diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index eb99201..0000000
Binary files a/.DS_Store and /dev/null differ
diff --git a/.gitignore b/.gitignore
index 8a34fce..9a99b8f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,15 @@ bazel-*
 data/factor_covariance.csv
 data/factor_exposure.csv
 data/specific_variance.csv
-data/topic_exposure.csv 
\ No newline at end of file
+data/topic_exposure.csv
+
+# Python bytecode / caches
+__pycache__/
+*.py[cod]
+.pytest_cache/
+
+# Packaging artifacts
+*.egg-info/
+
+# OS cruft
+.DS_Store 
\ No newline at end of file
diff --git a/.python-version b/.python-version
new file mode 100644
index 0000000..e4fba21
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.12
diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..adf6cc5
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,105 @@
+# Directory Map
+
+This is a map of the directory for reference.
+
+```
+.
+├── .DS_Store
+├── .gitignore
+├── .vscode
+│   └── settings.json
+├── AGENTS.md
+├── README.md
+├── data
+│   ├── BFI228.csv
+│   ├── blackrock_covariance.csv
+│   └── eighthr.data
+├── environment.yml
+├── figures
+│   ├── .DS_Store
+│   ├── blackrock_results.pdf
+│   ├── dist_comparison.pdf
+│   ├── model_selec_results_n=100_gaussian.pdf
+│   ├── model_selec_results_n=100_non_gaussian.pdf
+│   ├── model_selec_results_n=200_gaussian.pdf
+│   ├── model_selec_results_n=200_gaussian_fb.pdf
+│   ├── model_selec_results_n=200_non_gaussian.pdf
+│   ├── model_selec_results_n=200_non_gaussian_fb.pdf
+│   ├── model_selec_results_n=300_gaussian.pdf
+│   ├── model_selec_results_n=300_non_gaussian.pdf
+│   ├── model_selec_results_n=400_gaussian.pdf
+│   ├── model_selec_results_n=400_non_gaussian.pdf
+│   ├── model_selec_results_n=500_gaussian.pdf
+│   ├── model_selec_results_n=500_non_gaussian.pdf
+│   ├── ozone_results.pdf
+│   ├── reliability.pdf
+│   └── temp.pdf
+├── notebooks
+│   ├── .DS_Store
+│   ├── .ipynb_checkpoints
+│   │   ├── Development Notebook-checkpoint.ipynb
+│   │   ├── blackrock_css-checkpoint.ipynb
+│   │   ├── missing_data-checkpoint.ipynb
+│   │   ├── model_selection-checkpoint.ipynb
+│   │   ├── testing_data_generation_and_null_distribution-checkpoint.ipynb
+│   │   └── testing_subset_selection-checkpoint.ipynb
+│   ├── blackrock_css.ipynb
+│   ├── missing_data.ipynb
+│   ├── model_selection.ipynb
+│   ├── notebook_utils
+│   │   ├── .DS_Store
+│   │   ├── __pycache__
+│   │   │   ├── data_generation.cpython-310.pyc
+│   │   │   ├── missing_data.cpython-310.pyc
+│   │   │   └── utils.cpython-310.pyc
+│   │   ├── data_generation.py
+│   │   ├── missing_data.py
+│   │   └── utils.py
+│   ├── results
+│   │   ├── gaussian_results.csv
+│   │   └── non_gaussian_results
+│   ├── testing_data_generation_and_null_distribution.ipynb
+│   └── testing_subset_selection.ipynb
+├── pycss
+│   ├── .DS_Store
+│   ├── CSS.py
+│   ├── __init__.py
+│   ├── __pycache__
+│   │   ├── PCSS.cpython-310.pyc
+│   │   ├── __init__.cpython-310.pyc
+│   │   ├── css.cpython-310.pyc
+│   │   ├── hypothesis_testing.cpython-310.pyc
+│   │   ├── model_selection.cpython-310.pyc
+│   │   ├── subset_selection.cpython-310.pyc
+│   │   └── utils.cpython-310.pyc
+│   ├── model_selection.py
+│   ├── subset_selection.py
+│   └── utils.py
+├── pycss.egg-info
+│   ├── PKG-INFO
+│   ├── SOURCES.txt
+│   ├── dependency_links.txt
+│   ├── not-zip-safe
+│   ├── requires.txt
+│   └── top_level.txt
+├── requirements.txt
+├── setup.py
+└── tests
+    ├── .DS_Store
+    ├── __pycache__
+    │   ├── test_CSS.cpython-310-pytest-7.3.1.pyc
+    │   ├── test_PCSS.cpython-310-pytest-7.2.1.pyc
+    │   ├── test_PCSS.cpython-310-pytest-7.3.1.pyc
+    │   ├── test_css.cpython-310-pytest-7.2.1.pyc
+    │   ├── test_subset_selection.cpython-310-pytest-7.2.1.pyc
+    │   ├── test_subset_selection.cpython-310-pytest-7.3.1.pyc
+    │   ├── test_utils.cpython-310-pytest-7.2.1.pyc
+    │   └── test_utils.cpython-310-pytest-7.3.1.pyc
+    ├── test_CSS.py
+    ├── test_subset_selection.py
+    ├── test_utils.py
+    └── utils
+        ├── .DS_Store
+        └── __pycache__
+            └── test_general.cpython-310-pytest-7.2.1.pyc
+```
diff --git a/README.md b/README.md
index df8da7e..af4d286 100644
--- a/README.md
+++ b/README.md
@@ -2,17 +2,17 @@
 
 ## Installation
 
-1. If you do not have conda installed already, please install it. There are many ways to get conda. We recommend installing Mambaforge which is a conda installation with mamba installed by default and set to use conda-forge as the default set of package repositories. 
+This fork uses [uv](https://docs.astral.sh/uv/). From the repo root:
 
-2. Clone the git repo:
 ```
-git clone git@github.com:AnavSood/CSS.git
+uv sync
+uv run pytest tests/
 ```
 
