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  • 15 commits
  • 13 files changed
  • 5 contributors

Commits on Mar 14, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#270)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    pre-commit-ci[bot] and pre-commit-ci[bot] authored Mar 14, 2024
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Commits on Mar 18, 2024

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Commits on Mar 19, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#272)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    pre-commit-ci[bot] and pre-commit-ci[bot] authored Mar 19, 2024
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Commits on Mar 26, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#273)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    pre-commit-ci[bot] and pre-commit-ci[bot] authored Mar 26, 2024
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Commits on Apr 9, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#274)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Philipp A <flying-sheep@web.de>
    3 people authored Apr 9, 2024
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Commits on Apr 16, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#275)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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    pre-commit-ci[bot] and pre-commit-ci[bot] authored Apr 16, 2024
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Commits on Apr 23, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#276)

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    pre-commit-ci[bot] and pre-commit-ci[bot] authored Apr 23, 2024
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Commits on Apr 25, 2024

  1. fix typo (#279)

    Co-authored-by: Philipp A <flying-sheep@web.de>
    Zethson and flying-sheep authored Apr 25, 2024
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Commits on Apr 30, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#280)

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    pre-commit-ci[bot] and pre-commit-ci[bot] authored Apr 30, 2024
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Commits on May 6, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#281)

    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    pre-commit-ci[bot] and pre-commit-ci[bot] authored May 6, 2024
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Commits on May 14, 2024

  1. [pre-commit.ci] pre-commit autoupdate (#282)

    * [pre-commit.ci] pre-commit autoupdate
    
    updates:
    - [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](astral-sh/ruff-pre-commit@v0.4.3...v0.4.4)
    
    * Apply automatic changes
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <pre-commit-ci[bot]@users.noreply.github.com>
    pre-commit-ci[bot] and pre-commit-ci[bot] authored May 14, 2024
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Commits on May 18, 2024

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Commits on May 21, 2024

  1. Update required python versions according to scientific python SPEC 0 (

    …#284)
    
    * Update required python versions according to scientific python SPEC 0
    
    * Update minimum version in remaining places
    
    * No need to test 3.11
    
    * Update .gitignore
    
    * Update README
    grst authored May 21, 2024
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  2. Require myst-nb >= 1.1.0 (#285)

    Fixes issue with images rendering too large in tutorials. 
    Close #192
    grst authored May 21, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/test.yaml
Original file line number Diff line number Diff line change
@@ -17,7 +17,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python: ["3.9", "3.10"]
python: ["3.10", "3.12"]
os: [ubuntu-latest]
# one that matches "project-name".lower().replace('-', '_'), one that doesn’t:
package-name: [project_name, package_alt]
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -13,6 +13,7 @@ __pycache__/
/.pytest_cache/
/.cache/
/data/
/node_modules/

# IDEs
/.idea/
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@ repos:
- id: prettier
# Hooks that are run for scripts
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.2.2
rev: v0.4.4
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -48,7 +48,7 @@ and how to customize it for your needs.

### Install dependencies

You need `git >=2.28` and `python >=3.9`. In addition you need to install the following Python dependencies:
You need `git >=2.28` and `python >=3.10`. In addition you need to install the following Python dependencies:

```bash
pip install cruft pre-commit
6 changes: 5 additions & 1 deletion scripts/pyproject.toml
Original file line number Diff line number Diff line change
@@ -57,7 +57,11 @@ addopts = [
"-pnetwork", "--disable-network",
"-presponsemock"
]
filterwarnings = ["error"]
filterwarnings = [
"error",
# https://github.com/man-group/pytest-plugins/issues/224
"ignore::DeprecationWarning:pytest_shutil",
]

[tool.ruff]
line-length = 120
6 changes: 3 additions & 3 deletions {{cookiecutter.project_name}}/.github/workflows/test.yaml
Original file line number Diff line number Diff line change
@@ -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

1 change: 1 addition & 0 deletions {{cookiecutter.project_name}}/.gitignore
Original file line number Diff line number Diff line change
@@ -18,6 +18,7 @@ __pycache__/
/.pytest_cache/
/.cache/
/data/
/node_modules/

# docs
/docs/generated/
4 changes: 2 additions & 2 deletions {{cookiecutter.project_name}}/.pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -11,15 +11,15 @@ repos:
hooks:
- id: prettier
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.2.2
rev: v0.4.4
hooks:
- id: ruff
types_or: [python, pyi, jupyter]
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.5.0
rev: v4.6.0
hooks:
- id: detect-private-key
- id: check-ast
2 changes: 1 addition & 1 deletion {{cookiecutter.project_name}}/README.md
Original file line number Diff line number Diff line change
@@ -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 {{ cookiecutter.project_name }}:
10 changes: 5 additions & 5 deletions {{cookiecutter.project_name}}/docs/conf.py
Original file line number Diff line number Diff line change
@@ -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": "{{cookiecutter.github_user}}", # 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": "{{cookiecutter.github_user}}",
"github_repo": "{{cookiecutter.project_repo}}",
"github_version": "main",
"conf_py_path": "/docs/",
}

# -- General configuration ---------------------------------------------------
2 changes: 1 addition & 1 deletion {{cookiecutter.project_name}}/docs/contributing.md
Original file line number Diff line number Diff line change
@@ -54,7 +54,7 @@ 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
2 changes: 1 addition & 1 deletion {{cookiecutter.project_name}}/docs/template_usage.md
Original file line number Diff line number Diff line change
@@ -309,7 +309,7 @@ You can find a long list of checks that this template disables by default sittin
```toml
ignore = [
# ...
# __magic__ methods are are often self-explanatory, allow missing docstrings
# __magic__ methods are often self-explanatory, allow missing docstrings
"D105",
# ...
]
6 changes: 3 additions & 3 deletions {{cookiecutter.project_name}}/pyproject.toml
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@ name = "{{ cookiecutter.project_name }}"
version = "0.0.1"
description = "{{ cookiecutter.project_description }}"
readme = "README.md"
requires-python = ">=3.9"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
{name = "{{ cookiecutter.author_full_name }}"},
@@ -33,7 +33,7 @@ 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",
@@ -104,7 +104,7 @@ 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",