From fc4169b2573a602775c222560fbf8ae0ccd548d1 Mon Sep 17 00:00:00 2001
From: scverse-bot <None>
Date: Thu, 22 Feb 2024 18:38:33 +0000
Subject: [PATCH] Update template to v0.3.1

---
 .cruft.json                        |  7 +++---
 .github/workflows/release.yaml.rej | 10 ++++++++
 .pre-commit-config.yaml.rej        | 34 +++++++++++++++++++++++++++
 docs/contributing.md               |  3 ++-
 pyproject.toml                     |  8 +++----
 pyproject.toml.rej                 | 37 ++++++++++++++++++++++++++++++
 6 files changed, 91 insertions(+), 8 deletions(-)
 create mode 100644 .github/workflows/release.yaml.rej
 create mode 100644 .pre-commit-config.yaml.rej
 create mode 100644 pyproject.toml.rej

diff --git a/.cruft.json b/.cruft.json
index 36edd93..108db7e 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
   "context": {
     "cookiecutter": {
       "project_name": "infercnvpy",
@@ -12,7 +12,8 @@
       "project_repo": "https://github.com/icbi-lab/infercnvpy",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,
@@ -24,5 +25,5 @@
     }
   },
   "directory": null,
-  "checkout": "v0.3.0"
+  "checkout": "v0.3.1"
 }
diff --git a/.github/workflows/release.yaml.rej b/.github/workflows/release.yaml.rej
new file mode 100644
index 0000000..f65d3cd
--- /dev/null
+++ b/.github/workflows/release.yaml.rej
@@ -0,0 +1,10 @@
+diff a/.github/workflows/release.yaml b/.github/workflows/release.yaml	(rejected hunks)
+@@ -11,7 +11,7 @@ jobs:
+     runs-on: ubuntu-latest
+     environment:
+       name: pypi
+-      url: https://pypi.org/p/{{ cookiecutter.package_name }}
++      url: https://pypi.org/p/infercnvpy
+     permissions:
+       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+     steps:
diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej
new file mode 100644
index 0000000..831fbdc
--- /dev/null
+++ b/.pre-commit-config.yaml.rej
@@ -0,0 +1,34 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -6,29 +6,18 @@ default_stages:
+   - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-  - repo: https://github.com/psf/black
+-    rev: "24.2.0"
+-    hooks:
+-      - id: black
+-  - repo: https://github.com/asottile/blacken-docs
+-    rev: 1.16.0
+-    hooks:
+-      - id: blacken-docs
+   - repo: https://github.com/pre-commit/mirrors-prettier
+     rev: v4.0.0-alpha.8
+     hooks:
+       - id: prettier
+-        # Newer versions of node don't work on systems that have an older version of GLIBC
+-        # (in particular Ubuntu 18.04 and Centos 7)
+-        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+-        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+-        # https://github.com/jupyterlab/jupyterlab/issues/12675
+-        language_version: "17.9.1"
+   - repo: https://github.com/astral-sh/ruff-pre-commit
+     rev: v0.2.2
+     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
+     hooks:
diff --git a/docs/contributing.md b/docs/contributing.md
index 4794249..2db1e48 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +157,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
diff --git a/pyproject.toml b/pyproject.toml
index afd54be..1fd6f3b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -103,7 +103,7 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -130,10 +130,10 @@ ignore = [
     "D213",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]
@@ -147,5 +147,5 @@ skip = [
     "docs/changelog.md",
     "docs/references.bib",
     "docs/references.md",
-    "docs/notebooks/example.ipynb"
+    "docs/notebooks/example.ipynb",
 ]
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..19c02aa
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,37 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -21,13 +21,13 @@ urls.Home-page = "https://github.com/icbi-lab/infercnvpy"
+ dependencies = [
+     "anndata",
+     # for debug logging (referenced from the issue template)
+-    "session-info"
++    "session-info",
+ ]
+ 
+ [project.optional-dependencies]
+ dev = [
+     "pre-commit",
+-    "twine>=4.0.2"
++    "twine>=4.0.2",
+ ]
+ doc = [
+     "docutils>=0.8,!=0.18.*,!=0.19.*",
+@@ -61,12 +61,15 @@ addopts = [
+     "--import-mode=importlib",  # allow using test files with same name
+ ]
+ 
+-[tool.black]
+-line-length = 120
+-
+ [tool.ruff]
+-src = ["src"]
+ line-length = 120
++src = ["src"]
++extend-include = ["*.ipynb"]
++
++[tool.ruff.format]
++docstring-code-format = true
++
++[tool.ruff.lint]
+ select = [
+     "F",  # Errors detected by Pyflakes
+     "E",  # Error detected by Pycodestyle