diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 092fd29..6aa33c6 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -19,7 +19,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest] + os: ["ubuntu-latest"] python-version: ["3.8"] steps: #---------------------------------------------- diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7bfec00..fca127b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,8 +23,8 @@ jobs: strategy: fail-fast: false matrix: - # TODO(amir): turn on `macos-latest` and `windows-latest` - os: [ubuntu-latest] + # TODO(amir): enable `windows-latest`, `macos-latest` and fix possible `poetry` issues and glmnet + os: ["ubuntu-latest"] python-version: ["3.8", "3.9", "3.10"] steps: #---------------------------------------------- diff --git a/CHANGELOG.md b/CHANGELOG.md index dc1f651..e2fac53 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,13 +4,28 @@ - We follow [Semantic Versioning](http://semver.org/) to document any notable changes. - Please checkout [SlickML Official Releases](https://github.com/slickml/slick-ml/releases) for more details. ---- +--- ## 📍 Unreleased Version X.X.X - XXXX-XX-XX ### 🛠 Fixed ### 🔥 Added +--- + +## 📍 Version 0.2.0-beta.1 - 2022-11-13 + +### 🛠 Fixed +- [#167](https://github.com/slickml/slick-ml/pull/167), [#160](https://github.com/slickml/slick-ml/pull/160) fixed `dependencies`, `tox.ini` and `README.md`. +- [#164](https://github.com/slickml/slick-ml/pull/164) refactored `XGBoostBayesianOptimizer` class. +- [#161](https://github.com/slickml/slick-ml/pull/161) fixed `XGBoostFeatureSelector` `callbacks` to work smoothly. +- [#157](https://github.com/slickml/slick-ml/pull/157) fixed `codecov-action` to use `v3`. +- [#156](https://github.com/slickml/slick-ml/pull/156) refactored `XGBoostFeatureSelector` class. +- [#155](https://github.com/slickml/slick-ml/pull/155) fixed default PR reviewers. +### 🔥 Added +- [#162](https://github.com/slickml/slick-ml/pull/162) added `BaseXGBoostEstimator` class. +- [#158](https://github.com/slickml/slick-ml/pull/158) added `conftest.py` for `pytest` unit-tests. +- [#153](https://github.com/slickml/slick-ml/pull/153), [#159](https://github.com/slickml/slick-ml/pull/159) added ascii banner arts to `poe greet` command. --- diff --git a/README.md b/README.md index 77e343c..f0a0a3e 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,17 @@ +
+ [![build](https://github.com/slickml/slick-ml/actions/workflows/ci.yml/badge.svg)](https://github.com/slickml/slick-ml/actions/workflows/ci.yml) [![docs](https://github.com/slickml/slick-ml/actions/workflows/cd.yml/badge.svg)](https://github.com/slickml/slick-ml/actions/workflows/cd.yml) [![codecov](https://codecov.io/gh/slickml/slick-ml/branch/master/graph/badge.svg?token=Z7XP51MB4K)](https://codecov.io/gh/slickml/slick-ml) +![dependencies](https://img.shields.io/librariesio/github/slickml/slick-ml) [![license](https://img.shields.io/github/license/slickml/slick-ml)](https://github.com/slickml/slick-ml/blob/master/LICENSE/) [![downloads](https://pepy.tech/badge/slickml)](https://pepy.tech/project/slickml) ![pypi_version](https://img.shields.io/pypi/v/slickml) ![python_version](https://img.shields.io/pypi/pyversions/slickml) [![slack_invite](https://badgen.net/badge/Join/SlickML%20Slack/purple?icon=slack)](https://www.slickml.com/slack-invite) +![twitter_url](https://img.shields.io/twitter/url?style=social&url=https%3A%2F%2Ftwitter.com%2FSlickML) - +

diff --git a/poetry.lock b/poetry.lock index f8d919c..f83d94c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -62,7 +62,7 @@ tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy [[package]] name = "Babel" -version = "2.10.3" +version = "2.11.0" description = "Internationalization utilities" category = "dev" optional = false @@ -250,7 +250,7 @@ python-versions = ">=3.6" [[package]] name = "exceptiongroup" -version = "1.0.0" +version = "1.0.2" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false @@ -445,11 +445,11 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.16.2" +version = "6.17.1" description = "IPython Kernel for Jupyter" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] appnope = {version = "*", markers = "platform_system == \"Darwin\""} @@ -554,7 +554,7 @@ python-versions = ">=3.7" [[package]] name = "jsonschema" -version = "4.16.0" +version = "4.17.0" description = "An implementation of JSON Schema validation for Python" category = "dev" optional = false @@ -589,7 +589,7 @@ test = ["flake8 (>=3.9.2,<4)", "flake8-docstrings (>=1.6.0,<2)", "flake8-import- [[package]] name = "jupyter-client" -version = "7.4.4" +version = "7.4.5" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -610,13 +610,14 @@ test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-com [[package]] name = "jupyter-core" -version = "4.11.2" +version = "5.0.0" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] +platformdirs = "*" pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} traitlets = "*" @@ -772,11 +773,11 @@ test = ["pytest (<5.4)", "pytest-cov"] [[package]] name = "mypy" -version = "0.971" +version = "0.990" description = "Optional static typing for Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] mypy-extensions = ">=0.4.3" @@ -785,6 +786,7 @@ typing-extensions = ">=3.10" [package.extras] dmypy = ["psutil (>=4.0)"] +install-types = ["pip"] python2 = ["typed-ast (>=1.4.0,<2)"] reports = ["lxml"] @@ -846,7 +848,7 @@ python-versions = ">=3.5" [[package]] name = "networkx" -version = "2.8.7" +version = "2.8.8" description = "Python package for creating and manipulating graphs and networks" category = "main" optional = false @@ -854,14 +856,14 @@ python-versions = ">=3.8" [package.extras] default = ["matplotlib (>=3.4)", "numpy (>=1.19)", "pandas (>=1.3)", "scipy (>=1.8)"] -developer = ["mypy (>=0.981)", "pre-commit (>=2.20)"] -doc = ["nb2plots (>=0.6)", "numpydoc (>=1.4)", "pillow (>=9.1)", "pydata-sphinx-theme (>=0.9)", "sphinx (>=5)", "sphinx-gallery (>=0.10)", "texext (>=0.6.6)"] +developer = ["mypy (>=0.982)", "pre-commit (>=2.20)"] +doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (>=5.2)", "sphinx-gallery (>=0.11)", "texext (>=0.6.6)"] extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.9)", "sympy (>=1.10)"] -test = ["codecov (>=2.1)", "pytest (>=7.1)", "pytest-cov (>=3.0)"] +test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] [[package]] name = "numba" -version = "0.56.3" +version = "0.56.4" description = "compiling Python code using LLVM" category = "main" optional = false @@ -933,7 +935,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pathspec" -version = "0.10.1" +version = "0.10.2" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -975,7 +977,7 @@ python-versions = "*" [[package]] name = "Pillow" -version = "9.2.0" +version = "9.3.0" description = "Python Imaging Library (Fork)" category = "main" optional = false @@ -987,7 +989,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa [[package]] name = "pip" -version = "22.3" +version = "22.3.1" description = "The PyPA recommended tool for installing Python packages." category = "dev" optional = false @@ -1003,15 +1005,15 @@ python-versions = ">=3.6" [[package]] name = "platformdirs" -version = "2.5.2" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "2.5.4" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] +docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"] +test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -1042,7 +1044,7 @@ poetry_plugin = ["poetry (>=1.0,<2.0)"] [[package]] name = "prompt-toolkit" -version = "3.0.31" +version = "3.0.32" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -1053,7 +1055,7 @@ wcwidth = "*" [[package]] name = "psutil" -version = "5.9.3" +version = "5.9.4" description = "Cross-platform lib for process and system monitoring in Python." category = "dev" optional = false @@ -1134,7 +1136,7 @@ diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyrsistent" -version = "0.18.1" +version = "0.19.2" description = "Persistent/Functional/Immutable data structures" category = "dev" optional = false @@ -1202,7 +1204,7 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.5" +version = "2022.6" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1210,7 +1212,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "304" +version = "305" description = "Python for Window Extensions" category = "dev" optional = false @@ -1310,7 +1312,7 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"] [[package]] name = "setuptools" -version = "65.5.0" +version = "65.5.1" description = "Easily download, build, install, upgrade, and uninstall Python packages" category = "main" optional = false @@ -1318,7 +1320,7 @@ python-versions = ">=3.7" [package.extras] docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] -testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] [[package]] @@ -1573,6 +1575,69 @@ build = ["cython (>=0.29.26)"] develop = ["cython (>=0.29.26)"] docs = ["ipykernel", "jupyter_client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] +[[package]] +name = "statsmodels" +version = "0.13.3" +description = "Statistical computations and models for Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = {version = ">=1.17", markers = "python_version != \"3.10\" or platform_system != \"Windows\" or platform_python_implementation == \"PyPy\""} +packaging = ">=21.3" +pandas = ">=0.25" +patsy = ">=0.5.2" +scipy = {version = ">=1.3", markers = "(python_version > \"3.7\" or platform_system != \"Windows\" or platform_machine != \"x86\") and python_version < \"3.12\""} + +[package.extras] +build = ["cython (>=0.29.32)"] +develop = ["Jinja2", "colorama", "cython (>=0.29.32)", "cython (>=0.29.32,<3.0.0)", "flake8", "isort", "joblib", "matplotlib (>=3)", "oldest-supported-numpy (>=2022.4.18)", "pytest (>=7.0.1,<7.1.0)", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools_scm[toml] (>=7.0.0,<7.1.0)"] +docs = ["ipykernel", "jupyter_client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] + +[[package]] +name = "statsmodels" +version = "0.13.4" +description = "Statistical computations and models for Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = {version = ">=1.17", markers = "python_version != \"3.10\" or platform_system != \"Windows\" or platform_python_implementation == \"PyPy\""} +packaging = ">=21.3" +pandas = ">=0.25" +patsy = ">=0.5.2" +scipy = {version = ">=1.3", markers = "(python_version > \"3.9\" or platform_system != \"Windows\" or platform_machine != \"x86\") and python_version < \"3.12\""} + +[package.extras] +build = ["cython (>=0.29.32)"] +develop = ["Jinja2", "colorama", "cython (>=0.29.32)", "cython (>=0.29.32,<3.0.0)", "flake8", "isort", "joblib", "matplotlib (>=3)", "oldest-supported-numpy (>=2022.4.18)", "pytest (>=7.0.1,<7.1.0)", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools_scm[toml] (>=7.0.0,<7.1.0)"] +docs = ["ipykernel", "jupyter_client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] + +[[package]] +name = "statsmodels" +version = "0.13.5" +description = "Statistical computations and models for Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = [ + {version = ">=1.17", markers = "python_version != \"3.10\" or platform_system != \"Windows\" or platform_python_implementation == \"PyPy\""}, + {version = ">=1.22.3", markers = "python_version == \"3.10\" and platform_system == \"Windows\" and platform_python_implementation != \"PyPy\""}, +] +packaging = ">=21.3" +pandas = ">=0.25" +patsy = ">=0.5.2" +scipy = {version = ">=1.3", markers = "(python_version > \"3.9\" or platform_system != \"Windows\" or platform_machine != \"x86\") and python_version < \"3.12\""} + +[package.extras] +build = ["cython (>=0.29.32)"] +develop = ["Jinja2", "colorama", "cython (>=0.29.32)", "cython (>=0.29.32,<3.0.0)", "flake8", "isort", "joblib", "matplotlib (>=3)", "oldest-supported-numpy (>=2022.4.18)", "pytest (>=7.0.1,<7.1.0)", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=7.0.0,<7.1.0)"] +docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] + [[package]] name = "threadpoolctl" version = "3.1.0" @@ -1695,7 +1760,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.16.6" +version = "20.16.7" description = "Virtual Python