Merge pull request #78 from blei-lab/achille/prepare_release

Achille/prepare release

Author: velezbeltran

MANIFEST.in

@@ -5,3 +5,4 @@ six>=1.14.0
 tox
 twine
 scipy
+poetry

ci/requirements.txt

@@ -1,8 +1,42 @@
-[build-system]
-requires = [
-    "setuptools>=30.3.0",
+[tool.poetry]
+name = "treeffuser"
+version = "0.1.0"
+description = ""
+authors = [
+    "Nicolas Beltran-Velez <[email protected]>",
+    "Alessandro Antonio Grande <[email protected]>",
+    "Achille Nazaret <[email protected]>",
+]
+license = "MIT"
+readme = "README.rst"
+packages = [{include = "treeffuser", from= "src"}]
+repository = "https://github.com/blei-lab/treeffuser"
+include = [
+    "pyproject.toml",
+    "AUTHORS.rst",
+    "README.rst",
+    "LICENSE"
 ]
 
+[tool.poetry.dependencies]
+python = "^3.9"
+numpy = "^1.24"
+jaxtyping = "^0.2.19"
+einops = "^0.8.0"
+scipy = "^1.13.1"
+tqdm = "^4.66.4"
+lightgbm = "^4.3.0"
+ml-collections = "^0.1.1"
+scikit-learn = "^1.5.0"
+
+[tool.poetry.dev-dependencies]
+pytest = "^8.2.2"
+tox = "^3.20.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
 [tool.ruff.per-file-ignores]
 "ci/*" = ["S"]
 
@@ -56,3 +90,6 @@ target-version = ["py38"]
 
 [tool.ruff.format]
 indent-style="space"
+
+[tool.pytest.ini_options]
+pythonpath = "src"

pyproject.toml

@@ -4,12 +4,12 @@
 
 import numpy as np
 from einops import repeat
-from sklearn.metrics import r2_score
 
 from treeffuser._score_models import LightGBMScore
 from treeffuser.sde.sdes import VESDE
 
 from .utils import generate_bimodal_linear_regression_data
+from .utils import r2_score
 
 
 def test_linear_regression():

requirements.txt

@@ -1,9 +1,10 @@
 import numpy as np
 from scipy.stats import ks_2samp
-from sklearn.model_selection import train_test_split
 
 from treeffuser import LightGBMTreeffuser
-from utils import gaussian_mixture_pdf
+
+from .utils import gaussian_mixture_pdf
+from .utils import train_test_split
 
 
 def test_treeffuser_bimodal_linear_regression():

setup.py renamed to setup_deprecated.py

@@ -60,3 +60,34 @@ def gaussian_mixture_pdf(
     density = weight1 * gaussian_pdf(x, loc1, scale1, log=False)
     density += (1 - weight1) * gaussian_pdf(x, loc2, scale2, log=False)
     return np.log(density) if log else density
+
+
+def train_test_split(X, y, test_size=0.2, random_state=None):
+    """
+    Split the data into training and test sets.
+    """
+    n = X.shape[0]
+    if random_state is not None:
+        rng = np.random.default_rng(random_state)
+    else:
+        rng = np.random.default_rng()
+    idx = rng.permutation(n)
+    n_test = int(n * test_size)
+    idx_train = idx[n_test:]
+    idx_test = idx[:n_test]
+    return X[idx_train], X[idx_test], y[idx_train], y[idx_test]
+
+
+def r2_score(y_true, y_pred):
+    """
+    Compute the R^2 score.
+    """
+    y_true = y_true.flatten()
+    y_pred = y_pred.flatten()
+
+    y_mean = np.mean(y_true)
+    ss_tot = np.sum((y_true - y_mean) ** 2)
+    ss_res = np.sum((y_true - y_pred) ** 2)
+
+    r2 = 1 - ss_res / ss_tot
+    return r2

tests/test_score_models.py

@@ -8,19 +8,13 @@ commands =
 passenv =
     *
 
-; a generative tox configuration, see: https://tox.wiki/en/latest/user_guide.html#generative-environments
-# TODO: This should be fixed for the final release
 [tox]
+skipsdist = true
 envlist =
     clean,
     check,
     {py310,pypy310, py39,pypy39},
     report
-    #clean,
-    #check,
-    #docs,
-    #{py38,py39,py310,py311,py312,pypy38,pypy39,pypy310},
-    #report
 ignore_basepython_conflict = true
 
 [testenv]
@@ -40,24 +34,25 @@ setenv =
 passenv =
     *
 usedevelop = false
+allowlist_externals = poetry
 deps =
     pytest
     pytest-cov
 commands =
-    {posargs:pytest --cov --cov-report=term-missing --cov-report=xml -vv tests}
+    poetry install
+    poetry run pytest --cov --cov-report=term-missing --cov-report=xml -vv tests
 
 [testenv:check]
 deps =
     docutils
-    check-manifest
     pre-commit
     readme-renderer
     pygments
     isort
 skip_install = true
+allowlist_externals = poetry
 commands =
-    python setup.py check --strict --metadata --restructuredtext
-    check-manifest .
+    poetry check
     pre-commit run --all-files --show-diff-on-failure
 
 [testenv:docs]