-3. Set up your conda environment. The list of packages that will be installed inside your conda environment can be seen in `environment.yml`.
-```
-mamba update -y conda
-# create a development virtual environment with useful tools
-mamba env create
-conda activate CSS
-```
+`pycss` itself is pure Python. The original Cython
+[choldate](https://github.com/modusdatascience/choldate) dependency is
+replaced by a pure-NumPy implementation in `pycss/chol.py`; the original
+package is vendored under `vendor/choldate/` (with the build fixes from
+[choldate PR #8](https://github.com/modusdatascience/choldate/pull/8)) as a
+dev-only dependency so the replacement is tested against it
+(`tests/test_chol.py`). Reference benchmarks live in `benchmarks/`.
diff --git a/benchmarks/RESULTS.md b/benchmarks/RESULTS.md
new file mode 100644
index 0000000..72703a0
--- /dev/null
+++ b/benchmarks/RESULTS.md
@@ -0,0 +1,25 @@
+# Reference Benchmarks: cholupdate
+
+**Date:** 2026-07-18
+
+**Machine:**
+- Architecture: arm64
+- OS: macOS 26.5.2
+- Python: 3.12.13
+
+## Results
+
+```
+cholupdate micro-benchmark (mean per call)
+     p   numpy (ms)  choldate (ms)  numpy/choldate
+    10       0.0278         0.0006            49.7
+    50       0.1346         0.0022            62.4
+   100       0.2716         0.0072            37.9
+   250       0.7090         0.0359            19.7
+   500       1.5132         0.1415            10.7
+  1000       3.4433         0.5547             6.2
+
+swapping_css end-to-end (p=100, k=10, single init)
+numpy backend:    0.005 s
+choldate backend: 0.003 s
+```
diff --git a/benchmarks/bench_chol.py b/benchmarks/bench_chol.py
new file mode 100644
index 0000000..17c07f0
--- /dev/null
+++ b/benchmarks/bench_chol.py
@@ -0,0 +1,66 @@
+"""Reference benchmark: pure-NumPy cholupdate vs vendored Cython choldate.
+
+Run from the repo root: uv run python benchmarks/bench_chol.py
+Numbers are for reference only; optimization is not a project goal.
+"""
+import time
+
+import numpy as np
+
+import pycss.subset_selection as ss
+from pycss.chol import cholupdate as np_cholupdate
+
+try:
+    from choldate import cholupdate as c_cholupdate
+except ImportError:
+    c_cholupdate = None
+
+
+def bench_update(fn, p, reps=200, seed=0):
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((p, p))
+    A = M @ M.T + p * np.eye(p)
+    R0 = np.ascontiguousarray(np.linalg.cholesky(A).T)
+    xs = rng.standard_normal((reps, p))
+    start = time.perf_counter()
+    for i in range(reps):
+        fn(R0.copy(), xs[i].copy())
+    return (time.perf_counter() - start) / reps
+
+
+def bench_swapping(backend, p=100, k=10, seed=0):
+    """Time swapping_css with pycss.subset_selection's cholupdate swapped out."""
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((2 * p, p))
+    Sigma = M.T @ M / (2 * p)
+    original = ss.cholupdate
+    ss.cholupdate = backend
+    try:
+        start = time.perf_counter()
+        ss.swapping_css(Sigma, k, S_init=np.arange(k))
+        return time.perf_counter() - start
+    finally:
+        ss.cholupdate = original
+
+
+def main():
+    print("cholupdate micro-benchmark (mean per call)")
+    print(f"{'p':>6} {'numpy (ms)':>12} {'choldate (ms)':>14} {'numpy/choldate':>15}")
+    for p in [10, 50, 100, 250, 500, 1000]:
+        t_np = bench_update(np_cholupdate, p) * 1e3
+        if c_cholupdate is not None:
+            t_c = bench_update(c_cholupdate, p) * 1e3
+            print(f"{p:>6} {t_np:>12.4f} {t_c:>14.4f} {t_np / t_c:>15.1f}")
+        else:
+            print(f"{p:>6} {t_np:>12.4f} {'n/a':>14} {'n/a':>15}")
+
+    print("\nswapping_css end-to-end (p=100, k=10, single init)")
+    t_np = bench_swapping(np_cholupdate)
+    print(f"numpy backend:    {t_np:.3f} s")
+    if c_cholupdate is not None:
+        t_c = bench_swapping(c_cholupdate)
+        print(f"choldate backend: {t_c:.3f} s")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/superpowers/plans/2026-07-17-choldate-build-and-numpy-replacement.md b/docs/superpowers/plans/2026-07-17-choldate-build-and-numpy-replacement.md
new file mode 100644
index 0000000..992ebd8
--- /dev/null
+++ b/docs/superpowers/plans/2026-07-17-choldate-build-and-numpy-replacement.md
@@ -0,0 +1,731 @@
+# choldate Build Fix + Pure-NumPy Replacement Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Make the pycss fork build cleanly with uv, vendor a build-fixed copy of the original Cython `choldate` package as a dev dependency, verify a pure-NumPy `cholupdate`/`choldowndate` replacement against it, and record reference benchmarks.
+
+**Architecture:** The original `choldate` (Cython) gets vendored into `vendor/choldate/` with PEP 518 build fixes taken from upstream PR modusdatascience/choldate#8, wired in as a uv dev-only dependency so it never becomes a runtime requirement. `pycss/chol.py` is rewritten to be an exact drop-in for `choldate`'s API (in-place on upper-triangular `R`, mutates `x`, returns `None`, numerically stable `hypot`). Parity tests compare the two implementations and both against direct re-factorization; a benchmark script records relative performance.
+
+**Tech Stack:** Python ≥3.10 (uv-managed), setuptools + Cython (vendored package only), NumPy, pytest.
+
+## Global Constraints
+
+- All environment management through `uv` — never conda (`environment.yml`/`requirements.txt` are upstream leftovers; do not use or update them).
+- `choldate` must remain a **dev-only** dependency; `pycss`'s runtime Cholesky code stays pure NumPy.
+- Working directory for every command: `/Users/jsperger/code/column-subset-selection-recipe/CSS-column-subset-selection` (this repo — the workspace root above it is not a git repo).
+- Pre-existing test failures (if the baseline run in Task 1 shows any) are recorded, not fixed, in this plan.
+- Do not commit `__pycache__`/`.pyc`/build artifacts (some are already tracked — leave them alone, but don't add more).
+- Optimization is not a goal; benchmarks are for reference only.
+
+---
+
+### Task 1: uv project baseline
+
+Make the fork a clean uv-managed project and establish the test baseline before touching choldate.
+
+**Files:**
+- Modify: `pyproject.toml`
+- Create: `.python-version`, `uv.lock` (generated)
+
+**Interfaces:**
+- Produces: a working `.venv` where `uv run pytest` executes the existing suite; later tasks assume `uv sync` and `uv run` work from the repo root.
+
+- [ ] **Step 1: Update `pyproject.toml`**
+
+`pycss` is pure Python, so drop `Cython` from both the build requires and the dependency list (it was only ever needed for choldate), and add `requires-python`. Replace the whole file with:
+
+```toml
+[project]
+name = "pycss"
+version = "0.0.9"
+description = "CSS Package"
+authors = [{ name = "Anav Sood", email = "anavsood@gmail.com" }]
+requires-python = ">=3.10"
+dependencies = [
+    "scipy",
+    "numpy",
+    "matplotlib",
+    "tqdm",
+    "pandas",
+    "seaborn",
+    "pytest",
+    "jupyter",
+    "cvxpy",
+    "scs",
+    "pingouin",
+    "clarabel",
+    "mosek",
+]
+
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["pycss"]
+```
+
+- [ ] **Step 2: Pin a Python for uv**
+
+```bash
+echo "3.12" > .python-version
+```
+
+- [ ] **Step 3: Create the environment and install**
+
+```bash
+uv sync
+```
+
+Expected: uv creates `.venv`, resolves dependencies, writes `uv.lock`, and installs `pycss` itself (editable by default for the project). If `mosek` fails to resolve for the pinned Python, report back rather than working around it — it's an upstream dependency choice.
+
+- [ ] **Step 4: Verify the package imports**
+
+```bash
+uv run python -c "from pycss.CSS import CSS; from pycss.chol import cholupdate; print('ok')"
+```
+
+Expected: `ok`
+
+- [ ] **Step 5: Run the existing test suite to record the baseline**
+
+```bash
+uv run pytest tests/ -q
+```
+
