From 2c923a439edb2eab73dd24a259a18d446d409c26 Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Mon, 20 Nov 2023 23:30:28 +0000
Subject: [PATCH 1/6] Updated files with 'repo_helper'.

---
 .github/workflows/docs_test_action.yml |  2 +-
 .github/workflows/flake8.yml           |  8 ++++----
 .github/workflows/mypy.yml             |  6 +++---
 .github/workflows/python_ci.yml        |  8 ++++----
 .github/workflows/python_ci_linux.yml  | 22 +++++++++++-----------
 .github/workflows/python_ci_macos.yml  |  8 ++++----
 .pre-commit-config.yaml                | 15 +++++++++------
 .readthedocs.yml                       | 10 +++++++---
 README.rst                             |  6 +++---
 doc-source/index.rst                   |  6 +++---
 doc-source/requirements.txt            | 18 +++++++++---------
 tox.ini                                | 20 +++++++++++++++++++-
 12 files changed, 77 insertions(+), 52 deletions(-)

diff --git a/.github/workflows/docs_test_action.yml b/.github/workflows/docs_test_action.yml
index d258e8d..917a145 100644
--- a/.github/workflows/docs_test_action.yml
+++ b/.github/workflows/docs_test_action.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
index 84e9436..5b6260e 100644
--- a/.github/workflows/flake8.yml
+++ b/.github/workflows/flake8.yml
@@ -16,11 +16,11 @@ permissions:
 jobs:
   Run:
     name: "Flake8"
-    runs-on: "ubuntu-18.04"
+    runs-on: "ubuntu-20.04"
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
@@ -33,7 +33,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: "3.6"
 
@@ -43,7 +43,7 @@ jobs:
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install tox
+          python -m pip install tox~=3.0
 
       - name: "Run Flake8"
         if: steps.changes.outputs.code == 'true'
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
index db8ab06..882a62f 100644
--- a/.github/workflows/mypy.yml
+++ b/.github/workflows/mypy.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
@@ -38,7 +38,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: "3.6"
 
@@ -47,7 +47,7 @@ jobs:
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade tox virtualenv!=20.16.0
+          python -m pip install --upgrade tox~=3.0 virtualenv!=20.16.0
 
       - name: "Run mypy"
         if: steps.changes.outputs.code == 'true'
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
index e17433e..a82f667 100644
--- a/.github/workflows/python_ci.yml
+++ b/.github/workflows/python_ci.yml
@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -50,7 +50,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
@@ -60,14 +60,14 @@ jobs:
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade tox virtualenv!=20.16.0
+          python -m pip install --upgrade tox~=3.0 virtualenv!=20.16.0
 
       - name: "Run Tests for Python ${{ matrix.config.python-version }}"
         if: steps.setup-python.outcome == 'success'
         run: python -m tox -e "${{ matrix.config.testenvs }}" -s false
 
       - name: "Upload Coverage 🚀"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: ${{ always() && steps.setup-python.outcome == 'success' }}
         with:
           name: "coverage-${{ matrix.config.python-version }}"
diff --git a/.github/workflows/python_ci_linux.yml b/.github/workflows/python_ci_linux.yml
index 80ee082..204685a 100644
--- a/.github/workflows/python_ci_linux.yml
+++ b/.github/workflows/python_ci_linux.yml
@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -51,7 +51,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
@@ -61,7 +61,7 @@ jobs:
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade tox virtualenv!=20.16.0
+          python -m pip install --upgrade tox~=3.0 virtualenv!=20.16.0
           python -m pip install --upgrade coverage_pyver_pragma
 
       - name: "Run Tests for Python ${{ matrix.config.python-version }}"
@@ -69,7 +69,7 @@ jobs:
         run: python -m tox -e "${{ matrix.config.testenvs }}" -s false
 
       - name: "Upload Coverage 🚀"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: ${{ always() && steps.setup-python.outcome == 'success' }}
         with:
           name: "coverage-${{ matrix.config.python-version }}"
@@ -81,10 +81,10 @@ jobs:
     runs-on: "ubuntu-20.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: 3.8
 
