From 1ac56db758b4e8602123c2d4978b21757a5d91b2 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 21 May 2024 13:44:01 +0000 Subject: [PATCH] Update template to v0.4.0 --- .cruft.json | 4 ++-- .github/workflows/test.yaml.rej | 16 ++++++++++++++++ .gitignore.rej | 9 +++++++++ README.md | 2 +- docs/conf.py | 2 +- docs/conf.py.rej | 16 ++++++++++++++++ docs/contributing.md.rej | 10 ++++++++++ pyproject.toml | 2 +- pyproject.toml.rej | 19 +++++++++++++++++++ 9 files changed, 75 insertions(+), 5 deletions(-) create mode 100644 .github/workflows/test.yaml.rej create mode 100644 .gitignore.rej create mode 100644 docs/conf.py.rej create mode 100644 docs/contributing.md.rej create mode 100644 pyproject.toml.rej diff --git a/.cruft.json b/.cruft.json index f44d9ec..38fa6a1 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": "genomic-features", diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej new file mode 100644 index 0000000..e165fb8 --- /dev/null +++ b/.github/workflows/test.yaml.rej @@ -0,0 +1,16 @@ +diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks) +@@ -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.rej b/.gitignore.rej new file mode 100644 index 0000000..9d0a7e9 --- /dev/null +++ b/.gitignore.rej @@ -0,0 +1,9 @@ +diff a/.gitignore b/.gitignore (rejected hunks) +@@ -18,6 +18,7 @@ __pycache__/ + /.pytest_cache/ + /.cache/ + /data/ ++/node_modules/ + + # docs + /docs/generated/ diff --git a/README.md b/README.md index 1da1df8..0576f88 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ Check out the [documentation][link-docs], in particular the [basic tutorial][lin ## 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 genomic-features: diff --git a/docs/conf.py b/docs/conf.py index 0b296d9..b6df430 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 diff --git a/docs/conf.py.rej b/docs/conf.py.rej new file mode 100644 index 0000000..17c78da --- /dev/null +++ b/docs/conf.py.rej @@ -0,0 +1,16 @@ +diff a/docs/conf.py b/docs/conf.py (rejected hunks) +@@ -36,10 +36,10 @@ needs_sphinx = "4.0" + + html_context = { + "display_github": True, # Integrate GitHub +- "github_user": "ivirshup", # 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": "ivirshup", ++ "github_repo": "https://github.com/scverse/genomic-features", ++ "github_version": "main", ++ "conf_py_path": "/docs/", + } + + # -- General configuration --------------------------------------------------- diff --git a/docs/contributing.md.rej b/docs/contributing.md.rej new file mode 100644 index 0000000..e003d40 --- /dev/null +++ b/docs/contributing.md.rej @@ -0,0 +1,10 @@ +diff a/docs/contributing.md b/docs/contributing.md (rejected hunks) +@@ -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 d6242d4..3c46026 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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..83bd2f7 --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,19 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "genomic-features" + version = "0.0.1" + description = "Genomic annotations using BioConductor resources in Python." + readme = "README.md" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Isaac Virshup"}, +@@ -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",