PyMassSpec · domdfcoding · Mar 17, 2026 · Mar 17, 2026 · Mar 17, 2026
diff --git a/.github/workflows/docs_test_action.yml b/.github/workflows/docs_test_action.yml
@@ -9,11 +9,10 @@ on:
       - 'imgbot'
   pull_request:
 
-permissions:
-  contents: read
-
 jobs:
   docs:
+    permissions:
+      contents: read
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️

diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -10,12 +10,11 @@ on:
       - 'imgbot'
   pull_request:
 
-permissions:
-  contents: read
-
 jobs:
   Run:
     name: "Flake8"
+    permissions:
+      contents: read
     runs-on: "ubuntu-22.04"
 
     steps:

diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
@@ -10,11 +10,10 @@ on:
       - 'imgbot'
   pull_request:
 
-permissions:
-  contents: read
-
 jobs:
   Run:
+    permissions:
+      contents: read
     name: "mypy / ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
 

diff --git a/.github/workflows/octocheese.yml b/.github/workflows/octocheese.yml
@@ -6,11 +6,10 @@ on:
   schedule:
     - cron: 0 12 * * *
 
-permissions:
-  contents: write
-
 jobs:
   Run:
+    permissions:
+      contents: write
     runs-on: ubuntu-latest
     steps:
       - uses: domdfcoding/octocheese@master

diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
@@ -11,13 +11,11 @@ on:
 
   pull_request:
 
-permissions:
-  actions: write
-  issues: write
-  contents: read
-
 jobs:
   tests:
+    permissions:
+      actions: write
+      contents: read
     name: "windows-2022 / Python ${{ matrix.config.python-version }}"
     runs-on: "windows-2022"
     continue-on-error: ${{ matrix.config.experimental }}

diff --git a/.github/workflows/python_ci_linux.yml b/.github/workflows/python_ci_linux.yml
@@ -12,13 +12,11 @@ on:
       - '*'
   pull_request:
 
-permissions:
-  actions: write
-  issues: write
-  contents: read
-
 jobs:
   tests:
+    permissions:
+      actions: write
+      contents: read
     name: "ubuntu-22.04 / Python ${{ matrix.config.python-version }}"
     runs-on: "ubuntu-22.04"
     continue-on-error: ${{ matrix.config.experimental }}
@@ -79,6 +77,9 @@ jobs:
 
   Coverage:
     needs: tests
+    permissions:
+      actions: write
+      contents: read
     runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
@@ -128,7 +129,10 @@ jobs:
 
   Deploy:
     needs: tests
-
+    permissions:
+      actions: write
+      issues: write
+      contents: read
     runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout 🛎️
@@ -159,7 +163,7 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-          skip_existing: true
+          skip-existing: true
 
       - name: Close milestone 🚪
         if: startsWith(github.ref, 'refs/tags/')

diff --git a/.github/workflows/python_ci_macos.yml b/.github/workflows/python_ci_macos.yml
@@ -11,13 +11,11 @@ on:
 
   pull_request:
 
-permissions:
-  actions: write
-  issues: write
-  contents: read
-
 jobs:
   tests:
+    permissions:
+      actions: write
+      contents: read
     name: "macos-${{ matrix.config.os-ver }} / Python ${{ matrix.config.python-version }}"
     runs-on: "macos-${{ matrix.config.os-ver }}"
     continue-on-error: ${{ matrix.config.experimental }}

diff --git a/.gitignore b/.gitignore
@@ -47,7 +47,6 @@ docs/_build/
 doc/build
 target/
 .ipynb_checkpoints
-.python-version
 celerybeat-schedule
 celerybeat.pid
 *.sage.py

diff --git 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: v0.13.0
+   rev: v0.14.0
    hooks:
     - id: reformat-pyproject
 
