small improvements to claude

.claude/rules/uv.md

@@ -0,0 +1,12 @@
+---
+description: Enforce uv as the package manager for all Python operations
+globs:
+  - "**/*.py"
+  - "**/pyproject.toml"
+---
+
+- Always use `uv run` to execute commands — never bare `python`, `pytest`, `ruff`, or other tools.
+- Never use `pip install` — use `uv sync` (with `--group` flags) to manage dependencies.
+- The `uv.lock` file is the source of truth for resolved dependency versions.
+- When adding dependencies, add them to `pyproject.toml` and run `uv sync`.
+- HSSM uses PEP 735 dependency groups: `--group dev`, `--group notebook`, `--group docs`.

.gitignore

@@ -63,7 +63,6 @@ ENV/
 
 # Also ignore lock files
 poetry.lock
-uv.lock
 
 # Editor cruft
 .idea/
@@ -88,7 +87,6 @@ hssm_paper/
 
 *.so
 .python-version
-uv.lock
 explorations/
 *.nbconvert.ipynb
 pypi-token

.pre-commit-config.yaml

@@ -1,17 +1,25 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.14.13
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        exclude: ^mkdocs\.yml$
+      - id: check-added-large-files
+        args: ['--maxkb=99900']
+      - id: check-merge-conflict
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1 # Use the sha / tag you want to point at
+    rev: v1.19.1
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: [types-PyYAML]

CLAUDE.md

@@ -2,7 +2,7 @@
 
 ## What is HSSM?
 
-HSSM (Hierarchical Sequential Sampling Models) is a Python package for Bayesian inference on sequential sampling models (DDM, LBA, etc.) using PyMC and bambi. It provides a high-level API for defining, fitting, and analyzing these models.
+HSSM (Hierarchical Sequential Sampling Models) is a Python package for Bayesian inference on sequential sampling models (DDM, LBA, etc.) using PyMC and bambi. It provides a high-level API for defining, fitting, and analyzing these models. This is the user-facing package in the HSSM ecosystem. For ecosystem-wide context, see the HSSMSpine repo.
 
 ## Project Structure
 
@@ -100,6 +100,7 @@ Two separate skip mechanisms for notebooks:
 | `coverage.yml` | Code coverage |
 | `build_docs.yml` | Build documentation |
 | `build_and_publish.yml` | Release to PyPI (triggered on release publish) |
+| `prepare-release.yml` | Release preparation automation |
 
 ## Known Issues / Notes
 

pyproject.toml

@@ -59,6 +59,7 @@ dev = [
     "pytest-rerunfailures>=15.0",
     "pytest-timeout>=2.3.1",
     "ruff>=0.15.0",
+    "types-PyYAML",
     "pre-commit>=4.1.0",
     "onnxruntime>=1.17.1",
 ]

tests/test_rlssm_config.py

@@ -113,7 +113,7 @@ class TestRLSSMConfigCreation:
         {"v": "subject_wise_function"},
     )
 
-    testcase2 = (
+    testcase2: tuple = (
         "minimal_rlssm",
         minimal_rlssm_config,
         "minimal_rlssm",