aspire-inference 0.1.0a2__tar.gz

aspire_inference-0.1.0a2/.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on:
+  push:
+    branches: [ main, release* ]
+  pull_request:
+    branches: [ main, release* ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.11.x"
+          args: 'format --check'

aspire_inference-0.1.0a2/.github/workflows/publish.yml

@@ -0,0 +1,47 @@
+name: Publish Python distribution to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  pypi-publish:
+    name: Upload release to PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

aspire_inference-0.1.0a2/.github/workflows/tests.yml

@@ -0,0 +1,38 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, release* ]
+  pull_request:
+    branches: [ main, release* ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    name: Python ${{ matrix.python-version }} (${{ matrix.os }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [Ubuntu]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    runs-on: ${{ matrix.os }}-latest
+
+    steps:
+    - name: Checkout repository and submodules
+      uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install torch --index-url https://download.pytorch.org/whl/cpu
+        pip install -e .[test,torch,jax,minipcn,emcee,blackjax]
+    - name: Test with pytest
+      run: |
+        python -m pytest

aspire_inference-0.1.0a2/.gitignore

@@ -0,0 +1,165 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Project-specific
+outdir/

aspire_inference-0.1.0a2/.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.11.8
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        additional_dependencies:
+        - tomli

aspire_inference-0.1.0a2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Michael J. Williams
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

aspire_inference-0.1.0a2/PKG-INFO

@@ -0,0 +1,48 @@
+Metadata-Version: 2.4
+Name: aspire-inference
+Version: 0.1.0a2
+Summary: Accelerate Sequential Posterior Inference via REuse
+Author-email: "Michael J. Williams" <michaeljw1@googlemail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/mj-will/aspire
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: array-api-compat
+Requires-Dist: wrapt
+Requires-Dist: h5py
+Provides-Extra: jax
+Requires-Dist: jax; extra == "jax"
+Requires-Dist: jaxlib; extra == "jax"
+Requires-Dist: flowjax; extra == "jax"
+Provides-Extra: torch
+Requires-Dist: torch; extra == "torch"
+Requires-Dist: zuko; extra == "torch"
+Provides-Extra: minipcn
+Requires-Dist: minipcn; extra == "minipcn"
+Provides-Extra: emcee
+Requires-Dist: emcee; extra == "emcee"
+Provides-Extra: blackjax
+Requires-Dist: blackjax; extra == "blackjax"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-requires; extra == "test"
+Dynamic: license-file
+
+# aspire: Accelerated Sequential Posterior Inference via REuse
+
+aspire is a framework for reusing existing posterior samples to obtain new results at a reduced code.
+
+## Installation
+
+aspire can be installed from PyPI using `pip`
+
+```
+pip install aspire-inference
+```
+
+**Important:** the name of `aspire` on PyPI is `aspire-inference` but once installed
+the package can be imported and used as `aspire`.

aspire_inference-0.1.0a2/README.md

@@ -0,0 +1,14 @@
+# aspire: Accelerated Sequential Posterior Inference via REuse
+
+aspire is a framework for reusing existing posterior samples to obtain new results at a reduced code.
+
+## Installation
+
+aspire can be installed from PyPI using `pip`
+
+```
+pip install aspire-inference
+```
+
+**Important:** the name of `aspire` on PyPI is `aspire-inference` but once installed
+the package can be imported and used as `aspire`.

