From 6a427adbe0557fe4129165ff80dd652c7475de1a Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 09:25:47 +0200 Subject: [PATCH 01/12] Add Hatch --- .pre-commit-config.yaml | 59 - README.md | 5 +- examples/backend.py | 4 +- examples/classification.py | 4 - poetry.lock | 4284 ----------------- pyproject.old.toml | 198 + pyproject.toml | 228 +- {gpjax => src/gpjax}/__init__.py | 0 {gpjax => src/gpjax}/citation.py | 0 {gpjax => src/gpjax}/dataset.py | 0 .../gpjax}/decision_making/__init__.py | 0 .../gpjax}/decision_making/decision_maker.py | 0 .../decision_making/posterior_handler.py | 0 .../gpjax}/decision_making/search_space.py | 0 .../test_functions/__init__.py | 0 .../test_functions/continuous_functions.py | 0 .../test_functions/non_conjugate_functions.py | 0 .../utility_functions/__init__.py | 0 .../decision_making/utility_functions/base.py | 0 .../utility_functions/expected_improvement.py | 0 .../probability_of_improvement.py | 0 .../utility_functions/thompson_sampling.py | 0 .../decision_making/utility_maximizer.py | 0 {gpjax => src/gpjax}/decision_making/utils.py | 0 {gpjax => src/gpjax}/distributions.py | 0 {gpjax => src/gpjax}/fit.py | 0 {gpjax => src/gpjax}/gps.py | 0 {gpjax => src/gpjax}/integrators.py | 0 {gpjax => src/gpjax}/kernels/__init__.py | 0 .../gpjax}/kernels/approximations/__init__.py | 0 .../gpjax}/kernels/approximations/rff.py | 0 {gpjax => src/gpjax}/kernels/base.py | 0 .../gpjax}/kernels/computations/__init__.py | 0 .../gpjax}/kernels/computations/base.py | 0 .../kernels/computations/basis_functions.py | 0 .../kernels/computations/constant_diagonal.py | 0 .../gpjax}/kernels/computations/dense.py | 0 .../gpjax}/kernels/computations/diagonal.py | 0 .../gpjax}/kernels/computations/eigen.py | 0 .../gpjax}/kernels/non_euclidean/__init__.py | 0 .../gpjax}/kernels/non_euclidean/graph.py | 0 .../gpjax}/kernels/non_euclidean/utils.py | 0 .../gpjax}/kernels/nonstationary/__init__.py | 0 .../gpjax}/kernels/nonstationary/arccosine.py | 0 .../gpjax}/kernels/nonstationary/linear.py | 0 .../kernels/nonstationary/polynomial.py | 0 .../gpjax}/kernels/stationary/__init__.py | 0 .../gpjax}/kernels/stationary/base.py | 0 .../gpjax}/kernels/stationary/matern12.py | 0 .../gpjax}/kernels/stationary/matern32.py | 0 .../gpjax}/kernels/stationary/matern52.py | 0 .../gpjax}/kernels/stationary/periodic.py | 0 .../kernels/stationary/powered_exponential.py | 0 .../kernels/stationary/rational_quadratic.py | 0 .../gpjax}/kernels/stationary/rbf.py | 0 .../gpjax}/kernels/stationary/utils.py | 0 .../gpjax}/kernels/stationary/white.py | 0 {gpjax => src/gpjax}/likelihoods.py | 0 {gpjax => src/gpjax}/lower_cholesky.py | 0 {gpjax => src/gpjax}/mean_functions.py | 0 {gpjax => src/gpjax}/objectives.py | 0 {gpjax => src/gpjax}/parameters.py | 0 {gpjax => src/gpjax}/progress_bar.py | 0 {gpjax => src/gpjax}/scan.py | 0 {gpjax => src/gpjax}/typing.py | 0 {gpjax => src/gpjax}/variational_families.py | 0 tests/test_kernels/test_nonstationary.py | 5 +- tests/test_kernels/test_stationary.py | 5 +- 68 files changed, 337 insertions(+), 4455 deletions(-) delete mode 100644 .pre-commit-config.yaml delete mode 100644 poetry.lock create mode 100644 pyproject.old.toml rename {gpjax => src/gpjax}/__init__.py (100%) rename {gpjax => src/gpjax}/citation.py (100%) rename {gpjax => src/gpjax}/dataset.py (100%) rename {gpjax => src/gpjax}/decision_making/__init__.py (100%) rename {gpjax => src/gpjax}/decision_making/decision_maker.py (100%) rename {gpjax => src/gpjax}/decision_making/posterior_handler.py (100%) rename {gpjax => src/gpjax}/decision_making/search_space.py (100%) rename {gpjax => src/gpjax}/decision_making/test_functions/__init__.py (100%) rename {gpjax => src/gpjax}/decision_making/test_functions/continuous_functions.py (100%) rename {gpjax => src/gpjax}/decision_making/test_functions/non_conjugate_functions.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_functions/__init__.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_functions/base.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_functions/expected_improvement.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_functions/probability_of_improvement.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_functions/thompson_sampling.py (100%) rename {gpjax => src/gpjax}/decision_making/utility_maximizer.py (100%) rename {gpjax => src/gpjax}/decision_making/utils.py (100%) rename {gpjax => src/gpjax}/distributions.py (100%) rename {gpjax => src/gpjax}/fit.py (100%) rename {gpjax => src/gpjax}/gps.py (100%) rename {gpjax => src/gpjax}/integrators.py (100%) rename {gpjax => src/gpjax}/kernels/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/approximations/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/approximations/rff.py (100%) rename {gpjax => src/gpjax}/kernels/base.py (100%) rename {gpjax => src/gpjax}/kernels/computations/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/computations/base.py (100%) rename {gpjax => src/gpjax}/kernels/computations/basis_functions.py (100%) rename {gpjax => src/gpjax}/kernels/computations/constant_diagonal.py (100%) rename {gpjax => src/gpjax}/kernels/computations/dense.py (100%) rename {gpjax => src/gpjax}/kernels/computations/diagonal.py (100%) rename {gpjax => src/gpjax}/kernels/computations/eigen.py (100%) rename {gpjax => src/gpjax}/kernels/non_euclidean/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/non_euclidean/graph.py (100%) rename {gpjax => src/gpjax}/kernels/non_euclidean/utils.py (100%) rename {gpjax => src/gpjax}/kernels/nonstationary/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/nonstationary/arccosine.py (100%) rename {gpjax => src/gpjax}/kernels/nonstationary/linear.py (100%) rename {gpjax => src/gpjax}/kernels/nonstationary/polynomial.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/__init__.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/base.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/matern12.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/matern32.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/matern52.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/periodic.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/powered_exponential.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/rational_quadratic.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/rbf.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/utils.py (100%) rename {gpjax => src/gpjax}/kernels/stationary/white.py (100%) rename {gpjax => src/gpjax}/likelihoods.py (100%) rename {gpjax => src/gpjax}/lower_cholesky.py (100%) rename {gpjax => src/gpjax}/mean_functions.py (100%) rename {gpjax => src/gpjax}/objectives.py (100%) rename {gpjax => src/gpjax}/parameters.py (100%) rename {gpjax => src/gpjax}/progress_bar.py (100%) rename {gpjax => src/gpjax}/scan.py (100%) rename {gpjax => src/gpjax}/typing.py (100%) rename {gpjax => src/gpjax}/variational_families.py (100%) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 958818a7c..000000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,59 +0,0 @@ -minimum_pre_commit_version: 2.15.0 -ci: - autofix_prs: false -repos: - - repo: https://github.com/psf/black - rev: 23.3.0 - hooks: - - id: black - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - exclude_types: [json, binary] - - repo: https://github.com/codespell-project/codespell - rev: v2.2.2 - hooks: - - id: codespell - types_or: [python, markdown] - additional_dependencies: [tomli] - - repo: https://github.com/PyCQA/isort - rev: 5.12.0 - hooks: - - id: isort - exclude: examples/ - - repo: local - hooks: - - id: commitizen - name: commitizen - entry: cz check - args: [--commit-msg-file] - require_serial: true - language: system - stages: [commit-msg] - - id: absolufy-imports - name: absolufy-imports - entry: absolufy-imports - require_serial: true - language: system - types: [python] - - id: ruff - name: ruff - entry: ruff check - args: ["--exit-non-zero-on-fix"] - require_serial: true - language: system - types: [python] - exclude: examples/ - # - repo: https://github.com/econchick/interrogate - # rev: 1.5.0 - # hooks: - # - id: interrogate - # args: - # [ - # "gpjax", - # "--config", - # "pyproject.toml", - # ] - # pass_filenames: false diff --git a/README.md b/README.md index 721d4d747..82b9115f7 100644 --- a/README.md +++ b/README.md @@ -205,13 +205,14 @@ configuration in development mode. ```bash git clone https://github.com/JaxGaussianProcesses/GPJax.git cd GPJax -poetry install +hatch env create +hatch shell ``` > We recommend you check your installation passes the supplied unit tests: > > ```python -> poetry run pytest +> hatch run dev:test > ``` # Citing GPJax diff --git a/examples/backend.py b/examples/backend.py index 8e8bbe3a9..3e81b4b0e 100644 --- a/examples/backend.py +++ b/examples/backend.py @@ -269,10 +269,10 @@ # %% import typing as tp -from jaxtyping import Float, Num +from jaxtyping import Num from gpjax.mean_functions import AbstractMeanFunction -from gpjax.parameters import Parameter, Real +from gpjax.parameters import Parameter from gpjax.typing import ScalarFloat, Array diff --git a/examples/classification.py b/examples/classification.py index c53cf4354..e6e2229f8 100644 --- a/examples/classification.py +++ b/examples/classification.py @@ -27,14 +27,11 @@ config.update("jax_enable_x64", True) -from time import time -import blackjax from flax import nnx import jax import jax.numpy as jnp import jax.random as jr import jax.scipy as jsp -import jax.tree_util as jtu from jaxtyping import ( Array, Float, @@ -43,7 +40,6 @@ import matplotlib.pyplot as plt import optax as ox import 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+documentation = "https://docs.jaxgaussianprocesses.com/" +keywords = ["gaussian-processes jax machine-learning bayesian"] +packages = [{ include = "gpjax" }] + +[tool.poetry.dependencies] +python = ">=3.10,<3.12" +jax = "<0.4.28" +jaxlib = "<0.4.28" +optax = "^0.2.1" +jaxtyping = "^0.2.10" +tqdm = "^4.66.2" +tensorflow-probability = "^0.24.0" +beartype = "^0.16.1" +cola-ml = "0.0.5" +jaxopt = "^0.8.3" +flax = "^0.8.4" +numpy = "<2.0.0" + +[tool.poetry.group.dev.dependencies] +ruff = "~0" +pre-commit = "^3.2.2" +interrogate = "^1.5.0" +codespell = "^2.2.4" +pytest = "^7.2.2" +pytest-cov = "^4.0.0" +pytest-pretty = "^1.1.1" +pytest-xdist = "^3.2.1" +coverage = "^7.2.2" +absolufy-imports = "^0.3.1" +xdoctest = "^1.1.1" +mktestdocs = "^0.2.1" +asv = "^0.6.0" + + +[tool.poetry.group.docs.dependencies] +mkdocs = "^1.5.3" +mkdocs-material = "^9.5.12" +mkdocstrings = { version = "^0.25.1", extras = ["python"] } +mkdocs-jupyter = "^0.24.3" +mkdocs-gen-files = "^0.5.0" +mkdocs-literate-nav = "^0.6.0" +mkdocs-git-authors-plugin = "^0.7.0" +matplotlib = "^3.7.1" +seaborn = "^0.12.2" +networkx = "^3.0" +jupytext = "^1.14.5" +ipython = "^8.11.0" +ipykernel = "^6.22.0" +watermark = "^2.3.1" +blackjax = "^0.9.6" +ipywidgets = "^8.0.5" +pandas = "^1.5.3" +pymdown-extensions = "^10.7.1" +nbconvert = "^7.16.2" +markdown-katex = "^202406.1035" +scikit-learn = "^1.5.1" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.black] # https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#configuration-via-a-file +line-length = 88 +target-version = ["py310"] + +[tool.pytest.ini_options] # https://docs.pytest.org/en/latest/reference/reference.html#ini-options-ref +# addopts = "--color=yes --doctest-modules --exitfirst --failed-first --strict-config --strict-markers --typeguard-packages=my_package --verbosity=2 --junitxml=reports/pytest.xml" +filterwarnings = ["error", "ignore::DeprecationWarning"] +testpaths = ["gpjax", "tests"] +xfail_strict = true + +[tool.ruff] # https://github.com/charliermarsh/ruff +fix = true +cache-dir = "~/.cache/ruff" +exclude = ["docs/", "examples/"] +line-length = 88 +src = ["gpjax", "tests"] +target-version = "py310" + +[tool.ruff.lint] +dummy-variable-rgx = "^_$" +select = [ + "F", + # pycodestyle + "E", + "W", + # flake8-2020 + "YTT", + # flake8-bugbear + "B", + # flake8-quotes + "Q", + # pylint + "PLE", + "PLR", + "PLW", + # misc lints + "PIE", + # flake8-pyi + "PYI", + # tidy imports + "TID", + # implicit string concatenation + "ISC", +] +ignore = [ + # calls in argument defaults + "B008", + # space before : (needed for how black formats slicing) + # "E203", # not yet implemented + # module level import not at top of file + "E402", + # do not assign a lambda expression, use a def + "E731", + "E501", + "S303", + "S307", + "RET504", + "S101", + "F722", + 'PLR2004', + "PLR0913", +] +unfixable = ["ERA001", "F401", "F841", "T201", "T203"] + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.ruff.lint.per-file-ignores] +"gpjax/__init__.py" = ['I', 'F401', 'E402', 'D104'] +"gpjax/progress_bar.py" = ["TCH004"] +"gpjax/scan.py" = ["PLR0913"] +"gpjax/citation.py" = ["F811"] +"tests/test_base/test_module.py" = ["PLR0915"] +"tests/test_objectives.py" = ["PLR0913"] +"docs/examples/barycentres.py" = ["PLR0913"] + + +[tool.isort] +profile = "black" +combine_as_imports = true +force_sort_within_sections = true +force_grid_wrap = 2 +skip = 'docs' + +[tool.coverage.report] # https://coverage.readthedocs.io/en/latest/config.html#report +fail_under = 50 +precision = 1 +show_missing = true +skip_covered = true +exclude_lines = ["if TYPE_CHECKING:"] + +[tool.coverage.run] # https://coverage.readthedocs.io/en/latest/config.html#run +branch = true +command_line = "--module pytest" +data_file = "reports/.coverage" +source = ["src"] + +[tool.coverage.xml] # https://coverage.readthedocs.io/en/latest/config.html#xml +output = "reports/coverage.xml" + +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" + +[tool.poetry-dynamic-versioning.substitution] +files = ["gpjax/__init__.py"] + +[tool.codespell] +ignore-words-list = "fro" # Frobenius + +[tool.interrogate] +ignore-init-method = true +ignore-init-module = true +fail-under = 64 +exclude = [ + "setup.py", + "docs", + "tests", + "gpjax/__init__.py", + "gpjax/citation.py", +] +verbose = 2 +quiet = false +color = true diff --git a/pyproject.toml b/pyproject.toml index 396e3f928..8d68dd623 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,85 +1,136 @@ -[tool.poetry] +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] name = "gpjax" -version = "0.9.0" -description = "Gaussian processes in JAX." -authors = [ - "Thomas Pinder ", - "Daniel Dodd ", -] -license = "Apache-2.0" +dynamic = ["version"] +description = 'Gaussian processes in JAX.' readme = "README.md" -homepage = "https://github.com/JaxGaussianProcesses/GPJax" -repository = "https://github.com/JaxGaussianProcesses/GPJax" -include = ["LICENSE"] -documentation = "https://docs.jaxgaussianprocesses.com/" +requires-python = ">=3.9, <3.13" +license = "Apache-2.0" keywords = ["gaussian-processes jax machine-learning bayesian"] -packages = [{ include = "gpjax" }] - -[tool.poetry.dependencies] -python = ">=3.10,<3.12" -jax = "<0.4.28" -jaxlib = "<0.4.28" -optax = "^0.2.1" -jaxtyping = "^0.2.10" -tqdm = "^4.66.2" -tensorflow-probability = "^0.24.0" -beartype = "^0.16.1" -cola-ml = "0.0.5" -jaxopt = "^0.8.3" -flax = "^0.8.4" -numpy = "<2.0.0" - -[tool.poetry.group.dev.dependencies] -ruff = "~0" -pre-commit = "^3.2.2" -interrogate = "^1.5.0" -codespell = "^2.2.4" -pytest = "^7.2.2" -pytest-cov = "^4.0.0" -pytest-pretty = "^1.1.1" -pytest-xdist = "^3.2.1" -coverage = "^7.2.2" -absolufy-imports = "^0.3.1" -xdoctest = "^1.1.1" -mktestdocs = "^0.2.1" -asv = "^0.6.0" - - -[tool.poetry.group.docs.dependencies] -mkdocs = "^1.5.3" -mkdocs-material = "^9.5.12" -mkdocstrings = { version = "^0.25.1", extras = ["python"] } -mkdocs-jupyter = "^0.24.3" -mkdocs-gen-files = "^0.5.0" -mkdocs-literate-nav = "^0.6.0" -mkdocs-git-authors-plugin = "^0.7.0" -matplotlib = "^3.7.1" -seaborn = "^0.12.2" -networkx = "^3.0" -jupytext = "^1.14.5" -ipython = "^8.11.0" -ipykernel = "^6.22.0" -watermark = "^2.3.1" -blackjax = "^0.9.6" -ipywidgets = "^8.0.5" -pandas = "^1.5.3" -pymdown-extensions = "^10.7.1" -nbconvert = "^7.16.2" -markdown-katex = "^202406.1035" -scikit-learn = "^1.5.1" +authors = [{ name = "Thomas Pinder", email = "tompinder@live.co.uk" }] +classifiers = [ + "Development Status :: 4 - Beta", + "Programming Language :: Python", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy", +] +dependencies = [ + "jax<0.4.28", + "jaxlib<0.4.28", + "optax>0.2.1", + "jaxtyping>0.2.10", + "tqdm>4.66.2", + "tensorflow-probability>=0.24.0", + "beartype>0.16.1", + "cola-ml==0.0.5", + "jaxopt==0.8.2", + "flax>=0.8.5", + "numpy<2.0.0", +] -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.hatch.envs.default] +installer = "uv" +python = "3.10" + +[tool.hatch.envs.docs] +dependencies = [ + "mkdocs>=1.5.3", + "mkdocs-material>=9.5.12", + "mkdocstrings[python]>=0.25.1", + "mkdocs-jupyter>=0.24.3", + "mkdocs-gen-files>=0.5.0", + "mkdocs-literate-nav>=0.6.0", + "mkdocs-git-authors-plugin>=0.7.0", + "matplotlib>=3.7.1", + "seaborn>=0.12.2", + "networkx>=3.0", + "jupytext>=1.14.5", + "ipython>=8.11.0", + "ipykernel>=6.22.0", + "watermark>=2.3.1", + "blackjax>=0.9.6", + "ipywidgets>=8.0.5", + "pandas>=1.5.3", + "pymdown-extensions>=10.7.1", + "nbconvert>=7.16.2", + "markdown-katex>=202406.1035", + "scikit-learn>=1.5.1", +] +python = "3.10" + +[tool.hatch.envs.docs.scripts] +build = ["python docs/scripts/gen_examples.py --execute", "mkdocs build"] +serve = "mkdocs serve --dev-addr localhost:8000" + +[tool.hatch.envs.dev] +dependencies = [ + "ruff>=0.6", + "pre-commit>=3.2.2", + "interrogate>=1.5.0", + "codespell>=2.2.4", + "pytest>=7.2.2", + "pytest-cov>=4.0.0", + "pytest-pretty>=1.1.1", + "pytest-xdist>=3.2.1", + "coverage>=7.2.2", + "absolufy-imports>=0.3.1", + "xdoctest>=1.1.1", + "mktestdocs>=0.2.1", + "isort", +] + +[tool.hatch.envs.dev.scripts] +format = [ + "black ./src ./tests", + "isort ./src ./tests", + "ruff format ./src ./tests", + "ruff check --fix .", +] +test = "pytest -vv -n auto ." + +[project.urls] +Documentation = "https://docs.jaxgaussianprocesses.com/" +Issues = "https://github.com/JaxGaussianProcesses/GPJax/issues" +Source = "https://github.com/JaxGaussianProcesses/GPJax" + +[tool.hatch.version] +path = "src/gpjax/__init__.py" + +[tool.hatch.envs.types] +extra-dependencies = ["mypy>=1.0.0"] +[tool.hatch.envs.types.scripts] +check = "mypy --install-types --non-interactive {args:src/gpjax tests}" + +[tool.coverage.run] +source_pkgs = ["gpjax", "tests"] +branch = true +parallel = true +omit = ["src/gpjax/__init__.py"] + +[tool.coverage.paths] +gpjax = ["src/gpjax", "*/gpjax/src/gpjax"] +tests = ["tests", "*/gpjax/tests"] + +[tool.coverage.report] +exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"] +fail_under = 50 +precision = 1 +show_missing = true +skip_covered = true [tool.black] # https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#configuration-via-a-file line-length = 88 target-version = ["py310"] [tool.pytest.ini_options] # https://docs.pytest.org/en/latest/reference/reference.html#ini-options-ref -# addopts = "--color=yes --doctest-modules --exitfirst --failed-first --strict-config --strict-markers --typeguard-packages=my_package --verbosity=2 --junitxml=reports/pytest.xml" filterwarnings = ["error", "ignore::DeprecationWarning"] -testpaths = ["gpjax", "tests"] +testpaths = ["src/gpjax"] xfail_strict = true [tool.ruff] # https://github.com/charliermarsh/ruff @@ -87,7 +138,7 @@ fix = true cache-dir = "~/.cache/ruff" exclude = ["docs/", "examples/"] line-length = 88 -src = ["gpjax", "tests"] +src = ["src/gpjax", "tests"] target-version = "py310" [tool.ruff.lint] @@ -148,39 +199,12 @@ convention = "numpy" "tests/test_objectives.py" = ["PLR0913"] "docs/examples/barycentres.py" = ["PLR0913"] - [tool.isort] profile = "black" combine_as_imports = true force_sort_within_sections = true force_grid_wrap = 2 -skip = 'docs' - -[tool.coverage.report] # https://coverage.readthedocs.io/en/latest/config.html#report -fail_under = 50 -precision = 1 -show_missing = true -skip_covered = true -exclude_lines = ["if TYPE_CHECKING:"] - -[tool.coverage.run] # https://coverage.readthedocs.io/en/latest/config.html#run -branch = true -command_line = "--module pytest" -data_file = "reports/.coverage" -source = ["src"] - -[tool.coverage.xml] # https://coverage.readthedocs.io/en/latest/config.html#xml -output = "reports/coverage.xml" - -[tool.poetry-dynamic-versioning] -enable = true -vcs = "git" - -[tool.poetry-dynamic-versioning.substitution] -files = ["gpjax/__init__.py"] - -[tool.codespell] -ignore-words-list = "fro" # Frobenius +skip = 'examples' [tool.interrogate] ignore-init-method = true @@ -190,8 +214,8 @@ exclude = [ "setup.py", "docs", "tests", - "gpjax/__init__.py", - "gpjax/citation.py", + "src/gpjax/__init__.py", + "src/gpjax/citation.py", ] verbose = 2 quiet = false diff --git a/gpjax/__init__.py b/src/gpjax/__init__.py similarity index 100% rename from gpjax/__init__.py rename to src/gpjax/__init__.py diff --git a/gpjax/citation.py b/src/gpjax/citation.py similarity index 100% rename from gpjax/citation.py rename to src/gpjax/citation.py diff --git a/gpjax/dataset.py b/src/gpjax/dataset.py similarity index 100% rename from gpjax/dataset.py rename to src/gpjax/dataset.py diff --git a/gpjax/decision_making/__init__.py b/src/gpjax/decision_making/__init__.py similarity index 100% rename from gpjax/decision_making/__init__.py rename to src/gpjax/decision_making/__init__.py diff --git a/gpjax/decision_making/decision_maker.py b/src/gpjax/decision_making/decision_maker.py similarity index 100% rename from gpjax/decision_making/decision_maker.py rename to src/gpjax/decision_making/decision_maker.py diff --git a/gpjax/decision_making/posterior_handler.py b/src/gpjax/decision_making/posterior_handler.py similarity index 100% rename from gpjax/decision_making/posterior_handler.py rename to src/gpjax/decision_making/posterior_handler.py diff --git a/gpjax/decision_making/search_space.py b/src/gpjax/decision_making/search_space.py similarity index 100% rename from gpjax/decision_making/search_space.py rename to src/gpjax/decision_making/search_space.py diff --git a/gpjax/decision_making/test_functions/__init__.py b/src/gpjax/decision_making/test_functions/__init__.py similarity index 100% rename from gpjax/decision_making/test_functions/__init__.py rename to src/gpjax/decision_making/test_functions/__init__.py diff --git a/gpjax/decision_making/test_functions/continuous_functions.py b/src/gpjax/decision_making/test_functions/continuous_functions.py similarity index 100% rename from gpjax/decision_making/test_functions/continuous_functions.py rename to src/gpjax/decision_making/test_functions/continuous_functions.py diff --git a/gpjax/decision_making/test_functions/non_conjugate_functions.py b/src/gpjax/decision_making/test_functions/non_conjugate_functions.py similarity index 100% rename from gpjax/decision_making/test_functions/non_conjugate_functions.py rename to src/gpjax/decision_making/test_functions/non_conjugate_functions.py diff --git a/gpjax/decision_making/utility_functions/__init__.py b/src/gpjax/decision_making/utility_functions/__init__.py similarity index 100% rename from gpjax/decision_making/utility_functions/__init__.py rename to src/gpjax/decision_making/utility_functions/__init__.py diff --git a/gpjax/decision_making/utility_functions/base.py b/src/gpjax/decision_making/utility_functions/base.py similarity index 100% rename from gpjax/decision_making/utility_functions/base.py rename to src/gpjax/decision_making/utility_functions/base.py diff --git a/gpjax/decision_making/utility_functions/expected_improvement.py b/src/gpjax/decision_making/utility_functions/expected_improvement.py similarity index 100% rename from gpjax/decision_making/utility_functions/expected_improvement.py rename to src/gpjax/decision_making/utility_functions/expected_improvement.py diff --git a/gpjax/decision_making/utility_functions/probability_of_improvement.py b/src/gpjax/decision_making/utility_functions/probability_of_improvement.py similarity index 100% rename from gpjax/decision_making/utility_functions/probability_of_improvement.py rename to src/gpjax/decision_making/utility_functions/probability_of_improvement.py diff --git a/gpjax/decision_making/utility_functions/thompson_sampling.py b/src/gpjax/decision_making/utility_functions/thompson_sampling.py similarity index 100% rename from gpjax/decision_making/utility_functions/thompson_sampling.py rename to src/gpjax/decision_making/utility_functions/thompson_sampling.py diff --git a/gpjax/decision_making/utility_maximizer.py b/src/gpjax/decision_making/utility_maximizer.py similarity index 100% rename from gpjax/decision_making/utility_maximizer.py rename to src/gpjax/decision_making/utility_maximizer.py diff --git a/gpjax/decision_making/utils.py b/src/gpjax/decision_making/utils.py similarity index 100% rename from gpjax/decision_making/utils.py rename to src/gpjax/decision_making/utils.py diff --git a/gpjax/distributions.py b/src/gpjax/distributions.py similarity index 100% rename from gpjax/distributions.py rename to src/gpjax/distributions.py diff --git a/gpjax/fit.py b/src/gpjax/fit.py similarity index 100% rename from gpjax/fit.py rename to src/gpjax/fit.py diff --git a/gpjax/gps.py b/src/gpjax/gps.py similarity index 100% rename from gpjax/gps.py rename to src/gpjax/gps.py diff --git a/gpjax/integrators.py b/src/gpjax/integrators.py similarity index 100% rename from gpjax/integrators.py rename to src/gpjax/integrators.py diff --git a/gpjax/kernels/__init__.py b/src/gpjax/kernels/__init__.py similarity index 100% rename from gpjax/kernels/__init__.py rename to src/gpjax/kernels/__init__.py diff --git a/gpjax/kernels/approximations/__init__.py b/src/gpjax/kernels/approximations/__init__.py similarity index 100% rename from gpjax/kernels/approximations/__init__.py rename to src/gpjax/kernels/approximations/__init__.py diff --git a/gpjax/kernels/approximations/rff.py b/src/gpjax/kernels/approximations/rff.py similarity index 100% rename from gpjax/kernels/approximations/rff.py rename to src/gpjax/kernels/approximations/rff.py diff --git a/gpjax/kernels/base.py b/src/gpjax/kernels/base.py similarity index 100% rename from gpjax/kernels/base.py rename to src/gpjax/kernels/base.py diff --git a/gpjax/kernels/computations/__init__.py b/src/gpjax/kernels/computations/__init__.py similarity index 100% rename from gpjax/kernels/computations/__init__.py rename to src/gpjax/kernels/computations/__init__.py diff --git a/gpjax/kernels/computations/base.py b/src/gpjax/kernels/computations/base.py similarity index 100% rename from gpjax/kernels/computations/base.py rename to src/gpjax/kernels/computations/base.py diff --git a/gpjax/kernels/computations/basis_functions.py b/src/gpjax/kernels/computations/basis_functions.py similarity index 100% rename from gpjax/kernels/computations/basis_functions.py rename to src/gpjax/kernels/computations/basis_functions.py diff --git a/gpjax/kernels/computations/constant_diagonal.py b/src/gpjax/kernels/computations/constant_diagonal.py similarity index 100% rename from gpjax/kernels/computations/constant_diagonal.py rename to src/gpjax/kernels/computations/constant_diagonal.py diff --git a/gpjax/kernels/computations/dense.py b/src/gpjax/kernels/computations/dense.py similarity index 100% rename from gpjax/kernels/computations/dense.py rename to src/gpjax/kernels/computations/dense.py diff --git a/gpjax/kernels/computations/diagonal.py b/src/gpjax/kernels/computations/diagonal.py similarity index 100% rename from gpjax/kernels/computations/diagonal.py rename to src/gpjax/kernels/computations/diagonal.py diff --git a/gpjax/kernels/computations/eigen.py b/src/gpjax/kernels/computations/eigen.py similarity index 100% rename from gpjax/kernels/computations/eigen.py rename to src/gpjax/kernels/computations/eigen.py diff --git a/gpjax/kernels/non_euclidean/__init__.py b/src/gpjax/kernels/non_euclidean/__init__.py similarity index 100% rename from gpjax/kernels/non_euclidean/__init__.py rename to src/gpjax/kernels/non_euclidean/__init__.py diff --git a/gpjax/kernels/non_euclidean/graph.py b/src/gpjax/kernels/non_euclidean/graph.py similarity index 100% rename from gpjax/kernels/non_euclidean/graph.py rename to src/gpjax/kernels/non_euclidean/graph.py diff --git a/gpjax/kernels/non_euclidean/utils.py b/src/gpjax/kernels/non_euclidean/utils.py similarity index 100% rename from gpjax/kernels/non_euclidean/utils.py rename to src/gpjax/kernels/non_euclidean/utils.py diff --git a/gpjax/kernels/nonstationary/__init__.py b/src/gpjax/kernels/nonstationary/__init__.py similarity index 100% rename from gpjax/kernels/nonstationary/__init__.py rename to src/gpjax/kernels/nonstationary/__init__.py diff --git a/gpjax/kernels/nonstationary/arccosine.py b/src/gpjax/kernels/nonstationary/arccosine.py similarity index 100% rename from gpjax/kernels/nonstationary/arccosine.py rename to src/gpjax/kernels/nonstationary/arccosine.py diff --git a/gpjax/kernels/nonstationary/linear.py b/src/gpjax/kernels/nonstationary/linear.py similarity index 100% rename from gpjax/kernels/nonstationary/linear.py rename to src/gpjax/kernels/nonstationary/linear.py diff --git a/gpjax/kernels/nonstationary/polynomial.py b/src/gpjax/kernels/nonstationary/polynomial.py similarity index 100% rename from gpjax/kernels/nonstationary/polynomial.py rename to src/gpjax/kernels/nonstationary/polynomial.py diff --git a/gpjax/kernels/stationary/__init__.py b/src/gpjax/kernels/stationary/__init__.py similarity index 100% rename from gpjax/kernels/stationary/__init__.py rename to src/gpjax/kernels/stationary/__init__.py diff --git a/gpjax/kernels/stationary/base.py b/src/gpjax/kernels/stationary/base.py similarity index 100% rename from gpjax/kernels/stationary/base.py rename to src/gpjax/kernels/stationary/base.py diff --git a/gpjax/kernels/stationary/matern12.py b/src/gpjax/kernels/stationary/matern12.py similarity index 100% rename from gpjax/kernels/stationary/matern12.py rename to src/gpjax/kernels/stationary/matern12.py diff --git a/gpjax/kernels/stationary/matern32.py b/src/gpjax/kernels/stationary/matern32.py similarity index 100% rename from gpjax/kernels/stationary/matern32.py rename to src/gpjax/kernels/stationary/matern32.py diff --git a/gpjax/kernels/stationary/matern52.py b/src/gpjax/kernels/stationary/matern52.py similarity index 100% rename from gpjax/kernels/stationary/matern52.py rename to src/gpjax/kernels/stationary/matern52.py diff --git a/gpjax/kernels/stationary/periodic.py b/src/gpjax/kernels/stationary/periodic.py similarity index 100% rename from gpjax/kernels/stationary/periodic.py rename to src/gpjax/kernels/stationary/periodic.py diff --git a/gpjax/kernels/stationary/powered_exponential.py b/src/gpjax/kernels/stationary/powered_exponential.py similarity index 100% rename from gpjax/kernels/stationary/powered_exponential.py rename to src/gpjax/kernels/stationary/powered_exponential.py diff --git a/gpjax/kernels/stationary/rational_quadratic.py b/src/gpjax/kernels/stationary/rational_quadratic.py similarity index 100% rename from gpjax/kernels/stationary/rational_quadratic.py rename to src/gpjax/kernels/stationary/rational_quadratic.py diff --git a/gpjax/kernels/stationary/rbf.py b/src/gpjax/kernels/stationary/rbf.py similarity index 100% rename from gpjax/kernels/stationary/rbf.py rename to src/gpjax/kernels/stationary/rbf.py diff --git a/gpjax/kernels/stationary/utils.py b/src/gpjax/kernels/stationary/utils.py similarity index 100% rename from gpjax/kernels/stationary/utils.py rename to src/gpjax/kernels/stationary/utils.py diff --git a/gpjax/kernels/stationary/white.py b/src/gpjax/kernels/stationary/white.py similarity index 100% rename from gpjax/kernels/stationary/white.py rename to src/gpjax/kernels/stationary/white.py diff --git a/gpjax/likelihoods.py b/src/gpjax/likelihoods.py similarity index 100% rename from gpjax/likelihoods.py rename to src/gpjax/likelihoods.py diff --git a/gpjax/lower_cholesky.py b/src/gpjax/lower_cholesky.py similarity index 100% rename from gpjax/lower_cholesky.py rename to src/gpjax/lower_cholesky.py diff --git a/gpjax/mean_functions.py b/src/gpjax/mean_functions.py similarity index 100% rename from gpjax/mean_functions.py rename to src/gpjax/mean_functions.py diff --git a/gpjax/objectives.py b/src/gpjax/objectives.py similarity index 100% rename from gpjax/objectives.py rename to src/gpjax/objectives.py diff --git a/gpjax/parameters.py b/src/gpjax/parameters.py similarity index 100% rename from gpjax/parameters.py rename to src/gpjax/parameters.py diff --git a/gpjax/progress_bar.py b/src/gpjax/progress_bar.py similarity index 100% rename from gpjax/progress_bar.py rename to src/gpjax/progress_bar.py diff --git a/gpjax/scan.py b/src/gpjax/scan.py similarity index 100% rename from gpjax/scan.py rename to src/gpjax/scan.py diff --git a/gpjax/typing.py b/src/gpjax/typing.py similarity index 100% rename