@@ -94,7 +94,7 @@ jobs:
           python -m pip install --upgrade "coveralls>=3.0.0" coverage_pyver_pragma
 
       - name: "Download Coverage 🪂"
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           path: coverage
 
@@ -112,7 +112,7 @@ jobs:
 
       - name: "Upload Combined Coverage Artefact 🚀"
         if: ${{ steps.show.outcome != 'failure' }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: "combined-coverage"
           path: .coverage
@@ -130,11 +130,11 @@ jobs:
     runs-on: "ubuntu-20.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
         if: startsWith(github.ref, 'refs/tags/')
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         if: startsWith(github.ref, 'refs/tags/')
         with:
           python-version: 3.8
@@ -143,7 +143,7 @@ jobs:
         if: startsWith(github.ref, 'refs/tags/')
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade tox
+          python -m pip install --upgrade tox~=3.0
 
       - name: Build distributions 📦
         if: startsWith(github.ref, 'refs/tags/')
diff --git a/.github/workflows/python_ci_macos.yml b/.github/workflows/python_ci_macos.yml
index 66485d5..fb705fb 100644
--- a/.github/workflows/python_ci_macos.yml
+++ b/.github/workflows/python_ci_macos.yml
@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v2"
+        uses: "actions/checkout@v3"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -50,7 +50,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v2"
+        uses: "actions/setup-python@v4"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
@@ -60,14 +60,14 @@ jobs:
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade tox virtualenv!=20.16.0
+          python -m pip install --upgrade tox~=3.0 virtualenv!=20.16.0
 
       - name: "Run Tests for Python ${{ matrix.config.python-version }}"
         if: steps.setup-python.outcome == 'success'
         run: python -m tox -e "${{ matrix.config.testenvs }}" -s false
 
       - name: "Upload Coverage 🚀"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: ${{ always() && steps.setup-python.outcome == 'success' }}
         with:
           name: "coverage-${{ matrix.config.python-version }}"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fb9051c..f45a5f0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,9 +3,12 @@
 
 exclude: ^$
 
+ci:
+  autoupdate_schedule: quarterly
+
 repos:
  - repo: https://github.com/repo-helper/pyproject-parser
-   rev: v0.7.0
+   rev: v0.9.0
    hooks:
     - id: reformat-pyproject
 
@@ -40,7 +43,7 @@ repos:
     - id: bind-requirements
 
  - repo: https://github.com/domdfcoding/flake8-dunder-all
-   rev: v0.2.2
+   rev: v0.3.0
    hooks:
     - id: ensure-dunder-all
       files: ^notebook2script/.*\.py$
@@ -51,7 +54,7 @@ repos:
     - id: flake2lint
 
  - repo: https://github.com/pre-commit/pygrep-hooks
-   rev: v1.9.0
+   rev: v1.10.0
    hooks:
     - id: python-no-eval
     - id: rst-backticks
@@ -67,7 +70,7 @@ repos:
        - --keep-runtime-typing
 
  - repo: https://github.com/Lucas-C/pre-commit-hooks
-   rev: v1.2.0
+   rev: v1.5.1
    hooks:
     - id: remove-crlf
     - id: forbid-crlf
@@ -78,13 +81,13 @@ repos:
     - id: snippet-fmt
 
  - repo: https://github.com/python-formate/formate
-   rev: v0.4.10
+   rev: v0.5.0
    hooks:
     - id: formate
       exclude: ^(doc-source/conf|__pkginfo__|setup)\.(_)?py$
 
  - repo: https://github.com/domdfcoding/dep_checker
-   rev: v0.7.0
+   rev: v0.7.1
    hooks:
     - id: dep_checker
       args:
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 41d2e57..4a2ec5f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -9,9 +9,13 @@ formats:
  - pdf
  - htmlzip
 python:
-  version: 3.8
   install:
    - requirements: requirements.txt
    - requirements: doc-source/requirements.txt
-   - method: pip
-     path: .
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.9'
+  jobs:
+    post_create_environment:
+     - pip install .
diff --git a/README.rst b/README.rst
index 578aa4d..64b41dd 100644
--- a/README.rst
+++ b/README.rst
@@ -55,8 +55,8 @@ notebook2script
 	:target: https://github.com/PyMassSpec/notebook2script/actions?query=workflow%3A%22mypy%22
 	:alt: mypy status
 