aspire_inference-0.1.0a2/aspire_inference.egg-info/PKG-INFO

@@ -0,0 +1,48 @@
+Metadata-Version: 2.4
+Name: aspire-inference
+Version: 0.1.0a2
+Summary: Accelerate Sequential Posterior Inference via REuse
+Author-email: "Michael J. Williams" <michaeljw1@googlemail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/mj-will/aspire
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: array-api-compat
+Requires-Dist: wrapt
+Requires-Dist: h5py
+Provides-Extra: jax
+Requires-Dist: jax; extra == "jax"
+Requires-Dist: jaxlib; extra == "jax"
+Requires-Dist: flowjax; extra == "jax"
+Provides-Extra: torch
+Requires-Dist: torch; extra == "torch"
+Requires-Dist: zuko; extra == "torch"
+Provides-Extra: minipcn
+Requires-Dist: minipcn; extra == "minipcn"
+Provides-Extra: emcee
+Requires-Dist: emcee; extra == "emcee"
+Provides-Extra: blackjax
+Requires-Dist: blackjax; extra == "blackjax"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-requires; extra == "test"
+Dynamic: license-file
+
+# aspire: Accelerated Sequential Posterior Inference via REuse
+
+aspire is a framework for reusing existing posterior samples to obtain new results at a reduced code.
+
+## Installation
+
+aspire can be installed from PyPI using `pip`
+
+```
+pip install aspire-inference
+```
+
+**Important:** the name of `aspire` on PyPI is `aspire-inference` but once installed
+the package can be imported and used as `aspire`.

aspire_inference-0.1.0a2/aspire_inference.egg-info/SOURCES.txt

@@ -0,0 +1,42 @@
+.gitignore
+.pre-commit-config.yaml
+LICENSE
+README.md
+pyproject.toml
+.github/workflows/lint.yml
+.github/workflows/publish.yml
+.github/workflows/tests.yml
+aspire_inference.egg-info/PKG-INFO
+aspire_inference.egg-info/SOURCES.txt
+aspire_inference.egg-info/dependency_links.txt
+aspire_inference.egg-info/requires.txt
+aspire_inference.egg-info/top_level.txt
+examples/basic_example.py
+src/aspire/__init__.py
+src/aspire/aspire.py
+src/aspire/history.py
+src/aspire/plot.py
+src/aspire/samples.py
+src/aspire/transforms.py
+src/aspire/utils.py
+src/aspire/flows/__init__.py
+src/aspire/flows/base.py
+src/aspire/flows/jax/__init__.py
+src/aspire/flows/jax/flows.py
+src/aspire/flows/jax/utils.py
+src/aspire/flows/torch/__init__.py
+src/aspire/flows/torch/flows.py
+src/aspire/samplers/__init__.py
+src/aspire/samplers/base.py
+src/aspire/samplers/importance.py
+src/aspire/samplers/mcmc.py
+src/aspire/samplers/smc/__init__.py
+src/aspire/samplers/smc/base.py
+src/aspire/samplers/smc/blackjax.py
+src/aspire/samplers/smc/emcee.py
+src/aspire/samplers/smc/minipcn.py
+tests/conftest.py
+tests/integration_tests/conftest.py
+tests/integration_tests/test_integration.py
+tests/test_flows/test_jax_flows/test_flowjax_flows.py
+tests/test_flows/test_torch_flows/test_zuko_flows.py

aspire_inference-0.1.0a2/aspire_inference.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

aspire_inference-0.1.0a2/aspire_inference.egg-info/requires.txt

@@ -0,0 +1,27 @@
+matplotlib
+numpy
+array-api-compat
+wrapt
+h5py
+
+[blackjax]
+blackjax
+
+[emcee]
+emcee
+
+[jax]
+jax
+jaxlib
+flowjax
+
+[minipcn]
+minipcn
+
+[test]
+pytest
+pytest-requires
+
+[torch]
+torch
+zuko