@@ -18,7 +18,6 @@ repos:
     - id: check-added-large-files
     - id: check-ast
     - id: fix-byte-order-marker
-    - id: check-byte-order-marker
     - id: check-case-conflict
     - id: check-executables-have-shebangs
     - id: check-json
@@ -33,7 +32,7 @@ repos:
     - id: end-of-file-fixer
 
  - repo: https://github.com/domdfcoding/pre-commit-hooks
-   rev: v0.4.0
+   rev: v0.6.0
    hooks:
     - id: requirements-txt-sorter
       args:
@@ -61,8 +60,8 @@ repos:
     - id: rst-directive-colons
     - id: rst-inline-touching-normal
 
- - repo: https://github.com/asottile/pyupgrade
-   rev: v3.3.0
+ - repo: https://github.com/python-formate/pyupgrade
+   rev: '2e49872'
    hooks:
     - id: pyupgrade
       args:
@@ -81,13 +80,18 @@ repos:
     - id: snippet-fmt
 
  - repo: https://github.com/python-formate/formate
-   rev: v0.8.0
+   rev: v1.2.0
    hooks:
     - id: formate
       exclude: ^(doc-source/conf|__pkginfo__|setup)\.(_)?py$
+      additional_dependencies:
+       - formate-trailing-commas>=0.1.1
+      types_or:
+       - python
+       - pyi
 
  - repo: https://github.com/python-coincidence/dep_checker
-   rev: v0.8.0
+   rev: v0.9.0
    hooks:
     - id: dep_checker
       args:

diff --git a/.style.yapf b/.style.yapf
@@ -312,7 +312,7 @@ split_before_dict_set_generator=True
 #
 #   foo = ('This is a really long string: {}, {}, {}, {}'
 #          .format(a, b, c, d))
-split_before_dot=False
+split_before_dot=True
 
 # Split after the opening paren which surrounds an expression if it doesn't
 # fit on a single line.

diff --git a/README.rst b/README.rst
@@ -98,11 +98,11 @@ notebook2script
 	:target: https://github.com/PyMassSpec/notebook2script/commit/master
 	:alt: GitHub last commit
 
-.. |maintained| image:: https://img.shields.io/maintenance/yes/2025
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2026
 	:alt: Maintenance
 
 .. |pypi-downloads| image:: https://img.shields.io/pypi/dm/notebook2script
-	:target: https://pypi.org/project/notebook2script/
+	:target: https://pypistats.org/packages/notebook2script
 	:alt: PyPI - Downloads
 
 .. end shields

diff --git a/doc-source/index.rst b/doc-source/index.rst
@@ -104,7 +104,7 @@ notebook2script
 		:last-commit:
 		:alt: GitHub last commit
 
-	.. |maintained| maintained-shield:: 2025
+	.. |maintained| maintained-shield:: 2026
 		:alt: Maintenance
 
 	.. |pypi-downloads| pypi-shield::

diff --git a/doc-source/requirements.txt b/doc-source/requirements.txt
@@ -6,6 +6,7 @@ furo==2021.06.18b36
 html-section>=0.3.0
 roman>=4.0
 seed-intersphinx-mapping>=1.2.2
+setuptools<81
 sphinx>=3.0.3
 sphinx-copybutton>=0.5.2
 sphinx-debuginfo>=0.2.2

diff --git a/formate.toml b/formate.toml
@@ -5,6 +5,7 @@ reformat-generics = 40
 noqa-reformat = 60
 ellipsis-reformat = 70
 squish_stubs = 80
+newline_after_equals = 90
 
 [hooks.yapf]
 priority = 30
@@ -27,32 +28,15 @@ lines_between_types = 0
 use_parentheses = true
 remove_redundant_aliases = true
 default_section = "THIRDPARTY"
-known_third_party = [
-    "astroid",
-    "click",
-    "coincidence",
-    "consolekit",
-    "coverage",
-    "coverage_pyver_pragma",
-    "domdf_python_tools",
-    "github",
-    "importlib_metadata",
-    "ipython",
-    "isort",
-    "nbconvert",
-    "pre_commit_hooks",
-    "pylint",
-    "pytest",
-    "pytest_cov",
-    "pytest_randomly",
-    "pytest_rerunfailures",
-    "pytest_timeout",
-    "requests",
-    "yapf_isort",
-]
 known_first_party = [ "notebook2script",]
 line_length = 115
 