Environment builder" category = "dev" optional = false @@ -1739,11 +1804,11 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "xgboost" -version = "1.6.2" +version = "1.7.1" description = "XGBoost Python Package" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] numpy = "*" @@ -1754,6 +1819,7 @@ dask = ["dask", "distributed", "pandas"] datatable = ["datatable"] pandas = ["pandas"] plotting = ["graphviz", "matplotlib"] +pyspark = ["cloudpickle", "pyspark", "scikit-learn"] scikit-learn = ["scikit-learn"] [[package]] @@ -1771,7 +1837,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools" [metadata] lock-version = "1.1" python-versions = ">=3.8,<3.11" -content-hash = "252eabff08611b7ee7acaa1479913b4b7a5dd622896c054c68ba7d038e99f797" +content-hash = "ad8fda1bd3ae9e82d29dbe61c2801d9ffba2fb7cfed7bb5b2762788c338c2fb5" [metadata.files] add-trailing-comma = [ @@ -1798,8 +1864,8 @@ attrs = [ {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"}, ] Babel = [ - {file = "Babel-2.10.3-py3-none-any.whl", hash = "sha256:ff56f4892c1c4bf0d814575ea23471c230d544203c7748e8c68f0089478d48eb"}, - {file = "Babel-2.10.3.tar.gz", hash = "sha256:7614553711ee97490f732126dc077f8d0ae084ebc6a96e23db1482afabdb2c51"}, + {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"}, + {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"}, ] backcall = [ {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"}, @@ -2015,8 +2081,8 @@ 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Machine Learning in Python" license = "MIT" authors = [ @@ -64,7 +64,7 @@ statsmodels = "^0.13" # --- machine-learning --- scikit-learn = "^1.1" -xgboost = "^1.6" +xgboost = "^1.7" glmnet = "^2.2" shap = "^0.41" @@ -112,7 +112,7 @@ flake8-commas = "^2.1" # - flake8-typing-imports==1.12.0 # - flake8-use-fstring==1.4 # - pep8-naming==0.13.1 -mypy = "^0.971" +mypy = "^0.990" # --- unit-testing --- pytest = "^7.2" @@ -138,7 +138,7 @@ watchdog = "^2.1" [build-system] -requires = ["poetry-core>=1.2.0"] +requires = ["poetry-core>=1.3.2"] build-backend = "poetry.core.masonry.api" diff --git a/tox.ini b/tox.ini index 395fd6d..a7d820b 100644 --- a/tox.ini +++ b/tox.ini @@ -1,28 +1,23 @@ +# References: +# - https://tox.wiki/en/latest/ +# - https://tox.wiki/en/latest/config.html +# - https://tox.readthedocs.io/_/downloads/en/latest/pdf/ +# - https://tox.wiki/en/latest/example/package.html#poetry +# - https://github.com/awslabs/secrets-helper/blob/master/tox.ini +# - https://tox.wiki/en/latest/config.html#substitutions-for-virtualenv-related-sections + + [tox] isolated_build = True -# TODO(amir): figure out how to roll-out python v3.8 and 3.10 -# currently we get `ERROR: py38: InterpreterNotFound: python3.8` while I have py38 installed -# via pyenv; seems like poetry and tox have sometimes conflicts envlist = py39 [testenv] allowlist_externals = poetry commands = - # TODO(amir): tox sometimes seems stupid; for example sometimes it demands `numpy` to be installed - # first to install other dependencies such as `glmnet`; so, something like command below is needed - # to explicitly, wipe out other installations - # `poetry run python -m pip install --exists-action w numpy` - # however, I found out if you try `poe tox` commands twice; it will pass! so weird! we might need to dig in more - # or `poe tox -r` which should recreates the env sometimes wont work as well; so try twice :D poetry install -vv poe greet poe check - # TODO(amir): command `poe test` cannot be used here due to a bug in `tox` - # `poe test` will run the tests; however, the coverage report will be all zero - # reference: https://www.pythonfixing.com/2021/10/fixed-tox-0-coverage.html - # https://tox.wiki/en/latest/config.html#substitutions-for-virtualenv-related-sections - # so, we explicitly tell tox the coverage source directory via `--cov={envsitepackagesdir}/slickml` - poetry run python -m pytest --cov={envsitepackagesdir}/slickml --cov-report=term --cov-report=html --cov-config=.coveragerc --tb=short -ra -v tests/ + poe test poe sphinx poetry build poe clean \ No newline at end of file