_github": True, # Integrate GitHub
- "github_user": "theislab", # 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": "theislab",
+ "github_repo": "https://github.com/theislab/ehrdata",
+ "github_version": "main",
+ "conf_py_path": "/docs/",
}
# -- General configuration ---------------------------------------------------
diff --git a/docs/contributing.md b/docs/contributing.md
index 22c89ba..e00aced 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -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
diff --git a/pyproject.toml b/pyproject.toml
index ad094f7..0a73275 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ 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",
@@ -108,7 +108,7 @@ 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",
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..dc64183
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,10 @@
+diff a/pyproject.toml b/pyproject.toml (rejected hunks)
+@@ -7,7 +7,7 @@ name = "ehrdata"
+ version = "0.0.1"
+ description = "A data structure for EHR data."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+ {name = "Xinyue Zhang"},