from gpjax/typing.py rename to src/gpjax/typing.py diff --git a/gpjax/variational_families.py b/src/gpjax/variational_families.py similarity index 100% rename from gpjax/variational_families.py rename to src/gpjax/variational_families.py diff --git a/tests/test_kernels/test_nonstationary.py b/tests/test_kernels/test_nonstationary.py index 7d968e5ca..836e66f53 100644 --- a/tests/test_kernels/test_nonstationary.py +++ b/tests/test_kernels/test_nonstationary.py @@ -40,7 +40,10 @@ def params_product(params: dict[str, list]) -> list[dict[str, Any]]: - return [dict(zip(params.keys(), values)) for values in product(*params.values())] + return [ + dict(zip(params.keys(), values, strict=False)) + for values in product(*params.values()) + ] TESTED_KERNELS = [ diff --git a/tests/test_kernels/test_stationary.py b/tests/test_kernels/test_stationary.py index ce490e65c..05faa82ef 100644 --- a/tests/test_kernels/test_stationary.py +++ b/tests/test_kernels/test_stationary.py @@ -44,7 +44,10 @@ def params_product(params: dict[str, list]) -> list[dict[str, Any]]: - return [dict(zip(params.keys(), values)) for values in product(*params.values())] + return [ + dict(zip(params.keys(), values, strict=False)) + for values in product(*params.values()) + ] TESTED_KERNELS = [ From a3e7b22ef8b0cc24768ed5d9003b26349ee4dd09 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 15:38:39 +0200 Subject: [PATCH 02/12] Update workflows --- .github/workflows/build_docs.yml | 15 +-- .github/workflows/integration.yml | 20 +-- .github/workflows/test_docs.yml | 14 +-- .github/workflows/tests.yml | 24 +--- examples/graph_kernels.py | 2 +- pyproject.old.toml | 198 ------------------------------ pyproject.toml | 6 +- 7 files changed, 20 insertions(+), 259 deletions(-) delete mode 100644 pyproject.old.toml diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 92c65c5f8..58e1dab1f 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -46,20 +46,15 @@ jobs: - name: Install KaTeX run: | npm install katex - # Install Poetry and build the documentation - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: 1.5.1 - virtualenvs-create: false - virtualenvs-in-project: false - installer-parallel: true + + # Install Hatch + - name: Install Hatch + uses: pypa/hatch@install - name: Build the documentation with MKDocs run: | - poetry install --all-extras --with docs conda install pandoc - poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build + hatch run docs:build - name: Deploy Page 🚀 uses: JamesIves/github-pages-deploy-action@v4.4.1 diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml index 5aa90b148..e6e3de216 100644 --- a/.github/workflows/integration.yml +++ b/.github/workflows/integration.yml @@ -25,22 +25,10 @@ jobs: with: python-version: ${{ matrix.python-version }} - # Install Poetry - - name: Install Poetry - uses: snok/install-poetry@v1.3.3 - with: - version: 1.5.1 - - # Configure Poetry to use the virtual environment in the project - - name: Setup Poetry - run: | - poetry config virtualenvs.in-project true - - # Install the dependencies - - name: Install Package - run: | - poetry install --with docs + # Install Hatch + - name: Install Hatch + uses: pypa/hatch@install # Run the unit tests and build the coverage report - name: Run Integration Tests - run: poetry run python tests/integration_tests.py + run: hatch run python tests/integration_tests.py diff --git a/.github/workflows/test_docs.yml b/.github/workflows/test_docs.yml index 129de0e39..2435843c0 100644 --- a/.github/workflows/test_docs.yml +++ b/.github/workflows/test_docs.yml @@ -33,17 +33,11 @@ jobs: auto-update-conda: true python-version: ${{ matrix.python-version }} - # Install Poetry and build the documentation - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: 1.5.1 - virtualenvs-create: false - virtualenvs-in-project: false - installer-parallel: true + # Install Hatch + - name: Install Hatch + uses: pypa/hatch@install - name: Build the documentation with MKDocs run: | - poetry install --all-extras --with docs conda install pandoc - poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build + hatch run docs:build diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 967896bf5..82c42cf12 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -25,32 +25,18 @@ jobs: with: python-version: ${{ matrix.python-version }} - # Install Poetry - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: 1.5.1 - virtualenvs-create: false - virtualenvs-in-project: false - installer-parallel: true - - # Configure Poetry to use the virtual environment in the project - - name: Setup Poetry - run: | - poetry config virtualenvs.in-project true + # Install Hatch + - name: Install Hatch + uses: pypa/hatch@install # Install the dependencies - - name: Install Package - run: | - poetry install --with dev - - name: Check docstrings run: | - poetry run xdoctest ./gpjax + hatch run xdoctest ./gpjax # Run the unit tests and build the coverage report - name: Run Tests - run: poetry run pytest -v --cov=./gpjax --cov-report=xml:./coverage.xml + run: hatch run dev:coverage - name: Upload code coverage uses: codecov/codecov-action@v3 diff --git a/examples/graph_kernels.py b/examples/graph_kernels.py index e9a28b9a7..e5e532db5 100644 --- a/examples/graph_kernels.py +++ b/examples/graph_kernels.py @@ -152,7 +152,7 @@ # For this reason, we simply perform gradient descent on the GP's marginal # log-likelihood term as in the # [regression notebook](https://docs.jaxgaussianprocesses.com/examples/regression/). -# We do this using the BFGS optimiser provided in `scipy` via 'jaxopt'. +# We do this using the BFGS optimiser. # %% likelihood = gpx.likelihoods.Gaussian(num_datapoints=D.n) diff --git a/pyproject.old.toml b/pyproject.old.toml deleted file mode 100644 index 396e3f928..000000000 --- a/pyproject.old.toml +++ /dev/null @@ -1,198 +0,0 @@ -[tool.poetry] -name = "gpjax" -version = "0.9.0" -description = "Gaussian processes in JAX." -authors = [ - "Thomas Pinder ", - "Daniel Dodd ", -] -license = "Apache-2.0" -readme = "README.md" -homepage = "https://github.com/JaxGaussianProcesses/GPJax" -repository = "https://github.com/JaxGaussianProcesses/GPJax" -include = ["LICENSE"] -documentation = "https://docs.jaxgaussianprocesses.com/" -keywords = ["gaussian-processes jax machine-learning bayesian"] -packages = [{ include = "gpjax" }] - -[tool.poetry.dependencies] -python = ">=3.10,<3.12" -jax = "<0.4.28" -jaxlib = "<0.4.28" -optax = "^0.2.1" -jaxtyping = "^0.2.10" -tqdm = "^4.66.2" -tensorflow-probability = "^0.24.0" -beartype = "^0.16.1" -cola-ml = "0.0.5" -jaxopt = "^0.8.3" -flax = "^0.8.4" -numpy = "<2.0.0" - -[tool.poetry.group.dev.dependencies] -ruff = "~0" -pre-commit = "^3.2.2" -interrogate = "^1.5.0" -codespell = "^2.2.4" -pytest = "^7.2.2" -pytest-cov = "^4.0.0" -pytest-pretty = "^1.1.1" -pytest-xdist = "^3.2.1" -coverage = "^7.2.2" -absolufy-imports = "^0.3.1" -xdoctest = "^1.1.1" -mktestdocs = "^0.2.1" -asv = "^0.6.0" - - -[tool.poetry.group.docs.dependencies] -mkdocs = "^1.5.3" -mkdocs-material = "^9.5.12" -mkdocstrings = { version = "^0.25.1", extras = ["python"] } -mkdocs-jupyter = "^0.24.3" -mkdocs-gen-files = "^0.5.0" -mkdocs-literate-nav = "^0.6.0" -mkdocs-git-authors-plugin = "^0.7.0" -matplotlib = "^3.7.1" -seaborn = "^0.12.2" -networkx = "^3.0" -jupytext = "^1.14.5" -ipython = "^8.11.0" -ipykernel = "^6.22.0" -watermark = "^2.3.1" -blackjax = "^0.9.6" -ipywidgets = "^8.0.5" -pandas = "^1.5.3" -pymdown-extensions = "^10.7.1" -nbconvert = "^7.16.2" -markdown-katex = "^202406.1035" -scikit-learn = "^1.5.1" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" - -[tool.black] # https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#configuration-via-a-file -line-length = 88 -target-version = ["py310"] - -[tool.pytest.ini_options] # https://docs.pytest.org/en/latest/reference/reference.html#ini-options-ref -# addopts = "--color=yes --doctest-modules --exitfirst --failed-first --strict-config --strict-markers --typeguard-packages=my_package --verbosity=2 --junitxml=reports/pytest.xml" -filterwarnings = ["error", "ignore::DeprecationWarning"] -testpaths = ["gpjax", "tests"] -xfail_strict = true - -[tool.ruff] # https://github.com/charliermarsh/ruff -fix = true -cache-dir = "~/.cache/ruff" -exclude = ["docs/", "examples/"] -line-length = 88 -src = ["gpjax", "tests"] -target-version = "py310" - -[tool.ruff.lint] -dummy-variable-rgx = "^_$" -select = [ - "F", - # pycodestyle - "E", - "W", - # flake8-2020 - "YTT", - # flake8-bugbear - "B", - # flake8-quotes - "Q", - # pylint - "PLE", - "PLR", - "PLW", - # misc lints - "PIE", - # flake8-pyi - "PYI", - # tidy imports - "TID", - # implicit string concatenation - "ISC", -] -ignore = [ - # calls in argument defaults - "B008", - # space before : (needed for how black formats slicing) - # "E203", # not yet implemented - # module level import not at top of file - "E402", - # do not assign a lambda expression, use a def - "E731", - "E501", - "S303", - "S307", - "RET504", - "S101", - "F722", - 'PLR2004', - "PLR0913", -] -unfixable = ["ERA001", "F401", "F841", "T201", "T203"] - -[tool.ruff.lint.pydocstyle] -convention = "numpy" - -[tool.ruff.lint.per-file-ignores] -"gpjax/__init__.py" = ['I', 'F401', 'E402', 'D104'] -"gpjax/progress_bar.py" = ["TCH004"] -"gpjax/scan.py" = ["PLR0913"] -"gpjax/citation.py" = ["F811"] -"tests/test_base/test_module.py" = ["PLR0915"] -"tests/test_objectives.py" = ["PLR0913"] -"docs/examples/barycentres.py" = ["PLR0913"] - - -[tool.isort] -profile = "black" -combine_as_imports = true -force_sort_within_sections = true -force_grid_wrap = 2 -skip = 'docs' - -[tool.coverage.report] # https://coverage.readthedocs.io/en/latest/config.html#report -fail_under = 50 -precision = 1 -show_missing = true -skip_covered = true -exclude_lines = ["if TYPE_CHECKING:"] - -[tool.coverage.run] # https://coverage.readthedocs.io/en/latest/config.html#run -branch = true -command_line = "--module pytest" -data_file = "reports/.coverage" -source = ["src"] - -[tool.coverage.xml] # https://coverage.readthedocs.io/en/latest/config.html#xml -output = "reports/coverage.xml" - -[tool.poetry-dynamic-versioning] -enable = true -vcs = "git" - -[tool.poetry-dynamic-versioning.substitution] -files = ["gpjax/__init__.py"] - -[tool.codespell] -ignore-words-list = "fro" # Frobenius - -[tool.interrogate] -ignore-init-method = true -ignore-init-module = true -fail-under = 64 -exclude = [ - "setup.py", - "docs", - "tests", - "gpjax/__init__.py", - "gpjax/citation.py", -] -verbose = 2 -quiet = false -color = true diff --git a/pyproject.toml b/pyproject.toml index 8d68dd623..17495b5a1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -93,6 +93,7 @@ format = [ "ruff check --fix .", ] test = "pytest -vv -n auto ." +coverage = "pytest -vv --cov=./gpjax --cov-report=xml:./coverage.xml" [project.urls] Documentation = "https://docs.jaxgaussianprocesses.com/" @@ -102,11 +103,6 @@ Source = "https://github.com/JaxGaussianProcesses/GPJax" [tool.hatch.version] path = "src/gpjax/__init__.py" -[tool.hatch.envs.types] -extra-dependencies = ["mypy>=1.0.0"] -[tool.hatch.envs.types.scripts] -check = "mypy --install-types --non-interactive {args:src/gpjax tests}" - [tool.coverage.run] source_pkgs = ["gpjax", "tests"] branch = true From a9ad8de25ced282df195ec01fe188f23b421b7a2 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 15:44:47 +0200 Subject: [PATCH 03/12] Update workflows --- .github/workflows/integration.yml | 2 +- {src/gpjax => gpjax}/__init__.py | 0 {src/gpjax => gpjax}/citation.py | 0 {src/gpjax => gpjax}/dataset.py | 0 .../decision_making/__init__.py | 0 .../decision_making/decision_maker.py | 0 .../decision_making/posterior_handler.py | 0 .../decision_making/search_space.py | 0 .../test_functions/__init__.py | 0 .../test_functions/continuous_functions.py | 0 .../test_functions/non_conjugate_functions.py | 0 .../utility_functions/__init__.py | 0 .../decision_making/utility_functions/base.py | 0 .../utility_functions/expected_improvement.py | 0 .../probability_of_improvement.py | 0 .../utility_functions/thompson_sampling.py | 0 .../decision_making/utility_maximizer.py | 0 {src/gpjax => gpjax}/decision_making/utils.py | 0 {src/gpjax => gpjax}/distributions.py | 0 {src/gpjax => gpjax}/fit.py | 0 {src/gpjax => gpjax}/gps.py | 0 {src/gpjax => gpjax}/integrators.py | 0 {src/gpjax => gpjax}/kernels/__init__.py | 0 .../kernels/approximations/__init__.py | 0 .../kernels/approximations/rff.py | 0 {src/gpjax => gpjax}/kernels/base.py | 0 .../kernels/computations/__init__.py | 0 .../kernels/computations/base.py | 0 .../kernels/computations/basis_functions.py | 0 .../kernels/computations/constant_diagonal.py | 0 .../kernels/computations/dense.py | 0 .../kernels/computations/diagonal.py | 0 .../kernels/computations/eigen.py | 0 .../kernels/non_euclidean/__init__.py | 0 .../kernels/non_euclidean/graph.py | 0 .../kernels/non_euclidean/utils.py | 0 .../kernels/nonstationary/__init__.py | 0 .../kernels/nonstationary/arccosine.py | 0 .../kernels/nonstationary/linear.py | 0 .../kernels/nonstationary/polynomial.py | 0 .../kernels/stationary/__init__.py | 0 .../kernels/stationary/base.py | 0 .../kernels/stationary/matern12.py | 0 .../kernels/stationary/matern32.py | 0 .../kernels/stationary/matern52.py | 0 .../kernels/stationary/periodic.py | 0 .../kernels/stationary/powered_exponential.py | 0 .../kernels/stationary/rational_quadratic.py | 0 .../gpjax => gpjax}/kernels/stationary/rbf.py | 0 .../kernels/stationary/utils.py | 0 .../kernels/stationary/white.py | 0 {src/gpjax => gpjax}/likelihoods.py | 0 {src/gpjax => gpjax}/lower_cholesky.py | 0 {src/gpjax => gpjax}/mean_functions.py | 0 {src/gpjax => gpjax}/objectives.py | 0 {src/gpjax => gpjax}/parameters.py | 0 {src/gpjax => gpjax}/progress_bar.py | 0 {src/gpjax => gpjax}/scan.py | 0 {src/gpjax => gpjax}/typing.py | 0 {src/gpjax => gpjax}/variational_families.py | 0 pyproject.toml | 22 ++++++++++--------- 61 files changed, 13 insertions(+), 11 deletions(-) rename {src/gpjax => gpjax}/__init__.py (100%) rename {src/gpjax => gpjax}/citation.py (100%) rename {src/gpjax => gpjax}/dataset.py (100%) rename {src/gpjax => gpjax}/decision_making/__init__.py (100%) rename {src/gpjax => gpjax}/decision_making/decision_maker.py (100%) rename {src/gpjax => gpjax}/decision_making/posterior_handler.py (100%) rename {src/gpjax => gpjax}/decision_making/search_space.py (100%) rename {src/gpjax => gpjax}/decision_making/test_functions/__init__.py (100%) rename {src/gpjax => gpjax}/decision_making/test_functions/continuous_functions.py (100%) rename {src/gpjax => gpjax}/decision_making/test_functions/non_conjugate_functions.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_functions/__init__.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_functions/base.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_functions/expected_improvement.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_functions/probability_of_improvement.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_functions/thompson_sampling.py (100%) rename {src/gpjax => gpjax}/decision_making/utility_maximizer.py (100%) rename {src/gpjax => gpjax}/decision_making/utils.py (100%) rename {src/gpjax => gpjax}/distributions.py (100%) rename {src/gpjax => gpjax}/fit.py (100%) rename {src/gpjax => gpjax}/gps.py (100%) rename {src/gpjax => gpjax}/integrators.py (100%) rename {src/gpjax => gpjax}/kernels/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/approximations/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/approximations/rff.py (100%) rename {src/gpjax => gpjax}/kernels/base.py (100%) rename {src/gpjax => gpjax}/kernels/computations/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/computations/base.py (100%) rename {src/gpjax => gpjax}/kernels/computations/basis_functions.py (100%) rename {src/gpjax => gpjax}/kernels/computations/constant_diagonal.py (100%) rename {src/gpjax => gpjax}/kernels/computations/dense.py (100%) rename {src/gpjax => gpjax}/kernels/computations/diagonal.py (100%) rename {src/gpjax => gpjax}/kernels/computations/eigen.py (100%) rename {src/gpjax => gpjax}/kernels/non_euclidean/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/non_euclidean/graph.py (100%) rename {src/gpjax => gpjax}/kernels/non_euclidean/utils.py (100%) rename {src/gpjax => gpjax}/kernels/nonstationary/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/nonstationary/arccosine.py (100%) rename {src/gpjax => gpjax}/kernels/nonstationary/linear.py (100%) rename {src/gpjax => gpjax}/kernels/nonstationary/polynomial.