From bd79d93ccd4629df9758f064c5f3bbe3c67f5868 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 17:15:42 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v6.0.0)
- [github.com/snakemake/snakefmt: v0.6.1 → v0.11.5](https://github.com/snakemake/snakefmt/compare/v0.6.1...v0.11.5)
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 22.6.0 → 26.3.1](https://github.com/psf/black-pre-commit-mirror/compare/22.6.0...26.3.1)
- [github.com/PyCQA/isort.git: 5.10.1 → 8.0.1](https://github.com/PyCQA/isort.git/compare/5.10.1...8.0.1)
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 95b4eba..be855b7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
   - repo: https://github.com/snakemake/snakefmt
-    rev: v0.6.1
+    rev: v0.11.5
     hooks:
       - id: snakefmt
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.3.1
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort.git
-    rev: 5.10.1
+    rev: 8.0.1
     hooks:
       - id: isort
   - repo: https://github.com/python-poetry/poetry

From d8459249880925ef40a2c30c3ef796dda7e2b1dd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 17:15:55 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mccoy/workflow/rules/report.smk | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/mccoy/workflow/rules/report.smk b/mccoy/workflow/rules/report.smk
index 1ce6e07..7ff6490 100644
--- a/mccoy/workflow/rules/report.smk
+++ b/mccoy/workflow/rules/report.smk
@@ -53,26 +53,22 @@ rule report:
         loader = jinja2.FileSystemLoader(report_dir)
         env = jinja2.Environment(loader=loader, autoescape=jinja2.select_autoescape())
 
-
         def include_file_unsafe(name):
             if name:
                 return Path(str(name)).read_text()
             return ""
 
-
         def include_file(name):
             if name:
                 return markupsafe.Markup(include_file_unsafe(name))
             return ""
 
-
         def include_raw(name):
             if name:
                 file = report_dir / name
                 return markupsafe.Markup(file.read_text())
             return ""
 
-
         env.globals['include_file_unsafe'] = include_file_unsafe
         env.globals['include_file'] = include_file
         env.globals['include_raw'] = include_raw
@@ -90,7 +86,6 @@ rule report:
         except Exception as err:
             print(f"could not render template: {err}")
 
-
         with open(output_path, 'w') as f:
             print(f"Writing result to {output_path}")
             f.write(result)