From 0b566853976dd3331ce4b49fa068dc4ee3403785 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Dec 2023 20:34:54 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit automatically updated.
MIME-Version: 1.0
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updates:
- [github.com/psf/black: 23.9.1 → 23.12.1](https://github.com/psf/black/compare/23.9.1...23.12.1)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.292...v0.1.9)
- [github.com/pre-commit/mirrors-eslint: v8.51.0 → v8.56.0](https://github.com/pre-commit/mirrors-eslint/compare/v8.51.0...v8.56.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 19737907..df0b167b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.12.1
     hooks:
       - id: black
         types: [python]
@@ -32,7 +32,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.292"
+    rev: "v0.1.9"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -48,7 +48,7 @@ repos:
   #         - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v8.51.0
+    rev: v8.56.0
     hooks:
       - id: eslint
         types: [file]

From a58d889dd55fc72229d082f0a6266c79e9cc445b Mon Sep 17 00:00:00 2001
From: slackline <nshephard@protonmail.com>
Date: Wed, 10 Jan 2024 10:23:46 +0000
Subject: [PATCH 2/2] Fixing pytest-regtest issue
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

New releases of `pytest-regtest>=2.0.0` on PyPI are currently broken as the released packages don't appear to include
the Python code for the module itself. This has been reported upstream and when fixed I will remove the dependency.

+ [pytest-regtest #20](https://gitlab.com/uweschmitt/pytest-regtest/-/issues/20)

At the same time I've...

+ Made the `pre-commit` updates that were automated in #253 where the `pytest-regtest` issue cropped up
+ Added `no-commit-to-branch` check to `pre-commit` hooks which protects against commits to `master` locally.
+ Introduced `NPY201` checks under `ruff` linting to check for forthcoming Numpy2 deprecations.

Numpy2 is due to be released early later this year (first release candidate is scheduled 2024-02-01).

This may introduce some breaking changes, a broad overview is available [here](https://pythonspeed.com/articles/numpy-2/).

Mentioned in that article is that `scikit-image` has issues, which is indirect because the package has an optional
dependency on `matplotlib` (I've discovered this whilst working on `skan` issues).

The official [NumPy 2.0 migration guide — NumPy v2.0.dev0
Manual](https://numpy.org/devdocs/numpy_2_0_migration_guide.html) suggests that `ruff` can be leveraged to address the
mentioned changes under [Ruff Plugin](https://numpy.org/devdocs/numpy_2_0_migration_guide.html#ruff-plugin).

A useful summary of how to handle potential problems is provided at
[Numpy #24300](numpy/numpy#24300) and broadly suggests pinning `numpy<2.0` for releases whilst
development proceeds on resolving issues.
---
 .pre-commit-config.yaml | 5 +++--
 lib/pyproject.toml      | 6 +++++-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index df0b167b..605b7df2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -19,6 +19,7 @@ repos:
       - id: fix-byte-order-marker
       - id: name-tests-test
         args: ["--pytest-test-first"]
+      - id: no-commit-to-branch # Protects main/master by default
       - id: requirements-txt-fixer
       - id: trailing-whitespace
 
@@ -32,7 +33,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.1.9"
+    rev: "v0.1.11"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -48,7 +49,7 @@ repos:
   #         - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v8.56.0
+    rev: v9.0.0-alpha.0
     hooks:
       - id: eslint
         types: [file]
diff --git a/lib/pyproject.toml b/lib/pyproject.toml
index 0f68ee3a..26a587e1 100644
--- a/lib/pyproject.toml
+++ b/lib/pyproject.toml
@@ -40,7 +40,7 @@ tests = [
   "pytest>=7.0",
   "pytest-cov",
   "pytest-mpl",
-  "pytest-regtest",
+  "pytest-regtest<2.0.0",
   "pytest-xdist"
 ]
 docs = [
@@ -135,5 +135,9 @@ select = ["B", "E", "F", "W", "I001"]
 # Allow autofix for all enabled rules (when `--fix`) is provided.
 fixable = ["A", "B", "C", "D", "E", "F", "R", "S", "W", "U", "I001"]
 
+[tool.ruff.lint]
+extend-select = ["NPY201"]
+preview = true
+
 [project.scripts]
 find_pg = "pgfinder.find_pg:main"