From 21c514b7d04d2a06e02790d6c952ae0976837ef5 Mon Sep 17 00:00:00 2001
From: Shane Steinert-Threlkeld <ssshanest@gmail.com>
Date: Thu, 5 Mar 2026 14:29:01 -0800
Subject: [PATCH 1/6] Prepare ULTK for release: fix packaging, source bugs, and
 tests
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

## Packaging

- Bump version from invalid `0.0.1c` to PEP 440-compliant `0.1.0`
- Add `tqdm` to runtime dependencies (imported by `effcomm/optimization.py`
  and `language/sampling.py` but was missing from `pyproject.toml`)
- Move dev-only tools (`mypy`, `pytest`, `scipy-stubs`) out of `dependencies`
  and into a `[dependency-groups] dev` section so they are not installed by
  end-users of the library
- Delete `setup.py` legacy shim, which conflicted with the `uv_build` backend

## Source-code bug fixes

- `language/sampling.py` `all_meanings()`: fix `Meaning` construction to use
  the tuple-based API (boolean values indexed parallel to `universe.referents`)
  instead of passing a raw referent subset-tuple, which broke after the
  `FrozenDict`→tuple refactor
- `language/language.py` `Expression` default: replace
  `Meaning(FrozenDict(), ...)` with `Meaning(tuple(), ...)` and remove the
  now-unused `FrozenDict` import
- `language/grammar/grammar.py`:
  - `complement()`: replace the non-existent `.referents` attribute with
    `tuple(not val for val in self.meaning.mapping)`
  - `draw_referent()`: replace `.referents` attribute access with correct
    `zip(universe.referents, mapping)` iteration

## Test fixes

- `test_language.py`: replace all `FrozenDict({ref: bool})` `Meaning`
  constructors with `tuple(bool for ref in ...)`, fix `isAnimal` helper to
  iterate via `zip(universe.referents, mapping)` instead of dict `.items()`,
  rename duplicate `test_exp_subset` method to `test_exp_can_express_positive`
  so both positive and negative can_express tests actually run, remove unused
  `FrozenDict` import
- `test_grammar.py`: fix `goal_meaning` to use the tuple-based `Meaning` API

## CI workflows

- Replace `actions/setup-python` + `pip` with `astral-sh/setup-uv@v5` + `uv`
  in all three workflows (`test.yml`, `docs.yml`, `pypi-publish.yml`)
- `test.yml`: `uv sync --group dev` + `uv run pytest src/tests/`
- `docs.yml`: `uv sync` + `uv run pdoc ...`; upgrade to Python 3.13
- `pypi-publish.yml`: replace `python -m build` with `uv build`

## Documentation

- `README.md`: update install instructions to recommend `uv sync`, note
  Python 3.13 requirement, update testing section to use `uv run pytest`
- `CLAUDE.md`: update commands to use `uv sync --group dev` and
  `uv run pytest src/tests/`

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/docs.yml           | 12 ++----
 .github/workflows/pypi-publish.yml   | 11 ++---
 .github/workflows/test.yml           | 15 +++----
 CLAUDE.md                            | 64 ++++++++++++++++++++++++++++
 README.md                            | 22 ++++++++--
 pyproject.toml                       |  9 ++--
 setup.py                             |  4 --
 src/tests/test_grammar.py            |  2 +-
 src/tests/test_language.py           | 25 +++++------
 src/ultk/language/grammar/grammar.py |  7 +--
 src/ultk/language/language.py        |  3 +-
 src/ultk/language/sampling.py        |  3 +-
 uv.lock                              | 20 ++++++---
 13 files changed, 132 insertions(+), 65 deletions(-)
 create mode 100644 CLAUDE.md
 delete mode 100644 setup.py

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index c51430d5..16fcf5ef 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -19,16 +19,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
+      - uses: astral-sh/setup-uv@v5
 
-      # ADJUST THIS: install all dependencies (including pdoc)
-      - run: pip install -e .
-      - run: pip install pdoc
-      # ADJUST THIS: build your documentation into docs/.
-      # We use a custom build script for pdoc itself, ideally you just run `pdoc -o docs/ ...` here.
-      - run: pdoc src/ultk -d google --math -o ./docs
+      - run: uv sync
+      - run: uv run pdoc src/ultk -d google --math -o ./docs
 
       - uses: actions/upload-pages-artifact@v3
         with:
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
index b8fc563b..4424989b 100644
--- a/.github/workflows/pypi-publish.yml
+++ b/.github/workflows/pypi-publish.yml
@@ -13,15 +13,10 @@ jobs:
       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
     # retrieve your distributions here
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-          python-version: '3.11'
-    - name: Install package 
-      run:  pip install --upgrade build
-            pip install -e .
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v5
     - name: Build dist
-      run:  python -m build
+      run: uv build
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0eb9eba2..f40ff1d2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -6,14 +6,9 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-      - name: Install package 
-        run: pip install -e .
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Install dependencies
+        run: uv sync --group dev
       - name: Test with pytest
-        run: |
-          pip install pytest 
-          pytest
\ No newline at end of file
+        run: uv run pytest src/tests/
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 00000000..c973cad7
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,64 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+ULTK (Unnatural Language ToolKit) is a Python library for computational semantic typology research — specifically for "efficient communication" analyses that explain natural language structure in terms of competing pressures: minimizing cognitive complexity vs. maximizing communicative accuracy.
+
+## Commands
+
+```bash
+# Install all dependencies (including dev group for tests)
+uv sync --group dev
+
+# Run all tests
+uv run pytest src/tests/
+
+# Run a single test file
+uv run pytest src/tests/test_language.py
+
+# Run a single test by name
+uv run pytest src/tests/test_language.py::TestLanguage::test_name
+
+# Format code (Black is enforced via CI on PRs)
+black src/
+```
+
+Tests are discovered automatically by pytest from `src/tests/`. The CI workflow runs `uv run pytest src/tests/` from the repo root.
+
+## Architecture
+
+### Two Main Modules
+
+**`ultk.language`** — Core data structures for semantic representations:
+- `semantics.py`: `Referent` (immutable semantic object), `Universe` (collection of Referents with a prior distribution), `Meaning` (mapping from Universe to arbitrary type T — e.g., booleans for truth values)
+- `language.py`: `Expression` (form + meaning pair), `Language` (frozenset of Expressions sharing a Universe). Helper `aggregate_expression_complexity()` bridges language and effcomm.
+- `sampling.py`: Generators for all meanings, expressions, and languages from a universe — used to enumerate the full hypothesis space.
+- `grammar/`: A probabilistic context-free grammar (PCFG) framework for building expressions as programs in a Language of Thought. `grammar.py` defines `Rule` and `Grammar`/`GrammaticalExpression`; `likelihood.py` provides scoring functions; `inference.py` handles MDL/Bayesian inference.
+
+**`ultk.effcomm`** — Efficient communication analysis tools:
+- `agent.py`: RSA (Rational Speech Act) agents — `LiteralSpeaker`, `LiteralListener`, `PragmaticSpeaker`, `PragmaticListener` — represented as weight matrices.
+- `informativity.py`: `informativity()` and `communicative_success()` — compute how well a language supports communication (vectorized as `diag(prior) @ S @ R ⊙ U`).
+- `tradeoff.py`: Pareto front computation (`pareto_optimal_languages`, `non_dominated_2d`, `dominates`) for simplicity/informativeness trade-off analysis.
+- `optimization.py`: `EvolutionaryOptimizer` — iterative algorithm to approximate the Pareto frontier via mutations (`AddExpression`, `RemoveExpression`).
+- `sampling.py`: `get_hypothetical_variants()` — generates null-hypothesis languages by permuting speaker weight matrices.
+- `analysis.py`: Aggregation utilities for building results DataFrames.
+
+**`ultk.util`**:
+- `frozendict.py`: `FrozenDict` — an immutable dict used extensively as keys in frozen dataclasses.
+- `io.py`: I/O helpers.
+
+### Key Design Patterns
+
+- Core objects (`Universe`, `Meaning`, `Expression`) are **frozen/immutable** (`@dataclass(frozen=True)` or manual `_frozen` flag), enabling hashing and use as dict keys.
+- `Meaning` stores its mapping as a `tuple[T, ...]` indexed parallel to `Universe.referents`, with `_ref_to_idx` for O(1) lookup. Access via `meaning[referent]`.
+- `Language` stores expressions as a `frozenset` — order-independent, hashable.
+- Grammar rules are defined via Python type annotations; `Rule.from_callable()` introspects function signatures to build rules automatically.
+
+### Examples
+
+`src/examples/` contains complete worked analyses:
+- `indefinites/` — efficient communication analysis of indefinite pronouns
+- `modals/` — semantic universals for modals
+- `learn_quant/` — quantifier learning
diff --git a/README.md b/README.md
index 326d8606..46ee05d3 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,21 @@ Read the [documentation](https://clmbr.shane.st/ultk).
 
 ## Installing ULTK
 
-First, set up a virtual environment (e.g. via [miniconda](https://docs.conda.io/en/latest/miniconda.html), `conda create -n ultk python=3.11`, and `conda activate ultk`).
+ULTK requires Python 3.13+. We recommend using [uv](https://docs.astral.sh/uv/) to manage dependencies.
 
 1. Download or clone this repository and navigate to the root folder.
 
-2. Install ULTK (We recommend doing this inside a virtual environment)
+2. Install ULTK and all dependencies:
 
-    `pip install -e .`
+    ```
+    uv sync
+    ```
+
+    Alternatively, if you prefer pip inside an activated virtual environment:
+
+    ```
+    pip install -e .
+    ```
 
 ## Getting started
 
@@ -33,7 +41,13 @@ The source code is available on github [here](https://github.com/CLMBRs/ultk).
 
 ## Testing
 
-Unit tests are written in [pytest](https://docs.pytest.org/en/7.3.x/) and executed via running `pytest` in the `src/tests` folder.
+Unit tests are written in [pytest](https://docs.pytest.org/en/7.3.x/) and executed via:
+
+```
+uv run pytest src/tests/
+```
+
+Or, if inside an activated virtual environment: `pytest src/tests/`.
 
 ## References
 
diff --git a/pyproject.toml b/pyproject.toml
index 93b49731..0033cd37 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "ultk"
-version = "0.0.1c"
+version = "0.1.0"
 authors = [
   { name="Chris Haberland", email="haberc@uw.edu"},
   { name="Nathaniel Imel", email="nimel@uci.edu"},
@@ -16,18 +16,19 @@ classifiers = [
 ]
 license = {file = "LICENSE.txt"}
 dependencies = [
-    "mypy",
     "numpy",
     "nltk",
     "pyyaml",
     "pandas",
     "plotnine",
     "pathos",
-    "pytest",
     "scipy>=1.7.3",
-    "scipy-stubs[scipy]>=1.16.3.3",
+    "tqdm",
 ]
 
+[dependency-groups]
+dev = ["mypy", "pytest", "scipy-stubs[scipy]>=1.16.3.3"]
+
 [project.urls]
 "Homepage" = "https://clmbr.shane.st/ultk"
 "Bug Tracker" = "https://github.com/CLMBRs/ultk/issues"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 1abbd068..00000000
--- a/setup.py
+++ /dev/null
@@ -1,4 +0,0 @@
-import setuptools
-
-if __name__ == "__main__":
-    setuptools.setup()
diff --git a/src/tests/test_grammar.py b/src/tests/test_grammar.py
index ef9906ed..18664cb6 100644
--- a/src/tests/test_grammar.py
+++ b/src/tests/test_grammar.py
@@ -25,7 +25,7 @@ def test_meaning(self):
         parsed_expression = TestGrammar.grammar.parse(TestGrammar.geq2_expr_str)
         expr_meaning = parsed_expression.evaluate(TestGrammar.universe)
         goal_meaning = Meaning(
-            {referent: referent.num > 2 for referent in TestGrammar.referents},
+            tuple(referent.num > 2 for referent in TestGrammar.referents),
             TestGrammar.universe,
         )
         assert expr_meaning == goal_meaning
diff --git a/src/tests/test_language.py b/src/tests/test_language.py
index c4010877..9943e850 100644
--- a/src/tests/test_language.py
+++ b/src/tests/test_language.py
@@ -4,7 +4,6 @@
 
 from ultk.language.language import Expression, Language
 from ultk.language.semantics import Referent, Universe, Meaning
-from ultk.util.frozendict import FrozenDict
 
 
 class TestLanguage:
@@ -27,35 +26,35 @@ class TestLanguage:
     dog = Expression(
         form="dog",
         meaning=Meaning(
-            mapping=FrozenDict({ref: ref.name == "dog" for ref in uni_refs}),
+            mapping=tuple(ref.name == "dog" for ref in uni_refs),
             universe=uni,
         ),
     )
     cat = Expression(
         form="cat",
         meaning=Meaning(
-            mapping=FrozenDict({ref: ref.name == "cat" for ref in uni_refs}),
+            mapping=tuple(ref.name == "cat" for ref in uni_refs),
             universe=uni,
         ),
     )
     tree = Expression(
         form="tree",
         meaning=Meaning(
-            mapping=FrozenDict({ref: ref.name == "tree" for ref in uni_refs}),
+            mapping=tuple(ref.name == "tree" for ref in uni_refs),
             universe=uni,
         ),
     )
     shroom = Expression(
         form="shroom",
         meaning=Meaning(
-            mapping=FrozenDict({ref: ref.name == "shroom" for ref in uni_refs}),
+            mapping=tuple(ref.name == "shroom" for ref in uni_refs),
             universe=uni,
         ),
     )
     bird = Expression(
         form="bird",
         meaning=Meaning(
-            mapping=FrozenDict({ref: ref.name == "bird" for ref in uni_refs}),
+            mapping=tuple(ref.name == "bird" for ref in uni_refs),
             universe=uni,
         ),
     )
@@ -65,7 +64,7 @@ class TestLanguage:
     lang_subset_expr = Language(expressions=tuple([dog, cat, tree]))
     lang_of_different_order = Language(expressions=tuple([dog, cat, shroom, tree]))
 
-    def test_exp_subset(self):
+    def test_exp_can_express_positive(self):
         assert TestLanguage.dog.can_express(Referent("dog", {"phylum": "animal"}))
 
     def test_exp_subset(self):
@@ -83,11 +82,9 @@ def test_language_universe_check(self):
                     Expression(
                         form="dog",
                         meaning=Meaning(
-                            mapping=FrozenDict(
-                                {
-                                    ref: ref.name == "dog"
-                                    for ref in TestLanguage.uni.referents
-                                }
+                            mapping=tuple(
+                                ref.name == "dog"
+                                for ref in TestLanguage.uni.referents
                             ),
                             universe=TestLanguage.uni2,
                         ),
@@ -98,8 +95,8 @@ def test_language_universe_check(self):
     def test_language_degree(self):
         def isAnimal(exp: Expression) -> bool:
             print("checking phylum of " + str(exp))
-            for k, v in exp.meaning.mapping.items():
-                if v and k.phylum != "animal":
+            for ref, v in zip(exp.meaning.universe.referents, exp.meaning.mapping):
+                if v and ref.phylum != "animal":
                     return False
             return True
 
diff --git a/src/ultk/language/grammar/grammar.py b/src/ultk/language/grammar/grammar.py
index 7be0ab86..004fda79 100644
--- a/src/ultk/language/grammar/grammar.py
+++ b/src/ultk/language/grammar/grammar.py
@@ -168,15 +168,16 @@ def complement(self) -> Meaning:
         the expression evaluates to False."""
 
         return Meaning(
-            tuple(set(self.meaning.universe.referents) - set(self.meaning.referents)),
+            tuple(not val for val in self.meaning.mapping),
             self.meaning.universe,
         )
 
     def draw_referent(self, complement=False):
         """Get a random referent from the meaning's referents."""
+        universe_refs = self.meaning.universe.referents
         if complement:
-            return random.choice(list(self.complement().referents))
-        return random.choice(list(self.meaning.referents))
+            return random.choice([r for r, v in zip(universe_refs, self.meaning.mapping) if not v])
+        return random.choice([r for r, v in zip(universe_refs, self.meaning.mapping) if v])
 
     def to_dict(self) -> dict:
         the_dict = super().to_dict()
diff --git a/src/ultk/language/language.py b/src/ultk/language/language.py
index a89b6004..e20c7234 100644
--- a/src/ultk/language/language.py
+++ b/src/ultk/language/language.py
@@ -16,7 +16,6 @@
 from dataclasses import dataclass
 from typing import Callable, Generic, Iterable, TypeVar
 from ultk.language.semantics import Meaning, Referent, Universe
-from ultk.util.frozendict import FrozenDict
 
 # TODO: require Python 3.12 and use type parameter syntax instead? https://docs.python.org/3/reference/compound_stmts.html#type-params
 T = TypeVar("T")
@@ -30,7 +29,7 @@ class Expression(Generic[T]):
     # useful for hashing in certain cases
     # (e.g. a GrammaticalExpression which has not yet been evaluate()'d and so does not yet have a Meaning)
     form: str = ""
-    meaning: Meaning[T] = Meaning(FrozenDict(), Universe(tuple(), tuple()))
+    meaning: Meaning[T] = Meaning(tuple(), Universe(tuple(), tuple()))
 
     def can_express(self, referent: Referent) -> bool:
         """Return True if the expression can express the input single meaning point and false otherwise."""
diff --git a/src/ultk/language/sampling.py b/src/ultk/language/sampling.py
index 23dcb167..b6297db0 100644
--- a/src/ultk/language/sampling.py
+++ b/src/ultk/language/sampling.py
@@ -32,7 +32,8 @@ def all_meanings(universe: Universe) -> Generator[Meaning, None, None]:
     """Generate all Meanings (sets of Referents) from a given Universe."""
     referents = universe.referents
     for refset in powerset(referents):
-        yield Meaning(refset, universe)
+        refset_set = set(refset)
+        yield Meaning(tuple(ref in refset_set for ref in referents), universe)
 
 
 def all_expressions(meanings: Iterable[Meaning]) -> Generator[Expression, None, None]:
diff --git a/uv.lock b/uv.lock
index 64b3f092..1cc56a1f 100644
--- a/uv.lock
+++ b/uv.lock
@@ -934,31 +934,41 @@ wheels = [
 
 [[package]]
 name = "ultk"
-version = "0.0.1rc0"
+version = "0.1.0"
 source = { editable = "." }
 dependencies = [
-    { name = "mypy" },
     { name = "nltk" },
     { name = "numpy" },
     { name = "pandas" },
     { name = "pathos" },
     { name = "plotnine" },
-    { name = "pytest" },
     { name = "pyyaml" },
     { name = "scipy" },
+    { name = "tqdm" },
+]
+
+[package.dev-dependencies]
+dev = [
+    { name = "mypy" },
+    { name = "pytest" },
     { name = "scipy-stubs", extra = ["scipy"] },
 ]
 
 [package.metadata]
 requires-dist = [
-    { name = "mypy" },
     { name = "nltk" },
     { name = "numpy" },
     { name = "pandas" },
     { name = "pathos" },
     { name = "plotnine" },
-    { name = "pytest" },
     { name = "pyyaml" },
     { name = "scipy", specifier = ">=1.7.3" },
+    { name = "tqdm" },
+]
+
+[package.metadata.requires-dev]
+dev = [
+    { name = "mypy" },
+    { name = "pytest" },
     { name = "scipy-stubs", extras = ["scipy"], specifier = ">=1.16.3.3" },
 ]

From 1c56bcf613892b77395a8d978418d740e2b75dd1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Thu, 5 Mar 2026 22:33:33 +0000
Subject: [PATCH 2/6] Automated black formatting