+[hooks.trailing_commas]
+priority = 21
+
+[hooks.trailing_commas.kwargs]
+format_ImportFrom = false
+
 [config]
 indent = "	"
 line_length = 115
diff --git a/justfile b/justfile
@@ -12,6 +12,9 @@ unused-imports:
 incomplete-defs:
 	tox -e lint -- --select MAN
 
+commas:
+	tox -e lint -- --select C810,C812,C813,C814,C815,C816
+
 vdiff:
 	git diff $(repo-helper show version -q)..HEAD
 

diff --git a/make_conda_recipe.py b/make_conda_recipe.py
@@ -84,7 +84,7 @@
     - {author}
     - github.com/{github_username}
 
-"""
+""",
 			)
 
 print(f"Wrote recipe to {recipe_dir / 'meta.yaml'}")

diff --git a/tox.ini b/tox.ini
@@ -29,7 +29,7 @@ requires =
     pip>=21,!=22.2
     tox-envlist>=0.2.1
     tox~=3.0
-    virtualenv!=20.16.0
+    virtualenv!=20.16.0,<20.39
 
 [envlists]
 test = py37, py38, py39, py310
@@ -90,22 +90,24 @@ 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
+    git+https://github.com/python-formate/flake8-noqa.git@v1.2.2-python-formate.0
     flake8-pyi>=20.10.0,<=22.8.0
     flake8-pytest-style>=1.3.0,<2
     flake8-quotes>=3.3.0
     flake8-slots>=0.1.0
     flake8-sphinx-links>=0.0.4
     flake8-strftime>=0.1.1
     flake8-typing-imports>=1.10.0
+    flake8-params>=0.1.0
+    flake8-unused-fstrings>=2.0.0
+    git+https://github.com/python-formate/flake8-commas.git@4.0.0-python-formate.0
     git+https://github.com/domdfcoding/restructuredtext-lint.git@fix-deprecations
     git+https://github.com/domdfcoding/flake8-rst-docstrings-sphinx.git
     git+https://github.com/domdfcoding/flake8-rst-docstrings.git
     git+https://github.com/python-formate/flake8-unused-arguments.git@magic-methods
     git+https://github.com/python-formate/flake8-missing-annotations.git
     git+https://github.com/domdfcoding/pydocstyle.git@stub-functions
     pygments>=2.7.1
-    importlib_metadata<4.5.0; python_version<'3.8'
 commands = python3 -m flake8_rst_docstrings_sphinx notebook2script tests --allow-toolbox {posargs}
 
 [testenv:perflint]
@@ -164,11 +166,11 @@ rst-directives =
     license-info
 rst-roles = choosealicense
 per-file-ignores =
-    notebook2script/pointless_checker/__init__.py: PRM002
-    notebook2script/pointless_checker/base.py: PRM002
-    notebook2script/pointless.py: PRM002
     tests/*: 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 PRM001 PRM002 PRM003
     */*.pyi: 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 PRM001 PRM002 PRM003
+    notebook2script/pointless.py: PRM002
+    notebook2script/pointless_checker/__init__.py: PRM002
+    notebook2script/pointless_checker/base.py: PRM002
 pytest-parametrize-names-type = csv
 inline-quotes = "
 multiline-quotes = """
-Original file line number
+Diff line change
@@ Expand Up / @@ -84,7 +84,7 @@ @@
         - {author}
         - github.com/{github_username}
-    """
+    """,
     			)
     print(f"Wrote recipe to {recipe_dir / 'meta.yaml'}")
@@ Expand Down @@