Merge pull request #1383 from EpistasisLab/dev

Package build and PyPI deployment updates

Author: jay-m-dev

.github/workflows/publish_package.yml

@@ -20,10 +20,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
 
     - name: Build package
-      run: python setup.py sdist bdist_wheel
+      run: python -m build
 
     - name: Upload to PyPI
       env:

.gitignore

@@ -17,4 +17,5 @@ build/*
 *.egg
 *.coverage*
 docs/documentation/
-mkdocs.yml
+mkdocs.yml
+dist/

pyproject.toml

@@ -1,23 +1,88 @@
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=61", "setuptools_scm>=7.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tool.pytest.ini_options]
-addopts = "--cov=tpot"
-testpaths = [
-    "tpot/tests",
+[project]
+name = "TPOT"
+description = "Tree-based Pipeline Optimization Tool"
+readme = "README.md"
+requires-python = ">=3.10,<3.14"
+license = { text = "LGPL-3.0" }
+authors = [
+    { name = "Pedro Ribeiro" }
 ]
+keywords = [
+    "pipeline optimization",
+    "hyperparameter optimization",
+    "data science",
+    "machine learning",
+    "genetic programming",
+    "evolutionary computation"
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "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"
+]
+dependencies = [
+    "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",
+]
+
+dynamic = ["version"]
+
+[project.optional-dependencies]
+skrebate = ["skrebate>=0.3.4"]
+mdr = ["scikit-mdr>=0.4.4"]
+sklearnex = ["scikit-learn-intelex>=2023.2.1"]
+amltk = ["amltk>=1.12.1"]
+testing = [
+    "pytest>=6.0",
+    "pytest-cov>=2.0",
+    "mypy>=0.910",
+    "flake8>=3.9",
+    "tox>=3.24"
+]
+
+[project.urls]
+Homepage = "https://github.com/EpistasisLab/tpot"
+
+[project.scripts]
+tpot = "tpot:main"
+
+[tool.setuptools]
+packages = ["tpot"]
+zip-safe = true
+
+[tool.setuptools.package-data]
+tpot = ["py.typed"]
+
+[tool.flake8]
+max-line-length = 120
 
-[tool.mypy]
-mypy_path = "tpot"
-check_untyped_defs = true
-disallow_any_generics = true
-ignore_missing_imports = true
-no_implicit_optional = true
-show_error_codes = true
-strict_equality = true
-warn_redundant_casts = true
-warn_return_any = true
-warn_unreachable = true
-warn_unused_configs = true
-no_implicit_reexport = true
+[tool.setuptools_scm]
+# setuptools_scm gets the version from Git tags, e.g git tag v1.1.0
+# then python -m build embeds the version into the package

requirements_dev.txt

@@ -4,6 +4,7 @@ minversion = 3.28.0
 # envlist = py310, flake8, mypy
 envlist = py310, py311, py312, py313
 isolated_build = true
+skip_missing_interpreters = true
 
 [gh-actions]
 python =
@@ -16,8 +17,9 @@ python =
 [testenv]
 setenv =
     PYTHONPATH = {toxinidir}
+extras = testing
 deps =
-    -r{toxinidir}/requirements_dev.txt
+    setuptools>=65.0.0
 commands =
     pytest --basetemp={envtmpdir}
 
@@ -28,6 +30,7 @@ commands = flake8 tpot
 
 [testenv:mypy]
 basepython = python3.10
+extras = testing
 deps =
-    -r{toxinidir}/requirements_dev.txt
+    setuptools>=65.0.0
 commands = mypy tpot

setup.cfg

@@ -1,36 +1,6 @@
-"""
-This file is part of the TPOT library.
+try:
+    from importlib.metadata import version
+except ImportError:
+    from importlib_metadata import version  # for Python < 3.8
 
-The current version of TPOT was developed at Cedars-Sinai by:
-    - Pedro Henrique Ribeiro (https://github.com/perib, https://www.linkedin.com/in/pedro-ribeiro/)
-    - Anil Saini ([email protected])
-    - Jose Hernandez ([email protected])
-    - Jay Moran ([email protected])
-    - Nicholas Matsumoto ([email protected])
-    - Hyunjun Choi ([email protected])
-    - Gabriel Ketron ([email protected])
-    - Miguel E. Hernandez ([email protected])
-    - Jason Moore ([email protected])
-
-The original version of TPOT was primarily developed at the University of Pennsylvania by:
-    - Randal S. Olson ([email protected])
-    - Weixuan Fu ([email protected])
-    - Daniel Angell ([email protected])
-    - Jason Moore ([email protected])
-    - and many more generous open-source contributors
-
-TPOT is free software: you can redistribute it and/or modify
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation, either version 3 of
-the License, or (at your option) any later version.
-
-TPOT is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with TPOT. If not, see <http://www.gnu.org/licenses/>.
-
-"""
-__version__ = '1.1.0'
+__version__ = version("tpot")