---
 src/tests/test_language.py           |  3 +--
 src/ultk/language/grammar/grammar.py | 15 ++++++++++++---
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/tests/test_language.py b/src/tests/test_language.py
index 9943e850..0186d844 100644
--- a/src/tests/test_language.py
+++ b/src/tests/test_language.py
@@ -83,8 +83,7 @@ def test_language_universe_check(self):
                         form="dog",
                         meaning=Meaning(
                             mapping=tuple(
-                                ref.name == "dog"
-                                for ref in TestLanguage.uni.referents
+                                ref.name == "dog" for ref in TestLanguage.uni.referents
                             ),
                             universe=TestLanguage.uni2,
                         ),
diff --git a/src/ultk/language/grammar/grammar.py b/src/ultk/language/grammar/grammar.py
index 004fda79..6e84599b 100644
--- a/src/ultk/language/grammar/grammar.py
+++ b/src/ultk/language/grammar/grammar.py
@@ -100,7 +100,12 @@ def _and(p1: bool, p2: bool) -> bool:
         rhs: tuple[Any, ...] | None = tuple(arg.annotation for arg in args.values())
         # if one type annotation is class, a type of Referent, treat this as a terminal, no children = None RHS
         # TODO: make this more general?
-        if rhs and len(rhs) == 1 and inspect.isclass(rhs[0]) and issubclass(rhs[0], Referent):
+        if (
+            rhs
+            and len(rhs) == 1
+            and inspect.isclass(rhs[0])
+            and issubclass(rhs[0], Referent)
+        ):
             rhs = None
         return cls(
             name=rule_name,
@@ -176,8 +181,12 @@ def draw_referent(self, complement=False):
         """Get a random referent from the meaning's referents."""
         universe_refs = self.meaning.universe.referents
         if complement:
-            return random.choice([r for r, v in zip(universe_refs, self.meaning.mapping) if not v])
-        return random.choice([r for r, v in zip(universe_refs, self.meaning.mapping) if v])
+            return random.choice(
+                [r for r, v in zip(universe_refs, self.meaning.mapping) if not v]
+            )
+        return random.choice(
+            [r for r, v in zip(universe_refs, self.meaning.mapping) if v]
+        )
 
     def to_dict(self) -> dict:
         the_dict = super().to_dict()

From cc40dc00331a16a41aeed718220b95b92006e90d Mon Sep 17 00:00:00 2001
From: Shane Steinert-Threlkeld <ssshanest@gmail.com>
Date: Thu, 5 Mar 2026 14:41:56 -0800
Subject: [PATCH 3/6] python version in pypi-publish

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pypi-publish.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
index 4424989b..30cce4c6 100644
--- a/.github/workflows/pypi-publish.yml
+++ b/.github/workflows/pypi-publish.yml
@@ -15,6 +15,8 @@ jobs:
     # retrieve your distributions here
     - uses: actions/checkout@v4
     - uses: astral-sh/setup-uv@v5
+      with:
+        python-version: "3.13"
     - name: Build dist
       run: uv build
     - name: Publish package distributions to PyPI

From b32f63c6b8fa4ec82a8521620a3bfd462d4c64ed Mon Sep 17 00:00:00 2001
From: Shane Steinert-Threlkeld <ssshanest@gmail.com>
Date: Thu, 5 Mar 2026 14:50:07 -0800
Subject: [PATCH 4/6] add pdoc to dev group, update docs workflow

---
 .github/workflows/docs.yml |  2 +-
 README.md                  |  1 +
 pyproject.toml             |  2 +-
 uv.lock                    | 90 ++++++++++++++++++++++++++++++++++++++
 4 files changed, 93 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 16fcf5ef..b6107dfa 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v5
 
-      - run: uv sync
+      - run: uv sync --group dev
       - run: uv run pdoc src/ultk -d google --math -o ./docs
 
       - uses: actions/upload-pages-artifact@v3
diff --git a/README.md b/README.md
index 46ee05d3..326e834b 100644
--- a/README.md
+++ b/README.md
@@ -44,6 +44,7 @@ The source code is available on github [here](https://github.com/CLMBRs/ultk).
 Unit tests are written in [pytest](https://docs.pytest.org/en/7.3.x/) and executed via:
 
 ```
+uv sync --group dev
 uv run pytest src/tests/
 ```
 
diff --git a/pyproject.toml b/pyproject.toml
index 0033cd37..bdcab423 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
 ]
 
 [dependency-groups]
-dev = ["mypy", "pytest", "scipy-stubs[scipy]>=1.16.3.3"]
+dev = ["mypy", "pytest", "scipy-stubs[scipy]>=1.16.3.3", "pdoc"]
 
 [project.urls]
 "Homepage" = "https://clmbr.shane.st/ultk"
diff --git a/uv.lock b/uv.lock
index 1cc56a1f..49d01317 100644
--- a/uv.lock
+++ b/uv.lock
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     { url = "https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12", size = 7484, upload-time = "2025-10-18T21:55:41.639Z" },
 ]
 
+[[package]]
+name = "jinja2"
+version = "3.1.6"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "markupsafe" },
+]
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+wheels = [
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+]
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 [[package]]
 name = "joblib"
 version = "1.5.3"
@@ -247,6 +259,67 @@ wheels = [
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 ]
 
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+version = "2.5.5"
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+]
+
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 name = "matplotlib"
 version = "3.10.8"
@@ -541,6 +614,21 @@ wheels = [
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 ]
 
+[[package]]
+name = "pdoc"
+version = "16.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "jinja2" },
+    { name = "markdown2" },
+    { name = "markupsafe" },
+    { name = "pygments" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ac/fe/ab3f34a5fb08c6b698439a2c2643caf8fef0d61a86dd3fdcd5501c670ab8/pdoc-16.0.0.tar.gz", hash = "sha256:fdadc40cc717ec53919e3cd720390d4e3bcd40405cb51c4918c119447f913514", size = 111890, upload-time = "2025-10-27T16:02:16.345Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/16/a1/56a17b7f9e18c2bb8df73f3833345d97083b344708b97bab148fdd7e0b82/pdoc-16.0.0-py3-none-any.whl", hash = "sha256:070b51de2743b9b1a4e0ab193a06c9e6c12cf4151cf9137656eebb16e8556628", size = 100014, upload-time = "2025-10-27T16:02:15.007Z" },
+]
+
 [[package]]
 name = "pillow"
 version = "12.0.0"
@@ -950,6 +1038,7 @@ dependencies = [
 [package.dev-dependencies]
 dev = [
     { name = "mypy" },
+    { name = "pdoc" },
     { name = "pytest" },
     { name = "scipy-stubs", extra = ["scipy"] },
 ]
@@ -969,6 +1058,7 @@ requires-dist = [
 [package.metadata.requires-dev]
 dev = [
     { name = "mypy" },
+    { name = "pdoc" },
     { name = "pytest" },
     { name = "scipy-stubs", extras = ["scipy"], specifier = ">=1.16.3.3" },
 ]

From 8fde82abaa46c37e43138d7abc7b4fb50d788e09 Mon Sep 17 00:00:00 2001
From: Shane Steinert-Threlkeld <ssshanest@gmail.com>
Date: Thu, 5 Mar 2026 14:51:55 -0800
Subject: [PATCH 5/6] Update .github/workflows/test.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f40ff1d2..f66f3144 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,6 +8,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.13"
       - name: Install dependencies
         run: uv sync --group dev
       - name: Test with pytest

From d5598b352076fdf504d0a498318ce5b6efe77127 Mon Sep 17 00:00:00 2001
From: Shane Steinert-Threlkeld <ssshanest@gmail.com>
Date: Thu, 5 Mar 2026 15:15:59 -0800
Subject: [PATCH 6/6] init.py for pytest

---
 src/tests/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 src/tests/__init__.py

diff --git a/src/tests/__init__.py b/src/tests/__init__.py
new file mode 100644
index 00000000..e69de29b