+Expected: tests run. Record pass/fail counts. If there are failures, copy the failing test names into the commit message body as "pre-existing baseline failures" — do **not** fix them in this plan.
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add pyproject.toml .python-version uv.lock
+git commit -m "build: make pycss a uv-managed project; drop unused Cython build dep"
+```
+
+---
+
+### Task 2: Vendor choldate with a working build
+
+Vendor the original Cython implementation into `vendor/choldate/` with the PEP 518 fixes from upstream PR #8 (rewritten more cleanly: static build requires in `pyproject.toml` instead of PR #8's `pip install` fallbacks inside `setup.py`), and install it as a uv dev dependency.
+
+**Files:**
+- Create: `vendor/choldate/pyproject.toml`
+- Create: `vendor/choldate/setup.py`
+- Create: `vendor/choldate/choldate/__init__.py`
+- Create: `vendor/choldate/choldate/_choldate.pyx` (copied verbatim from upstream)
+- Create: `vendor/choldate/LICENSE` (copied from upstream)
+- Modify: `pyproject.toml` (add dev group + uv source)
+- Delete: `choldate/` (stale empty directory left over from the removed submodule)
+
+**Interfaces:**
+- Produces: importable `choldate` module in the dev environment with `cholupdate(R, x)` and `choldowndate(R, x)` — both operate **in place** on a C-ordered upper-triangular float64 factor `R` (where `A = R.T @ R`), also mutate `x` in place, and return `None`. Tasks 3, 4, 5, and 7 import it exactly as `from choldate import cholupdate, choldowndate`.
+
+- [ ] **Step 1: Fetch upstream source**
+
+```bash
+git clone --depth 1 https://github.com/modusdatascience/choldate.git /private/tmp/claude-501/-Users-jsperger-code-column-subset-selection-recipe/b586afd9-f053-441d-ac82-b70f702e35bb/scratchpad/choldate-upstream
+```
+
+Expected: clone succeeds. Inspect `choldate-upstream/choldate/_choldate.pyx` exists.
+
+- [ ] **Step 2: Copy the source files we're vendoring**
+
+Copy only the `.pyx` and license — we write our own packaging and `__init__.py` (upstream's may carry Python-2-era code we don't want):
+
+```bash
+mkdir -p vendor/choldate/choldate
+cp /private/tmp/claude-501/-Users-jsperger-code-column-subset-selection-recipe/b586afd9-f053-441d-ac82-b70f702e35bb/scratchpad/choldate-upstream/choldate/_choldate.pyx vendor/choldate/choldate/_choldate.pyx
+cp /private/tmp/claude-501/-Users-jsperger-code-column-subset-selection-recipe/b586afd9-f053-441d-ac82-b70f702e35bb/scratchpad/choldate-upstream/LICENSE* vendor/choldate/ 2>/dev/null || cp /private/tmp/claude-501/-Users-jsperger-code-column-subset-selection-recipe/b586afd9-f053-441d-ac82-b70f702e35bb/scratchpad/choldate-upstream/COPYING* vendor/choldate/LICENSE 2>/dev/null
+ls vendor/choldate/
+```
+
+Expected: `_choldate.pyx` and a license file present. If no license file exists upstream, note that in the commit message and skip it (the repo is marked BSD-3-Clause on GitHub).
+
+- [ ] **Step 3: Write `vendor/choldate/choldate/__init__.py`**
+
+```python
+from choldate._choldate import cholupdate, choldowndate
+
+__all__ = ["cholupdate", "choldowndate"]
+```
+
+- [ ] **Step 4: Write `vendor/choldate/pyproject.toml`**
+
+```toml
+[build-system]
+requires = ["setuptools>=64", "cython", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "choldate"
+version = "0.1.0+pycss.vendored"
+description = "Rank-1 Cholesky update/downdate. Vendored from modusdatascience/choldate with the PEP 518 build fixes proposed in upstream PR #8."
+requires-python = ">=3.10"
+dependencies = ["numpy"]
+
+[tool.setuptools]
+packages = ["choldate"]
+```
+
+- [ ] **Step 5: Write `vendor/choldate/setup.py`**
+
+```python
+import numpy
+from Cython.Build import cythonize
+from setuptools import Extension, setup
+
+setup(
+    ext_modules=cythonize(
+        [
+            Extension(
+                "choldate._choldate",
+                ["choldate/_choldate.pyx"],
+                include_dirs=[numpy.get_include()],
+            )
+        ],
+        language_level=3,
+    ),
+)
+```
+
+- [ ] **Step 6: Remove the stale submodule leftover**
+
+```bash
+rmdir choldate
+```
+
+Expected: succeeds (the directory is empty). If it is not empty, stop and look — that would mean untracked local files worth surfacing before deleting anything.
+
+- [ ] **Step 7: Register choldate as a dev dependency in the root `pyproject.toml`**
+
+Append to `pyproject.toml`:
+
+```toml
+[dependency-groups]
+dev = ["choldate"]
+
+[tool.uv.sources]
+choldate = { path = "vendor/choldate" }
+```
+
+- [ ] **Step 8: Build and install**
+
+```bash
+uv sync
+```
+
+Expected: uv builds the `choldate` wheel from `vendor/choldate` (compiling the Cython extension) and installs it. This is the step the previous attempt never got working — if compilation fails, apply these contingencies in order, re-running `uv sync` after each:
+
+1. Error mentions `abs` from `libc.math` (Cython 3 removed the ambiguous `abs`): edit `vendor/choldate/choldate/_choldate.pyx`, changing `from libc.math cimport abs as cabs` to `from libc.math cimport fabs as cabs`. This is semantically identical for the float arguments used.
+2. Other Cython-3 syntax errors in the `.pyx`: pin the old toolchain instead of patching — in `vendor/choldate/pyproject.toml` change `"cython"` to `"cython<3"` in `[build-system].requires`.
+3. Error mentions missing C compiler: run `xcode-select --install` and report to the user that Command Line Tools are needed.
+
+Record which (if any) contingency was needed in the commit message.
+
+- [ ] **Step 9: Smoke-test the import**
+
+```bash
+uv run python -c "from choldate import cholupdate, choldowndate; print('choldate ok')"
+```
+
+Expected: `choldate ok`
+
+- [ ] **Step 10: Commit**
+
+```bash
+git add vendor/ pyproject.toml uv.lock
+git commit -m "build: vendor choldate with PEP 518 build fixes as uv dev dependency
+
+Vendors modusdatascience/choldate (BSD-3-Clause) with the build
+modernization from upstream PR #8 so the original Cython implementation
+builds under uv. Dev-only dependency: pycss runtime does not require it.
+Replaces the git submodule approach from e8c0faa that never built."
+```
+
+---
+
+### Task 3: Correctness tests for the vendored choldate
+
+Prove the vendored build is actually correct (not just importable) by checking it against direct re-factorization. These tests also define the ground-truth harness reused in Task 4.
+
+**Files:**
+- Create: `tests/__init__.py` (empty)
+- Create: `tests/test_choldate_vendored.py`
+
+**Interfaces:**
+- Consumes: `from choldate import cholupdate, choldowndate` (Task 2).
+- Produces: helper functions `random_spd(p, seed)` and `upper_factor(A)` with these exact signatures, which Task 4's tests import via `from tests.test_choldate_vendored import random_spd, upper_factor`.
+
+- [ ] **Step 1: Make `tests/` an importable package**
+
+Create an empty `tests/__init__.py` so test modules can import helpers from each other (pytest then puts the repo root — the package parent — on `sys.path`):
+
+```bash
+touch tests/__init__.py
+```
+
+- [ ] **Step 2: Write the test file**
+
+```python
+import numpy as np
+import pytest
+
+choldate = pytest.importorskip("choldate")
+
+
+def random_spd(p, seed):
+    """A well-conditioned random symmetric positive-definite matrix."""
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((p, p))
+    return M @ M.T + p * np.eye(p)
+
+
+def upper_factor(A):
+    """C-ordered upper-triangular R with A = R.T @ R."""
+    return np.ascontiguousarray(np.linalg.cholesky(A).T)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A)
+    choldate.cholupdate(R, x.copy())
+
+    expected = upper_factor(A + np.outer(x, x))
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_matches_refactorization(p):
+    # Downdate A + x x^T by x; must recover the factor of A (A stays PD).
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A + np.outer(x, x))
+    choldate.choldowndate(R, x.copy())
+
+    expected = upper_factor(A)