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/__init__.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/base.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/matern12.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/matern32.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/matern52.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/periodic.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/powered_exponential.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/rational_quadratic.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/rbf.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/utils.py (100%) rename {src/gpjax => gpjax}/kernels/stationary/white.py (100%) rename {src/gpjax => gpjax}/likelihoods.py (100%) rename {src/gpjax => gpjax}/lower_cholesky.py (100%) rename {src/gpjax => gpjax}/mean_functions.py (100%) rename {src/gpjax => gpjax}/objectives.py (100%) rename {src/gpjax => gpjax}/parameters.py (100%) rename {src/gpjax => gpjax}/progress_bar.py (100%) rename {src/gpjax => gpjax}/scan.py (100%) rename {src/gpjax => gpjax}/typing.py (100%) rename {src/gpjax => gpjax}/variational_families.py (100%) diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml index e6e3de216..7601a73bf 100644 --- a/.github/workflows/integration.yml +++ b/.github/workflows/integration.yml @@ -31,4 +31,4 @@ jobs: # Run the unit tests and build the coverage report - name: Run Integration Tests - run: hatch run python tests/integration_tests.py + run: hatch run docs:integration diff --git a/src/gpjax/__init__.py b/gpjax/__init__.py similarity index 100% rename from src/gpjax/__init__.py rename to gpjax/__init__.py diff --git a/src/gpjax/citation.py b/gpjax/citation.py similarity index 100% rename from src/gpjax/citation.py rename to gpjax/citation.py diff --git a/src/gpjax/dataset.py b/gpjax/dataset.py similarity index 100% rename from src/gpjax/dataset.py rename to gpjax/dataset.py diff --git a/src/gpjax/decision_making/__init__.py b/gpjax/decision_making/__init__.py similarity index 100% rename from src/gpjax/decision_making/__init__.py rename to gpjax/decision_making/__init__.py diff --git a/src/gpjax/decision_making/decision_maker.py b/gpjax/decision_making/decision_maker.py similarity index 100% rename from src/gpjax/decision_making/decision_maker.py rename to gpjax/decision_making/decision_maker.py diff --git a/src/gpjax/decision_making/posterior_handler.py b/gpjax/decision_making/posterior_handler.py similarity index 100% rename from src/gpjax/decision_making/posterior_handler.py rename to gpjax/decision_making/posterior_handler.py diff --git a/src/gpjax/decision_making/search_space.py b/gpjax/decision_making/search_space.py similarity index 100% rename from src/gpjax/decision_making/search_space.py rename to gpjax/decision_making/search_space.py diff --git a/src/gpjax/decision_making/test_functions/__init__.py b/gpjax/decision_making/test_functions/__init__.py similarity index 100% rename from src/gpjax/decision_making/test_functions/__init__.py rename to gpjax/decision_making/test_functions/__init__.py diff --git a/src/gpjax/decision_making/test_functions/continuous_functions.py b/gpjax/decision_making/test_functions/continuous_functions.py similarity index 100% rename from src/gpjax/decision_making/test_functions/continuous_functions.py rename to gpjax/decision_making/test_functions/continuous_functions.py diff --git a/src/gpjax/decision_making/test_functions/non_conjugate_functions.py b/gpjax/decision_making/test_functions/non_conjugate_functions.py similarity index 100% rename from src/gpjax/decision_making/test_functions/non_conjugate_functions.py rename to gpjax/decision_making/test_functions/non_conjugate_functions.py diff --git a/src/gpjax/decision_making/utility_functions/__init__.py b/gpjax/decision_making/utility_functions/__init__.py similarity index 100% rename from src/gpjax/decision_making/utility_functions/__init__.py rename to gpjax/decision_making/utility_functions/__init__.py diff --git a/src/gpjax/decision_making/utility_functions/base.py b/gpjax/decision_making/utility_functions/base.py similarity index 100% rename from src/gpjax/decision_making/utility_functions/base.py rename to gpjax/decision_making/utility_functions/base.py diff --git a/src/gpjax/decision_making/utility_functions/expected_improvement.py b/gpjax/decision_making/utility_functions/expected_improvement.py similarity index 100% rename from src/gpjax/decision_making/utility_functions/expected_improvement.py rename to gpjax/decision_making/utility_functions/expected_improvement.py diff --git a/src/gpjax/decision_making/utility_functions/probability_of_improvement.py b/gpjax/decision_making/utility_functions/probability_of_improvement.py similarity index 100% rename from src/gpjax/decision_making/utility_functions/probability_of_improvement.py rename to gpjax/decision_making/utility_functions/probability_of_improvement.py diff --git a/src/gpjax/decision_making/utility_functions/thompson_sampling.py b/gpjax/decision_making/utility_functions/thompson_sampling.py similarity index 100% rename from src/gpjax/decision_making/utility_functions/thompson_sampling.py rename to gpjax/decision_making/utility_functions/thompson_sampling.py diff --git a/src/gpjax/decision_making/utility_maximizer.py b/gpjax/decision_making/utility_maximizer.py similarity index 100% rename from src/gpjax/decision_making/utility_maximizer.py rename to gpjax/decision_making/utility_maximizer.py diff --git a/src/gpjax/decision_making/utils.py b/gpjax/decision_making/utils.py similarity index 100% rename from src/gpjax/decision_making/utils.py rename to gpjax/decision_making/utils.py diff --git a/src/gpjax/distributions.py b/gpjax/distributions.py similarity index 100% rename from src/gpjax/distributions.py rename to gpjax/distributions.py diff --git a/src/gpjax/fit.py b/gpjax/fit.py similarity index 100% rename from src/gpjax/fit.py rename to gpjax/fit.py diff --git a/src/gpjax/gps.py b/gpjax/gps.py similarity index 100% rename from src/gpjax/gps.py rename to gpjax/gps.py diff --git a/src/gpjax/integrators.py b/gpjax/integrators.py similarity index 100% rename from src/gpjax/integrators.py rename to gpjax/integrators.py diff --git a/src/gpjax/kernels/__init__.py b/gpjax/kernels/__init__.py similarity index 100% rename from src/gpjax/kernels/__init__.py rename to gpjax/kernels/__init__.py diff --git a/src/gpjax/kernels/approximations/__init__.py b/gpjax/kernels/approximations/__init__.py similarity index 100% rename from src/gpjax/kernels/approximations/__init__.py rename to gpjax/kernels/approximations/__init__.py diff --git a/src/gpjax/kernels/approximations/rff.py b/gpjax/kernels/approximations/rff.py similarity index 100% rename from src/gpjax/kernels/approximations/rff.py rename to gpjax/kernels/approximations/rff.py diff --git a/src/gpjax/kernels/base.py b/gpjax/kernels/base.py similarity index 100% rename from src/gpjax/kernels/base.py rename to gpjax/kernels/base.py diff --git a/src/gpjax/kernels/computations/__init__.py b/gpjax/kernels/computations/__init__.py similarity index 100% rename from src/gpjax/kernels/computations/__init__.py rename to gpjax/kernels/computations/__init__.py diff --git a/src/gpjax/kernels/computations/base.py b/gpjax/kernels/computations/base.py similarity index 100% rename from src/gpjax/kernels/computations/base.py rename to gpjax/kernels/computations/base.py diff --git a/src/gpjax/kernels/computations/basis_functions.py b/gpjax/kernels/computations/basis_functions.py similarity index 100% rename from src/gpjax/kernels/computations/basis_functions.py rename to gpjax/kernels/computations/basis_functions.py diff --git a/src/gpjax/kernels/computations/constant_diagonal.py b/gpjax/kernels/computations/constant_diagonal.py similarity index 100% rename from src/gpjax/kernels/computations/constant_diagonal.py rename to gpjax/kernels/computations/constant_diagonal.py diff --git a/src/gpjax/kernels/computations/dense.py b/gpjax/kernels/computations/dense.py similarity index 100% rename from src/gpjax/kernels/computations/dense.py rename to gpjax/kernels/computations/dense.py diff --git a/src/gpjax/kernels/computations/diagonal.py b/gpjax/kernels/computations/diagonal.py similarity index 100% rename from src/gpjax/kernels/computations/diagonal.py rename to gpjax/kernels/computations/diagonal.py diff --git a/src/gpjax/kernels/computations/eigen.py b/gpjax/kernels/computations/eigen.py similarity index 100% rename from src/gpjax/kernels/computations/eigen.py rename to gpjax/kernels/computations/eigen.py diff --git a/src/gpjax/kernels/non_euclidean/__init__.py b/gpjax/kernels/non_euclidean/__init__.py similarity index 100% rename from src/gpjax/kernels/non_euclidean/__init__.py rename to gpjax/kernels/non_euclidean/__init__.py diff --git a/src/gpjax/kernels/non_euclidean/graph.py b/gpjax/kernels/non_euclidean/graph.py similarity index 100% rename from src/gpjax/kernels/non_euclidean/graph.py rename to gpjax/kernels/non_euclidean/graph.py diff --git a/src/gpjax/kernels/non_euclidean/utils.py b/gpjax/kernels/non_euclidean/utils.py similarity index 100% rename from src/gpjax/kernels/non_euclidean/utils.py rename to gpjax/kernels/non_euclidean/utils.py diff --git a/src/gpjax/kernels/nonstationary/__init__.py b/gpjax/kernels/nonstationary/__init__.py similarity index 100% rename from src/gpjax/kernels/nonstationary/__init__.py rename to gpjax/kernels/nonstationary/__init__.py diff --git a/src/gpjax/kernels/nonstationary/arccosine.py b/gpjax/kernels/nonstationary/arccosine.py similarity index 100% rename from src/gpjax/kernels/nonstationary/arccosine.py rename to gpjax/kernels/nonstationary/arccosine.py diff --git a/src/gpjax/kernels/nonstationary/linear.py b/gpjax/kernels/nonstationary/linear.py similarity index 100% rename from src/gpjax/kernels/nonstationary/linear.py rename to gpjax/kernels/nonstationary/linear.py diff --git a/src/gpjax/kernels/nonstationary/polynomial.py b/gpjax/kernels/nonstationary/polynomial.py similarity index 100% rename from src/gpjax/kernels/nonstationary/polynomial.py rename to gpjax/kernels/nonstationary/polynomial.py diff --git a/src/gpjax/kernels/stationary/__init__.py b/gpjax/kernels/stationary/__init__.py similarity index 100% rename from src/gpjax/kernels/stationary/__init__.py rename to gpjax/kernels/stationary/__init__.py diff --git a/src/gpjax/kernels/stationary/base.py b/gpjax/kernels/stationary/base.py similarity index 100% rename from src/gpjax/kernels/stationary/base.py rename to gpjax/kernels/stationary/base.py diff --git a/src/gpjax/kernels/stationary/matern12.py b/gpjax/kernels/stationary/matern12.py similarity index 100% rename from src/gpjax/kernels/stationary/matern12.py rename to gpjax/kernels/stationary/matern12.py diff --git a/src/gpjax/kernels/stationary/matern32.py b/gpjax/kernels/stationary/matern32.py similarity index 100% rename from src/gpjax/kernels/stationary/matern32.py rename to gpjax/kernels/stationary/matern32.py diff --git a/src/gpjax/kernels/stationary/matern52.py b/gpjax/kernels/stationary/matern52.py similarity index 100% rename from src/gpjax/kernels/stationary/matern52.py rename to gpjax/kernels/stationary/matern52.py diff --git a/src/gpjax/kernels/stationary/periodic.py b/gpjax/kernels/stationary/periodic.py similarity index 100% rename from src/gpjax/kernels/stationary/periodic.py rename to gpjax/kernels/stationary/periodic.py diff --git a/src/gpjax/kernels/stationary/powered_exponential.py b/gpjax/kernels/stationary/powered_exponential.py similarity index 100% rename from src/gpjax/kernels/stationary/powered_exponential.py rename to gpjax/kernels/stationary/powered_exponential.py diff --git a/src/gpjax/kernels/stationary/rational_quadratic.py b/gpjax/kernels/stationary/rational_quadratic.py similarity index 100% rename from src/gpjax/kernels/stationary/rational_quadratic.py rename to gpjax/kernels/stationary/rational_quadratic.py diff --git a/src/gpjax/kernels/stationary/rbf.py b/gpjax/kernels/stationary/rbf.py similarity index 100% rename from src/gpjax/kernels/stationary/rbf.py rename to gpjax/kernels/stationary/rbf.py diff --git a/src/gpjax/kernels/stationary/utils.py b/gpjax/kernels/stationary/utils.py similarity index 100% rename from src/gpjax/kernels/stationary/utils.py rename to gpjax/kernels/stationary/utils.py diff --git a/src/gpjax/kernels/stationary/white.py b/gpjax/kernels/stationary/white.py similarity index 100% rename from src/gpjax/kernels/stationary/white.py rename to gpjax/kernels/stationary/white.py diff --git a/src/gpjax/likelihoods.py b/gpjax/likelihoods.py similarity index 100% rename from src/gpjax/likelihoods.py rename to gpjax/likelihoods.py diff --git a/src/gpjax/lower_cholesky.py b/gpjax/lower_cholesky.py similarity index 100% rename from src/gpjax/lower_cholesky.py rename to gpjax/lower_cholesky.py diff --git a/src/gpjax/mean_functions.py b/gpjax/mean_functions.py similarity index 100% rename from src/gpjax/mean_functions.py rename to gpjax/mean_functions.py diff --git a/src/gpjax/objectives.py b/gpjax/objectives.py similarity index 100% rename from src/gpjax/objectives.py rename to gpjax/objectives.py diff --git a/src/gpjax/parameters.py b/gpjax/parameters.py similarity index 100% rename from src/gpjax/parameters.py rename to gpjax/parameters.py diff --git a/src/gpjax/progress_bar.py b/gpjax/progress_bar.py similarity index 100% rename from src/gpjax/progress_bar.py rename to gpjax/progress_bar.py diff --git a/src/gpjax/scan.py b/gpjax/scan.py similarity index 100% rename from src/gpjax/scan.py rename to gpjax/scan.py diff --git a/src/gpjax/typing.py b/gpjax/typing.py similarity index 100% rename from src/gpjax/typing.py rename to gpjax/typing.py diff --git a/src/gpjax/variational_families.py b/gpjax/variational_families.py similarity index 100% rename from src/gpjax/variational_families.py rename to gpjax/variational_families.py diff --git a/pyproject.toml b/pyproject.toml index 17495b5a1..32df9ca1c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,6 +67,7 @@ python = "3.10" [tool.hatch.envs.docs.scripts] build = ["python docs/scripts/gen_examples.py --execute", "mkdocs build"] serve = "mkdocs serve --dev-addr localhost:8000" +integration = "python tests/integration_tests.py" [tool.hatch.envs.dev] dependencies = [ @@ -87,13 +88,14 @@ dependencies = [ [tool.hatch.envs.dev.scripts] format = [ - "black ./src ./tests", - "isort ./src ./tests", - "ruff format ./src ./tests", + "black ./gpjax ./tests", + "isort ./gpjax ./tests", + "ruff format ./gpjax ./tests", "ruff check --fix .", ] test = "pytest -vv -n auto ." coverage = "pytest -vv --cov=./gpjax --cov-report=xml:./coverage.xml" +docstrings = "xdoctest ./gpjax" [project.urls] Documentation = "https://docs.jaxgaussianprocesses.com/" @@ -101,16 +103,16 @@ Issues = "https://github.com/JaxGaussianProcesses/GPJax/issues" Source = "https://github.com/JaxGaussianProcesses/GPJax" [tool.hatch.version] -path = "src/gpjax/__init__.py" +path = "gpjax/__init__.py" [tool.coverage.run] source_pkgs = ["gpjax", "tests"] branch = true parallel = true -omit = ["src/gpjax/__init__.py"] +omit = ["gpjax/__init__.py"] [tool.coverage.paths] -gpjax = ["src/gpjax", "*/gpjax/src/gpjax"] +gpjax = ["gpjax", "*/gpjax/"] tests = ["tests", "*/gpjax/tests"] [tool.coverage.report] @@ -126,7 +128,7 @@ target-version = ["py310"] [tool.pytest.ini_options] # https://docs.pytest.org/en/latest/reference/reference.html#ini-options-ref filterwarnings = ["error", "ignore::DeprecationWarning"] -testpaths = ["src/gpjax"] +testpaths = ["gpjax"] xfail_strict = true [tool.ruff] # https://github.com/charliermarsh/ruff @@ -134,7 +136,7 @@ fix = true cache-dir = "~/.cache/ruff" exclude = ["docs/", "examples/"] line-length = 88 -src = ["src/gpjax", "tests"] +src = ["gpjax", "tests"] target-version = "py310" [tool.ruff.lint] @@ -210,8 +212,8 @@ exclude = [ "setup.py", "docs", "tests", - "src/gpjax/__init__.py", - "src/gpjax/citation.py", + "gpjax/__init__.py", + "gpjax/citation.py", ] verbose = 2 quiet = false From b9247a419cf39acd863f35ebedfd3d2f53a7c96c Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 15:49:00 +0200 Subject: [PATCH 04/12] Update workflows --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 82c42cf12..b61355c3c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,7 +32,7 @@ jobs: # Install the dependencies - name: Check docstrings run: | - hatch run xdoctest ./gpjax + hatch run dev:docstrings # Run the unit tests and build the coverage report - name: Run Tests From a48d758416ee2439431ede92b6ba378b04218660 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 15:59:20 +0200 Subject: [PATCH 05/12] Add networkx --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 32df9ca1c..a28ae14b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,7 @@ dependencies = [ "xdoctest>=1.1.1", "mktestdocs>=0.2.1", "isort", + "networkx", ] [tool.hatch.envs.dev.scripts] @@ -93,8 +94,8 @@ format = [ "ruff format ./gpjax ./tests", "ruff check --fix .", ] -test = "pytest -vv -n auto ." -coverage = "pytest -vv --cov=./gpjax --cov-report=xml:./coverage.xml" +test = "pytest . -vv -n auto" +coverage = "pytest . -vv --cov=./gpjax --cov-report=xml:./coverage.xml" docstrings = "xdoctest ./gpjax" [project.urls] From 4979ec6556da63711ecc3558fc9d6cf15184cc77 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 16:20:03 +0200 Subject: [PATCH 06/12] Update tests --- pyproject.toml | 4 ++-- .../test_utility_functions/test_utility_functions.py | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a28ae14b4..712868e29 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,8 +94,8 @@ format = [ "ruff format ./gpjax ./tests", "ruff check --fix .", ] -test = "pytest . -vv -n auto" -coverage = "pytest . -vv --cov=./gpjax --cov-report=xml:./coverage.xml" +test = "pytest . -v -n auto" +coverage = "pytest . -v --cov=./gpjax --cov-report=xml:./coverage.xml" docstrings = "xdoctest ./gpjax" [project.urls] diff --git a/tests/test_decision_making/test_utility_functions/test_utility_functions.py b/tests/test_decision_making/test_utility_functions/test_utility_functions.py index f92c52f72..49f1ed358 100644 --- a/tests/test_decision_making/test_utility_functions/test_utility_functions.py +++ b/tests/test_decision_making/test_utility_functions/test_utility_functions.py @@ -42,6 +42,7 @@ generate_dummy_conjugate_posterior, generate_dummy_non_conjugate_posterior, ) +from jaxtyping import TypeCheckError @pytest.mark.filterwarnings( @@ -121,7 +122,7 @@ def test_non_conjugate_posterior_raises_error( posterior = generate_dummy_non_conjugate_posterior(dataset) posteriors = {OBJECTIVE: posterior} datasets = {OBJECTIVE: dataset} - with pytest.raises(ValueError): + with pytest.raises(TypeCheckError): utility_function = utility_function_builder(**utility_function_kwargs) utility_function.build_utility_function( posteriors=posteriors, datasets=datasets, key=key From 217e9e8350efeedcf3b12e76249542b139b279c1 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 17:33:10 +0200 Subject: [PATCH 07/12] Add formatters --- examples/backend.py | 57 +++++++------------ examples/barycentres.py | 16 +++--- examples/bayesian_optimisation.py | 38 +++++++++---- examples/classification.py | 21 ++++--- examples/collapsed_vi.py | 17 +++--- examples/constructing_new_kernels.py | 19 ++++--- examples/decision_making.py | 21 +++---- examples/deep_kernels.py | 25 ++++---- examples/graph_kernels.py | 16 +++--- examples/intro_to_gps.py | 8 ++- examples/intro_to_kernels.py | 22 ++++--- examples/likelihoods_guide.py | 15 ++--- examples/oceanmodelling.py | 24 +++++--- examples/poisson.py | 11 ++-- examples/regression.py | 15 +++-- examples/uncollapsed_vi.py | 11 ++-- examples/utils.py | 2 +- examples/yacht.py | 13 +++-- .../test_functions/continuous_functions.py | 7 +-- gpjax/distributions.py | 4 +- gpjax/gps.py | 24 +++----- gpjax/kernels/approximations/rff.py | 3 +- gpjax/kernels/computations/base.py | 3 +- gpjax/kernels/computations/eigen.py | 3 +- gpjax/kernels/stationary/matern12.py | 1 + pyproject.toml | 19 +++++-- .../test_utility_functions.py | 2 +- 27 files changed, 222 insertions(+), 195 deletions(-) diff --git a/examples/backend.py b/examples/backend.py index 3e81b4b0e..48e27f04c 100644 --- a/examples/backend.py +++ b/examples/backend.py @@ -1,20 +1,3 @@ -# -*- coding: utf-8 -*- -# --- -# jupyter: -# jupytext: -# cell_metadata_filter: -all -# custom_cell_magics: kql -# text_representation: -# extension: .py -# format_name: percent -# format_version: '1.3' -# jupytext_version: 1.11.2 -# kernelspec: -# display_name: gpjax -# language: python -# name: python3 -# --- - # %% [markdown] # # Backend Module Design # @@ -28,34 +11,48 @@ # # %% +import typing as tp + +from flax import nnx + # Enable Float64 for more stable matrix inversions. from jax import ( config, grad, ) - -config.update("jax_enable_x64", True) - import jax.numpy as jnp +import jax.tree_util as jtu from jaxtyping import ( Float, + Num, install_import_hook, ) import matplotlib as mpl import matplotlib.pyplot as plt -from gpjax.mean_functions import Constant +from examples.utils import use_mpl_style +from gpjax.mean_functions import ( + AbstractMeanFunction, + Constant, +) from gpjax.parameters import ( + DEFAULT_BIJECTION, Parameter, + PositiveReal, Real, + transform, +) +from gpjax.typing import ( + Array, + ScalarFloat, ) +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from flax import nnx - -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() @@ -86,7 +83,6 @@ # `Parameter` will be transformed by GPJax. # %% -from gpjax.parameters import PositiveReal issubclass(PositiveReal, Parameter) @@ -130,8 +126,6 @@ # see how you can define your own bijectors and parameter types. # %% -from gpjax.parameters import DEFAULT_BIJECTION, transform - print(DEFAULT_BIJECTION[constant_param._tag]) # %% [markdown] @@ -195,7 +189,6 @@ # parameter's value by 1. # %% -import jax.tree_util as jtu updated_state = jtu.tree_map(lambda x: x + 1, state) print(updated_state) @@ -236,7 +229,6 @@ # altering the way in which we invoke `nnx.split`. # %% -from gpjax.parameters import PositiveReal graphdef, positive_reals, other_params = nnx.split(posterior, PositiveReal, ...) print(positive_reals) @@ -267,13 +259,6 @@ # mean function. Let's now implement that using the new NNX backend. # %% -import typing as tp - -from jaxtyping import Num - -from gpjax.mean_functions import AbstractMeanFunction -from gpjax.parameters import Parameter -from gpjax.typing import ScalarFloat, Array class LinearMeanFunction(AbstractMeanFunction): diff --git a/examples/barycentres.py b/examples/barycentres.py index 62e06753b..27fe7210a 100644 --- a/examples/barycentres.py +++ b/examples/barycentres.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -30,14 +30,12 @@ # # %% -# Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) - import typing as tp import jax + +# Enable Float64 for more stable matrix inversions. +from jax import config import jax.numpy as jnp import jax.random as jr import jax.scipy.linalg as jsl @@ -45,10 +43,14 @@ import matplotlib.pyplot as plt import tensorflow_probability.substrates.jax.distributions as tfd +from examples.utils import use_mpl_style + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style key = jr.key(123) diff --git a/examples/bayesian_optimisation.py b/examples/bayesian_optimisation.py index ac660a693..faeca6c70 100644 --- a/examples/bayesian_optimisation.py +++ b/examples/bayesian_optimisation.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -23,28 +23,43 @@ # (GPs), so if you're not familiar with them, check out our [GP introduction notebook](https://docs.jaxgaussianprocesses.com/examples/intro_to_gps/). # %% -# Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) +from typing import ( + List, + Tuple, +) import jax + +# Enable Float64 for more stable matrix inversions. +from jax import config import jax.numpy as jnp import jax.random as jr -from jaxtyping import install_import_hook, Float, Int +from jaxopt import ScipyBoundedMinimize +from jaxtyping import ( + Float, + Int, + install_import_hook, +) import matplotlib as mpl -import matplotlib.pyplot as plt from matplotlib import cm +import matplotlib.pyplot as plt import optax as ox import tensorflow_probability.substrates.jax as tfp -from typing import List, Tuple + +from examples.utils import use_mpl_style +from gpjax.parameters import Static +from gpjax.typing import ( + Array, + FunctionalSample, + ScalarFloat, +) + +config.update("jax_enable_x64", True) + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from gpjax.typing import Array, FunctionalSample, ScalarFloat -from jaxopt import ScipyBoundedMinimize -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() @@ -227,7 +242,6 @@ def standardised_forrester(x: Float[Array, "N 1"]) -> Float[Array, "N 1"]: # %% -from gpjax.parameters import Static def return_optimised_posterior( diff --git a/examples/classification.py b/examples/classification.py index e6e2229f8..360f5b2fd 100644 --- a/examples/classification.py +++ b/examples/classification.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -22,13 +22,12 @@ # with non-Gaussian likelihoods via maximum a posteriori (MAP). We focus on a classification task here. # %% -# Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) - +import cola from flax import nnx import jax + +# Enable Float64 for more stable matrix inversions. +from jax import config import jax.numpy as jnp import jax.random as jr import jax.scipy as jsp @@ -41,10 +40,15 @@ import optax as ox import tensorflow_probability.substrates.jax as tfp +from examples.utils import use_mpl_style +from gpjax.lower_cholesky import lower_cholesky + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style tfd = tfp.distributions identity_matrix = jnp.eye @@ -206,8 +210,7 @@ # datapoints below. # %% -import cola -from gpjax.lower_cholesky import lower_cholesky + gram, cross_covariance = (kernel.gram, kernel.cross_covariance) jitter = 1e-6 diff --git a/examples/collapsed_vi.py b/examples/collapsed_vi.py index 959515920..b2a1f90cf 100644 --- a/examples/collapsed_vi.py +++ b/examples/collapsed_vi.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax_beartype # language: python @@ -27,11 +27,10 @@ # %% # Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) - -from jax import jit +from jax import ( + config, + jit, +) import jax.numpy as jnp import jax.random as jr from jaxtyping import install_import_hook @@ -39,10 +38,14 @@ import matplotlib.pyplot as plt import optax as ox +from examples.utils import use_mpl_style + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() diff --git a/examples/constructing_new_kernels.py b/examples/constructing_new_kernels.py index 96d085259..ceb8b4863 100644 --- a/examples/constructing_new_kernels.py +++ b/examples/constructing_new_kernels.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -24,9 +24,6 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - import jax.numpy as jnp import jax.random as jr from jaxtyping import ( @@ -37,10 +34,20 @@ import matplotlib.pyplot as plt import tensorflow_probability.substrates.jax as tfp +from examples.utils import use_mpl_style +from gpjax.kernels.computations import DenseKernelComputation +from gpjax.parameters import ( + DEFAULT_BIJECTION, + PositiveReal, + Static, +) + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style tfb = tfp.bijectors @@ -206,8 +213,6 @@ # %% -from gpjax.kernels.computations import DenseKernelComputation -from gpjax.parameters import DEFAULT_BIJECTION, Static, PositiveReal def angular_distance(x, y, c): diff --git a/examples/decision_making.py b/examples/decision_making.py index e281e55d4..4274d0d44 100644 --- a/examples/decision_making.py +++ b/examples/decision_making.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -36,37 +36,32 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - - import jax.numpy as jnp import jax.random as jr import matplotlib as mpl import matplotlib.pyplot as plt import optax as ox +from examples.utils import use_mpl_style import gpjax as gpx -from gpjax.decision_making.utility_functions import ( - ThompsonSampling, -) +from gpjax.decision_making.decision_maker import UtilityDrivenDecisionMaker +from gpjax.decision_making.posterior_handler import PosteriorHandler +from gpjax.decision_making.search_space import ContinuousSearchSpace +from gpjax.decision_making.utility_functions import ThompsonSampling from gpjax.decision_making.utility_maximizer import ( ContinuousSinglePointUtilityMaximizer, ) -from gpjax.decision_making.decision_maker import UtilityDrivenDecisionMaker from gpjax.decision_making.utils import ( OBJECTIVE, build_function_evaluator, ) -from gpjax.decision_making.posterior_handler import PosteriorHandler -from gpjax.decision_making.search_space import ContinuousSearchSpace from gpjax.typing import ( Array, Float, ) +config.update("jax_enable_x64", True) -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() @@ -259,7 +254,7 @@ def forrester(x: Float[Array, "N 1"]) -> Float[Array, "N 1"]: ) # %% [markdown] - +# # It is worth noting that `ThompsonSampling` is not the only utility function we could use, # since our module also provides e.g. `ProbabilityOfImprovement`, `ExpectedImprovment`, # which were briefly discussed in [our previous introduction to Bayesian optimisation](https://docs.jaxgaussianprocesses.com/examples/bayesian_optimisation/). diff --git a/examples/deep_kernels.py b/examples/deep_kernels.py index b41538c39..2ebb0d349 100644 --- a/examples/deep_kernels.py +++ b/examples/deep_kernels.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -26,22 +26,16 @@ # Gaussian process model's kernel through a neural network can offer a solution to this. # %% -# Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) - from dataclasses import ( dataclass, field, ) from flax import nnx -from gpjax.kernels.computations import ( - AbstractKernelComputation, - DenseKernelComputation, -) import jax + +# Enable Float64 for more stable matrix inversions. +from jax import config import jax.numpy as jnp import jax.random as jr from jaxtyping import ( @@ -54,13 +48,20 @@ import optax as ox from scipy.signal import sawtooth +from examples.utils import use_mpl_style +from gpjax.kernels.computations import ( + AbstractKernelComputation, + DenseKernelComputation, +) + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx from gpjax.kernels.base import AbstractKernel -from examples.utils import use_mpl_style - # set the default style for plotting use_mpl_style() cols = mpl.rcParams["axes.prop_cycle"].by_key()["color"] diff --git a/examples/graph_kernels.py b/examples/graph_kernels.py index e5e532db5..0bd9db41b 100644 --- a/examples/graph_kernels.py +++ b/examples/graph_kernels.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -25,13 +25,10 @@ # [kernels notebook](https://docs.jaxgaussianprocesses.com/examples/constructing_new_kernels). # %% -# Enable Float64 for more stable matrix inversions. -from jax import config - -config.update("jax_enable_x64", True) - import random +# Enable Float64 for more stable matrix inversions. +from jax import config import jax.numpy as jnp import jax.random as jr from jaxtyping import install_import_hook @@ -39,12 +36,15 @@ import matplotlib.pyplot as plt import networkx as nx +from examples.utils import use_mpl_style + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style - # set the default style for plotting use_mpl_style() diff --git a/examples/intro_to_gps.py b/examples/intro_to_gps.py index 9fc0eeae9..699bde903 100644 --- a/examples/intro_to_gps.py +++ b/examples/intro_to_gps.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -121,7 +121,11 @@ import pandas as pd import seaborn as sns import tensorflow_probability.substrates.jax as tfp -from examples.utils import confidence_ellipse, use_mpl_style + +from examples.utils import ( + confidence_ellipse, + use_mpl_style, +) # set the default style for plotting use_mpl_style() diff --git a/examples/intro_to_kernels.py b/examples/intro_to_kernels.py index 396aa9361..b4340ffac 100644 --- a/examples/intro_to_kernels.py +++ b/examples/intro_to_kernels.