-.. |requires| image:: https://dependency-dash.herokuapp.com/github/PyMassSpec/notebook2script/badge.svg
-	:target: https://dependency-dash.herokuapp.com/github/PyMassSpec/notebook2script/
+.. |requires| image:: https://dependency-dash.repo-helper.uk/github/PyMassSpec/notebook2script/badge.svg
+	:target: https://dependency-dash.repo-helper.uk/github/PyMassSpec/notebook2script/
 	:alt: Requirements Status
 
 .. |coveralls| image:: https://img.shields.io/coveralls/github/PyMassSpec/notebook2script/master?logo=coveralls
@@ -98,7 +98,7 @@ notebook2script
 	:target: https://github.com/PyMassSpec/notebook2script/commit/master
 	:alt: GitHub last commit
 
-.. |maintained| image:: https://img.shields.io/maintenance/yes/2022
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2023
 	:alt: Maintenance
 
 .. |pypi-downloads| image:: https://img.shields.io/pypi/dm/notebook2script
diff --git a/doc-source/index.rst b/doc-source/index.rst
index 3d899c9..bc1f936 100644
--- a/doc-source/index.rst
+++ b/doc-source/index.rst
@@ -58,8 +58,8 @@ notebook2script
 		:workflow: mypy
 		:alt: mypy status
 
-	.. |requires| image:: https://dependency-dash.herokuapp.com/github/PyMassSpec/notebook2script/badge.svg
-		:target: https://dependency-dash.herokuapp.com/github/PyMassSpec/notebook2script/
+	.. |requires| image:: https://dependency-dash.repo-helper.uk/github/PyMassSpec/notebook2script/badge.svg
+		:target: https://dependency-dash.repo-helper.uk/github/PyMassSpec/notebook2script/
 		:alt: Requirements Status
 
 	.. |coveralls| coveralls-shield::
@@ -104,7 +104,7 @@ notebook2script
 		:last-commit:
 		:alt: GitHub last commit
 
-	.. |maintained| maintained-shield:: 2022
+	.. |maintained| maintained-shield:: 2023
 		:alt: Maintenance
 
 	.. |pypi-downloads| pypi-shield::
diff --git a/doc-source/requirements.txt b/doc-source/requirements.txt
index 72b7cb9..aa976f8 100644
--- a/doc-source/requirements.txt
+++ b/doc-source/requirements.txt
@@ -1,18 +1,18 @@
 git+https://github.com/domdfcoding/sphinx-click.git
-default-values>=0.5.0
-extras-require>=0.2.0
-furo>=2020.11.19b18
-html-section>=0.1.0
-seed-intersphinx-mapping>=0.3.1
+default-values>=0.6.0
+extras-require>=0.5.0
+furo==2021.06.18b36
+html-section>=0.3.0
+seed-intersphinx-mapping>=1.2.2
 sphinx>=3.0.3
 sphinx-copybutton>=0.2.12
-sphinx-debuginfo>=0.1.0
-sphinx-licenseinfo>=0.1.1
+sphinx-debuginfo>=0.2.2
+sphinx-licenseinfo>=0.3.1
 sphinx-notfound-page>=0.5
 sphinx-prompt>=1.1.0
 sphinx-pyproject>=0.1.0
 sphinx-tabs>=1.1.13
-sphinx-toolbox>=2.13.0
+sphinx-toolbox>=3.5.0
 sphinxcontrib-httpdomain>=1.7.0
 sphinxemoji>=0.1.6
-toctree-plus>=0.5.0
+toctree-plus>=0.6.1
diff --git a/tox.ini b/tox.ini
index 41c1575..eac1465 100644
--- a/tox.ini
+++ b/tox.ini
@@ -3,6 +3,10 @@
 #     * tox
 #     * envlists
 #     * testenv
+#     * testenv:.package
+#     * testenv:py313-dev
+#     * testenv:py312-dev
+#     * testenv:py312
 #     * testenv:docs
 #     * testenv:build
 #     * testenv:lint
@@ -23,6 +27,7 @@ isolated_build = True
 requires =
     pip>=21,!=22.2
     tox-envlist>=0.2.1
+    tox~=3.0
     virtualenv!=20.16.0
 