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+def test_cholupdate_is_in_place_and_returns_none():
+    A = random_spd(5, seed=0)
+    x = np.arange(1.0, 6.0)
+    R = upper_factor(A)
+    x_before = x.copy()
+
+    result = choldate.cholupdate(R, x)
+
+    assert result is None
+    assert not np.array_equal(x, x_before)  # choldate mutates x too
+```
+
+- [ ] **Step 3: Run the new tests**
+
+```bash
+uv run pytest tests/test_choldate_vendored.py -v
+```
+
+Expected: all PASS. A failure here means the vendored build is miscompiled or the upstream algorithm assumption is wrong — stop and investigate before proceeding (do not loosen tolerances to get to green).
+
+- [ ] **Step 4: Confirm adding `tests/__init__.py` didn't break existing collection**
+
+```bash
+uv run pytest tests/ -q --collect-only
+```
+
+Expected: all existing test modules still collect (same module count as the Task 1 baseline).
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add tests/__init__.py tests/test_choldate_vendored.py
+git commit -m "test: verify vendored choldate against direct re-factorization"
+```
+
+---
+
+### Task 4: Rewrite `pycss/chol.py` cholupdate as an exact choldate drop-in
+
+The current `chol.py` differs from choldate observably: it copies `x` instead of mutating it, returns `R`, and uses the numerically naive `sqrt(a**2 + b**2)` instead of a stable `hypot`. Rewrite it to match choldate's contract exactly, test-first.
+
+**Files:**
+- Create: `tests/test_chol.py`
+- Modify: `pycss/chol.py`
+
+**Interfaces:**
+- Consumes: `random_spd`, `upper_factor` from `tests/test_choldate_vendored.py` (Task 3); `from choldate import cholupdate` for parity tests.
+- Produces: `pycss.chol.cholupdate(R, x)` — in place on upper-triangular C-ordered float64 `R` (`A = R.T @ R` becomes `A + x x^T`), mutates `x`, returns `None`. The existing call site `update_cholesky_after_removing_first` (`pycss/subset_selection.py:208`) already ignores the return value and passes a copied `x`, so it needs no change.
+
+- [ ] **Step 1: Write the failing tests**
+
+Create `tests/test_chol.py`:
+
+```python
+import numpy as np
+import pytest
+
+from pycss.chol import cholupdate
+from tests.test_choldate_vendored import random_spd, upper_factor
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A)
+    cholupdate(R, x.copy())
+
+    expected = upper_factor(A + np.outer(x, x))
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+def test_cholupdate_is_in_place_and_returns_none():
+    A = random_spd(5, seed=0)
+    x = np.arange(1.0, 6.0)
+    R = upper_factor(A)
+    x_before = x.copy()
+
+    result = cholupdate(R, x)
+
+    assert result is None
+    assert not np.array_equal(x, x_before)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_parity_with_choldate(p):
+    choldate = pytest.importorskip("choldate")
+    rng = np.random.default_rng(p + 1000)
+    A = random_spd(p, seed=p + 1000)
+    x = rng.standard_normal(p)
+
+    R_np, x_np = upper_factor(A), x.copy()
+    R_c, x_c = upper_factor(A), x.copy()
+
+    cholupdate(R_np, x_np)
+    choldate.cholupdate(R_c, x_c)
+
+    np.testing.assert_allclose(R_np, R_c, rtol=1e-12, atol=1e-14)
+    np.testing.assert_allclose(x_np, x_c, rtol=1e-12, atol=1e-14)
+```
+
+- [ ] **Step 2: Run the tests to verify they fail**
+
+```bash
+uv run pytest tests/test_chol.py -v
+```
+
+Expected: `test_cholupdate_is_in_place_and_returns_none` FAILS (current implementation returns `R` and does not mutate `x`); the parity test FAILS on `x` mutation. The refactorization test may pass — that's fine; the failing tests are what drive the rewrite.
+
+- [ ] **Step 3: Rewrite `pycss/chol.py`**
+
+Replace the file's `cholupdate` with:
+
+```python
+import numpy as np
+
+
+def cholupdate(R, x):
+    """Rank-1 update of an upper-triangular Cholesky factor, in place.
+
+    Drop-in replacement for choldate.cholupdate: given upper-triangular
+    `R` with `A = R.T @ R`, overwrites `R` with the factor of
+    `A + np.outer(x, x)`. Both `R` and `x` are modified in place and
+    nothing is returned, matching the choldate API exactly.
+    """
+    p = len(x)
+    for k in range(p):
+        r = np.hypot(R[k, k], x[k])
+        c = r / R[k, k]
+        s = x[k] / R[k, k]
+        R[k, k] = r
+        R[k, k + 1:] = (R[k, k + 1:] + s * x[k + 1:]) / c
+        x[k + 1:] = c * x[k + 1:] - s * R[k, k + 1:]
+```
+
+- [ ] **Step 4: Run the tests to verify they pass**
+
+```bash
+uv run pytest tests/test_chol.py -v
+```
+
+Expected: all PASS (parity tests skip only if choldate failed to install, which Task 2 rules out).
+
+- [ ] **Step 5: Run the full suite to catch call-site regressions**
+
+```bash
+uv run pytest tests/ -q
+```
+
+Expected: same results as the Task 1 baseline (no new failures). `update_cholesky_after_removing_first` is exercised via the swapping-CSS tests.
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add pycss/chol.py tests/test_chol.py
+git commit -m "fix: make pure-NumPy cholupdate an exact choldate drop-in
+
+Match choldate semantics (in-place on R and x, returns None) and use
+np.hypot for numerical stability instead of naive sqrt of squares."
+```
+
+---
+
+### Task 5: Add pure-NumPy choldowndate
+
+pycss only calls `cholupdate` today, but the R port and full choldate replacement need the downdate too; it completes API parity with the vendored package.
+
+**Files:**
+- Modify: `pycss/chol.py`
+- Modify: `tests/test_chol.py`
+
+**Interfaces:**
+- Consumes: `random_spd`, `upper_factor` helpers; `from choldate import choldowndate` for parity.
+- Produces: `pycss.chol.choldowndate(R, x)` — same in-place contract as `cholupdate`, subtracting `np.outer(x, x)`.
+
+- [ ] **Step 1: Write the failing tests**
+
+Append to `tests/test_chol.py` (and extend the top import to `from pycss.chol import cholupdate, choldowndate`):
+
+```python
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A + np.outer(x, x))
+    choldowndate(R, x.copy())
+
+    expected = upper_factor(A)
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_parity_with_choldate(p):
+    choldate = pytest.importorskip("choldate")
+    rng = np.random.default_rng(p + 2000)
+    A = random_spd(p, seed=p + 2000)
+    x = rng.standard_normal(p)
+    R0 = upper_factor(A + np.outer(x, x))
+
+    R_np, x_np = R0.copy(), x.copy()
+    R_c, x_c = R0.copy(), x.copy()
+
+    choldowndate(R_np, x_np)
+    choldate.choldowndate(R_c, x_c)
+
+    np.testing.assert_allclose(R_np, R_c, rtol=1e-12, atol=1e-14)
+    np.testing.assert_allclose(x_np, x_c, rtol=1e-12, atol=1e-14)
+```
+
+- [ ] **Step 2: Run the tests to verify they fail**
+
+```bash
+uv run pytest tests/test_chol.py -v
+```
+
+Expected: the two new tests FAIL with `ImportError: cannot import name 'choldowndate' from 'pycss.chol'` (collection error is acceptable — it demonstrates the function doesn't exist).
+
+- [ ] **Step 3: Implement `choldowndate` in `pycss/chol.py`**
+
+Append:
+
+```python
+def choldowndate(R, x):
+    """Rank-1 downdate of an upper-triangular Cholesky factor, in place.
+
+    Drop-in replacement for choldate.choldowndate: given upper-triangular
+    `R` with `A = R.T @ R`, overwrites `R` with the factor of
+    `A - np.outer(x, x)` (which must remain positive definite). Both `R`
+    and `x` are modified in place and nothing is returned.
+    """
+    p = len(x)
+    for k in range(p):
+        r = np.sqrt((R[k, k] - x[k]) * (R[k, k] + x[k]))
+        c = r / R[k, k]
+        s = x[k] / R[k, k]
+        R[k, k] = r
+        R[k, k + 1:] = (R[k, k + 1:] - s * x[k + 1:]) / c
+        x[k + 1:] = c * x[k + 1:] - s * R[k, k + 1:]
+```
+
+- [ ] **Step 4: Run the tests to verify they pass**
+
+```bash
+uv run pytest tests/test_chol.py -v
+```
+
+Expected: all PASS.
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add pycss/chol.py tests/test_chol.py
+git commit -m "feat: add pure-NumPy choldowndate for full choldate API parity"
