From ab9ba98f6d7eb95592516468ad6461d2e6a392e7 Mon Sep 17 00:00:00 2001 From: Mark Forrer Date: Mon, 16 Jun 2025 14:45:21 -0700 Subject: [PATCH 1/3] Update dependency management --- .github/workflows/publish_package.yml | 10 +- .github/workflows/tests.yml | 8 +- poetry.lock | 2716 +++++++++++++++++++++++++ pyproject.toml | 129 +- setup.py | 69 - tox.ini | 10 +- tpot/__init__.py | 17 +- tpot/_version.py | 2 +- 8 files changed, 2872 insertions(+), 89 deletions(-) create mode 100644 poetry.lock delete mode 100644 setup.py diff --git a/.github/workflows/publish_package.yml b/.github/workflows/publish_package.yml index 89f402a8..46a8dce7 100644 --- a/.github/workflows/publish_package.yml +++ b/.github/workflows/publish_package.yml @@ -20,14 +20,12 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel twine + curl -sSL https://install.python-poetry.org | python3 - - name: Build package - run: python setup.py sdist bdist_wheel + run: poetry build - name: Upload to PyPI env: - TWINE_USERNAME: __token__ - TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} - run: twine upload dist/* - + POETRY_PYPI_TOKEN_POETRY: ${{ secrets.PYPI_API_TOKEN }} + run: poetry publish diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6a4af6fd..f8834c1c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -21,6 +21,10 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install tox tox-gh-actions + sudo apt-get update + sudo apt-get install -y --no-install-recommends curl gcc + curl -sSL https://install.python-poetry.org | python3 - + export PATH="/root/.local/bin:$PATH" + poetry install --extras cpu --with dev,github-ci - name: Test with tox - run: tox \ No newline at end of file + run: poetry run tox \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..913d9e1e --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2716 @@ +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. + +[[package]] +name = "cachetools" +version = "6.1.0" +description = "Extensible memoizing collections and decorators" +optional = false +python-versions = ">=3.9" +groups = ["dev", "github-ci"] +files = [ + {file = "cachetools-6.1.0-py3-none-any.whl", hash = "sha256:1c7bb3cf9193deaf3508b7c5f2a79986c13ea38965c5adcff1f84519cf39163e"}, + {file = "cachetools-6.1.0.tar.gz", hash = "sha256:b4c4f404392848db3ce7aac34950d17be4d864da4b8b66911008e430bc544587"}, +] + +[[package]] +name = "certifi" +version = "2025.7.14" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.7" +groups = ["updates"] +files = [ + {file = "certifi-2025.7.14-py3-none-any.whl", hash = "sha256:6b31f564a415d79ee77df69d757bb49a5bb53bd9f756cbbe24394ffd6fc1f4b2"}, + {file = "certifi-2025.7.14.tar.gz", hash = "sha256:8ea99dbdfaaf2ba2f9bac77b9249ef62ec5218e7c2b2e903378ed5fccf765995"}, +] + +[[package]] +name = "chardet" +version = "5.2.0" +description = "Universal encoding detector for Python 3" +optional = false +python-versions = ">=3.7" +groups = ["dev", "github-ci"] +files = [ + {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, + {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.4.2" +description = "The Real First Universal Charset Detector. 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["pytest-enabler (>=2.2)"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[extras] +cpu = ["xgboost-cpu"] +cuda = ["xgboost"] +nn = ["torch"] +plot = ["matplotlib"] + +[metadata] +lock-version = "2.1" +python-versions = ">=3.10.0,<3.14.0" +content-hash = "601837e949b5307ff44ec8de188e041d994d427c9dafd22721c21351f65cdb5f" diff --git a/pyproject.toml b/pyproject.toml index 42772c7d..d0703091 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,123 @@ -[build-system] -requires = ["setuptools", "wheel"] -build-backend = "setuptools.build_meta" +[project] +name = "TPOT" +description = "Tree-based Pipeline Optimization