From df7dba47babae105680f4384da48a4960ce3be2d Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Sun, 13 Sep 2026 19:38:20 +0100
Subject: [PATCH 1/3] Updated files with 'repo_helper'.

---
 .github/workflows/conda_ci.yml         |  4 ++--
 .github/workflows/docs_test_action.yml |  4 ++--
 .github/workflows/flake8.yml           |  6 +++---
 .github/workflows/mypy.yml             |  6 +++---
 .github/workflows/python_ci.yml        |  6 +++---
 .github/workflows/python_ci_linux.yml  | 18 +++++++++---------
 .github/workflows/python_ci_macos.yml  |  6 +++---
 .pre-commit-config.yaml                | 14 +++++++++++---
 doc-source/conf.py                     |  2 +-
 justfile                               |  5 +++++
 pyproject.toml                         |  1 +
 tox.ini                                |  9 ++++++---
 12 files changed, 49 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/conda_ci.yml b/.github/workflows/conda_ci.yml
index 5ae172c..6307fbf 100644
--- a/.github/workflows/conda_ci.yml
+++ b/.github/workflows/conda_ci.yml
@@ -18,10 +18,10 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "3.11"
 
diff --git a/.github/workflows/docs_test_action.yml b/.github/workflows/docs_test_action.yml
index dc03fd3..76249f1 100644
--- a/.github/workflows/docs_test_action.yml
+++ b/.github/workflows/docs_test_action.yml
@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
index 1ecb7b9..1f5be86 100644
--- a/.github/workflows/flake8.yml
+++ b/.github/workflows/flake8.yml
@@ -19,10 +19,10 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
@@ -32,7 +32,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "3.9"
 
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
index 6406711..8b5717a 100644
--- a/.github/workflows/mypy.yml
+++ b/.github/workflows/mypy.yml
@@ -24,10 +24,10 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
@@ -37,7 +37,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "3.9"
 
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
index 04a7fb9..f323ace 100644
--- a/.github/workflows/python_ci.yml
+++ b/.github/workflows/python_ci.yml
@@ -36,11 +36,11 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
@@ -51,7 +51,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
diff --git a/.github/workflows/python_ci_linux.yml b/.github/workflows/python_ci_linux.yml
index 4e818dd..047f097 100644
--- a/.github/workflows/python_ci_linux.yml
+++ b/.github/workflows/python_ci_linux.yml
@@ -37,11 +37,11 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
@@ -52,7 +52,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
@@ -89,10 +89,10 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: 3.8
 
@@ -142,11 +142,11 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
         if: startsWith(github.ref, 'refs/tags/')
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         if: startsWith(github.ref, 'refs/tags/')
         with:
           python-version: 3.8
@@ -189,10 +189,10 @@ jobs:
     if: startsWith(github.ref, 'refs/tags/') || (startsWith(github.event.head_commit.message, 'Bump version') != true)
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: 3.11
 
diff --git a/.github/workflows/python_ci_macos.yml b/.github/workflows/python_ci_macos.yml
index 29b47e1..b516953 100644
--- a/.github/workflows/python_ci_macos.yml
+++ b/.github/workflows/python_ci_macos.yml
@@ -36,11 +36,11 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
-        uses: dorny/paths-filter@v2
+        uses: dorny/paths-filter@v4
         id: changes
         with:
           list-files: "json"
@@ -51,7 +51,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6216ff8..c846166 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,6 +5,7 @@ exclude: ^$
 
 ci:
   autoupdate_schedule: quarterly
+  skip: [taplo-lint]
 
 repos:
  - repo: https://github.com/repo-helper/pyproject-parser
@@ -21,7 +22,6 @@ repos:
     - id: check-case-conflict
     - id: check-executables-have-shebangs
     - id: check-json
-    - id: check-toml
     - id: check-yaml
     - id: check-merge-conflict
     - id: check-symlinks
@@ -31,8 +31,14 @@ repos:
     - id: mixed-line-ending
     - id: end-of-file-fixer
 
+ - repo: https://github.com/domdfcoding/taplo-pre-commit
+   rev: v0.10.0
+   hooks:
+    - id: taplo-lint
+      args: []
+
  - repo: https://github.com/domdfcoding/pre-commit-hooks
-   rev: v0.7.0
+   rev: v0.8.1
    hooks:
     - id: requirements-txt-sorter
       args:
@@ -78,9 +84,11 @@ repos:
     - id: forbid-crlf
 
  - repo: https://github.com/python-formate/snippet-fmt
-   rev: v0.1.5
+   rev: v0.3.1
    hooks:
     - id: snippet-fmt
+      additional_dependencies:
+       - formate-trailing-commas>=0.1.1
 
