documenteer 2.0.0a3__tar.gz → 2.0.0a4__tar.gz

{documenteer-2.0.0a3 → documenteer-2.0.0a4}/.github/workflows/ci-cron.yaml

@@ -5,11 +5,12 @@
 name: Periodic CI
 
 env:
-  PYTHON_VERSION: "3.12"
+  PYTHON_VERSION: "3.13"
 
 "on":
   schedule:
     - cron: "0 12 * * 1"
+  workflow_dispatch: {}
 
 jobs:
   lint:
@@ -44,6 +45,7 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
           tox-envs: 'lint'
           use-cache: false
+          tox-plugins: tox-uv
 
       - name: Report status
         if: failure()
@@ -61,7 +63,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.11"
           - "3.12"
           - "3.13"
         sphinx-version:
@@ -89,10 +90,8 @@ jobs:
           npm install
           npm run build
 
-      - name: Install graphviz
-        run: |
-          sudo apt-get update
-          sudo apt-get install graphviz
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
 
       - name: Run tests in tox
         uses: lsst-sqre/run-tox@v1
@@ -100,6 +99,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           tox-envs: "typing-sphinx${{ matrix.sphinx-version }},py-test-sphinx${{ matrix.sphinx-version }},demo"
           use-cache: false
+          tox-plugins: tox-uv
 
       - name: Report status
         if: failure()
@@ -119,12 +119,32 @@ jobs:
         with:
           fetch-depth: 0 # full history for setuptools_scm
 
+      - uses: actions/setup-node@v4
+        with:
+          cache: 'npm'
+          node-version-file: '.nvmrc'
+
+      - name: Authenticate GitHub Packages
+        run: |
+          echo "//npm.pkg.github.com/:_authToken=${NPM_PKG_TOKEN}" > ~/.npmrc
+        env:
+          NPM_PKG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: npm install and build
+        run: |
+          npm install
+          npm run build
+
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
+
       - name: Build docs in tox
         uses: lsst-sqre/run-tox@v1
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           tox-envs: "docs,docs-lint"
           use-cache: false
+          tox-plugins: tox-uv
 
       - name: Report status
         if: failure()
@@ -160,9 +180,8 @@ jobs:
           npm run build
 
       - name: Build and publish
-        uses: lsst-sqre/build-and-publish-to-pypi@v2
+        uses: lsst-sqre/build-and-publish-to-pypi@v3
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
           upload: false
 
       - name: Report status

{documenteer-2.0.0a3 → documenteer-2.0.0a4}/.github/workflows/ci.yaml

@@ -1,7 +1,7 @@
 name: CI
 
 env:
-  PYTHON_VERSION: '3.12' # Default Python version
+  PYTHON_VERSION: '3.13' # Default Python version
 
 'on':
   push:
@@ -50,6 +50,7 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           tox-envs: 'lint'
+          tox-plugins: tox-uv
 
   test:
     runs-on: ubuntu-latest
@@ -57,7 +58,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - '3.11'
           - '3.12'
           - '3.13'
         sphinx-version:
@@ -85,16 +85,15 @@ jobs:
           npm install
           npm run build
 
-      - name: Install graphviz
-        run: |
-          sudo apt-get update
-          sudo apt-get install graphviz
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
 
       - name: Run tox
         uses: lsst-sqre/run-tox@v1
         with:
           python-version: ${{ matrix.python-version }}
           tox-envs: 'py-test-sphinx${{ matrix.sphinx-version }},typing-sphinx${{ matrix.sphinx-version }},demo'
+          tox-plugins: tox-uv
 
   docs:
     runs-on: ubuntu-latest
@@ -104,14 +103,31 @@ jobs:
         with:
           fetch-depth: 0 # full history for setuptools_scm
 
-      - name: Install Graphviz
-        run: sudo apt-get install graphviz
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
+
+      - uses: actions/setup-node@v4
+        with:
+          cache: 'npm'
+          node-version-file: '.nvmrc'
+
+      - name: Authenticate GitHub Packages
+        run: |
+          echo "//npm.pkg.github.com/:_authToken=${NPM_PKG_TOKEN}" > ~/.npmrc
+        env:
+          NPM_PKG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: npm install and build
+        run: |
+          npm install
+          npm run build
 
       - name: Run tox
         uses: lsst-sqre/run-tox@v1
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           tox-envs: 'docs,docs-lint'
+          tox-plugins: tox-uv
 
       # Only attempt documentation uploads for tagged releases and pull
       # requests from ticket branches in the same repository.  This avoids
@@ -136,10 +152,25 @@ jobs:
         with:
           fetch-depth: 0 # full history for setuptools_scm
 
+      - uses: actions/setup-node@v4
+        with:
+          cache: 'npm'
+          node-version-file: '.nvmrc'
+
+      - name: Authenticate GitHub Packages
+        run: |
+          echo "//npm.pkg.github.com/:_authToken=${NPM_PKG_TOKEN}" > ~/.npmrc
+        env:
+          NPM_PKG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: npm install and build
+        run: |
+          npm install
+          npm run build
+
       - name: Build and publish
-        uses: lsst-sqre/build-and-publish-to-pypi@v2
+        uses: lsst-sqre/build-and-publish-to-pypi@v3
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
           upload: "false"
 
   pypi-publish:
@@ -163,12 +194,16 @@ jobs:
           cache: 'npm'
           node-version-file: '.nvmrc'
 
+      - name: Authenticate GitHub Packages
+        run: |
+          echo "//npm.pkg.github.com/:_authToken=${NPM_PKG_TOKEN}" > ~/.npmrc
+        env:
+          NPM_PKG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
       - name: npm install and build
         run: |
           npm install
           npm run build
 
       - name: Build and publish
-        uses: lsst-sqre/build-and-publish-to-pypi@v2
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
+        uses: lsst-sqre/build-and-publish-to-pypi@v3

documenteer-2.0.0a4/Makefile

@@ -0,0 +1,25 @@
+.PHONY: help
+help:
+	@echo "Make command reference"
+	@echo "  make init ........ (initialize for development)"
+	@echo "  make clean ....... (clean up build artifacts)"
+	@echo "  make update-deps . (update dependencies and pre-commit hooks)"
+
+.PHONY: init
+init:
+	rm -rf .tox
+	uv pip install --upgrade pre-commit tox tox-uv scriv
+	uv pip install -e ".[technote,pipelines]" --group dev
+	pre-commit install
+
+.PHONY: clean
+clean:
+	rm -rf .tox
+	rm -rf docs/_build
+	rm -rf docs/dev/api/contents/*.rst
+	make -C demo/rst-technote clean
+
+.PHONY: update-deps
+update-deps:
+	uv pip install --upgrade pre-commit
+	pre-commit autoupdate

{documenteer-2.0.0a3/src/documenteer.egg-info → documenteer-2.0.0a4}/PKG-INFO

@@ -1,29 +1,8 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: documenteer
-Version: 2.0.0a3
+Version: 2.0.0a4
 Summary: Rubin Observatory / LSST Sphinx documentation tools, extensions, and configurations.
-License: The MIT License (MIT)
-        
-        Copyright (c) 2015-2022 Association of Universities for Research in Astronomy, Inc. (AURA)
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Homepage, https://documenteer.lsst.io
 Project-URL: Source, https://github.com/lsst-sqre/documenteer
 Keywords: rubin,lsst
@@ -31,51 +10,39 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Framework :: Sphinx :: Extension
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Documentation
 Classifier: Topic :: Documentation :: Sphinx
 Classifier: Typing :: Typed
-Requires-Python: >=3.11
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
+License-File: licenses/README.md
+License-File: licenses/astropy-helpers.txt
+License-File: licenses/sphinx-issue.txt
+License-File: licenses/sphinx.txt
+License-File: licenses/sphinxcontrib-redoc.txt
 Requires-Dist: docutils>=0.20
 Requires-Dist: Sphinx<8.2,>=7
 Requires-Dist: PyYAML
 Requires-Dist: GitPython
 Requires-Dist: requests
 Requires-Dist: click
-Requires-Dist: sphinxcontrib-bibtex>=2.0.0
-Requires-Dist: setuptools
+Requires-Dist: sphinxcontrib-bibtex>=2.6.5
+Requires-Dist: pybtex>=0.25.0
 Requires-Dist: pydantic>=2.0.0
 Requires-Dist: urllib3
 Requires-Dist: pylatexenc
 Requires-Dist: tomlkit
-Provides-Extra: dev
-Requires-Dist: twine; extra == "dev"
-Requires-Dist: coverage[toml]; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-mock; extra == "dev"
-Requires-Dist: lxml; extra == "dev"
-Requires-Dist: cssselect; extra == "dev"
-Requires-Dist: defusedxml; extra == "dev"
-Requires-Dist: sphinx-click; extra == "dev"
-Requires-Dist: sphinxcontrib-autoprogram; extra == "dev"
-Requires-Dist: types-setuptools; extra == "dev"
-Requires-Dist: types-requests; extra == "dev"
-Requires-Dist: types-PyYAML; extra == "dev"
-Requires-Dist: types-docutils; extra == "dev"
-Requires-Dist: types-mock; extra == "dev"
 Provides-Extra: guide
 Requires-Dist: autodoc_pydantic; extra == "guide"
 Requires-Dist: sphinx_design; extra == "guide"
-Requires-Dist: pydata-sphinx-theme<0.13.0,>=0.10.0; extra == "guide"
+Requires-Dist: pydata-sphinx-theme<0.17.0,>=0.16.1; extra == "guide"
 Requires-Dist: sphinx-autodoc-typehints; extra == "guide"
 Requires-Dist: sphinx-automodapi; extra == "guide"
 Requires-Dist: sphinx-copybutton; extra == "guide"
@@ -86,18 +53,19 @@ Requires-Dist: myst-nb; extra == "guide"
 Requires-Dist: markdown-it-py[linkify]; extra == "guide"
 Requires-Dist: sphinxcontrib-mermaid>=1; extra == "guide"
 Requires-Dist: sphinxext-opengraph; extra == "guide"
-Requires-Dist: sphinxcontrib-redoc; extra == "guide"
 Requires-Dist: sphinxcontrib-jquery; extra == "guide"
 Requires-Dist: sphinxext-rediraffe; extra == "guide"
 Requires-Dist: sphinxcontrib-youtube; extra == "guide"
+Requires-Dist: sphinx-favicon; extra == "guide"
 Provides-Extra: technote
 Requires-Dist: technote<0.10.0,>=0.9.0; extra == "technote"
 Requires-Dist: sphinx-prompt; extra == "technote"
-Requires-Dist: sphinxcontrib-mermaid; extra == "technote"
+Requires-Dist: sphinxcontrib-mermaid>=1; extra == "technote"
 Requires-Dist: sphinx-diagrams; extra == "technote"
 Requires-Dist: sphinx_design; extra == "technote"
 Requires-Dist: myst-nb; extra == "technote"
 Requires-Dist: sphinxcontrib-youtube; extra == "technote"
+Dynamic: license-file
 
 [![Documentation](https://img.shields.io/badge/documenteer-lsst.io-brightgreen.svg)](https://documenteer.lsst.io)
 [![PyPI](https://img.shields.io/pypi/v/documenteer.svg?style=flat-square)](https://pypi.python.org/pypi/documenteer)

documenteer-2.0.0a4/changelog.d/20250224_102742_jsick_graphviz_ci.md

@@ -0,0 +1,17 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+-
+
+### New features
+
+-
+
+### Bug fixes
+
+-
+
+### Other changes
+
+- Adopt [ts-graphviz/setup-graphviz](https://github.com/ts-graphviz/setup-graphviz) for installing Graphviz in GitHub Actions CI workflows.

documenteer-2.0.0a4/changelog.d/20250625_141008_jsick_DM_51536.md

@@ -0,0 +1,17 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+- Dropped support for Python 3.11. Python 3.12 or later is now required.
+
+### New features
+
+-
+
+### Bug fixes
+
+-
+
+### Other changes
+
+- Updated how license information is encoded in `pyproject.toml`.

documenteer-2.0.0a4/changelog.d/20250630_113114_jsick_update_theme.md

@@ -0,0 +1,18 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+-
+
+### New features
+
+- Update to pydata-sphinx-theme 0.16
+- Adopt [sphinx-favicon](https://sphinx-favicon.readthedocs.io/en/stable/index.html) for managing favicons in user guides.
+
+### Bug fixes
+
+-
+
+### Other changes
+
+- Switch to dependency groups for development dependencies in `pyproject.toml`. With this change, Documenteer no longer publishes a `dev` extra to PyPI.

documenteer-2.0.0a4/changelog.d/20250703_103944_jsick_DM_51688.md

@@ -0,0 +1,23 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+-
+
+### New features
+
+- For embedding a redoc page for API documentation, Documenteer now provides its own `documenteer.ext.redoc` extension. This replaces the previous `sphinxcontrib.redoc` extension, which is not being actively maintained. This new extension is automatically configured through `documenteer.conf.guide`, and therefore should not require any changes for most user guide projects. `documenteer.ext.redoc` drops support for referencing an OpenAPI specification file from a web URL. FastAPI projects can use `documenteer.ext.openapi` to generate an OpenAPI specification file from the FastAPI app.
+
+- In Markdown content for technotes and guides, Mermaid diagrams can now be written in code fences using the `mermaid` language tag. This is also supported in GitHub's Markdown renderer. The traditional method of using the `mermaid` directive syntax is still supported.
+
+- Documenteer's `technote` and `guide` configurations now ignore pending Sphinx API deprecation warnings by default. This is to prevent the warnings from cluttering the build output, and are only useful for the Documenteer developers since the Sphinx version is constrained by Documenteer.
+
+### Bug fixes
+
+-
+
+### Other changes
+
+- Documenteer no longer depends on setuptools as a runtime dependency thanks to pybtex version 0.25 and `documenteer.ext.redoc`.
+
+- Documenteer's Sphinx extensions now provide proper extension metadata to support version-based cache busting and parallel builds.

documenteer-2.0.0a4/changelog.d/20250710_133037_jsick_DM_51727.md

@@ -0,0 +1,17 @@
+<!-- Delete the sections that don't apply -->
+
+### Backwards-incompatible changes
+
+-
+
+### New features
+
+- The `documenteer` `add-authors` and `sync-authors` CLI commands now uses the Ook web API to get author information, rather than directly reading `authordb.yaml` from lsst/lsst-texmf.
+
+### Bug fixes
+
+-
+
+### Other changes
+
+-

{documenteer-2.0.0a3 → documenteer-2.0.0a4}/docs/Makefile

@@ -1,7 +1,7 @@
 # Makefile for Sphinx documentation
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -n -W
+SPHINXOPTS    = -n
 SPHINXBUILD   = sphinx-build
 BUILDDIR      = _build
 

documenteer-2.0.0a4/licenses/README.md

@@ -0,0 +1,9 @@
+This directory contains third-party license information for projects that Documenteer is derived from or has adapted code from.
+See individual source files for specific attribution.
+
+See ../LICENSE for Documenteer's main license information.
+
+- sphinx.txt — https://www.sphinx-doc.org
+- sphinx-issue.txt — https://github.com/sloria/sphinx-issues
+- astropy-helpers - https://github.com/astropy/astropy-helpers
+- sphinxcontrib-redoc - https://sphinxcontrib-redoc.readthedocs.io/

documenteer-2.0.0a4/licenses/sphinxcontrib-redoc.txt

@@ -0,0 +1,23 @@
+Copyright (c) 2017, Ihor Kalnytskyi <ihor@kalnytskyi.com>.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{documenteer-2.0.0a3 → documenteer-2.0.0a4}/pyproject.toml

