diff --git a/.codecov.yml b/.codecov.yml
index d61d211..ba90ed6 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -13,4 +13,5 @@ comment:
   flags: []
   paths: []
 ignore:
-  - "openff/pablo/_version.py"
+  - "examples/"
+  - "docs/"
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..e5f2055
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+
+    groups:
+      dependencies:
+        patterns:
+          - "*"
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
new file mode 100644
index 0000000..75db4ad
--- /dev/null
+++ b/.github/workflows/lint.yaml
@@ -0,0 +1,47 @@
+name: GH Actions Lints
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  # Specific group naming so CI is only cancelled
+  # within same PR or on merge to main
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  lints:
+    if: "github.repository == 'openforcefield/openff-pablo'"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build information
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - uses: prefix-dev/setup-pixi@v0.8.0
+        with:
+          pixi-version: v0.50.0
+          activate-environment: lint
+
+      - run: ruff check openff
+
+      - run: pixi r typecheck
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/tests.yaml
similarity index 52%
rename from .github/workflows/gh-ci.yaml
rename to .github/workflows/tests.yaml
index 95483e9..5d20ff4 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.github/workflows/tests.yaml
@@ -1,4 +1,4 @@
-name: GH Actions CI
+name: GH Actions Tests
 on:
   push:
     branches:
@@ -23,14 +23,13 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  main-tests:
+  tests:
     if: "github.repository == 'openforcefield/openff-pablo'"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -43,38 +42,18 @@ jobs:
           df -h
           ulimit -a
 
-      - name: Install environment
-        uses: mamba-org/setup-micromamba@v2
+      - uses: prefix-dev/setup-pixi@v0.8.0
         with:
-          environment-file: devtools/conda-envs/test_env.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
+          pixi-version: v0.52.0
+          environments: test
 
-      - name: Install package
-        run: |
-          python --version
-          python -m pip install .
-
-      - name: Python information
-        run: |
-          which python
-          which pip
-          pip list
-          micromamba info
-          micromamba list
+      - run: pixi r slowtest -v --color=yes --cov=openff/pablo --cov-append --cov-report=xml
 
-      - name: Type check
-        if: runner.os == 'Linux'
-        run: |
-          basedpyright openff
+      - run: pixi r doctest -v --color=yes
 
-      - name: Run tests
-        run: |
-          pytest -n auto -v --color=yes
-
-    # - name: codecov
-    #   uses: codecov/codecov-action@v3
-    #   with:
-    #     file: coverage.xml
-    #     name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-    #     verbose: True
+      - name: Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          disable_search: true
+          fail_ci_if_error: false
diff --git a/.gitignore b/.gitignore
index df7a46f..79577a4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -116,4 +116,8 @@ poetry.lock
 # zed
 .zed/
 
+# pixi
+.pixi
+pixi.lock
+
 .ccd_cache
diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml
deleted file mode 100644
index bcf459b..0000000
--- a/devtools/conda-envs/docs_env.yaml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: pablo-docs
-channels:
-  - conda-forge
-dependencies:
-  # Base depends
-  - python>=3.11,<3.13
-  - pip
-
-  # Documentation
-  - myst-parser
-  - sphinx==6.1.2
-  - sphinx-notfound-page
-  - autodoc-pydantic
-  - sphinx-click
-
-  # Imports
-  - openff-units
-  - openff-toolkit>=0.17.0
-  - polars
-  - openmm
-  - mdtraj
-  - numpy
-  - nglview
-  - typer>=0.14
-  - mdanalysis
-  - rdkit
-  - pyxdg
-  - rustworkx
-  - gemmi
-
-  #  Pip-only installs
-  - pip:
-      - git+https://github.com/openforcefield/openff-sphinx-theme.git@main
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
deleted file mode 100644
index 534d55e..0000000
--- a/devtools/conda-envs/test_env.yaml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: pablo-test
-channels:
-  - conda-forge
-dependencies:
-  # Base depends (runtime and imports)
-  - pip
-  - python>=3.11
-  - openff-toolkit-base>=0.17.0
-  - rdkit
-  - openmm
-  - pyxdg
-  - rustworkx
-  - gemmi
-
-  # Lints
-  - basedpyright
-  - ruff
-
-  # Testing
-  - pytest
-  - pytest-xdist
-  - pytest-socket
-  # - pytest-cov
-  # - codecov
-
-  # Examples
-  - jupyterlab>=4
-  - ipywidgets>=8
-  - jupyterlab_execute_time
-  - jupyterlab-lsp
-  - jupyterlab_rise
-  - jedi-language-server
-  - jupyterlab_code_formatter
-  - black
-  - isort
-  - snakeviz
-  - nglview>=3.0.6,<3.1.0
-  - pdbfixer
-  - mdanalysis
-  - openff-interchange
-  - ambertools
-  - numpy
-  - pymol-open-source
-  - openff-nagl-base >= 0.5.2
-  - openff-nagl-models
-  - pytorch-cpu >= 2.6
-
-  - pip:
-      - git+https://github.com/openforcefield/openff-toolkit.git@main
diff --git a/openff/pablo/_utils.py b/openff/pablo/_utils.py
index e30f539..429fb76 100644
--- a/openff/pablo/_utils.py
+++ b/openff/pablo/_utils.py
@@ -18,7 +18,6 @@
 import rdkit.Chem.Draw
 import rdkit.Chem.rdDepictor
 import rdkit.Geometry
-from IPython.display import SVG
 from openff.toolkit import Molecule
 from openff.toolkit.topology._mm_molecule import _SimpleMolecule
 from openff.toolkit.topology.molecule import MoleculeLike
@@ -348,7 +347,7 @@ def draw_molecule(
     emphasize_atoms: list[int] | None = None,
     explicit_hydrogens: bool | None = None,
     color_by_element: bool | None = None,
-) -> SVG:
+):
     """Draw a molecule
 
     Parameters
@@ -392,6 +391,7 @@ def draw_molecule(
         When an atom or bond in highlight_atoms or highlight_bonds is missing
         from the image, including when it is present in the molecule but hidden.
     """
+    from IPython.display import SVG
 
     # We're working in RDKit
     try:
diff --git a/openff/pablo/residue.py b/openff/pablo/residue.py
index 51cc4c8..975a77e 100644
--- a/openff/pablo/residue.py
+++ b/openff/pablo/residue.py
@@ -542,6 +542,41 @@ def from_smiles(
         virtual_sites
             Virtual sites expected by the residue. See
             :py:data:`openff.pablo.ResidueDefinition.virtual_sites`
+
+        Examples
+        --------
+
+        To create a ``ResidueDefinition`` for a neutral cysteine residue:
+
+        >>> from openff.pablo.residue import ResidueDefinition
+        >>> from openff.pablo.chem import DISULFIDE_BOND, PEPTIDE_BOND
+        >>>
+        >>> ResidueDefinition.from_smiles(
+        ...     residue_name="CYS",
+        ...     mapped_smiles=r"[N:1]([C@@:2]([C:5]([S:6][H:13])([H:11])[H:12])([C:3]([O:7][H:14])=[O:4])[H:10])([H:8])[H:9]",
+        ...     atom_names={
+        ...         1: "N",
+        ...         2: "CA",
+        ...         3: "C",
+        ...         4: "O",
+        ...         5: "CB",
+        ...         6: "SG",
+        ...         7: "OXT",
+        ...         8: "H",
+        ...         9: "H2",
+        ...         10: "HA",
+        ...         11: "HB2",
+        ...         12: "HB3",
+        ...         13: "HG",
+        ...         14: "HXT",
+        ...     },
+        ...     leaving_atoms={7, 14, 13, 9},
+        ...     crosslink=DISULFIDE_BOND,
+        ...     linking_bond=PEPTIDE_BOND,
+        ...     description="CYSTEINE",
+        ... )
+        ResidueDefinition(...)
+
         """
         molecule = Molecule.from_mapped_smiles(
             mapped_smiles,
diff --git a/pyproject.toml b/pyproject.toml
index 878f132..3b8fb9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,19 +27,91 @@ dynamic = [
   "version",
 ]
 
-[project.optional-dependencies]
-test = [
-  "pytest>=6.0",
-  "pytest-xdist>=2.5",
-  "pytest-cov>=3.0",
-]
-doc = [
-  "sphinx",
-]
+[project.urls]
+source = "https://github.com/openforcefield/openff-pablo"
+documentation = "https://openff-pablo.readthedocs.io"
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64", "osx-64"]
+
+[tool.pixi.dependencies]
+openff-toolkit-base = ">=0.17.0"
+rdkit = "*"
+openmm = "*"
+numpy = "*"
+rustworkx = "*"
+pyxdg = "*"
+gemmi = "*"
+
+[tool.pixi.pypi-dependencies]
+openff-pablo = { path = ".", editable = true }
+
+[tool.pixi.feature.doc.dependencies]
+myst-parser = "*"
+sphinx = "==6.1.2"
+sphinx-notfound-page = "*"
+autodoc-pydantic = "*"
+sphinx-click = "*"
+
+[tool.pixi.feature.doc.pypi-dependencies]
+openff-sphinx-theme = { git = "https://github.com/openforcefield/openff-sphinx-theme.git", rev = "main" }
+
+[tool.pixi.feature.test.dependencies]
+pytest = "*"
+pytest-xdist = "*"
+pytest-cov = "*"
+codecov = "*"
+
+[tool.pixi.feature.example.dependencies]
+jupyterlab = ">=4"
+ipywidgets = ">=8"
+jupyterlab_execute_time = "*"
+jupyterlab-lsp = "*"
+jupyterlab_rise = "*"
+jedi-language-server = "*"
+jupyterlab_code_formatter = "*"
+black = "*"
+isort = "*"
+snakeviz = "*"
+nglview = ">=3.0.6,<3.1.0"
+
+[tool.pixi.feature.lint.dependencies]
+basedpyright = "*"
+ruff = "*"
+
+[tool.pixi.environments]
+test = { features = ["test", "test-tasks"], solve-group = "default" }
+doc = { features = ["doc", "doc-tasks"], solve-group = "default" }
+example = { features = ["example", "example-tasks"], solve-group = "default" }
+lint = { features = ["lint", "test", "doc", "example"], solve-group = "default" }
 
-# [project.urls]
-# source = "https://github.com/openforcefield/openff-pablo"
-# documentation = "https://openff-pablo.readthedocs.io"
+[tool.pixi.feature.test-tasks.tasks.slowtest]
+cmd = "pytest -n auto"
+cwd = "."
+
+[tool.pixi.feature.test-tasks.tasks.test]
+cmd = "pytest -n auto -m 'not slow'"
+cwd = "."
+
+[tool.pixi.feature.test-tasks.tasks.doctest]
+cmd = "pytest -n auto --doctest-glob 'docs/*.md' --doctest-glob 'docs/*.rst' --doctest-modules --ignore openff/pablo/_tests/ --ignore-glob docs/*.py openff/ docs/"
+cwd = "."
+[tool.pixi.feature.doc-tasks.tasks.doc]
+cmd = "sphinx-build -j auto docs docs/_build/html"
+cwd = "."
+
+[tool.pixi.feature.doc-tasks.tasks.watchdoc]
+cmd = "watchexec --on-busy-update restart -w openff -w docs --print-events 'sphinx-build -j auto docs docs/_build/html'"
+cwd = "."
+
+[tool.pixi.feature.example-tasks.tasks.lab]
+cmd = "jupyter lab"
+cwd = "examples"
+
+[tool.pixi.feature.lint.tasks.typecheck]
+cmd = "basedpyright openff"
+cwd = "."
 
 [tool.versioningit]
 default-version = "v0.0.0.dev0+VERSIONMISSING"
@@ -60,12 +132,8 @@ include = ["openff.*"]
 include = ["openff"]
 exclude = [
   ".soap",
-  "docs",
-  "examples",
-  "**/_tests/data",
   "**/node_modules",
   "**/__pycache__",
-  "**/.*",
 ]
 "ignore" = [
   ".soap",
@@ -76,6 +144,8 @@ exclude = [
   "**/__pycache__",
   "**/.*",
 ]
+"venvPath" = ".pixi/envs"
+"venv" = "lint"
 
 typeCheckingMode = "strict"
 
@@ -101,5 +171,10 @@ namespace-packages = ["openff/pablo/"]
 ignore = ["E731"]
 
 [tool.ruff.lint.isort]
-known-third-party = ["openff.toolkit", "openff.utilities", "openff.units"]
+known-third-party = [
+  "openff.toolkit",
+  "openff.utilities",
+  "openff.units",
+  "openff.utilities",
+]
 known-first-party = ["openff.pablo"]
diff --git a/readthedocs.yaml b/readthedocs.yaml
index c9ba525..4e3bde5 100644
--- a/readthedocs.yaml
+++ b/readthedocs.yaml
@@ -5,16 +5,17 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
-
-python:
-  install:
-    - method: pip
-      path: .
-
-sphinx:
-  configuration: docs/conf.py
-  fail_on_warning: true
-
-conda:
-  environment: devtools/conda-envs/docs_env.yaml
+    python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    pre_install:
+      # https://docs.readthedocs.com/platform/stable/build-customization.html#avoid-having-a-dirty-git-index
+      - git update-index --assume-unchanged pyproject.toml docs/conf.py
+    install:
+      - pixi install -e doc
+    build:
+      html:
+        - pixi run -e doc sphinx-build -W -T -b html docs $READTHEDOCS_OUTPUT/html