  - repo: https://github.com/python-formate/formate
    rev: v1.2.1
diff --git a/doc-source/conf.py b/doc-source/conf.py
index 6eeb631..3313ab9 100644
--- a/doc-source/conf.py
+++ b/doc-source/conf.py
@@ -93,7 +93,7 @@ def setup(app):
 
 	app.connect("config-inited", lambda app, config: better_header_layout(config))
 	app.connect("build-finished", copy_asset_files)
-	app.add_js_file("https://unpkg.com/twemoji@latest/dist/twemoji.min.js")
+	app.add_js_file("https://cdn.jsdelivr.net/npm/twemoji@14.0.2/dist/twemoji.min.js")
 	app.add_js_file("twemoji.js")
 	app.add_css_file("twemoji.css")
 	app.add_transform(sphinxemoji.EmojiSubstitutions)
diff --git a/justfile b/justfile
index 9cd8b78..4307956 100644
--- a/justfile
+++ b/justfile
@@ -23,3 +23,8 @@ bare-ignore:
 
 lint: unused-imports incomplete-defs bare-ignore
 	tox -n qa
+
+uncomm:
+  git status -uall --ignored
+
+# Custom commands can be added below this comment
diff --git a/pyproject.toml b/pyproject.toml
index b59319a..a1677b2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,6 +79,7 @@ extensions = [
     "html_section",
     "sphinx_toolbox.tweaks.footnote_symbols",
 ]
+sphinxemoji_source = "https://cdn.jsdelivr.net/npm/twemoji@14.0.2/dist/twemoji.min.js"
 gitstamp_fmt = "%d %b %Y"
 templates_path = [ "_templates",]
 html_static_path = [ "_static",]
diff --git a/tox.ini b/tox.ini
index 896f2f3..a688474 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,6 +4,10 @@
 #     * envlists
 #     * testenv
 #     * testenv:.package
+#     * testenv:py315-dev
+#     * testenv:py315
+#     * testenv:py314-dev
+#     * testenv:py314
 #     * testenv:py313-dev
 #     * testenv:py313
 #     * testenv:py312-dev
@@ -40,6 +44,7 @@ setenv =
     PYTHONDEVMODE=1
     PIP_DISABLE_PIP_VERSION_CHECK=1
     SETUPTOOLS_USE_DISTUTILS=stdlib
+download = True
 deps = -r{toxinidir}/tests/requirements.txt
 commands =
     python --version
@@ -51,13 +56,11 @@ setenv =
     PIP_DISABLE_PIP_VERSION_CHECK=1
 
 [testenv:py313]
-download = True
 setenv =
     PYTHONDEVMODE=1
     PIP_DISABLE_PIP_VERSION_CHECK=1
 
 [testenv:py312]
-download = True
 setenv =
     PYTHONDEVMODE=1
     PIP_DISABLE_PIP_VERSION_CHECK=1
@@ -144,7 +147,7 @@ skip_install = True
 ignore_errors = True
 changedir = {toxinidir}
 deps = pyupgrade-directories
-commands = pyup_dirs pymassspec_plot tests --py36-plus --recursive
+commands = pyup_dirs pymassspec_plot tests --py37-plus --recursive
 
 [testenv:coverage]
 basepython = python3.9

From b907b8c25b3aa1d8d3694141577aff76c310a7ea Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 13 Sep 2026 18:40:03 +0000
Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pymassspec_plot/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pymassspec_plot/__init__.py b/pymassspec_plot/__init__.py
index efe514c..a50c91e 100644
--- a/pymassspec_plot/__init__.py
+++ b/pymassspec_plot/__init__.py
@@ -79,7 +79,7 @@ def plot_ic(  # noqa: PRM002
 
 		.. code-block:: python
 
-			>>> plot_ic(im.get_ic_at_index(5), label='IC @ Index 5', linewidth=2)
+			>>> plot_ic(im.get_ic_at_index(5), label="IC @ Index 5", linewidth=2)
 
 		See :class:`matplotlib.lines.Line2D` for the list of possible keyword arguments.
 

From 6429c88e566c195c277ecc6e956d7343a468d761 Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Mon, 14 Sep 2026 21:43:40 +0000
Subject: [PATCH 3/3] Updated files with 'repo_helper'.

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c846166..93e4d37 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -84,7 +84,7 @@ repos:
     - id: forbid-crlf
 
  - repo: https://github.com/python-formate/snippet-fmt
-   rev: v0.3.1
+   rev: v0.3.2
    hooks:
     - id: snippet-fmt
       additional_dependencies: