Replace tox and pip with uv

Drop tox and pip as the dev/CI tooling in favor of uv: CI now uses
astral-sh/setup-uv + uv sync/uv run instead of tox environments, and
deploy.yml builds the sdist with `uv build --sdist` instead of `build`.
The CI-only git dependencies (petabtests, benchmark_models_petab) move
from tox's testenv `deps=` to a PEP 735 dependency-group. Also fixes
README's stated Python requirement to match pyproject.toml (>=3.12).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: dweindl

CLAUDE.md

@@ -0,0 +1,102 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## About This Project
+
+**libpetab-python** is the Python reference implementation of [PEtab](https://petab.readthedocs.io/), a standardized format for specifying parameter estimation problems in systems biology. It provides reading, writing, and validation of PEtab files.
+
+## Specs
+
+The PEtab specs can be found at:
+
+v1: https://github.com/PEtab-dev/PEtab/blob/main/doc/v1/documentation_data_format.rst
+
+v2: https://github.com/PEtab-dev/PEtab/blob/main/doc/v2/documentation_data_format.rst
+
+
+## Commands
+
+### Install for development
+```bash
+uv sync --extra tests --extra quality --extra vis --extra combine
+uv run pre-commit install
+```
+
+### Run tests
+```bash
+# All unit tests
+uv run pytest tests/
+
+# Single test file
+uv run pytest tests/v1/test_parameters.py
+
+# Single test
+uv run pytest tests/v1/test_parameters.py::test_get_optimization_parameter_scaling
+```
+
+### Linting and formatting
+```bash
+uv run pre-commit run --all-files
+```
+
+Uses **ruff** (linter + formatter), configured in `pyproject.toml` with 79-char line length.
+
+### Build docs
+```bash
+uv sync --extra doc --extra vis
+cd doc && make html
+```
+
+## Architecture
+
+### V1 vs V2 API
+
+The package has two versioned APIs:
+
+- **`petab.v1`** — stable, pandas-DataFrame-based API (PEtab 1.x spec). This is what most existing code uses.
+- **`petab.v2`** — newer Pydantic-based API with stricter typing (PEtab 2.x spec). Still evolving.
+
+Top-level `petab.*` imports are legacy shims that forward to `petab.v1`; new code should use the versioned subpackage explicitly.
+
+### Core Data Model
+
+A PEtab problem is a collection of tables (stored as pandas DataFrames in v1, Pydantic models in v2):
+
+| Table | Content |
+|-------|---------|
+| **parameter** | Parameters to estimate (id, scale, bounds, priors) |
+| **condition** | Experimental conditions (parameter overrides per experiment) |
+| **measurement** | Experimental data (observable, time, value, condition reference) |
+| **observable** | Observable definitions (formula, noise formula) |
+| **mapping** | Maps PEtab observables to model entities (optional) |
+| **visualization** | Plot specifications (optional) |
+
+The **`Problem`** class (`v1/problem.py`, `v2/core.py`) is the central container that loads all tables and the dynamical model.
+
+### Constants (`C.py`)
+
+All column names and allowed values are defined as constants in `petab/v1/C.py` (and `petab/v2/C.py`). Always use these instead of string literals (e.g., `C.PARAMETER_ID`, `C.ESTIMATE`, `C.LOG10`).
+
+### Model Abstraction
+
+The `models/` subpackage provides an abstract `Model` base class with concrete implementations for SBML (`sbml_model.py`) and PySB (`pysb_model.py`). Use `model_from_file()` to load a model without knowing the type.
+
+### Mathematical Expressions
+
+Observable and noise formulas are symbolic expressions parsed via a generated ANTLR grammar in `v1/math/_generated/` (auto-generated — do not edit directly). Use `sympify_petab()` to parse them. The `_generated/` directory is excluded from ruff linting.
+
+### Validation
+
+`lint.py` contains the validation logic. The `petablint` CLI entry point calls `lint_problem()`. Linting checks cross-table consistency, required columns, type correctness, and formula validity.
+
+### Parameter Mapping
+
+`parameter_mapping.py` handles the non-trivial logic of resolving which parameter value applies for a given observable/condition combination, including condition-specific overrides and placeholder substitution in formulas.
+
+## Key Conventions
+
+- **Deprecation policy:** features deprecated in a minor release are kept for ≥ 6 months before removal. Use `warnings.warn(..., DeprecationWarning, stacklevel=2)`. See `doc/development.rst` for the full release process.
+- **Docstrings:** Sphinx/reStructuredText style with `:param name:` and `:return:` tags.
+- **Test layout:** `tests/v1/` for v1 API tests, `tests/v2/` for v2. Test fixtures live in `tests/v1/test_petab.py`.
+- **Auto-generated files:** `petab/*/math/_generated/` — never edit manually.