+```
+
+---
+
+### Task 6: Reference benchmarks
+
+Micro-benchmark `cholupdate` (NumPy vs Cython) and one end-to-end `swapping_css` run with each backend. Reference numbers only — no optimization work.
+
+**Files:**
+- Create: `benchmarks/bench_chol.py`
+- Create: `benchmarks/RESULTS.md`
+
+**Interfaces:**
+- Consumes: `pycss.chol.cholupdate`, `choldate.cholupdate`, `pycss.subset_selection.swapping_css(Sigma, k, ...)`.
+- Produces: standalone script; nothing downstream depends on it.
+
+- [ ] **Step 1: Write `benchmarks/bench_chol.py`**
+
+```python
+"""Reference benchmark: pure-NumPy cholupdate vs vendored Cython choldate.
+
+Run from the repo root: uv run python benchmarks/bench_chol.py
+Numbers are for reference only; optimization is not a project goal.
+"""
+import time
+
+import numpy as np
+
+import pycss.subset_selection as ss
+from pycss.chol import cholupdate as np_cholupdate
+
+try:
+    from choldate import cholupdate as c_cholupdate
+except ImportError:
+    c_cholupdate = None
+
+
+def bench_update(fn, p, reps=200, seed=0):
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((p, p))
+    A = M @ M.T + p * np.eye(p)
+    R0 = np.ascontiguousarray(np.linalg.cholesky(A).T)
+    xs = rng.standard_normal((reps, p))
+    start = time.perf_counter()
+    for i in range(reps):
+        fn(R0.copy(), xs[i].copy())
+    return (time.perf_counter() - start) / reps
+
+
+def bench_swapping(backend, p=100, k=10, seed=0):
+    """Time swapping_css with pycss.subset_selection's cholupdate swapped out."""
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((2 * p, p))
+    Sigma = M.T @ M / (2 * p)
+    original = ss.cholupdate
+    ss.cholupdate = backend
+    try:
+        start = time.perf_counter()
+        ss.swapping_css(Sigma, k, S_init=np.arange(k))
+        return time.perf_counter() - start
+    finally:
+        ss.cholupdate = original
+
+
+def main():
+    print("cholupdate micro-benchmark (mean per call)")
+    print(f"{'p':>6} {'numpy (ms)':>12} {'choldate (ms)':>14} {'numpy/choldate':>15}")
+    for p in [10, 50, 100, 250, 500, 1000]:
+        t_np = bench_update(np_cholupdate, p) * 1e3
+        if c_cholupdate is not None:
+            t_c = bench_update(c_cholupdate, p) * 1e3
+            print(f"{p:>6} {t_np:>12.4f} {t_c:>14.4f} {t_np / t_c:>15.1f}")
+        else:
+            print(f"{p:>6} {t_np:>12.4f} {'n/a':>14} {'n/a':>15}")
+
+    print("\nswapping_css end-to-end (p=100, k=10, single init)")
+    t_np = bench_swapping(np_cholupdate)
+    print(f"numpy backend:    {t_np:.3f} s")
+    if c_cholupdate is not None:
+        t_c = bench_swapping(c_cholupdate)
+        print(f"choldate backend: {t_c:.3f} s")
+
+
+if __name__ == "__main__":
+    main()
+```
+
+- [ ] **Step 2: Run it**
+
+```bash
+uv run python benchmarks/bench_chol.py
+```
+
+Expected: the table prints with both columns populated (choldate importable) and both `swapping_css` runs return the same-length subset without error. If `swapping_css(Sigma, k, S_init=...)` raises a signature error, check `pycss/subset_selection.py:692` for the actual keyword names and adjust the call.
+
+- [ ] **Step 3: Record results**
+
+Create `benchmarks/RESULTS.md` containing the date (2026-07-17), the machine description (`uname -m`, macOS, Python version from `uv run python -V`), and the verbatim script output in a fenced code block.
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add benchmarks/
+git commit -m "bench: reference comparison of NumPy cholupdate vs Cython choldate"
+```
+
+---
+
+### Task 7: Documentation sync
+
+Update the fork's README and the workspace CLAUDE.md so the choldate story is accurate.
+
+**Files:**
+- Modify: `README.md` (fork root)
+- Modify: `../CLAUDE.md` (workspace — not part of this git repo; edit but don't commit here)
+
+**Interfaces:**
+- Consumes: outcomes of Tasks 1–6 (which contingencies fired, benchmark summary).
+
+- [ ] **Step 1: Replace the README installation section**
+
+Replace both installation sections of `README.md` (the uv section's choldate/rpy2 warning and the entire conda section) with:
+
+````markdown
+## Installation
+
+This fork uses [uv](https://docs.astral.sh/uv/). From the repo root:
+
+```
+uv sync
+uv run pytest tests/
+```
+
+`pycss` itself is pure Python. The original Cython
+[choldate](https://github.com/modusdatascience/choldate) dependency is
+replaced by a pure-NumPy implementation in `pycss/chol.py`; the original
+package is vendored under `vendor/choldate/` (with the build fixes from
+[choldate PR #8](https://github.com/modusdatascience/choldate/pull/8)) as a
+dev-only dependency so the replacement is tested against it
+(`tests/test_chol.py`). Reference benchmarks live in `benchmarks/`.
+````
+
+- [ ] **Step 2: Update the workspace `CLAUDE.md`**
+
+In `/Users/jsperger/code/column-subset-selection-recipe/CLAUDE.md`, rewrite "The choldate situation" section to reflect the new state: vendored build-fixed choldate at `vendor/choldate/` (dev-only), verified pure-NumPy `cholupdate`/`choldowndate` in `pycss/chol.py` with parity tests in `tests/test_chol.py`, benchmarks in `benchmarks/`. Update the Python commands section from `uv pip install -e .` to `uv sync`. Remove the "treat with skepticism / unverified" warnings — they will no longer be true.
+
+- [ ] **Step 3: Commit the fork's README**
+
+```bash
+git add README.md
+git commit -m "docs: document uv workflow and choldate replacement status"
+```
+
+---
+
+## Verification (whole plan)
+
+- `uv sync` from a clean checkout (delete `.venv`) succeeds and compiles the vendored choldate.
+- `uv run pytest tests/ -q` — all new tests pass; no regressions vs the Task 1 baseline.
+- `uv run python benchmarks/bench_chol.py` runs to completion with both backends.
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-Author: Anav Sood
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-pycss/utils.py
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diff --git a/pycss/chol.py b/pycss/chol.py
new file mode 100644
index 0000000..4f3b3cc
--- /dev/null
+++ b/pycss/chol.py
@@ -0,0 +1,39 @@
+import numpy as np
+
+
+def cholupdate(R, x):
+    """Rank-1 update of an upper-triangular Cholesky factor, in place.
+
+    Drop-in replacement for choldate.cholupdate: given upper-triangular
+    `R` with `A = R.T @ R`, overwrites `R` with the factor of
+    `A + np.outer(x, x)`. Both `R` and `x` are modified in place and
+    nothing is returned, matching the choldate API exactly.
+    """
+    p = len(x)
+    for k in range(p):
+        r = np.hypot(R[k, k], x[k])
+        c = r / R[k, k]
+        s = x[k] / R[k, k]
+        R[k, k] = r
+        R[k, k + 1:] = (R[k, k + 1:] + s * x[k + 1:]) / c
+        x[k + 1:] = c * x[k + 1:] - s * R[k, k + 1:]
+
+
+def choldowndate(R, x):
+    """Rank-1 downdate of an upper-triangular Cholesky factor, in place.
+
+    Drop-in replacement for choldate.choldowndate: given upper-triangular
+    `R` with `A = R.T @ R`, overwrites `R` with the factor of
+    `A - np.outer(x, x)` (which must remain positive definite). Both `R`
+    and `x` are modified in place and nothing is returned. Violating that
+    precondition yields NaN entries (with a RuntimeWarning), whereas the
+    original Cython choldate silently returns an incorrect finite factor.
+    """
+    p = len(x)
+    for k in range(p):
+        r = np.sqrt((R[k, k] - x[k]) * (R[k, k] + x[k]))
+        c = r / R[k, k]
+        s = x[k] / R[k, k]
+        R[k, k] = r
+        R[k, k + 1:] = (R[k, k + 1:] - s * x[k + 1:]) / c
+        x[k + 1:] = c * x[k + 1:] - s * R[k, k + 1:]
diff --git a/pycss/subset_selection.py b/pycss/subset_selection.py
index f663df8..dcb7106 100644
--- a/pycss/subset_selection.py
+++ b/pycss/subset_selection.py
@@ -3,7 +3,7 @@
 import itertools
 import math 
 import tqdm 
-from choldate import cholupdate
+from .chol import cholupdate
 from scipy.linalg import solve_triangular
 