 [envlists]
@@ -34,11 +39,17 @@ cov = py36, coverage
 setenv =
     PYTHONDEVMODE=1
     PIP_DISABLE_PIP_VERSION_CHECK=1
+    SETUPTOOLS_USE_DISTUTILS=stdlib
 deps = -r{toxinidir}/tests/requirements.txt
 commands =
     python --version
     python -m pytest --cov=notebook2script -r aR tests/ {posargs}
 
+[testenv:.package]
+setenv =
+    PYTHONDEVMODE=1
+    PIP_DISABLE_PIP_VERSION_CHECK=1
+
 [testenv:docs]
 setenv = SHOW_TODOS = 1
 passenv = SPHINX_BUILDER
@@ -48,12 +59,17 @@ deps = -r{toxinidir}/doc-source/requirements.txt
 commands = sphinx-build -M {env:SPHINX_BUILDER:html} . ./build {posargs}
 
 [testenv:build]
+setenv =
+    PYTHONDEVMODE=1
+    PIP_DISABLE_PIP_VERSION_CHECK=1
+    PIP_PREFER_BINARY=1
 skip_install = True
 changedir = {toxinidir}
 deps =
     build[virtualenv]>=0.3.1
     check-wheel-contents>=0.1.0
     twine>=3.2.0
+    cryptography<40; implementation_name == "pypy" and python_version <= "3.7"
 commands =
     python -m build --sdist --wheel "{toxinidir}"
     twine check dist/*.tar.gz dist/*.whl
@@ -123,6 +139,7 @@ passenv =
     COV_PYTHON_VERSION
     COV_PLATFORM
     COV_PYTHON_IMPLEMENTATION
+    *
 changedir = {toxinidir}
 deps =
     coverage>=5
@@ -134,7 +151,7 @@ commands =
 