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -24,23 +24,28 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - import jax.numpy as jnp import jax.random as jr -from jaxtyping import install_import_hook, Float +from jaxtyping import ( + Float, + install_import_hook, +) import matplotlib as mpl import matplotlib.pyplot as plt import optax as ox import pandas as pd +from sklearn.preprocessing import StandardScaler + +from examples.utils import use_mpl_style +from gpjax.parameters import PositiveReal +from gpjax.typing import Array + +config.update("jax_enable_x64", True) + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from gpjax.typing import Array -from sklearn.preprocessing import StandardScaler -from examples.utils import use_mpl_style key = jr.key(42) @@ -232,7 +237,6 @@ def forrester(x: Float[Array, "N"]) -> Float[Array, "N"]: # noqa: F821 # First we define our model, using the Matérn52 kernel, and construct our posterior *without* optimising the kernel hyperparameters: # %% -from gpjax.parameters import PositiveReal mean = gpx.mean_functions.Zero() kernel = gpx.kernels.Matern52( diff --git a/examples/likelihoods_guide.py b/examples/likelihoods_guide.py index 10597a265..4e210be55 100644 --- a/examples/likelihoods_guide.py +++ b/examples/likelihoods_guide.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -66,19 +66,20 @@ # a likelihood object. To do this, we'll need a dataset. # %% +import jax + # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - -import gpjax as gpx -import jax import jax.numpy as jnp import jax.random as jr import matplotlib.pyplot as plt import tensorflow_probability.substrates.jax as tfp from examples.utils import use_mpl_style +import gpjax as gpx + +config.update("jax_enable_x64", True) + tfd = tfp.distributions @@ -130,7 +131,7 @@ gpx.likelihoods.Gaussian(num_datapoints=D.n, obs_stddev=0.5) # %% [markdown] - +# # ### Prediction # # The `predict` method of a likelihood object transforms the latent distribution of diff --git a/examples/oceanmodelling.py b/examples/oceanmodelling.py index d46e89af8..e1d8041b5 100644 --- a/examples/oceanmodelling.py +++ b/examples/oceanmodelling.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -23,13 +23,15 @@ # # Surface drifters are measurement devices that measure the dynamics and circulation patterns of the world's oceans. Studying and predicting ocean currents are important to climate research, for example, forecasting and predicting oil spills, oceanographic surveying of eddies and upwelling, or providing information on the distribution of biomass in ecosystems. We will be using the [Gulf Drifters Open dataset](https://zenodo.org/record/4421585), which contains all publicly available surface drifter trajectories from the Gulf of Mexico spanning 28 years. # %% -from jax import config - -config.update("jax_enable_x64", True) -from dataclasses import dataclass, field +from dataclasses import ( + dataclass, + field, +) -from jax import hessian -from jax import config +from jax import ( + config, + hessian, +) import jax.numpy as jnp import jax.random as jr from jaxtyping import ( @@ -42,10 +44,15 @@ import pandas as pd import tensorflow_probability as tfp +from examples.utils import use_mpl_style +from gpjax.kernels.computations import DenseKernelComputation + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() @@ -213,7 +220,6 @@ def dataset_3d(pos, vel): # %% -from gpjax.kernels.computations import DenseKernelComputation class VelocityKernel(gpx.kernels.AbstractKernel): diff --git a/examples/poisson.py b/examples/poisson.py index 284cb54c8..9d2ec4966 100644 --- a/examples/poisson.py +++ b/examples/poisson.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: base # language: python @@ -24,21 +24,22 @@ # %% import blackjax +from flax import nnx import jax +from jax import config import jax.numpy as jnp import jax.random as jr import jax.tree_util as jtu +from jaxtyping import install_import_hook import matplotlib as mpl import matplotlib.pyplot as plt import tensorflow_probability.substrates.jax as tfp -from jax import config -from jaxtyping import install_import_hook -from flax import nnx + +from examples.utils import use_mpl_style with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style # Enable Float64 for more stable matrix inversions. config.update("jax_enable_x64", True) diff --git a/examples/regression.py b/examples/regression.py index c5ef2d50e..9dae4fc1b 100644 --- a/examples/regression.py +++ b/examples/regression.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -22,20 +22,23 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - import jax.numpy as jnp import jax.random as jr from jaxtyping import install_import_hook import matplotlib as mpl import matplotlib.pyplot as plt -from examples.utils import clean_legend + +from examples.utils import ( + clean_legend, + use_mpl_style, +) + +config.update("jax_enable_x64", True) + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style key = jr.key(123) diff --git a/examples/uncollapsed_vi.py b/examples/uncollapsed_vi.py index 073819a6d..f2fb52ae4 100644 --- a/examples/uncollapsed_vi.py +++ b/examples/uncollapsed_vi.py @@ -8,7 +8,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax_beartype # language: python @@ -33,9 +33,6 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - import jax.numpy as jnp import jax.random as jr from jaxtyping import install_import_hook @@ -44,11 +41,15 @@ import optax as ox import tensorflow_probability.substrates.jax as tfp +from examples.utils import use_mpl_style + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx import gpjax.kernels as jk -from examples.utils import use_mpl_style tfb = tfp.bijectors diff --git a/examples/utils.py b/examples/utils.py index b8d5a81f8..a87e8966b 100644 --- a/examples/utils.py +++ b/examples/utils.py @@ -1,8 +1,8 @@ from pathlib import Path -import matplotlib.pyplot as plt from matplotlib import transforms from matplotlib.patches import Ellipse +import matplotlib.pyplot as plt import numpy as np diff --git a/examples/yacht.py b/examples/yacht.py index 940dff153..a78d63af3 100644 --- a/examples/yacht.py +++ b/examples/yacht.py @@ -7,7 +7,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.11.2 +# jupytext_version: 1.16.4 # kernelspec: # display_name: gpjax # language: python @@ -26,11 +26,8 @@ # %% # Enable Float64 for more stable matrix inversions. from jax import config - -config.update("jax_enable_x64", True) - -import jax.random as jr import jax.numpy as jnp +import jax.random as jr from jaxtyping import install_import_hook import matplotlib as mpl import matplotlib.pyplot as plt @@ -43,10 +40,14 @@ from sklearn.model_selection import train_test_split from sklearn.preprocessing import StandardScaler +from examples.utils import use_mpl_style + +config.update("jax_enable_x64", True) + + with install_import_hook("gpjax", "beartype.beartype"): import gpjax as gpx -from examples.utils import use_mpl_style # set the default style for plotting use_mpl_style() diff --git a/gpjax/decision_making/test_functions/continuous_functions.py b/gpjax/decision_making/test_functions/continuous_functions.py index a04b4292b..ff3f82fda 100644 --- a/gpjax/decision_making/test_functions/continuous_functions.py +++ b/gpjax/decision_making/test_functions/continuous_functions.py @@ -139,12 +139,7 @@ def evaluate(self, x: Float[Array, "N D"]) -> Float[Array, "N 1"]: x1 = 4.0 * x[:, 0] - 2.0 x2 = 4.0 * x[:, 1] - 2.0 a = 1.0 + (x1 + x2 + 1.0) ** 2 * ( - 19.0 - - 14.0 * x1 - + 3.0 * (x1**2) - - 14.0 * x2 - + 6.0 * x1 * x2 - + 3.0 * (x2**2) + 19.0 - 14.0 * x1 + 3.0 * (x1**2) - 14.0 * x2 + 6.0 * x1 * x2 + 3.0 * (x2**2) ) b = 30.0 + (2.0 * x1 - 3.0 * x2) ** 2 * ( 18.0 diff --git a/gpjax/distributions.py b/gpjax/distributions.py index 3c6d7e82a..b8f7bb331 100644 --- a/gpjax/distributions.py +++ b/gpjax/distributions.py @@ -162,9 +162,7 @@ def affine_transformation(x): return vmap(affine_transformation)(Z) - def sample( - self, seed: KeyArray, sample_shape: Tuple[int, ...] - ): # pylint: disable=useless-super-delegation + def sample(self, seed: KeyArray, sample_shape: Tuple[int, ...]): # pylint: disable=useless-super-delegation r"""See `Distribution.sample`.""" return self._sample_n( seed, sample_shape[0] diff --git a/gpjax/gps.py b/gpjax/gps.py index be4ab211a..db11f8066 100644 --- a/gpjax/gps.py +++ b/gpjax/gps.py @@ -146,20 +146,17 @@ class Prior(AbstractPrior[M, K]): if tp.TYPE_CHECKING: @tp.overload - def __mul__(self, other: GL) -> "ConjugatePosterior[Prior[M, K], GL]": - ... + def __mul__(self, other: GL) -> "ConjugatePosterior[Prior[M, K], GL]": ... @tp.overload def __mul__( # noqa: F811 self, other: NGL - ) -> "NonConjugatePosterior[Prior[M, K], NGL]": - ... + ) -> "NonConjugatePosterior[Prior[M, K], NGL]": ... @tp.overload def __mul__( # noqa: F811 self, other: L - ) -> "AbstractPosterior[Prior[M, K], L]": - ... + ) -> "AbstractPosterior[Prior[M, K], L]": ... def __mul__(self, other): # noqa: F811 r"""Combine the prior with a likelihood to form a posterior distribution. @@ -195,20 +192,17 @@ def __mul__(self, other): # noqa: F811 if tp.TYPE_CHECKING: @tp.overload - def __rmul__(self, other: GL) -> "ConjugatePosterior[Prior[M, K], GL]": - ... + def __rmul__(self, other: GL) -> "ConjugatePosterior[Prior[M, K], GL]": ... @tp.overload def __rmul__( # noqa: F811 self, other: NGL - ) -> "NonConjugatePosterior[Prior[M, K], NGL]": - ... + ) -> "NonConjugatePosterior[Prior[M, K], NGL]": ... @tp.overload def __rmul__( # noqa: F811 self, other: L - ) -> "AbstractPosterior[Prior[M, K], L]": - ... + ) -> "AbstractPosterior[Prior[M, K], L]": ... def __rmul__(self, other): # noqa: F811 r"""Combine the prior with a likelihood to form a posterior distribution. @@ -722,15 +716,13 @@ def predict( @tp.overload -def construct_posterior(prior: P, likelihood: GL) -> ConjugatePosterior[P, GL]: - ... +def construct_posterior(prior: P, likelihood: GL) -> ConjugatePosterior[P, GL]: ... @tp.overload def construct_posterior( # noqa: F811 prior: P, likelihood: NGL -) -> NonConjugatePosterior[P, NGL]: - ... +) -> NonConjugatePosterior[P, NGL]: ... def construct_posterior(prior, likelihood): # noqa: F811 diff --git a/gpjax/kernels/approximations/rff.py b/gpjax/kernels/approximations/rff.py index b63e6cd08..dedcd3c4c 100644 --- a/gpjax/kernels/approximations/rff.py +++ b/gpjax/kernels/approximations/rff.py @@ -1,4 +1,5 @@ -"""Compute Random Fourier Feature (RFF) kernel approximations. """ +"""Compute Random Fourier Feature (RFF) kernel approximations.""" + import beartype.typing as tp import jax.random as jr from jaxtyping import Float diff --git a/gpjax/kernels/computations/base.py b/gpjax/kernels/computations/base.py index fe60b9f0e..5826f3b9e 100644 --- a/gpjax/kernels/computations/base.py +++ b/gpjax/kernels/computations/base.py @@ -74,8 +74,7 @@ def gram( @abc.abstractmethod def _cross_covariance( self, kernel: K, x: Num[Array, "N D"], y: Num[Array, "M D"] - ) -> Float[Array, "N M"]: - ... + ) -> Float[Array, "N M"]: ... def cross_covariance( self, kernel: K, x: Num[Array, "N D"], y: Num[Array, "M D"] diff --git a/gpjax/kernels/computations/eigen.py b/gpjax/kernels/computations/eigen.py index 091b63d50..97a1bff6f 100644 --- a/gpjax/kernels/computations/eigen.py +++ b/gpjax/kernels/computations/eigen.py @@ -26,7 +26,8 @@ from gpjax.typing import Array Kernel = tp.TypeVar( - "Kernel", bound="gpjax.kernels.non_euclidean.graph.GraphKernel" # noqa: F821 + "Kernel", + bound="gpjax.kernels.non_euclidean.graph.GraphKernel", # noqa: F821 ) diff --git a/gpjax/kernels/stationary/matern12.py b/gpjax/kernels/stationary/matern12.py index 9f99122e3..ddf2f1058 100644 --- a/gpjax/kernels/stationary/matern12.py +++ b/gpjax/kernels/stationary/matern12.py @@ -38,6 +38,7 @@ class Matern12(StationaryKernel): k(x, y) = \sigma^2\exp\Bigg(-\frac{\lvert x-y \rvert}{2\ell^2}\Bigg) $$ """ + name: str = "Matérn12" def __call__(self, x: Float[Array, " D"], y: Float[Array, " D"]) -> ScalarFloat: diff --git a/pyproject.toml b/pyproject.toml index 712868e29..8180496ad 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -85,18 +85,29 @@ dependencies = [ "mktestdocs>=0.2.1", "isort", "networkx", + "black", + "jupytext", ] [tool.hatch.envs.dev.scripts] -format = [ - "black ./gpjax ./tests", +black-format = ["black ./gpjax ./tests", "jupytext --pipe black examples/*.py"] +black-check = "black --check --diff ./gpjax ./tests" +imports-format = [ "isort ./gpjax ./tests", - "ruff format ./gpjax ./tests", - "ruff check --fix .", + 'isort examples/*.py --treat-comment-as-code "# %%" --float-to-top', ] +imports-check = [ + "isort ./gpjax ./tests -c", + 'isort examples/*.py -c --treat-comment-as-code "# %%" --float-to-top', +] +lint-format = ['ruff format ./gpjax ./tests ./examples'] +lint-check = ['ruff check --fix ./gpjax ./tests ./examples'] +format = ["black-format", "imports-format", "lint-format"] +check = ["black-check", "imports-check", "lint-check"] test = "pytest . -v -n auto" coverage = "pytest . -v --cov=./gpjax --cov-report=xml:./coverage.xml" docstrings = "xdoctest ./gpjax" +all-tests = ['check', 'docstrings', 'test'] [project.urls] Documentation = "https://docs.jaxgaussianprocesses.com/" diff --git a/tests/test_decision_making/test_utility_functions/test_utility_functions.py b/tests/test_decision_making/test_utility_functions/test_utility_functions.py index 49f1ed358..1ed3f4606 100644 --- a/tests/test_decision_making/test_utility_functions/test_utility_functions.py +++ b/tests/test_decision_making/test_utility_functions/test_utility_functions.py @@ -22,6 +22,7 @@ from beartype.typing import Type import jax.random as jr +from jaxtyping import TypeCheckError import pytest from gpjax.decision_making.test_functions.continuous_functions import ( @@ -42,7 +43,6 @@ generate_dummy_conjugate_posterior, generate_dummy_non_conjugate_posterior, ) -from jaxtyping import TypeCheckError @pytest.mark.filterwarnings( From af2f86e418706b9483fa04678982a71725d0a169 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 18:00:23 +0200 Subject: [PATCH 08/12] Drop Poetry refs --- .github/pull_request_template.md | 10 +- docs/contributing.md | 29 +---- docs/installation.md | 4 +- static/CONTRIBUTING.md | 207 ++++++++++++++++--------------- 4 files changed, 115 insertions(+), 135 deletions(-) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 6bca22c6f..143ba3c2a 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,14 +1,6 @@ -## Type of changes - -- [ ] Bug fix -- [ ] New feature -- [ ] Documentation / docstrings -- [ ] Tests -- [ ] Other - ## Checklist -- [ ] I've formatted the new code by running `poetry run pre-commit run --all-files --show-diff-on-failure` before committing. +- [ ] I've formatted the new code by running `hatch run dev:format` before committing. - [ ] I've added tests for new code. - [ ] I've added docstrings for the new code. diff --git a/docs/contributing.md b/docs/contributing.md index 10be7812a..578626b43 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -72,36 +72,19 @@ you through every detail! Always use a `feature` branch. It's good practice to avoid work on the ``main`` branch of any repository. -4. We use [Poetry](https://python-poetry.org/) for packaging and dependency management, and project requirements are in ``pyproject.toml``. We suggest using a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/) for -development. For those using Apple Silicon chips, we advise using [Conda miniforge](https://github.com/conda-forge/miniforge). Once the virtual environment is activated, run: +4. We use [Hatch](https://hatch.pypa.io/latest/) for packaging and dependency management. Project requirements are in ``pyproject.toml``. To install GPJax into a Hatch virtual environment, run: ```bash - $ poetry install + $ hatch env create ``` At this point we recommend you check your installation passes the supplied unit tests: ```bash - $ poetry run pytest + $ hatch run dev:all-tests ``` -5. Install the pre-commit hooks. - - ```bash - $ pre-commit install - ``` - - Please ensure you have done this before committing any files. If - successful, this will print the following output `pre-commit installed at - .git/hooks/pre-commit`. - -6. At this point you can manually run the pre-commit hooks with the following command: - - ```bash - poetry run pre-commit run --all-files - ``` - -7. Add changed files using `git add` and then `git commit` files to record your +5. Add changed files using `git add` and then `git commit` files to record your changes locally: ```bash @@ -122,7 +105,7 @@ development. For those using Apple Silicon chips, we advise using [Conda minifor $ git push -u origin my-feature ``` -8. Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull +6. Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull request' button to send your changes to the project's maintainers for review. @@ -159,7 +142,7 @@ request, we recommend you check the following: accepted. Test coverage can be checked with: ```bash - $ poetry run pytest tests --cov=./ --cov-report=html + $ hatch run dev:coverage ``` Navigate to the newly created folder `htmlcov` and open `index.html` to view diff --git a/docs/installation.md b/docs/installation.md index b711d70b6..73de52822 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -31,7 +31,7 @@ hardware acceleration support as detailed in the ```bash git clone https://github.com/thomaspinder/GPJax.git cd GPJax - poetry install + hatch shell create ``` !!! tip @@ -45,5 +45,5 @@ hardware acceleration support as detailed in the and recommend you check your installation passes the supplied unit tests: ```bash - poetry run pytest tests/ + hatch run dev:all-tests ``` diff --git a/static/CONTRIBUTING.md b/static/CONTRIBUTING.md index 5df3f4559..578626b43 100644 --- a/static/CONTRIBUTING.md +++ b/static/CONTRIBUTING.md @@ -1,147 +1,152 @@ -# Guidelines for Contributing +# Contributing -GPJax welcomes contributions from interested individuals or groups. These -guidelines help explain how you can contribute to the library +## How can I contribute? -There are 4 main ways of contributing to the library (in descending order of -difficulty or scope): +GPJax welcomes contributions from interested individuals or groups. There are +many ways to contribute, including: + +- Answering questions on our [discussions + page](https://github.com/JaxGaussianProcesses/GPJax/discussions). +- Raising [issues](https://github.com/JaxGaussianProcesses/GPJax/issues) related to bugs + or desired enhancements. +- Contributing or improving the + [docs](https://github.com/JaxGaussianProcesses/GPJax/tree/main/docs) or + [examples](https://github.com/JaxGaussianProcesses/GPJax/tree/master/docs/nbs). +- Fixing outstanding [issues](https://github.com/JaxGaussianProcesses/GPJax/issues) + (bugs). +- Extending or improving our [codebase](https://github.com/JaxGaussianProcesses/GPJax). -- Adding new or improved functionality to the existing codebase -- Fixing outstanding issues (bugs) with the existing codebase. They range from - low-level software bugs to higher-level design problems. -- Contributing or improving the documentation (`docs`) or examples - (`gpjax/docs/nbs`) -- Submitting issues related to bugs or desired enhancements ## Code of conduct As a contributor to GPJax, you can help us keep the community open and inclusive. Please read and follow our [Code of -Conduct](https://github.com/thomaspinder/GPJax/blob/master/.github/CODE_OF_CONDUCT.md). +Conduct](https://github.com/JaxGaussianProcesses/GPJax/blob/master/.github/CODE_OF_CONDUCT.md). -# Opening issues and getting support +## Opening issues and getting support Please open issues on [Github Issue -Tracker](https://github.com/thomaspinder/GPJax/issues/new/choose). +Tracker](https://github.com/JaxGaussianProcesses/GPJax/issues/new/choose). Here you can +mention You can ask a question or start a discussion in the [Discussion -section](https://github.com/thomaspinder/GPJax/discussions) on Github. +section](https://github.com/JaxGaussianProcesses/GPJax/discussions) on Github. -# Contributing code via pull requests +## Contributing to the source code -Please submit patches via pull requests. +Submitting code contributions to GPJax is done via a [GitHub pull +request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests). +Our preferred workflow is to first fork the [GitHub +repository](https://github.com/JaxGaussianProcesses/GPJax), clone it to your local +machine, and develop on a _feature branch_. Once you're happy with your changes, +install our `pre-commit hooks`, `commit` and `push` your code. -The preferred workflow for contributing is to fork the [GitHub -repository](https://github.com/thomaspinder/GPJax), clone it to your local -machine, and develop on a feature branch. Once you are ready to commit your -changes, install the pre-commit hooks with `pre-commit install` and the commit -and push your code as usual. +**New to this?** Don't panic, our [guide](#step-by-step-guide) below will walk +you through every detail! -## Steps: +!!! attention "Note" -1. Fork the [project repository](https://github.com/thomaspinder/GPJax) by - clicking on the 'Fork' button near the top right of the main repository page. - This creates a copy of the code under your GitHub user account. + Before opening a pull request we recommend you check our [pull request checklist](#pull-request-checklist). -2. Clone your fork of the GPJax repo from your GitHub account to your local - disk, and add the base repository as a remote: - ```bash - $ git clone git@github.com:/GPJax.git - $ cd GPJax - $ git remote add upstream git@github.com:GPJax.git - ``` +### Step-by-step guide: -3. Create a `feature` branch to hold your development changes: +1. Click [here](https://github.com/JaxGaussianProcesses/GPJax/fork) to Fork GPJax's + codebase (alternatively, click the 'Fork' button towards the top right of + the [main repository page](https://github.com/JaxGaussianProcesses/GPJax)). This + adds a copy of the codebase to your GitHub user account. - ```bash - $ git checkout -b my-feature - ``` +2. Clone your GPJax fork from your GitHub account to your local disk, and add + the base repository as a remote: + ```bash + $ git clone git@github.com:/GPJax.git + $ cd GPJax + $ git remote add upstream git@github.com:GPJax.git + ``` - Always use a `feature` branch. It's good practice to never routinely work on - the `master` branch of any repository. +3. Create a `feature` branch to hold your development changes: -4. Project requirements are in `requirements.txt`. + ```bash + $ git checkout -b my-feature + ``` + Always use a `feature` branch. It's good practice to avoid + work on the ``main`` branch of any repository. - We suggest using a [virtual - environment](https://docs.python-guide.org/dev/virtualenvs/) for development. - Once the virtual environment is activated, run: +4. We use [Hatch](https://hatch.pypa.io/latest/) for packaging and dependency management. Project requirements are in ``pyproject.toml``. To install GPJax into a Hatch virtual environment, run: - ```bash - $ pip install -e . - $ pip install -r requirements-dev.txt - ``` + ```bash + $ hatch env create + ``` -5. Install the pre-commit hooks. Please **ensure you do this before committing - any files**. This can be done by executing the following: - ```bash - $ pre-commit install - ``` - If successful, this will print the following output `pre-commit installed at - .git/hooks/pre-commit`. + At this point we recommend you check your installation passes the supplied unit tests: -6. Develop the feature on your feature branch. When you're done editing, format the new code with - ```bash - $ poetry run pre-commit run --all-files --show-diff-on-failure - ``` - If any errors are reported, fix them and re-run the command. + ```bash + $ hatch run dev:all-tests + ``` -7. Check all tests are passing - ```bash - poetry run pytest tests --n auto - ``` - If any tests fail, fix them and re-run the command. +5. Add changed files using `git add` and then `git commit` files to record your + changes locally: -8. Add changed files using `git add` and then `git commit` files: + ```bash + $ git add modified_files + $ git commit + ``` + After committing, it is a good idea to sync with the base repository in case + there have been any changes: - ```bash - $ git add modified_files - $ git commit - ``` + ```bash + $ git fetch upstream + $ git rebase upstream/main + ``` - to record your changes locally. After committing, it is a good idea to sync - with the base repository in case there have been any changes: + Then push the changes to your GitHub account with: - ```bash - $ git fetch upstream - $ git rebase upstream/main - ``` + ```bash + $ git push -u origin my-feature + ``` - Then push the changes to your GitHub account with: +6. Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull + request' button to send your changes to the project's maintainers for + review. - ```bash - $ git push -u origin my-feature - ``` +### Pull request checklist -9. Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull - request' button to send your changes to the project's maintainer for review. +We welcome both complete or "work in progress" pull requests. Before opening +one, we recommended you check the following guidelines to ensure a smooth review +process. -## Pull request checklist +**My contribution is a "work in progress":** -We recommended that your contribution complies with the following guidelines -before you submit a pull request: +Please prefix the title of incomplete contributions with `[WIP]` (to indicate a +work in progress). WIPs are useful to: -- If your pull request addresses an issue, please use the pull request title to - describe the issue and mention the issue number in the pull request - description. This will make sure a link back to the original issue is created. + 1. Indicate you are working on something to avoid duplicated work. + 2. Request broad review of functionality or API. + 3. Seek collaborators. -- All public methods must have informative docstrings +In the description of the pull request, we recommend you outline where work +needs doing. For example, do some tests need writing? -- Please prefix the title of incomplete contributions with `[WIP]` (to indicate - a work in progress). WIPs may be useful to (1) indicate you are working on - something to avoid duplicated work, (2) request broad review of functionality - or API, or (3) seek collaborators. +**My contribution is complete:** -- All other tests pass when everything is rebuilt from scratch. +If addressing an issue, please use the pull request title to describe the issue +and mention the issue number in the pull request description. This will make +sure a link back to the original issue is created. Then before making your pull +request, we recommend you check the following: -- Documentation and high-coverage tests are necessary for enhancements to be - accepted. + - Do all public methods have informative docstrings that describe their + function, input(s) and output(s)? + - Do the pre-commit hooks pass? + - Do the tests pass when everything is rebuilt from scratch? + - Documentation and high-coverage tests are necessary for enhancements to be + accepted. Test coverage can be checked with: -- Code with good test, check with: + ```bash + $ hatch run dev:coverage + ``` - ```bash - $ pip install -r requirements-dev.txt - $ pytest tests --cov=./ --cov-report=html - ``` + Navigate to the newly created folder `htmlcov` and open `index.html` to view + the coverage report. -#### This guide was derived from [PyMC's guide to contributing](https://github.com/pymc-devs/pymc/blob/main/CONTRIBUTING.md) +This guide was derived from [PyMC's guide to +contributing](https://github.com/pymc-devs/pymc/blob/main/CONTRIBUTING.md). From fb989defd27d1a60d7e6c4085b9fb2cbdb87a281 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Sun, 18 Aug 2024 22:23:06 +0200 Subject: [PATCH 09/12] Gaussian dist tests --- gpjax/testing.py | 48 ++++++++++++++++ gpjax/typing.py | 4 ++ pyproject.toml | 6 +- tests/conftest.py | 4 ++ tests/test_gaussian_distribution.py | 80 ++++++++++++++------------- tests/test_kernels/test_stationary.py | 3 +- tests/test_testing.py | 55 ++++++++++++++++++ 7 files changed, 159 insertions(+), 41 deletions(-) create mode 100644 gpjax/testing.py create mode 100644 tests/test_testing.py diff --git a/gpjax/testing.py b/gpjax/testing.py new file mode 100644 index 000000000..dc80db7c3 --- /dev/null +++ b/gpjax/testing.py @@ -0,0 +1,48 @@ +from beartype import typing as tp +from hypothesis import strategies as st +from hypothesis.extra.numpy import arrays +import jax.numpy as jnp +from jaxtyping import Float + +from gpjax.typing import ( + Array, + ScalarFloat, +) + +_JITTER = 1e-6 + + +@st.composite +def sample_univariate_gaussian_params(draw) -> tp.Tuple[ScalarFloat, ScalarFloat]: + loc = jnp.array(draw(st.floats()), dtype=jnp.float64) + scale = jnp.array( + draw(st.floats(min_value=_JITTER, exclude_min=True)), dtype=jnp.float64 + ) + return loc, scale + + +@st.composite +def sample_multivariate_gaussian_params( + draw, dim: int +) -> tp.Tuple[Float[Array, " N"], Float[Array, "N N"]]: + mean = draw( + arrays(dtype=float, shape=dim, elements=st.floats(min_value=-10, max_value=10)) + ) + lower_vals = draw( + arrays( + dtype=float, + shape=(dim, dim), + elements=st.floats(min_value=-10, max_value=10), + ) + ) + cov = jnp.dot(lower_vals, lower_vals.T) + cov += jnp.eye(dim) * _JITTER + return mean, cov + + +def is_psd(matrix: Float[Array, "N N"]) -> bool: + # try: + eig_vals = jnp.linalg.eigvals(matrix) + psd_status = jnp.all(eig_vals > 0.0) + # except jnp.linalg.Lin + return psd_status diff --git a/gpjax/typing.py b/gpjax/typing.py index c2cd18e8d..e1d9058d0 100644 --- a/gpjax/typing.py +++ b/gpjax/typing.py @@ -15,6 +15,7 @@ from typing import ( Callable, + Tuple, Union, ) @@ -43,6 +44,9 @@ VecNOrMatNM = Union[Float[Array, " N"], Float[Array, "N M"]] +UnivariateParams = Tuple[ScalarFloat, ScalarFloat] +MultivariateParams = Tuple[Float[Array, " N"], Float[Array, "N N"]] + FunctionalSample = Callable[[Float[Array, "N D"]], Float[Array, "N B"]] r""" Type alias for functions representing $B$ samples from a model, to be evaluated on any set of $N$ inputs (of dimension $D$) and returning the evaluations of each diff --git a/pyproject.toml b/pyproject.toml index 8180496ad..a734388fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ dependencies = [ "jaxopt==0.8.2", "flax>=0.8.5", "numpy<2.0.0", + "hypothesis", ] [tool.hatch.envs.default] @@ -63,6 +64,7 @@ dependencies = [ "scikit-learn>=1.5.1", ] python = "3.10" +installer = "uv" [tool.hatch.envs.docs.scripts] build = ["python docs/scripts/gen_examples.py --execute", "mkdocs build"] @@ -104,8 +106,8 @@ lint-format = ['ruff format ./gpjax ./tests ./examples'] lint-check = ['ruff check --fix ./gpjax ./tests ./examples'] format = ["black-format", "imports-format", "lint-format"] check = ["black-check", "imports-check", "lint-check"] -test = "pytest . -v -n auto" -coverage = "pytest . -v --cov=./gpjax --cov-report=xml:./coverage.xml" +test = "pytest . -v --hypothesis-profile local_dev -n auto" +coverage = "pytest . -v --hypothesis-profile ci --cov=./gpjax --cov-report=xml:./coverage.xml" docstrings = "xdoctest ./gpjax" all-tests = ['check', 'docstrings', 'test'] diff --git a/tests/conftest.py b/tests/conftest.py index 4902e7d4c..ff77c3977 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,3 +1,4 @@ +from hypothesis import settings from jax import config from jaxtyping import install_import_hook @@ -6,3 +7,6 @@ # import gpjax within import hook to apply beartype everywhere, before running tests with install_import_hook("gpjax", "beartype.beartype"): import gpjax # noqa: F401 + +settings.register_profile("ci", max_examples=100, deadline=None) +settings.register_profile("local_dev", max_examples=5, deadline=None) diff --git a/tests/test_gaussian_distribution.py b/tests/test_gaussian_distribution.py index dfe07c89e..618a34b65 100644 --- a/tests/test_gaussian_distribution.py +++ b/tests/test_gaussian_distribution.py @@ -16,20 +16,25 @@ from jax import config -import jax.numpy as jnp -import jax.random as jr -import pytest # Enable Float64 for more stable matrix inversions. config.update("jax_enable_x64", True) - import cola from cola.ops import ( Dense, Diagonal, ) +from hypothesis import ( + given, + strategies as st, +) +import jax.numpy as jnp +import jax.random as jr +import pytest from gpjax.distributions import GaussianDistribution +from gpjax.testing import sample_multivariate_gaussian_params +from gpjax.typing import MultivariateParams _key = jr.key(seed=42) @@ -38,20 +43,18 @@ MultivariateNormalFullCovariance, ) +MIN_DIM = 1 +MAX_DIM = 50 + def approx_equal(res: jnp.ndarray, actual: jnp.ndarray) -> bool: """Check if two arrays are approximately equal.""" return jnp.linalg.norm(res - actual) < 1e-5 -@pytest.mark.parametrize("n", [1, 2, 5, 100]) -def test_array_arguments(n: int) -> None: - key_mean, key_sqrt = jr.split(_key, 2) - mean = jr.uniform(key_mean, shape=(n,)) - sqrt = jr.uniform(key_sqrt, shape=(n, n)) - covariance = sqrt @ sqrt.T - # check that cholesky does not error - _L = jnp.linalg.cholesky(covariance) # noqa: F841 +@given(dim=st.integers(min_value=MIN_DIM, max_value=MAX_DIM), data=st.data()) +def test_array_arguments(dim: int, data: st.DataObject) -> None: + mean, covariance = data.draw(sample_multivariate_gaussian_params(dim)) dist = GaussianDistribution(loc=mean, scale=cola.PSD(Dense(covariance))) @@ -63,7 +66,7 @@ def test_array_arguments(n: int) -> None: assert isinstance(dist.scale, Dense) assert cola.PSD in dist.scale.annotations - y = jr.uniform(_key, shape=(n,)) + y = jr.uniform(_key, shape=(dim,)) tfp_dist = MultivariateNormalFullCovariance(loc=mean, covariance_matrix=covariance) @@ -71,11 +74,17 @@ def test_array_arguments(n: int) -> None: assert approx_equal(dist.kl_divergence(dist), 0.0) -@pytest.mark.parametrize("n", [1, 2, 5, 100]) -def test_diag_linear_operator(n: int) -> None: - key_mean, key_diag = jr.split(_key, 2) - mean = jr.uniform(key_mean, shape=(n,)) - diag = jr.uniform(key_diag, shape=(n,)) +@given( + params=st.integers(min_value=MIN_DIM, max_value=MAX_DIM).flatmap( + lambda n: sample_multivariate_gaussian_params(dim=n) + ) +) +def test_diag_linear_operator( + params: MultivariateParams, +) -> None: + mean, _covariance = params + n = mean.shape[0] + diag = jnp.sqrt(jnp.diag(_covariance)) # We purosely forget to add a PSD annotation to the diagonal matrix. dist_diag = GaussianDistribution(loc=mean, scale=Diagonal(diag**2)) @@ -104,15 +113,16 @@ def test_diag_linear_operator(n: int) -> None: assert approx_equal(dist_diag.kl_divergence(dist_diag), 0.0) -@pytest.mark.parametrize("n", [1, 2, 5, 100]) -def test_dense_linear_operator(n: int) -> None: - key_mean, key_sqrt = jr.split(_key, 2) - mean = jr.uniform(key_mean, shape=(n,)) - sqrt = jr.uniform(key_sqrt, shape=(n, n)) - covariance = sqrt @ sqrt.T - - sqrt = jnp.linalg.cholesky(covariance + jnp.eye(n) * 1e-10) - +@given( + params=st.integers(min_value=MIN_DIM, max_value=MAX_DIM).flatmap( + lambda n: sample_multivariate_gaussian_params(dim=n) + ) +) +def test_dense_linear_operator( + params: MultivariateParams, +) -> None: + mean, covariance = params + n = mean.shape[0] dist_dense = GaussianDistribution(loc=mean, scale=cola.PSD(Dense(covariance))) tfp_dist = MultivariateNormalFullCovariance(loc=mean, covariance_matrix=covariance) @@ -134,16 +144,10 @@ def test_dense_linear_operator(n: int) -> None: assert approx_equal(dist_dense.kl_divergence(dist_dense), 0.0) -@pytest.mark.parametrize("n", [1, 2, 5, 100]) -def test_kl_divergence(n: int) -> None: - key_a, key_b = jr.split(_key, 2) - mean_a = jr.uniform(key_a, shape=(n,)) - mean_b = jr.uniform(key_b, shape=(n,)) - sqrt_a = jr.uniform(key_a, shape=(n, n)) - sqrt_b = jr.uniform(key_b, shape=(n, n)) - covariance_a = sqrt_a @ sqrt_a.T - covariance_b = sqrt_b @ sqrt_b.T - +@given(dim=st.integers(min_value=MIN_DIM, max_value=MAX_DIM), data=st.data()) +def test_kl_divergence(dim: int, data: st.DataObject) -> None: + mean_a, covariance_a = data.draw(sample_multivariate_gaussian_params(dim)) + mean_b, covariance_b = data.draw(sample_multivariate_gaussian_params(dim)) dist_a = GaussianDistribution(loc=mean_a, scale=cola.PSD(Dense(covariance_a))) dist_b = GaussianDistribution(loc=mean_b, scale=cola.PSD(Dense(covariance_b))) @@ -159,5 +163,5 @@ def test_kl_divergence(n: int) -> None: ) with pytest.raises(ValueError): - incompatible = GaussianDistribution(loc=jnp.ones((2 * n,))) + incompatible = GaussianDistribution(loc=jnp.ones((2 * dim,))) incompatible.kl_divergence(dist_a) diff --git a/tests/test_kernels/test_stationary.py b/tests/test_kernels/test_stationary.py index 05faa82ef..7872feebb 100644 --- a/tests/test_kernels/test_stationary.py +++ b/tests/test_kernels/test_stationary.py @@ -38,6 +38,7 @@ PositiveReal, Static, ) +from gpjax.testing import is_psd # Enable Float64 for more stable matrix inversions. config.update("jax_enable_x64", True) @@ -199,7 +200,7 @@ def test_gram(test_init: StationaryKernel, n: int): Kxx = k.gram(x) assert isinstance(Kxx, LinearOperator) assert Kxx.shape == (n, n) - assert jnp.all(jnp.linalg.eigvalsh(Kxx.to_dense() + jnp.eye(n) * 1e-6) > 0.0) + assert is_psd(Kxx.to_dense() + jnp.eye(n) * 1e-6) @pytest.mark.parametrize( diff --git a/tests/test_testing.py b/tests/test_testing.py new file mode 100644 index 000000000..0a899eba8 --- /dev/null +++ b/tests/test_testing.py @@ -0,0 +1,55 @@ +from hypothesis import ( + given, + settings, + strategies as st, +) +import jax.numpy as jnp + +from gpjax.testing import ( + is_psd, + sample_multivariate_gaussian_params, + sample_univariate_gaussian_params, +) +from gpjax.typing import ( + MultivariateParams, + UnivariateParams, +) + + +@given(params=sample_univariate_gaussian_params()) +def test_univariate_sampling(params: UnivariateParams): + mu, scale = params + assert jnp.isreal(mu) + assert scale > 0 + assert mu.shape == () + assert scale.shape == () + + +@given( + params=st.integers(min_value=1, max_value=20).flatmap( + lambda n: sample_multivariate_gaussian_params(dim=n) + ) +) +def test_multivariate_validity( + params: MultivariateParams, +): + mu, cov = params + assert jnp.all(jnp.isreal(mu)) + assert is_psd(cov) + assert jnp.allclose(cov, cov.T) + + +@given(dim=st.integers(min_value=1, max_value=20), data=st.data()) +def test_multivariate_shape(dim: int, data: st.DataObject): + mu, cov = data.draw(sample_multivariate_gaussian_params(dim)) + assert mu.shape == (dim,) + assert cov.shape == (dim, dim) + + +@given(dim=st.integers(min_value=1, max_value=20), data=st.data()) +@settings(max_examples=3) +def test_is_psd(dim: int, data: st.DataObject): + _, cov = data.draw(sample_multivariate_gaussian_params(dim)) + negative_identity = -1 + jnp.diagonal(cov) * -1.0 + cov += negative_identity + assert not is_psd(cov) From b98a881f0915399d111a9edbbba489dc97583c7a Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Mon, 19 Aug 2024 06:55:32 +0200 Subject: [PATCH 10/12] Stabilise KL test --- gpjax/testing.py | 47 ++++++++++++++++++++++++++--- tests/conftest.py | 2 +- tests/test_gaussian_distribution.py | 16 +++++----- 3 files changed, 51 insertions(+), 14 deletions(-) diff --git a/gpjax/testing.py b/gpjax/testing.py index dc80db7c3..6350bb200 100644 --- a/gpjax/testing.py +++ b/gpjax/testing.py @@ -6,14 +6,42 @@ from gpjax.typing import ( Array, + MultivariateParams, ScalarFloat, + UnivariateParams, ) _JITTER = 1e-6 @st.composite -def sample_univariate_gaussian_params(draw) -> tp.Tuple[ScalarFloat, ScalarFloat]: +def stable_float(draw, min_value=-10, max_value=10, abs_threshold=1e-6) -> float: + """ + Strategy to generate floats between min_value and max_value, + excluding values with absolute value less than abs_threshold. + + Parameters: + - min_value: minimum value for the float (default: -10) + - max_value: maximum value for the float (default: 10) + - abs_threshold: absolute values below this will be excluded (default: 1e-6) + """ + value = draw( + st.floats( + min_value=min_value, + max_value=max_value, + allow_infinity=False, + allow_nan=False, + ) + ) + # If the value is too close to zero, move it outside the excluded range + if abs(value) < abs_threshold: + sign = 1 if value >= 0 else -1 + value = sign * (abs_threshold + (abs(value) % abs_threshold)) + return value + + +@st.composite +def sample_univariate_gaussian_params(draw) -> UnivariateParams: loc = jnp.array(draw(st.floats()), dtype=jnp.float64) scale = jnp.array( draw(st.floats(min_value=_JITTER, exclude_min=True)), dtype=jnp.float64 @@ -22,11 +50,13 @@ def sample_univariate_gaussian_params(draw) -> tp.Tuple[ScalarFloat, ScalarFloat @st.composite -def sample_multivariate_gaussian_params( - draw, dim: int -) -> tp.Tuple[Float[Array, " N"], Float[Array, "N N"]]: +def sample_multivariate_gaussian_params(draw, dim: int) -> MultivariateParams: mean = draw( - arrays(dtype=float, shape=dim, elements=st.floats(min_value=-10, max_value=10)) + arrays( + dtype=float, + shape=dim, + elements=stable_float(min_value=-10, max_value=10, abs_threshold=1e-3), + ) ) lower_vals = draw( arrays( @@ -46,3 +76,10 @@ def is_psd(matrix: Float[Array, "N N"]) -> bool: psd_status = jnp.all(eig_vals > 0.0) # except jnp.linalg.Lin return psd_status + + +def approx_equal( + res: Float[Array, "N N"], actual: Float[Array, "N N"], threshold: float = 1e-6 +) -> bool: + """Check if two arrays are approximately equal.""" + return jnp.linalg.norm(res - actual) < threshold diff --git a/tests/conftest.py b/tests/conftest.py index ff77c3977..d2716f5fc 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -8,5 +8,5 @@ with install_import_hook("gpjax", "beartype.beartype"): import gpjax # noqa: F401 -settings.register_profile("ci", max_examples=100, deadline=None) +settings.register_profile("ci", max_examples=300, deadline=None) settings.register_profile("local_dev", max_examples=5, deadline=None) diff --git a/tests/test_gaussian_distribution.py b/tests/test_gaussian_distribution.py index 618a34b65..2c854c6ad 100644 --- a/tests/test_gaussian_distribution.py +++ b/tests/test_gaussian_distribution.py @@ -33,7 +33,10 @@ import pytest from gpjax.distributions import GaussianDistribution -from gpjax.testing import sample_multivariate_gaussian_params +from gpjax.testing import ( + approx_equal, + sample_multivariate_gaussian_params, +) from gpjax.typing import MultivariateParams _key = jr.key(seed=42) @@ -44,12 +47,7 @@ ) MIN_DIM = 1 -MAX_DIM = 50 - - -def approx_equal(res: jnp.ndarray, actual: jnp.ndarray) -> bool: - """Check if two arrays are approximately equal.""" - return jnp.linalg.norm(res - actual) < 1e-5 +MAX_DIM = 20 @given(dim=st.integers(min_value=MIN_DIM, max_value=MAX_DIM), data=st.data()) @@ -159,7 +157,9 @@ def test_kl_divergence(dim: int, data: st.DataObject) -> None: ) assert approx_equal( - dist_a.kl_divergence(dist_b), tfp_dist_a.kl_divergence(tfp_dist_b) + dist_a.kl_divergence(dist_b), + tfp_dist_a.kl_divergence(tfp_dist_b), + threshold=1e-3, ) with pytest.raises(ValueError): From d81be40725894d230a8ef56fa1de86678f613bd1 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Mon, 19 Aug 2024 06:57:11 +0200 Subject: [PATCH 11/12] Fix linting --- gpjax/testing.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/gpjax/testing.py b/gpjax/testing.py index 6350bb200..bda3b3892 100644 --- a/gpjax/testing.py +++ b/gpjax/testing.py @@ -1,4 +1,3 @@ -from beartype import typing as tp from hypothesis import strategies as st from hypothesis.extra.numpy import arrays import jax.numpy as jnp @@ -7,7 +6,6 @@ from gpjax.typing import ( Array, MultivariateParams, - ScalarFloat, UnivariateParams, ) From 98b6c48cf1548e5f6d3cfd5ca22e6427ea5230f9 Mon Sep 17 00:00:00 2001 From: Thomas Pinder Date: Tue, 3 Sep 2024 21:54:06 +0200 Subject: [PATCH 12/12] Update tests --- gpjax/testing.py | 92 ++++++++++++++++++++++++++++++++++++++----- gpjax/typing.py | 1 + tests/test_dataset.py | 28 ++++++++----- tests/test_testing.py | 1 + 4 files changed, 103 insertions(+), 19 deletions(-) diff --git a/gpjax/testing.py b/gpjax/testing.py index bda3b3892..6bf04cd4f 100644 --- a/gpjax/testing.py +++ b/gpjax/testing.py @@ -2,7 +2,8 @@ from hypothesis.extra.numpy import arrays import jax.numpy as jnp from jaxtyping import Float - +from beartype import typing as tp +from jax._src.numpy.lax_numpy import _ScalarMeta as JAXDType from gpjax.typing import ( Array, MultivariateParams, @@ -13,7 +14,9 @@ @st.composite -def stable_float(draw, min_value=-10, max_value=10, abs_threshold=1e-6) -> float: +def stable_float( + draw: st.DrawFn, min_value=-10, max_value=10, abs_threshold=1e-6 +) -> float: """ Strategy to generate floats between min_value and max_value, excluding values with absolute value less than abs_threshold. @@ -39,7 +42,7 @@ def stable_float(draw, min_value=-10, max_value=10, abs_threshold=1e-6) -> float @st.composite -def sample_univariate_gaussian_params(draw) -> UnivariateParams: +def sample_univariate_gaussian_params(draw: st.DrawFn) -> UnivariateParams: loc = jnp.array(draw(st.floats()), dtype=jnp.float64) scale = jnp.array( draw(st.floats(min_value=_JITTER, exclude_min=True)), dtype=jnp.float64 @@ -48,7 +51,9 @@ def sample_univariate_gaussian_params(draw) -> UnivariateParams: @st.composite -def sample_multivariate_gaussian_params(draw, dim: int) -> MultivariateParams: +def sample_multivariate_gaussian_params( + draw: st.DrawFn, dim: int +) -> MultivariateParams: mean = draw( arrays( dtype=float, @@ -76,8 +81,77 @@ def is_psd(matrix: Float[Array, "N N"]) -> bool: return psd_status -def approx_equal( - res: Float[Array, "N N"], actual: Float[Array, "N N"], threshold: float = 1e-6 -) -> bool: - """Check if two arrays are approximately equal.""" - return jnp.linalg.norm(res - actual) < threshold +def shape_strategy( + min_length: int = 1, max_length=100, min_dims: int = 1, max_dims: int = 20 +) -> st.SearchStrategy[tp.Tuple[int, int]]: + return st.tuples( + st.integers(min_length, max_length), st.integers(min_dims, max_dims) + ) + + +@st.composite +def sample_jax_array( + draw: st.DrawFn, + length: int = 1, + dim: int = 1, + min_value: int = -100, + max_value: int = 100, + dtype: JAXDType = jnp.float64, + unique_vals: bool = True, +) -> Float[Array, "{length} {int}"]: + elements_strategy = st.floats( + min_value=min_value, max_value=max_value, allow_nan=False, allow_infinity=False + ) + array_vals = jnp.array( + draw( + arrays( + dtype=dtype, + shape=(length, dim), + elements=elements_strategy, + unique=unique_vals, + ) + ), + dtype=dtype, + ) + return array_vals + + +@st.composite +def sample_dynamic_jax_array_pair( + draw: st.DrawFn, + min_length: int = 1, + max_length: int = 100, + min_dims: int = 1, + max_dims: int = 20, + singleton_output: int = bool, + min_value: int = -100, + max_value: int = 100, + dtype: JAXDType = jnp.float64, + unique_vals: bool = True, +) -> tp.Tuple[Float[Array, "{length} {int}"], Float[Array, "{length} {int}"]]: + length, x_dim = draw(shape_strategy(min_length, max_length, min_dims, max_dims)) + if singleton_output: + y_dim = 1 + else: + y_dim = x_dim + X = draw( + sample_jax_array( + length=length, + dim=x_dim, + min_value=min_value, + max_value=max_value, + unique_vals=unique_vals, + dtype=dtype, + ) + ) + y = draw( + sample_jax_array( + length=length, + dim=y_dim, + min_value=min_value, + max_value=max_value, + unique_vals=unique_vals, + dtype=dtype, + ) + ) + return X, y diff --git a/gpjax/typing.py b/gpjax/typing.py index e1d9058d0..33aa8b5c3 100644 --- a/gpjax/typing.py +++ b/gpjax/typing.py @@ -46,6 +46,7 @@ UnivariateParams = Tuple[ScalarFloat, ScalarFloat] MultivariateParams = Tuple[Float[Array, " N"], Float[Array, "N N"]] +SingletonArrayPair = Tuple[Float[Array, "N D"], Float[Array, "N 1"]] FunctionalSample = Callable[[Float[Array, "N D"]], Float[Array, "N B"]] r""" Type alias for functions representing $B$ samples from a model, to be evaluated on diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 1896b21f3..b19122dcd 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -21,34 +21,43 @@ ValidationErrors = (ValueError, beartype.roar.BeartypeCallHintParamViolation) except ImportError: ValidationErrors = ValueError - +from hypothesis import given, strategies as st from jax import config import jax.numpy as jnp import jax.tree_util as jtu import pytest from gpjax.dataset import Dataset +from gpjax.testing import sample_dynamic_jax_array_pair +from gpjax.typing import SingletonArrayPair config.update("jax_enable_x64", True) -@pytest.mark.parametrize("n", [1, 2, 10]) -@pytest.mark.parametrize("in_dim", [1, 2, 10]) -def test_dataset_init(n: int, in_dim: int) -> None: +MIN_DIM = 1 +MAX_DIM = 20 + + +@given( + data_arrays=sample_dynamic_jax_array_pair( + min_length=1, max_length=100, min_dims=1, max_dims=20, singleton_output=True + ) +) +def test_dataset_init(data_arrays: SingletonArrayPair) -> None: # Create dataset - x = jnp.ones((n, in_dim)) - y = jnp.ones((n, 1)) + x, y = data_arrays + num_data, data_dim = x.shape D = Dataset(X=x, y=y) # Test dataset shapes - assert D.n == n - assert D.in_dim == in_dim + assert D.n == num_data + assert D.in_dim == data_dim # Test representation assert ( D.__repr__() - == f"Dataset(Number of observations: {n} - Input dimension: {in_dim})" + == f"Dataset(Number of observations: {num_data} - Input dimension: {data_dim})" ) # Ensure dataclass @@ -75,7 +84,6 @@ def test_dataset_add(n1: int, n2: int, in_dim: int) -> None: x2 = 2 * jnp.ones((n2, in_dim)) y2 = 2 * jnp.ones((n2, 1)) D2 = Dataset(X=x2, y=y2) - # Add datasets D = D1 + D2 diff --git a/tests/test_testing.py b/tests/test_testing.py index 0a899eba8..8449fc400 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -9,6 +9,7 @@ is_psd, sample_multivariate_gaussian_params, sample_univariate_gaussian_params, + approx_equal, ) from gpjax.typing import ( MultivariateParams,