 TOL = 1e-10
@@ -385,7 +385,7 @@ def check_greedy_css_inputs(Sigma, k, cutoffs, include, exclude, tol):
         raise ValueError('Exclude must be a numpy array of integers from 0 to p-1.')
     if len(include) != len(set_include):
         raise ValueError("Include has repeated elements.")
-    if len(exclude) != len(set_include):
+    if len(exclude) != len(set_exclude):
         raise ValueError("Exclude has repeated elements.")
     if len(set_exclude.intersection(set_include)) > 0:
         raise ValueError("Include and exclude must be disjoint.")
@@ -480,7 +480,7 @@ def greedy_css(Sigma,
             obj_vals = css_score(Sigma_R_active, tol=tol)
 
             # set the exclude objective values to infinity
-            obj_vals[np.in1d(idx_order[:num_active], exclude)] = np.inf
+            obj_vals[np.isin(idx_order[:num_active], exclude)] = np.inf
             # select next variable
             j_star = random_argmin(obj_vals)
 
@@ -552,7 +552,7 @@ def check_swapping_css_inputs(Sigma,
         raise ValueError('Exclude must be a numpy array of integers from 0 to p-1.')
     if len(include) != len(set_include):
         raise ValueError("Include has repeated elements.")
-    if len(exclude) != len(set_include):
+    if len(exclude) != len(set_exclude):
         raise ValueError("Exclude has repeated elements.")
     if len(set_exclude.intersection(set_include)) > 0:
         raise ValueError("Include and exclude must be disjoint.")
@@ -646,7 +646,7 @@ def swapping_css_with_init(Sigma,
                 obj_vals = css_score(Sigma_R[:num_active, :num_active], tol=tol)
 