@@ -2,7 +2,12 @@
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 name = "documenteer"
 description = "Rubin Observatory / LSST Sphinx documentation tools, extensions, and configurations."
-license = { file = "LICENSE" }
+license = "MIT"
+license-files = [
+    "LICENSE",
+    "licenses/README.md",
+    "licenses/*.txt",
+]
 readme = "README.md"
 keywords = ["rubin", "lsst"]
 # https://pypi.org/classifiers/
@@ -11,19 +16,17 @@ classifiers = [
     "Environment :: Console",
     "Framework :: Sphinx :: Extension",
     "Intended Audience :: Developers",
-    "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
     "Operating System :: POSIX",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Topic :: Documentation",
     "Topic :: Documentation :: Sphinx",
     "Typing :: Typed",
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 dynamic = ["version"]
 dependencies = [
     "docutils>=0.20",  # solves an extra div bug with the bibliography directive
@@ -32,8 +35,8 @@ dependencies = [
     "GitPython",
     "requests",
     "click",
-    "sphinxcontrib-bibtex>=2.0.0", # for pybtex extension
-    "setuptools", # for pkg_resources, used by pybtex
+    "sphinxcontrib-bibtex>=2.6.5", # drops setuptools hack
+    "pybtex>=0.25.0", # drops setuptools dependency
     "pydantic >= 2.0.0",
     "urllib3",
     "pylatexenc",
@@ -41,32 +44,11 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = [
-    "twine",
-    # Documenteer's testing and deployment deps
-    "coverage[toml]",
-    "pytest",
-    "pytest-mock",
-    # Test depedendencies for analyzing HTML output
-    "lxml",
-    "cssselect",
-    "defusedxml",  # used by Sphinx but not declared as a dependency
-    # Extensions for documenteer's own docs
-    "sphinx-click",
-    "sphinxcontrib-autoprogram",
-    # Type stubs
-    "types-setuptools",
-    "types-requests",
-    "types-PyYAML",
-    "types-docutils",
-    "types-mock",
-    # Testing dependencies
-]
 guide = [
     # Theme and extensions for Rubin user guide projects
     "autodoc_pydantic",
     "sphinx_design",
-    "pydata-sphinx-theme>=0.10.0,<0.13.0",
+    "pydata-sphinx-theme>=0.16.1,<0.17.0",
     "sphinx-autodoc-typehints",
     "sphinx-automodapi",
     "sphinx-copybutton",
@@ -77,22 +59,53 @@ guide = [
     "markdown-it-py[linkify]",
     "sphinxcontrib-mermaid>=1",
     "sphinxext-opengraph",
-    "sphinxcontrib-redoc",
     "sphinxcontrib-jquery",
     "sphinxext-rediraffe",
-    "sphinxcontrib-youtube"
+    "sphinxcontrib-youtube",
+    "sphinx-favicon"
 ]
 technote = [
     # Theme and extensions for technotes
     "technote>=0.9.0,<0.10.0",
     "sphinx-prompt",
-    "sphinxcontrib-mermaid",
+    "sphinxcontrib-mermaid>=1",
     "sphinx-diagrams",
     "sphinx_design",
     "myst-nb",
     "sphinxcontrib-youtube"
 ]
 
+[dependency-groups]
+test = [
+    "coverage[toml]",
+    "pytest",
+    "pytest-mock",
+    "pytest-responses",
+    # Test depedendencies for analyzing HTML output
+    "lxml",
+    "cssselect",
+    "defusedxml",  # used by Sphinx but not declared as a dependency
+]
+typing = [
+    "mypy",
+    "types-setuptools",
+    "types-requests",
+    "types-PyYAML",
+    "types-docutils",
+    "types-mock",
+    {include-group = "test"},  # include test dependencies for type checking
+]
+docs = [
+    # Extensions for documenteer's own docs
+    "sphinx-click",
+    "sphinxcontrib-autoprogram",
+]
+dev = [
+    {include-group = "test"},  # include test dependencies
+    {include-group = "typing"},  # include type checking dependencies
+    {include-group = "docs"},  # include docs dependencies
+]
+
 [project.urls]
 Homepage = "https://documenteer.lsst.io"
 Source = "https://github.com/lsst-sqre/documenteer"
@@ -166,6 +179,7 @@ warn_redundant_casts = true
 warn_unreachable = true
 warn_unused_ignores = true
 plugins = ["pydantic.mypy"]
+exclude = ["tests/roots/.*"]
 
 [tool.ruff]
 extend = "ruff-shared.toml"
@@ -208,9 +222,6 @@ extend-ignore = [
     "INP001",
     "D100"
 ]
-"src/documenteer/cli.py" = [
-    "T201",  # CLI scripts can print
-]
 
 [tool.ruff.lint.isort]
 known-first-party = ["documenteer", "tests"]