From f306c4b563b9027317660ea2f4b18f986c7da23f Mon Sep 17 00:00:00 2001 From: John Franklin Crenshaw <41785729+jfcrenshaw@users.noreply.github.com> Date: Mon, 26 Feb 2024 08:47:24 -0800 Subject: [PATCH] =?UTF-8?q?Moved=20np.trapz=20->=20scipy.integrate.trapezo?= =?UTF-8?q?id.=20Updated=20version=20requirem=E2=80=A6=20(#96)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Moved np.trapz -> scipy.integrate.trapezoid. Updated version requirements. Some linting. * Bumped python version array in github action. * Github action version numbers now strings. --- .github/workflows/main.yml | 4 +- poetry.lock | 3404 +++++++++++++++++++++++++---------- pyproject.toml | 60 +- pzflow/__init__.py | 2 +- pzflow/bijectors.py | 4 - pzflow/distributions.py | 2 +- pzflow/examples.py | 4 +- pzflow/flow.py | 3 +- pzflow/flowEnsemble.py | 6 +- tests/test_distributions.py | 4 +- tests/test_ensemble.py | 9 +- tests/test_examples.py | 1 + tests/test_utils.py | 1 - tests/test_version.py | 7 +- 14 files changed, 2463 insertions(+), 1048 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8b57e6f..9ba5c97 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -18,7 +18,7 @@ jobs: fail-fast: true matrix: os: [ubuntu-latest] - python-version: [3.7, 3.8, 3.9] + python-version: ["3.9", "3.10", "3.11"] runs-on: ${{ matrix.os }} steps: @@ -37,7 +37,7 @@ jobs: uses: actions/setup-python@v3 with: 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authors = ["John Franklin Crenshaw "] license = "MIT" @@ -9,38 +9,38 @@ readme = "README.md" [tool.poetry.dependencies] -python = "^3.8.1" -jax = "^0.4.2" -jaxlib = "^0.4.2" -optax = "^0.1.4" +python = "^3.9" +jax = ">=0.4.16" +jaxlib = ">=0.4.16" +optax = ">=0.1.4" pandas = ">=1.1" -dill = "^0.3.6" -tqdm = "^4.64.1" +dill = ">=0.3.6" +tqdm = ">=4.64.1" [tool.poetry.dev-dependencies] -pre-commit = "^3.0.3" -black = "^23.1.0" -mypy = "^0.931" -isort = "^5.12.0" -flake8 = "^6.0.0" -flake8-bugbear = "^23.1.20" -flake8-builtins = "^2.1.0" -flake8-comprehensions = "^3.10.1" -flake8-docstrings = "^1.7.0" -flake8-isort = "^6.0.0" -flake8-markdown = "^0.4.0" -flake8-print = "^5.0.0" -flake8-pytest-style = "^1.6.0" -flake8-simplify = "^0.19.3" -flake8-tidy-imports = "^4.8.0" -pandas-vet = "^0.2.3" -pep8-naming = "^0.13.3" -pytest = "^7.2.1" -pytest-cov = "^4.0.0" -pytest-xdist = "^3.1.0" -jupyter = "^1.0.0" -matplotlib = "^3.6.3" -toml = "^0.10.2" +pre-commit = ">=3.0.3" +black = ">=23.1.0" +mypy = ">=0.931" +isort = ">=5.12.0" +flake8 = ">=6.0.0" +flake8-bugbear = ">=23.1.20" +flake8-builtins = ">=2.1.0" +flake8-comprehensions = ">=3.10.1" +flake8-docstrings = ">=1.7.0" +flake8-isort = ">=6.0.0" +flake8-markdown = ">=0.4.0" +flake8-print = ">=5.0.0" +flake8-pytest-style = ">=1.6.0" +flake8-simplify = ">=0.19.3" +flake8-tidy-imports = ">=4.8.0" +pandas-vet = ">=0.2.3" +pep8-naming = ">=0.13.3" +pytest = ">=7.2.1" +pytest-cov = ">=4.0.0" +pytest-xdist = ">=3.1.0" +jupyter = ">=1.0.0" +matplotlib = ">=3.6.3" +toml = ">=0.10.2" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/pzflow/__init__.py b/pzflow/__init__.py index f24ec12..d5b3e0d 100644 --- a/pzflow/__init__.py +++ b/pzflow/__init__.py @@ -3,4 +3,4 @@ from pzflow.flow import Flow from pzflow.flowEnsemble import FlowEnsemble -__version__ = "3.1.2" +__version__ = "3.1.3" diff --git a/pzflow/bijectors.py b/pzflow/bijectors.py index f236c2c..215fbb2 100644 --- a/pzflow/bijectors.py +++ b/pzflow/bijectors.py @@ -143,7 +143,6 @@ def Chain( @InitFunction def init_fun(rng, input_dim, **kwargs): - all_params, forward_funs, inverse_funs = [], [], [] for init_f in init_funs: rng, layer_rng = random.split(rng) @@ -237,7 +236,6 @@ def ColorTransform( @InitFunction def init_fun(rng, input_dim, **kwargs): - # array of all the indices all_idx = jnp.arange(input_dim) # indices for columns to stick at the front @@ -462,7 +460,6 @@ def NeuralSplineCoupling( @InitFunction def init_fun(rng, input_dim, **kwargs): - if transformed_dim is None: upper_dim = input_dim // 2 # variables that determine NN params lower_dim = ( @@ -797,7 +794,6 @@ def Shuffle() -> Tuple[InitFunction, Bijector_Info]: @InitFunction def init_fun(rng, input_dim, **kwargs): - perm = random.permutation(rng, jnp.arange(input_dim)) inv_perm = jnp.argsort(perm) diff --git a/pzflow/distributions.py b/pzflow/distributions.py index a4b29b9..06cc8d8 100644 --- a/pzflow/distributions.py +++ b/pzflow/distributions.py @@ -133,6 +133,7 @@ def sample( ) return 2 * self.B * (samples - 0.5) + class CentBeta13(LatentDist): """A centered Beta distribution with alpha, beta = 13. @@ -228,7 +229,6 @@ def sample( return 2 * self.B * (samples - 0.5) - class Normal(LatentDist): """A multivariate Gaussian distribution with mean zero and unit variance. diff --git a/pzflow/examples.py b/pzflow/examples.py index 7222981..4d1c265 100644 --- a/pzflow/examples.py +++ b/pzflow/examples.py @@ -110,6 +110,8 @@ def get_example_flow() -> Flow: For more info: `print(example_flow().info)`. """ this_dir, _ = os.path.split(__file__) - flow_path = os.path.join(this_dir, f"{EXAMPLE_FILE_DIR}/example-flow.pzflow.pkl") + flow_path = os.path.join( + this_dir, f"{EXAMPLE_FILE_DIR}/example-flow.pzflow.pkl" + ) flow = Flow(file=flow_path) return flow diff --git a/pzflow/flow.py b/pzflow/flow.py index 343e95e..53c74d8 100644 --- a/pzflow/flow.py +++ b/pzflow/flow.py @@ -8,6 +8,7 @@ import optax import pandas as pd from jax import grad, jit, random +from jax.scipy.integrate import trapezoid from tqdm import tqdm from pzflow import distributions @@ -731,7 +732,7 @@ def check_flags(data): if normalize: # normalize so they integrate to one - pdfs = pdfs / jnp.trapz(y=pdfs, x=grid).reshape(-1, 1) + pdfs = pdfs / trapezoid(y=pdfs, x=grid).reshape(-1, 1) if nan_to_zero: # set NaN's equal to zero probability pdfs = jnp.nan_to_num(pdfs, nan=0.0) diff --git a/pzflow/flowEnsemble.py b/pzflow/flowEnsemble.py index 8cb6971..c4c4dc9 100644 --- a/pzflow/flowEnsemble.py +++ b/pzflow/flowEnsemble.py @@ -1,4 +1,5 @@ """Define FlowEnsemble object that holds an ensemble of normalizing flows.""" + from typing import Any, Callable, Sequence, Tuple import dill as pickle @@ -6,6 +7,7 @@ import numpy as np import pandas as pd from jax import random +from jax.scipy.integrate import trapezoid from pzflow import Flow, distributions from pzflow.bijectors import Bijector_Info, InitFunction @@ -336,7 +338,7 @@ def posterior( # return the ensemble of posteriors if normalize: ensemble = ensemble.reshape(-1, grid.size) - ensemble = ensemble / jnp.trapz(y=ensemble, x=grid).reshape( + ensemble = ensemble / trapezoid(y=ensemble, x=grid).reshape( -1, 1 ) ensemble = ensemble.reshape(inputs.shape[0], -1, grid.size) @@ -345,7 +347,7 @@ def posterior( # return mean over ensemble pdfs = ensemble.mean(axis=1) if normalize: - pdfs = pdfs / jnp.trapz(y=pdfs, x=grid).reshape(-1, 1) + pdfs = pdfs / trapezoid(y=pdfs, x=grid).reshape(-1, 1) return pdfs def sample( diff --git a/tests/test_distributions.py b/tests/test_distributions.py index 7346e3d..8b414d0 100644 --- a/tests/test_distributions.py +++ b/tests/test_distributions.py @@ -14,12 +14,11 @@ (Joint, (Normal(1), Uniform(1, 4)), ((), ())), (Joint, (Normal(1), Tdist(1)), ((), jnp.log(30.0))), (Joint, (Joint(Normal(1), Uniform(1)).info[1]), ((), ())), - (CentBeta13, (2, 4), ()) + (CentBeta13, (2, 4), ()), ], ) class TestDistributions: def test_returns_correct_shapes(self, distribution, inputs, params): - dist = distribution(*inputs) nsamples = 8 @@ -30,7 +29,6 @@ def test_returns_correct_shapes(self, distribution, inputs, params): assert log_prob.shape == (nsamples,) def test_control_sample_randomness(self, distribution, inputs, params): - dist = distribution(*inputs) nsamples = 8 diff --git a/tests/test_ensemble.py b/tests/test_ensemble.py index 97c2078..2080790 100644 --- a/tests/test_ensemble.py +++ b/tests/test_ensemble.py @@ -4,6 +4,7 @@ import pandas as pd import pytest from jax import random +from jax.scipy.integrate import trapezoid from pzflow import Flow, FlowEnsemble from pzflow.bijectors import Reverse, RollingSplineCoupling @@ -17,7 +18,6 @@ def test_log_prob(): - lpEns = flowEns.log_prob(x, returnEnsemble=True) assert lpEns.shape == (3, 2) @@ -36,7 +36,6 @@ def test_log_prob(): def test_posterior(): - grid = jnp.linspace(-1, 1, 5) pEns = flowEns.posterior(x, "x", grid, returnEnsemble=True) @@ -53,12 +52,11 @@ def test_posterior(): p0 = flow0.posterior(x, "x", grid, normalize=False) p1 = flow1.posterior(x, "x", grid, normalize=False) manualMean = (p0 + p1) / 2 - manualMean = manualMean / jnp.trapz(y=manualMean, x=grid).reshape(-1, 1) + manualMean = manualMean / trapezoid(y=manualMean, x=grid).reshape(-1, 1) assert jnp.allclose(pEnsMean, manualMean) def test_sample(): - # first test everything with returnEnsemble=False sEns = flowEns.sample(10, seed=0).values assert sEns.shape == (10, 2) @@ -81,7 +79,6 @@ def test_sample(): def test_conditional_sample(): - cEns = FlowEnsemble( ("x", "y"), RollingSplineCoupling(nlayers=2, n_conditions=2), @@ -122,7 +119,6 @@ def test_conditional_sample(): def test_train(): - data = random.normal(random.PRNGKey(0), shape=(100, 2)) data = pd.DataFrame(np.array(data), columns=("x", "y")) @@ -138,7 +134,6 @@ def test_train(): def test_load_ensemble(tmp_path): - flowEns = FlowEnsemble(("x", "y"), RollingSplineCoupling(nlayers=2), N=2) preSave = flowEns.sample(10, seed=0) diff --git a/tests/test_examples.py b/tests/test_examples.py index 1ef6f3f..6ce82c2 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -21,6 +21,7 @@ def test_get_city_data(): assert isinstance(data, pd.DataFrame) assert data.shape == (47_966, 5) + def test_get_checkerboard_data(): data = examples.get_checkerboard_data() assert isinstance(data, pd.DataFrame) diff --git a/tests/test_utils.py b/tests/test_utils.py index fd65cd6..3cee814 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -7,7 +7,6 @@ def test_build_bijector_from_info(): - x = jnp.array([[1.0, 2.0, 3.0, 4.0], [5.0, 6.0, 7.0, 8.0]]) init_fun, info1 = Chain( diff --git a/tests/test_version.py b/tests/test_version.py index 150ffc8..1accd8a 100644 --- a/tests/test_version.py +++ b/tests/test_version.py @@ -1,7 +1,10 @@ -import toml from pathlib import Path + +import toml + import pzflow + def test_versions_are_in_sync(): """Checks if the pyproject.toml and pzflow.__init__.py __version__ are in sync.""" @@ -10,5 +13,5 @@ def test_versions_are_in_sync(): pyproject_version = pyproject["tool"]["poetry"]["version"] package_init_version = pzflow.__version__ - + assert package_init_version == pyproject_version