                 # set the objective value to infinity for the excluded variables
-                obj_vals[np.in1d(idx_order[:num_active], exclude)] = np.inf
+                obj_vals[np.isin(idx_order[:num_active], exclude)] = np.inf
 
                 choices = np.flatnonzero(obj_vals == obj_vals.min())
 
@@ -814,7 +814,7 @@ def check_exhuastive_css_inputs(Sigma,
         raise ValueError('Exclude must be a numpy array of integers from 0 to p-1.')
     if len(include) != len(set_include):
         raise ValueError("Include has repeated elements.")
-    if len(exclude) != len(set_include):
+    if len(exclude) != len(set_exclude):
         raise ValueError("Exclude has repeated elements.")
     if len(set_exclude.intersection(set_include)) > 0:
         raise ValueError("Include and exclude must be disjoint.")
@@ -956,7 +956,7 @@ def check_greedy_subset_factor_inputs(Sigma, cutoffs, include, exclude, tol):
         raise ValueError('Exclude must be a numpy array of integers from 0 to p-1.')
     if len(include) != len(set_include):
         raise ValueError("Include has repeated elements.")
-    if len(exclude) != len(set_include):
+    if len(exclude) != len(set_exclude):
         raise ValueError("Exclude has repeated elements.")
     if len(set_exclude.intersection(set_include)) > 0:
         raise ValueError("Include and exclude must be disjoint.")
@@ -1041,7 +1041,7 @@ def greedy_subset_factor_selection(Sigma,
                 return np.concatenate([S[:num_selected], np.array([colinearity_errors[0][0]])]), reject
 
             # set the exclude objective values to infinity
-            obj_vals[np.in1d(idx_order[:num_active], exclude)] = np.inf
+            obj_vals[np.isin(idx_order[:num_active], exclude)] = np.inf
             # select next variable
             j_star = random_argmin(obj_vals)
 