aspire_inference-0.1.0a2/aspire_inference.egg-info/top_level.txt

@@ -0,0 +1 @@
+aspire

aspire_inference-0.1.0a2/examples/basic_example.py

@@ -0,0 +1,87 @@
+"""
+This examples demonstrates how to use aspire to fit a flow to a simple Gaussian
+likelihood with a uniform prior.
+"""
+
+import math
+from pathlib import Path
+
+from aspire import Aspire
+from aspire.plot import plot_comparison
+from aspire.samples import Samples
+from aspire.utils import AspireFile, configure_logger
+from scipy.stats import norm, uniform
+
+# Configure the logger
+configure_logger("INFO")
+
+outdir = Path("outdir") / "basic_example"
+outdir.mkdir(parents=True, exist_ok=True)
+
+# Number of dimensions
+dims = 4
+
+
+# Define the log likelihood and log prior
+def log_likelihood(samples: Samples):
+    # The log likelihood must accept a Samples object
+    # The samples object contains the samples in the attribute samples.x
+    return norm(2, 1).logpdf(samples.x).sum(axis=-1)
+
+
+def log_prior(samples: Samples):
+    return uniform(-10, 20).logpdf(samples.x).sum(axis=-1)
+
+
+# True evidence is analytic for a Gaussian likelihood and uniform prior
+true_log_evidence = -dims * math.log(20)
+
+# Generate some initial samples
+# These are slightly biased compared to the true posterior
+initial_samples = Samples(norm(2.5, 1.0).rvs(size=(5000, dims)))
+# Define the parameters and prior bounds
+parameters = [f"x_{i}" for i in range(dims)]
+prior_bounds = {p: [-10, 10] for p in parameters}
+
+# Define the aspire object
+aspire = Aspire(
+    log_likelihood=log_likelihood,
+    log_prior=log_prior,
+    dims=dims,
+    parameters=parameters,
+    prior_bounds=prior_bounds,
+)
+
+# Fit the flow to the initial samples
+history = aspire.fit(
+    initial_samples,
+    n_epochs=50,
+)
+# Plot the loss
+fig = history.plot_loss()
+fig.savefig(outdir / "loss.png")
+
+# Produce samples from the posterior
+samples = aspire.sample_posterior(5000)
+
+# Save the the results to a file
+# The AspireFile is a small wrapper around h5py.File that automatically
+# includes additional metadata
+with AspireFile(outdir / "aspire_result.h5", "w") as f:
+    aspire.save_config(f, "aspire_config")
+    samples.save(f, "posterior_samples")
+    history.save(f, "flow_history")
+
+fig = plot_comparison(
+    initial_samples,
+    samples,
+    samples,
+    per_samples_kwargs=[
+        dict(include_weights=True, color="C0"),
+        dict(include_weights=False, color="lightgrey"),
+        dict(include_weights=True, color="C1"),
+    ],
+    labels=["Training samples", "Samples (w/o weights)", "Posterior samples"],
+)
+
+fig.savefig(outdir / "comparison.png")

aspire_inference-0.1.0a2/pyproject.toml

@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools>=45", "setuptools-scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "aspire-inference"
+authors = [
+    {name = "Michael J. Williams", email = "michaeljw1@googlemail.com"},
+]
+description = "Accelerate Sequential Posterior Inference via REuse"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+    "matplotlib",
+    "numpy",
+    "array-api-compat",
+    "wrapt",
+    "h5py",
+]
+
+dynamic = ["version"]
+
+[project.optional-dependencies]
+jax = [
+    "jax",
+    "jaxlib",
+    "flowjax"
+]
+torch = [
+    "torch",
+    "zuko",
+]
+minipcn = [
+    "minipcn",
+]
+emcee = [
+    "emcee",
+]
+blackjax = [
+    "blackjax",
+]
+test = [
+    "pytest",
+    "pytest-requires",
+]
+
+[project.urls]
+Homepage = "https://github.com/mj-will/aspire"
+
+[tool.setuptools_scm]
+
+[tool.setuptools.package-dir]
+aspire = "src/aspire"
+
+[tool.ruff]
+line-length = 79
+indent-width = 4
+target-version = "py39"
+
+[tool.ruff.lint]
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+extend-select = ["I"]

aspire_inference-0.1.0a2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

aspire_inference-0.1.0a2/src/aspire/__init__.py

@@ -0,0 +1,19 @@
+"""
+aspire: Accelerated Sequential Posterior Inference via REuse
+"""
+
+import logging
+from importlib.metadata import PackageNotFoundError, version
+
+from .aspire import Aspire
+
+try:
+    __version__ = version("aspire")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+__all__ = [
+    "Aspire",
+]