Tool" +license = "LGPL-3.0" +version="0.0.0" # grabbed from _version.py by poetry-dynamic-versioning (see "dynamic" instances below) +dynamic = ["version"] +# TODO: this doesn't seem to match code comments +authors = [{ name = "Pedro Ribioro", email = "pedroribeiroh@gmail.com" }] +readme = "README.md" +#These cause tests to fail +project.urls = [ + "https://epistasislab.github.io/tpot/", + "https://github.com/EpistasisLab/tpot", +] +classifiers=[ + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Topic :: Scientific/Engineering :: Artificial Intelligence" +] +keywords = [ + "pipeline optimization", + "hyperparameter optimization", + "data science", + "machine learning", + "genetic programming", + "evolutionary computation" +] +requires-python=">=3.10.0,<3.14.0" + +# TODO: Specifically-listed deps from setup.py that aren't included here yet. +# 'optuna>=3.0.5', +# 'dask-expr>=1.0.12', +# 'dask-jobqueue>=0.8.5', +# 'func_timeout>=4.3.5', +# 'dill>=0.3.9' + +# TODO: Not yet integrated from setup.py +#extras_require={ +# 'skrebate': ['skrebate>=0.3.4'], +# 'mdr': ['scikit-mdr>=0.4.4'], +# 'sklearnex' : ['scikit-learn-intelex>=2023.2.1'], +# 'amltk' : ['amltk>=1.12.1'], +#} + +# TODO: several dependencies don't seem strictly needed in every context, but were needed +# to run the code as-is. + +dependencies = [ + "ConfigSpace>=1.1.1", + "distributed>=2024.4.2", + "func_timeout>=4.3.5", + "joblib>=1.1.1", + "lightgbm>=3.3.3", + "matplotlib>=3.6.2", + "networkx>=3.0", + "nose", + "numpy>=1.26.4", + "pandas>=2.2.0", + "scikit-learn>=1.6", + "scipy>=1.3.1", + "stopit>=1.1.1", + "tqdm>=4.36.1", + "traitlets>=5.8.0", + # TODO: setuptools was needed to make stopit work. + # stopit is a dead project. + #>>> import tpot + #Traceback (most recent call last): + # File "", line 1, in + # File "/code/tpot/__init__.py", line 48, in + # from . import utils + # File "/code/tpot/utils/__init__.py", line 36, in + # from . import eval_utils + # File "/code/tpot/utils/eval_utils.py", line 43, in + # from stopit import threading_timeoutable, TimeoutException + # File "/root/.cache/pypoetry/virtualenvs/tpot-MATOk_fk-py3.12/lib/python3.12/site-packages/stopit/__init__.py", line 10, in + # import pkg_resources + #ModuleNotFoundError: No module named 'pkg_resources' + "setuptools (>=80.9.0,<81.0.0)", +] + +[project.optional-dependencies] +cpu = ["xgboost-cpu>=3.0"] +cuda = ["xgboost>=3.0"] +nn = ["torch"] +plot = ["matplotlib"] + +[tool.poetry] + +[tool.poetry.group.dev] +optional = true +[tool.poetry.group.dev.dependencies] +nose = "*" +pytest = "*" +pytest-cov = "*" +mypy = "*" +flake8 = "*" +tox = "*" + +# Define in a separate group, so clients can optionally opt out. +[tool.poetry.group.updates.dependencies] +update_checker = ">=0.16" + + +[tool.poetry.requires-plugins] +poetry-dynamic-versioning = ">=1.0.0,<2.0.0" + +[tool.poetry-dynamic-versioning] +enable = true +# version = { git-tag = true } +# version = { attr = "tpot.__version__" } + +[tool.poetry.group.github-ci] +optional = true + +[tool.poetry.group.github-ci.dependencies] +tox-gh-actions = "*" [tool.pytest.ini_options] addopts = "--cov=tpot" @@ -20,4 +137,8 @@ warn_redundant_casts = true warn_return_any = true warn_unreachable = true warn_unused_configs = true -no_implicit_reexport = true \ No newline at end of file +no_implicit_reexport = true + +[build-system] +requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] +build-backend = "poetry_dynamic_versioning.backend" \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 281ffc4a..00000000 --- a/setup.py +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -#TODO update this -from setuptools import setup, find_packages - -def calculate_version(): - initpy = open('tpot/_version.py').read().split('\n') - version = list(filter(lambda x: '__version__' in