 [flake8]
 max-line-length = 120
-select = E111 E112 E113 E121 E122 E125 E127 E128 E129 E131 E133 E201 E202 E203 E211 E222 E223 E224 E225 E225 E226 E227 E228 E231 E241 E242 E251 E261 E262 E265 E271 E272 E303 E304 E306 E402 E502 E703 E711 E712 E713 E714 E721 W291 W292 W293 W391 W504 YTT101 YTT102 YTT103 YTT201 YTT202 YTT203 YTT204 YTT301 YTT302 YTT303 STRFTIME001 STRFTIME002 SXL001  PT001 PT002 PT003 PT006 PT007 PT008 PT009 PT010 PT011 PT012 PT013 PT014 PT015 PT016 PT017 PT018 PT019 PT020 PT021 RST201 RST202 RST203 RST204 RST205 RST206 RST207 RST208 RST210 RST211 RST212 RST213 RST214 RST215 RST216 RST217 RST218 RST219 RST299 RST301 RST302 RST303 RST304 RST305 RST306 RST399 RST401 RST499 RST900 RST901 RST902 RST903 Q001 Q002 Q003 A001 A002 A003 TYP001 TYP002 TYP003 TYP004 TYP005 TYP006 ENC001 ENC002 ENC003 ENC004 ENC011 ENC012 ENC021 ENC022 ENC023 ENC024 ENC025 ENC026 Y001,Y002 Y003 Y004 Y005 Y006 Y007 Y008 Y009 Y010 Y011 Y012 Y013 Y014 Y015 Y090 Y091 NQA001 NQA002 NQA003 NQA004 NQA005 NQA102 NQA103 E301 E302 E305 D100 D101 D102 D103 D104 D106 D201 D204 D207 D208 D209 D210 D211 D212 D213 D214 D215 D300 D301 D400 D402 D403 D404 D415 D417 DALL000  SLOT000 SLOT001 SLOT002
+select = E111 E112 E113 E121 E122 E125 E127 E128 E129 E131 E133 E201 E202 E203 E211 E222 E223 E224 E225 E225 E226 E227 E228 E231 E241 E242 E251 E261 E262 E265 E271 E272 E303 E304 E306 E402 E502 E703 E711 E712 E713 E714 E721 W291 W292 W293 W391 W504 YTT101 YTT102 YTT103 YTT201 YTT202 YTT203 YTT204 YTT301 YTT302 YTT303 STRFTIME001 STRFTIME002 SXL001  PT001 PT002 PT003 PT006 PT007 PT008 PT009 PT010 PT011 PT012 PT013 PT014 PT015 PT016 PT017 PT018 PT019 PT020 PT021 RST201 RST202 RST203 RST204 RST205 RST206 RST207 RST208 RST210 RST211 RST212 RST213 RST214 RST215 RST216 RST217 RST218 RST219 RST299 RST301 RST302 RST303 RST304 RST305 RST306 RST399 RST401 RST499 RST900 RST901 RST902 RST903 Q001 Q002 Q003 A001 A002 TYP001 TYP002 TYP003 TYP004 TYP005 TYP006 ENC001 ENC002 ENC003 ENC004 ENC011 ENC012 ENC021 ENC022 ENC023 ENC024 ENC025 ENC026 Y001,Y002 Y003 Y004 Y005 Y006 Y007 Y008 Y009 Y010 Y011 Y012 Y013 Y014 Y015 Y090 Y091 NQA001 NQA002 NQA003 NQA004 NQA005 NQA102 NQA103 E301 E302 E305 D100 D101 D102 D103 D104 D106 D201 D204 D207 D208 D209 D210 D211 D212 D213 D214 D215 D300 D301 D400 D402 D403 D404 D415 D417 DALL000  SLOT000 SLOT001 SLOT002
 extend-exclude = doc-source,old,build,dist,__pkginfo__.py,setup.py,venv
 rst-directives =
     TODO
@@ -162,6 +179,7 @@ plugins = coverage_pyver_pragma
 
 [coverage:report]
 fail_under = 80
+show_missing = True
 exclude_lines =
     raise AssertionError
     raise NotImplementedError

From 2bc5a7cfe094308b0d8fe7dfb43a378a4dae23b3 Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Fri, 8 Dec 2023 09:31:04 +0000
Subject: [PATCH 2/6] Updated files with 'repo_helper'.

---
 doc-source/requirements.txt | 6 +++---
 tox.ini                     | 2 --
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/doc-source/requirements.txt b/doc-source/requirements.txt
index aa976f8..1be307c 100644
--- a/doc-source/requirements.txt
+++ b/doc-source/requirements.txt
@@ -5,14 +5,14 @@ furo==2021.06.18b36
 html-section>=0.3.0
 seed-intersphinx-mapping>=1.2.2
 sphinx>=3.0.3
-sphinx-copybutton>=0.2.12
+sphinx-copybutton>=0.5.2
 sphinx-debuginfo>=0.2.2
 sphinx-licenseinfo>=0.3.1
-sphinx-notfound-page>=0.5
+sphinx-notfound-page>=0.8.3
 sphinx-prompt>=1.1.0
 sphinx-pyproject>=0.1.0
 sphinx-tabs>=1.1.13
 sphinx-toolbox>=3.5.0
 sphinxcontrib-httpdomain>=1.7.0
-sphinxemoji>=0.1.6
+sphinxemoji>=0.2.0
 toctree-plus>=0.6.1
diff --git a/tox.ini b/tox.ini
index eac1465..f0ab863 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,9 +4,7 @@
 #     * envlists
 #     * testenv
 #     * testenv:.package
-#     * testenv:py313-dev
 #     * testenv:py312-dev
-#     * testenv:py312
 #     * testenv:docs
 #     * testenv:build
 #     * testenv:lint

From 24a4a34b354c0253a15ea864cd0ac8145c01a13f Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Mon, 11 Dec 2023 16:54:26 +0000
Subject: [PATCH 3/6] Updated files with 'repo_helper'.