@@ -1117,7 +1117,7 @@ def check_swapping_subset_factor_inputs(Sigma,
         raise ValueError('Exclude must be a numpy array of integers from 0 to p-1.')
     if len(include) != len(set_include):
         raise ValueError("Include has repeated elements.")
-    if len(exclude) != len(set_include):
+    if len(exclude) != len(set_exclude):
         raise ValueError("Exclude has repeated elements.")
     if len(set_exclude.intersection(set_include)) > 0:
         raise ValueError("Include and exclude must be disjoint.")
@@ -1229,7 +1229,7 @@ def swapping_subset_factor_with_init(Sigma,
                     return np.concatenate([T, np.array([colinearity_errors[0][0]])]), reject, -np.inf
 
                 # set the objective value to infinity for the excluded variables
-                obj_vals[np.in1d(idx_order[:(d+1)], exclude)] = np.inf
+                obj_vals[np.isin(idx_order[:(d+1)], exclude)] = np.inf
 
                 choices = np.flatnonzero(obj_vals == obj_vals.min())
 
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..0a298af
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,34 @@
+[project]
+name = "pycss"
+version = "0.0.9"
+description = "CSS Package"
+authors = [{ name = "Anav Sood", email = "anavsood@gmail.com" }]
+requires-python = ">=3.10"
+dependencies = [
+    "scipy",
+    "numpy",
+    "matplotlib",
+    "tqdm",
+    "pandas",
+    "seaborn",
+    "pytest",
+    "jupyter",
+    "cvxpy",
+    "scs",
+    "pingouin",
+    "clarabel",
+    "mosek",
+]
+
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["pycss"]
+
+[dependency-groups]
+dev = ["choldate"]
+
+[tool.uv.sources]
+choldate = { path = "vendor/choldate" }
diff --git a/tests/.DS_Store b/tests/.DS_Store
deleted file mode 100644
index 8e8881e..0000000
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diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
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deleted file mode 100644
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diff --git a/tests/__pycache__/test_utils.cpython-310-pytest-7.2.1.pyc b/tests/__pycache__/test_utils.cpython-310-pytest-7.2.1.pyc
deleted file mode 100644
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diff --git a/tests/__pycache__/test_utils.cpython-310-pytest-7.3.1.pyc b/tests/__pycache__/test_utils.cpython-310-pytest-7.3.1.pyc
deleted file mode 100644
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diff --git a/tests/helpers.py b/tests/helpers.py
new file mode 100644
index 0000000..05a3668
--- /dev/null
+++ b/tests/helpers.py
@@ -0,0 +1,13 @@
+import numpy as np
+
+
+def random_spd(p, seed):
+    """A well-conditioned random symmetric positive-definite matrix."""
+    rng = np.random.default_rng(seed)
+    M = rng.standard_normal((p, p))
+    return M @ M.T + p * np.eye(p)
+
+
+def upper_factor(A):
+    """C-ordered upper-triangular R with A = R.T @ R."""
+    return np.ascontiguousarray(np.linalg.cholesky(A).T)
diff --git a/tests/test_chol.py b/tests/test_chol.py
new file mode 100644
index 0000000..10a018c
--- /dev/null
+++ b/tests/test_chol.py
@@ -0,0 +1,78 @@
+import numpy as np
+import pytest
+
+from pycss.chol import cholupdate, choldowndate
+from tests.helpers import random_spd, upper_factor
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A)
+    cholupdate(R, x.copy())
+
+    expected = upper_factor(A + np.outer(x, x))
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+def test_cholupdate_is_in_place_and_returns_none():
+    A = random_spd(5, seed=0)
+    x = np.arange(1.0, 6.0)
+    R = upper_factor(A)
+    x_before = x.copy()
+
+    result = cholupdate(R, x)
+
+    assert result is None
+    assert not np.array_equal(x, x_before)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_parity_with_choldate(p):
+    choldate = pytest.importorskip("choldate")
+    rng = np.random.default_rng(p + 1000)
+    A = random_spd(p, seed=p + 1000)
+    x = rng.standard_normal(p)
+
+    R_np, x_np = upper_factor(A), x.copy()
+    R_c, x_c = upper_factor(A), x.copy()
+
+    cholupdate(R_np, x_np)
+    choldate.cholupdate(R_c, x_c)
+
+    np.testing.assert_allclose(R_np, R_c, rtol=1e-12, atol=1e-14)
+    np.testing.assert_allclose(x_np, x_c, rtol=1e-12, atol=1e-14)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A + np.outer(x, x))
+    choldowndate(R, x.copy())
+
+    expected = upper_factor(A)
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_parity_with_choldate(p):
+    choldate = pytest.importorskip("choldate")
+    rng = np.random.default_rng(p + 2000)
+    A = random_spd(p, seed=p + 2000)
+    x = rng.standard_normal(p)
+    R0 = upper_factor(A + np.outer(x, x))
+
+    R_np, x_np = R0.copy(), x.copy()
+    R_c, x_c = R0.copy(), x.copy()
+
+    choldowndate(R_np, x_np)
+    choldate.choldowndate(R_c, x_c)
+
+    np.testing.assert_allclose(R_np, R_c, rtol=1e-12, atol=1e-14)
+    np.testing.assert_allclose(x_np, x_c, rtol=1e-12, atol=1e-14)
diff --git a/tests/test_choldate_vendored.py b/tests/test_choldate_vendored.py
new file mode 100644
index 0000000..025977d
--- /dev/null
+++ b/tests/test_choldate_vendored.py
@@ -0,0 +1,45 @@
+import numpy as np
+import pytest
+
+from tests.helpers import random_spd, upper_factor
+
+choldate = pytest.importorskip("choldate")
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_cholupdate_matches_refactorization(p):
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A)
+    choldate.cholupdate(R, x.copy())
+
+    expected = upper_factor(A + np.outer(x, x))
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+@pytest.mark.parametrize("p", [1, 2, 5, 20, 100])
+def test_choldowndate_matches_refactorization(p):
+    # Downdate A + x x^T by x; must recover the factor of A (A stays PD).
+    rng = np.random.default_rng(p)
+    A = random_spd(p, seed=p)
+    x = rng.standard_normal(p)
+
+    R = upper_factor(A + np.outer(x, x))
+    choldate.choldowndate(R, x.copy())
+
+    expected = upper_factor(A)
+    np.testing.assert_allclose(R, expected, rtol=1e-8, atol=1e-10)
+
+
+def test_cholupdate_is_in_place_and_returns_none():
+    A = random_spd(5, seed=0)
+    x = np.arange(1.0, 6.0)
+    R = upper_factor(A)
+    x_before = x.copy()
+
+    result = choldate.cholupdate(R, x)
+
+    assert result is None
+    assert not np.array_equal(x, x_before)  # choldate mutates x too
diff --git a/tests/utils/.DS_Store b/tests/utils/.DS_Store
deleted file mode 100644
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diff --git a/tests/utils/__pycache__/test_general.cpython-310-pytest-7.2.1.pyc b/tests/utils/__pycache__/test_general.cpython-310-pytest-7.2.1.pyc
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diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..b51edb3
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,3992 @@
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+    "python_full_version == '3.11.*' and sys_platform == 'emscripten'",
+    "python_full_version == '3.11.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+    "python_full_version < '3.11'",
+]
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+[[package]]
+name = "anyio"
+version = "4.14.2"
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diff --git a/vendor/choldate/.gitignore b/vendor/choldate/.gitignore
new file mode 100644
index 0000000..d1d02e9
--- /dev/null
+++ b/vendor/choldate/.gitignore
@@ -0,0 +1,6 @@
+build/
+*.egg-info/
+choldate/_choldate.c
+*.so
+__pycache__/
+*.pyc
diff --git a/vendor/choldate/LICENSE b/vendor/choldate/LICENSE
new file mode 100644
index 0000000..aeed1e3
--- /dev/null
+++ b/vendor/choldate/LICENSE
@@ -0,0 +1,9 @@
+Copyright (c) 2013, Jason Rudy
+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.
+Neither the name of Clinicast, Inc., nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+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.
\ No newline at end of file
diff --git a/vendor/choldate/choldate/__init__.py b/vendor/choldate/choldate/__init__.py
new file mode 100644
index 0000000..8e84706
--- /dev/null
+++ b/vendor/choldate/choldate/__init__.py
@@ -0,0 +1,3 @@
+from choldate._choldate import cholupdate, choldowndate
+
+__all__ = ["cholupdate", "choldowndate"]
diff --git a/vendor/choldate/choldate/_choldate.pxd b/vendor/choldate/choldate/_choldate.pxd
new file mode 100644
index 0000000..3f85960
--- /dev/null
+++ b/vendor/choldate/choldate/_choldate.pxd
@@ -0,0 +1,7 @@
+
+cimport numpy as np
+ctypedef np.float64_t FLOAT_t
+
+cpdef cholupdate(np.ndarray[FLOAT_t, ndim=2] R, np.ndarray[FLOAT_t, ndim=1] x)
+
+cpdef choldowndate(np.ndarray[FLOAT_t, ndim=2] R, np.ndarray[FLOAT_t, ndim=1] x)
\ No newline at end of file
diff --git a/vendor/choldate/choldate/_choldate.pyx b/vendor/choldate/choldate/_choldate.pyx
new file mode 100644
index 0000000..8cdfdae
--- /dev/null
+++ b/vendor/choldate/choldate/_choldate.pyx
@@ -0,0 +1,79 @@
+#cython: cdivision=True
+#cython: boundscheck=True
+#cython: wraparound=True
+
+from libc.math cimport sqrt
+from libc.math cimport abs as cabs
+import numpy as np
+
+cdef inline FLOAT_t hypot(FLOAT_t x,FLOAT_t y):
+    cdef FLOAT_t t
+    x = cabs(x)
+    y = cabs(y)
+    t = x if x < y else y
+    x = x if x > y else y
+    t = t/x
+    return x*sqrt(1+t*t)
+
+cdef inline FLOAT_t rypot(FLOAT_t x,FLOAT_t y):
+    cdef FLOAT_t t
+    x = cabs(x)
+    y = cabs(y)
+    t = x if x < y else y
+    x = x if x > y else y
+    t = t/x
+    return x*sqrt(1-t*t)
+
+cpdef cholupdate(np.ndarray[FLOAT_t, ndim=2] R, np.ndarray[FLOAT_t, ndim=1] x):
+    '''
+    Update the upper triangular Cholesky factor R with the rank 1 addition
+    implied by x such that:
+    R_'R_ = R'R + outer(x,x)
+    where R_ is the upper triangular Cholesky factor R after updating.  Note
+    that both x and R are modified in place.
+    '''
+    cdef unsigned int p
+    cdef unsigned int k
+    cdef unsigned int i
+    cdef FLOAT_t r
+    cdef FLOAT_t c
+    cdef FLOAT_t s
+    cdef FLOAT_t a
+    cdef FLOAT_t b
+
+    p = <unsigned int>len(x)
+    for k in range(p):
+        r = hypot(R[<unsigned int>k,<unsigned int>k], x[<unsigned int>k])
+        c = r / R[<unsigned int>k,<unsigned int>k]
+        s = x[<unsigned int>k] / R[<unsigned int>k,<unsigned int>k]
+        R[<unsigned int>k,<unsigned int>k] = r
+        #TODO: Use BLAS instead of inner for loop
+        for i in range(<unsigned int>(k+1),<unsigned int>p):
+            R[<unsigned int>k,<unsigned int>i] = (R[<unsigned int>k,<unsigned int>i] + s*x[<unsigned int>i]) / c
+            x[<unsigned int>i] = c * x[<unsigned int>i] - s * R[<unsigned int>k,<unsigned int>i]
+
+cpdef choldowndate(np.ndarray[FLOAT_t, ndim=2] R, np.ndarray[FLOAT_t, ndim=1] x):
+    '''
+    Update the upper triangular Cholesky factor R with the rank 1 subtraction
+    implied by x such that:
+    R_'R_ = R'R - outer(x,x)
+    where R_ is the upper triangular Cholesky factor R after updating.  Note
+    that both x and R are modified in place.
+    '''
+    cdef unsigned int p
+    cdef unsigned int k
+    cdef unsigned int i
+    cdef FLOAT_t r
+    cdef FLOAT_t c
+    cdef FLOAT_t s
+
+    p = <unsigned int>len(x)
+    for k in range(p):
+        r = rypot(R[<unsigned int>k,<unsigned int>k], x[<unsigned int>k])
+        c = r / R[<unsigned int>k,<unsigned int>k]
+        s = x[<unsigned int>k] / R[<unsigned int>k,<unsigned int>k]
+        R[<unsigned int>k,<unsigned int>k] = r
+        #TODO: Use BLAS instead of inner for loop
+        for i in range(<unsigned int>(k+1),<unsigned int>p):
+            R[<unsigned int>k,<unsigned int>i] = (R[<unsigned int>k,<unsigned int>i] - s*x[<unsigned int>i]) / c
+            x[<unsigned int>i] = c * x[<unsigned int>i] - s * R[<unsigned int>k,<unsigned int>i]
diff --git a/vendor/choldate/pyproject.toml b/vendor/choldate/pyproject.toml
new file mode 100644
index 0000000..15e147e
--- /dev/null
+++ b/vendor/choldate/pyproject.toml
@@ -0,0 +1,14 @@
+[build-system]
+requires = ["setuptools>=64", "cython", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "choldate"
+version = "0.1.0+pycss.vendored"
+description = "Rank-1 Cholesky update/downdate. Vendored from modusdatascience/choldate with the PEP 518 build fixes proposed in upstream PR #8."
+license = { file = "LICENSE" }
+requires-python = ">=3.10"
+dependencies = ["numpy"]
+
+[tool.setuptools]
+packages = ["choldate"]
diff --git a/vendor/choldate/setup.py b/vendor/choldate/setup.py
new file mode 100644
index 0000000..8f79ee3
--- /dev/null
+++ b/vendor/choldate/setup.py
@@ -0,0 +1,16 @@
+import numpy
+from Cython.Build import cythonize
+from setuptools import Extension, setup
+
+setup(
+    ext_modules=cythonize(
+        [
+            Extension(
+                "choldate._choldate",
+                ["choldate/_choldate.pyx"],
+                include_dirs=[numpy.get_include()],
+            )
+        ],
+        language_level=3,
+    ),
+)