From f8678407cdcd2d54d6fea44b8fe80228d8958878 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 16 Apr 2024 12:11:25 +0000
Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#74)
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* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)

* Fix spelling of seamless

* Skip some kinds of files w/ codespell

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Isaac Virshup <ivirshup@gmail.com>
---
 .pre-commit-config.yaml                            | 2 +-
 docs/how-to/ChIP_seq_genomic_ranges_tutorial.ipynb | 2 +-
 pyproject.toml                                     | 1 +
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3042a4c..2783077 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.3.7
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
diff --git a/docs/how-to/ChIP_seq_genomic_ranges_tutorial.ipynb b/docs/how-to/ChIP_seq_genomic_ranges_tutorial.ipynb
index 8b0ef93..342dea1 100644
--- a/docs/how-to/ChIP_seq_genomic_ranges_tutorial.ipynb
+++ b/docs/how-to/ChIP_seq_genomic_ranges_tutorial.ipynb
@@ -623,7 +623,7 @@
    "source": [
     "## Mapping chromosome annotation styles\n",
     "\n",
-    "In order to annotate the ranges in the dataframe with gene symbols, ensembl ids, strand direction, etc. the two dataframes need to be merged. To make this seemless we use the bioframe [assembly_info](https://bioframe.readthedocs.io/en/latest/api-resources.html#bioframe.io.assembly.assembly_info) to map the numeric Ensembl chromosome annotation with the \"chr\" notation of the CHIP-Seq dataset and remove any peaks with unmapped chromosome values. This step is optional but makes joining the two dataframes much simpler in the next step."
+    "In order to annotate the ranges in the dataframe with gene symbols, ensembl ids, strand direction, etc. the two dataframes need to be merged. To make this seamless we use the bioframe [assembly_info](https://bioframe.readthedocs.io/en/latest/api-resources.html#bioframe.io.assembly.assembly_info) to map the numeric Ensembl chromosome annotation with the \"chr\" notation of the CHIP-Seq dataset and remove any peaks with unmapped chromosome values. This step is optional but makes joining the two dataframes much simpler in the next step."
    ]
   },
   {
diff --git a/pyproject.toml b/pyproject.toml
index 3c48de4..d6242d4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -146,4 +146,5 @@ skip = [
 ]
 
 [tool.codespell]
+skip = ".git,*.pdf,*.svg,*.ipynb"
 ignore-words-list = "theis,coo,homogenous"