x, initpy))[0].split('\'')[1] - return version - - -package_version = calculate_version() - -setup( - name='TPOT', - python_requires='>=3.10, <3.14', - version=package_version, - author='Pedro Ribeiro', - packages=find_packages(), - url='https://github.com/EpistasisLab/tpot', - license='GNU/LGPLv3', #TODO - entry_points={'console_scripts': ['tpot=tpot:main', ]}, - description=('Tree-based Pipeline Optimization Tool'), - long_description=''' -A Python tool that automatically creates and optimizes machine learning pipelines using genetic programming. - - -''', - zip_safe=True, - install_requires=['numpy>=1.26.4', - 'scipy>=1.3.1', - 'scikit-learn>=1.6', - 'update_checker>=0.16', - 'tqdm>=4.36.1', - 'stopit>=1.1.1', - 'pandas>=2.2.0', - 'joblib>=1.1.1', - 'xgboost>=3.0.0', - 'matplotlib>=3.6.2', - 'traitlets>=5.8.0', - 'lightgbm>=3.3.3', - 'optuna>=3.0.5', - 'networkx>=3.0', - 'dask>=2024.4.2', - 'distributed>=2024.4.2', - 'dask-expr>=1.0.12', - 'dask-jobqueue>=0.8.5', - 'func_timeout>=4.3.5', - 'configspace>=1.1.1', - 'dill>=0.3.9', - 'seaborn>=0.13.2', - ], - extras_require={ - 'skrebate': ['skrebate>=0.3.4'], - 'mdr': ['scikit-mdr>=0.4.4'], - 'sklearnex' : ['scikit-learn-intelex>=2023.2.1'], - 'amltk' : ['amltk>=1.12.1'], - }, - classifiers=[ - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)', - 'Programming Language :: Python :: 3.10', - 'Programming Language :: Python :: 3.11', - 'Programming Language :: Python :: 3.12', - 'Programming Language :: Python :: 3.13', - 'Topic :: Scientific/Engineering :: Artificial Intelligence' - ], - keywords=['pipeline optimization', 'hyperparameter optimization', 'data science', 'machine learning', 'genetic programming', 'evolutionary computation'], -) diff --git a/tox.ini b/tox.ini index 1e07dabe..680fa3d5 100644 --- a/tox.ini +++ b/tox.ini @@ -16,8 +16,9 @@ python = [testenv] setenv = PYTHONPATH = {toxinidir} -deps = - -r{toxinidir}/requirements_dev.txt +deps = poetry +commands_pre = + poetry install --extras cpu --with dev,github-ci commands = pytest --basetemp={envtmpdir} @@ -28,6 +29,7 @@ commands = flake8 tpot [testenv:mypy] basepython = python3.10 -deps = - -r{toxinidir}/requirements_dev.txt +commands_pre = + poetry install --extras cpu --with dev,github-ci +deps = poetry commands = mypy tpot diff --git a/tpot/__init__.py b/tpot/__init__.py index abe05e81..23a38579 100644 --- a/tpot/__init__.py +++ b/tpot/__init__.py @@ -37,6 +37,8 @@ #TODO: are all the imports in the init files done correctly? #TODO clean up import organization +import warnings + from .individual import BaseIndividual from .graphsklearn import GraphPipeline @@ -54,6 +56,15 @@ from .tpot_estimator import TPOTClassifier, TPOTRegressor, TPOTEstimator, TPOTEstimatorSteadyState -from update_checker import update_check -from ._version import __version__ -update_check("tpot",__version__) \ No newline at end of file +# Optionally import update_checker and use it to noisily complain if this isn't exactly the latest +# TPOT release. +try: + from update_checker import update_check + from ._version import __version__ + update_check("tpot",__version__) +except ImportError: + warnings.warn( + ImportWarning( + "Optional update_check import is missing. Recency of TPOT version won't be checked." + ) + ) \ No newline at end of file diff --git a/tpot/_version.py b/tpot/_version.py index 45ac75c0..14850217 100644 --- a/tpot/_version.py +++ b/tpot/_version.py @@ -33,4 +33,4 @@ License along with TPOT. If not, see . """ -__version__ = '1.1.0' +__version__ = '0.0.0' # Managed via the git tag From 72454bc49dc6d116f2c5cf73a9fa5c5afeb672d0 Mon Sep 17 00:00:00 2001 From: Mark Forrer Date: Fri, 25 Jul 2025 14:16:35 -0700 Subject: [PATCH 2/3] Remove some additional files that *should* be superseded by `pyproject.toml` --- requirements_dev.txt | 6 ------ setup.cfg | 13 ------------- 2 files changed, 19 deletions(-) delete mode 100644 requirements_dev.txt delete mode 100644 setup.cfg diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index 86d2b5f9..00000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,6 +0,0 @@ -flake8==6.0.0 -tox==4.4.12 -pytest==7.3.0 -pytest-cov==4.0.0 -mypy==1.2.0 -setuptools \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index a619924a..00000000 --- a/setup.cfg +++ /dev/null @@ -1,13 +0,0 @@ -[options.extras_require] -testing = - pytest>=6.0 - pytest-cov>=2.0 - mypy>=0.910 - flake8>=3.9 - tox>=3.24 - -[options.package_data] -tpot = py.typed - -[flake8] -max-line-length = 120 \ No newline at end of file From b7162454a9d12556d3a72ba7b95ce8848e6a67d6 Mon Sep 17 00:00:00 2001 From: Mark Forrer Date: Mon, 4 Aug 2025 12:02:37 -0700 Subject: [PATCH 3/3] Define cuda and cpu extras as exclusive --- poetry.lock | 8 ++++---- pyproject.toml | 5 ++--- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 913d9e1e..0423eb3a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1508,7 +1508,7 @@ description = "NVIDIA Collective Communication Library (NCCL) Runtime" optional = true python-versions = ">=3" groups = ["main"] -markers = "platform_system == \"Linux\" and platform_machine != \"aarch64\" and (extra == \"cuda\" or platform_machine == \"x86_64\") and (extra == \"cuda\" or extra == \"nn\")" +markers = "platform_system == \"Linux\" and extra != \"cpu\" and extra == \"cuda\" and platform_machine != \"aarch64\" or platform_system == \"Linux\" and platform_machine == \"x86_64\" and extra == \"nn\"" files = [ {file = "nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:5c196e95e832ad30fbbb50381eb3cbd1fadd5675e587a548563993609af19522"}, {file = "nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:694cf3879a206553cc9d7dbda76b13efaf610fdb70a50cba303de1b0d1530ac6"}, @@ -2619,7 +2619,7 @@ description = "XGBoost Python Package" optional = true python-versions = ">=3.10" groups = ["main"] -markers = "extra == \"cuda\"" +markers = "extra != \"cpu\" and extra == \"cuda\"" files = [ {file = "xgboost-3.0.2-py3-none-macosx_10_15_x86_64.whl", hash = "sha256:923f46cd1b25c0a39fc98e969fa0a72a1a84feb7f55797cb3385962cd8d3b2d4"}, {file = "xgboost-3.0.2-py3-none-macosx_12_0_arm64.whl", hash = "sha256:5c4e377c86df815669939646b3abe7a20559e4d4c0f5c2ab10c31252e7a9d7d9"}, @@ -2650,7 +2650,7 @@ description = "XGBoost Python Package" optional = true python-versions = ">=3.10" groups = ["main"] -markers = "extra == \"cpu\"" +markers = "extra != \"cuda\" and extra == \"cpu\"" files = [ {file = "xgboost_cpu-3.0.2-py3-none-manylinux2014_aarch64.whl", hash = "sha256:c02637ef56960eef23e8f2ec27e0af76585f035a9ce02a10477630bd83675efa"}, {file = "xgboost_cpu-3.0.2-py3-none-manylinux2014_x86_64.whl", hash = "sha256:95ac1e6af1227b856222c71454c7da8766a5c8fbb5a30c6977c48b27d196155a"}, @@ -2713,4 +2713,4 @@ plot = ["matplotlib"] [metadata] lock-version = "2.1" python-versions = ">=3.10.0,<3.14.0" -content-hash = "601837e949b5307ff44ec8de188e041d994d427c9dafd22721c21351f65cdb5f" +content-hash = "25b65b8b92cca43d163247b6065488aa141f5ec753e00a726ae9f3a54acf33f1" diff --git a/pyproject.toml b/pyproject.toml index d0703091..1df7afbe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,6 @@ dynamic = ["version"] # TODO: this doesn't seem to match code comments authors = [{ name = "Pedro Ribioro", email = "pedroribeiroh@gmail.com" }] readme = "README.md" -#These cause tests to fail project.urls = [ "https://epistasislab.github.io/tpot/", "https://github.com/EpistasisLab/tpot", @@ -83,8 +82,8 @@ dependencies = [ ] [project.optional-dependencies] -cpu = ["xgboost-cpu>=3.0"] -cuda = ["xgboost>=3.0"] +cpu = ["xgboost-cpu (>=3.0) ; extra != 'cuda'"] +cuda = ["xgboost (>=3.0) ; extra != 'cpu'"] nn = ["torch"] plot = ["matplotlib"]