---
 tox.ini | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index f0ab863..50f7661 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,7 +4,9 @@
 #     * envlists
 #     * testenv
 #     * testenv:.package
+#     * testenv:py313-dev
 #     * testenv:py312-dev
+#     * testenv:py312
 #     * testenv:docs
 #     * testenv:build
 #     * testenv:lint
@@ -66,7 +68,8 @@ changedir = {toxinidir}
 deps =
     build[virtualenv]>=0.3.1
     check-wheel-contents>=0.1.0
-    twine>=3.2.0
+    twine>=3.2.0; python_version < "3.13"
+    twine@git+https://github.com/pypa/twine; python_version >= "3.13"
     cryptography<40; implementation_name == "pypy" and python_version <= "3.7"
 commands =
     python -m build --sdist --wheel "{toxinidir}"
@@ -86,7 +89,7 @@ deps =
     flake8-dunder-all>=0.1.1
     flake8-encodings>=0.1.0
     flake8-github-actions>=0.1.0
-    flake8-noqa>=1.1.0,<=1.2.2
+    flake8-noqa>=1.1.0
     flake8-pyi>=20.10.0,<=22.8.0
     flake8-pytest-style>=1.3.0
     flake8-quotes>=3.3.0

From 49b2f6d32ebfe60af7a9b32b275b74e2fcc2804f Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Mon, 22 Jan 2024 16:49:29 +0000
Subject: [PATCH 4/6] Updated files with 'repo_helper'.

---
 README.rst           | 2 +-
 doc-source/index.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index 64b41dd..cf96662 100644
--- a/README.rst
+++ b/README.rst
@@ -98,7 +98,7 @@ notebook2script
 	:target: https://github.com/PyMassSpec/notebook2script/commit/master
 	:alt: GitHub last commit
 
-.. |maintained| image:: https://img.shields.io/maintenance/yes/2023
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2024
 	:alt: Maintenance
 
 .. |pypi-downloads| image:: https://img.shields.io/pypi/dm/notebook2script
diff --git a/doc-source/index.rst b/doc-source/index.rst
index bc1f936..348c99c 100644
--- a/doc-source/index.rst
+++ b/doc-source/index.rst
@@ -104,7 +104,7 @@ notebook2script
 		:last-commit:
 		:alt: GitHub last commit
 
-	.. |maintained| maintained-shield:: 2023
+	.. |maintained| maintained-shield:: 2024
 		:alt: Maintenance
 
 	.. |pypi-downloads| pypi-shield::

From 7827b8d55c96f2c5c7c0cf27c7cda01bd5a90001 Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 16:33:41 +0000
Subject: [PATCH 5/6] Updated files with 'repo_helper'.

---
 .readthedocs.yml | 3 +++
 tox.ini          | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 4a2ec5f..e928b70 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -19,3 +19,6 @@ build:
   jobs:
     post_create_environment:
      - pip install .
+    post_install:
+     - pip install sphinxcontrib-applehelp==1.0.4 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.1
+       sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5
diff --git a/tox.ini b/tox.ini
index 50f7661..e8cca84 100644
--- a/tox.ini
+++ b/tox.ini
@@ -89,7 +89,7 @@ deps =
     flake8-dunder-all>=0.1.1
     flake8-encodings>=0.1.0
     flake8-github-actions>=0.1.0
-    flake8-noqa>=1.1.0
+    flake8-noqa>=1.1.0,<=1.2.2
     flake8-pyi>=20.10.0,<=22.8.0
     flake8-pytest-style>=1.3.0
     flake8-quotes>=3.3.0

From 859fa60f770126bc50f44734ffaf70629afa3299 Mon Sep 17 00:00:00 2001
From: "repo-helper[bot]" <74742576+repo-helper[bot]@users.noreply.github.com>
Date: Mon, 5 Feb 2024 11:40:59 +0000
Subject: [PATCH 6/6] Updated files with 'repo_helper'.

---
 .github/workflows/docs_test_action.yml |  2 +-
 .github/workflows/flake8.yml           |  4 ++--
 .github/workflows/mypy.yml             |  4 ++--
 .github/workflows/python_ci.yml        |  4 ++--
 .github/workflows/python_ci_linux.yml  | 12 ++++++------
 .github/workflows/python_ci_macos.yml  |  4 ++--
 .pre-commit-config.yaml                | 12 ++++++------
 7 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/docs_test_action.yml b/.github/workflows/docs_test_action.yml
index 917a145..331606e 100644
--- a/.github/workflows/docs_test_action.yml
+++ b/.github/workflows/docs_test_action.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
index 5b6260e..d7c372d 100644
--- a/.github/workflows/flake8.yml
+++ b/.github/workflows/flake8.yml
@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
@@ -33,7 +33,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: "3.6"
 
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
index 882a62f..c707651 100644
--- a/.github/workflows/mypy.yml
+++ b/.github/workflows/mypy.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2
@@ -38,7 +38,7 @@ jobs:
 
       - name: Setup Python 🐍
         if: steps.changes.outputs.code == 'true'
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: "3.6"
 
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
index a82f667..151df52 100644
--- a/.github/workflows/python_ci.yml
+++ b/.github/workflows/python_ci.yml
@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -50,7 +50,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
diff --git a/.github/workflows/python_ci_linux.yml b/.github/workflows/python_ci_linux.yml
index 204685a..7dc7a99 100644
--- a/.github/workflows/python_ci_linux.yml
+++ b/.github/workflows/python_ci_linux.yml
@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -51,7 +51,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
@@ -81,10 +81,10 @@ jobs:
     runs-on: "ubuntu-20.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: 3.8
 
@@ -130,11 +130,11 @@ jobs:
     runs-on: "ubuntu-20.04"
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
         if: startsWith(github.ref, 'refs/tags/')
 
       - name: Setup Python 🐍
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         if: startsWith(github.ref, 'refs/tags/')
         with:
           python-version: 3.8
diff --git a/.github/workflows/python_ci_macos.yml b/.github/workflows/python_ci_macos.yml
index fb705fb..f64cbbe 100644
--- a/.github/workflows/python_ci_macos.yml
+++ b/.github/workflows/python_ci_macos.yml
@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v3"
+        uses: "actions/checkout@v4"
 
       - name: Check for changed files
         if: startsWith(github.ref, 'refs/tags/') != true
@@ -50,7 +50,7 @@ jobs:
       - name: Setup Python 🐍
         id: setup-python
         if: ${{ steps.changes.outputs.code == 'true' || steps.changes.outcome == 'skipped' }}
-        uses: "actions/setup-python@v4"
+        uses: "actions/setup-python@v5"
         with:
           python-version: "${{ matrix.config.python-version }}"
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f45a5f0..78fe63d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,7 +8,7 @@ ci:
 
 repos:
  - repo: https://github.com/repo-helper/pyproject-parser
-   rev: v0.9.0
+   rev: v0.9.1
    hooks:
     - id: reformat-pyproject
 
@@ -43,13 +43,13 @@ repos:
     - id: bind-requirements
 
  - repo: https://github.com/domdfcoding/flake8-dunder-all
-   rev: v0.3.0
+   rev: v0.3.1
    hooks:
     - id: ensure-dunder-all
       files: ^notebook2script/.*\.py$
 
  - repo: https://github.com/domdfcoding/flake2lint
-   rev: v0.4.2
+   rev: v0.4.3
    hooks:
     - id: flake2lint
 
@@ -76,18 +76,18 @@ repos:
     - id: forbid-crlf
 
  - repo: https://github.com/python-formate/snippet-fmt
-   rev: v0.1.4
+   rev: v0.1.5
    hooks:
     - id: snippet-fmt
 
  - repo: https://github.com/python-formate/formate
-   rev: v0.5.0
+   rev: v0.7.0
    hooks:
     - id: formate
       exclude: ^(doc-source/conf|__pkginfo__|setup)\.(_)?py$
 
  - repo: https://github.com/domdfcoding/dep_checker
-   rev: v0.7.1
+   rev: v0.8.0
    hooks:
     - id: dep_checker
       args: