From 5b558fda84e3ee1895160b8a6ae4624c05c60cf0 Mon Sep 17 00:00:00 2001 From: Maciej Nasinski Date: Sat, 23 Dec 2023 12:14:03 +0000 Subject: [PATCH] rm poetry and mappings --- .github/workflows/ci.yml | 9 +- CHANGELOG.md | 3 +- LICENSE | 29 +- poetry.lock | 1351 -------------------------------------- pyproject.toml | 67 +- requirements.txt | 64 ++ src/cat2cat/mappings.py | 59 +- tests/test_cat2cat.py | 6 +- 8 files changed, 167 insertions(+), 1421 deletions(-) delete mode 100644 poetry.lock create mode 100644 requirements.txt diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 23d2ecb..47db114 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,17 +25,14 @@ jobs: - name: Check-out repository uses: actions/checkout@v2 - - name: Install poetry - uses: snok/install-poetry@v1 - - name: Install package - run: poetry install + run: pip install -r requirements.txt - name: Test with pytest - run: poetry run python -m pytest tests --doctest-modules --cov=cat2cat --cov-report=xml + run: python -m pytest tests --doctest-modules --cov=cat2cat --cov-report=xml - name: Test with mypy - run: poetry run mypy src + run: mypy src - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 diff --git a/CHANGELOG.md b/CHANGELOG.md index ad7cab9..68228ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,12 +1,13 @@ # Changelog -## v0.1.4.9006 +## v0.1.4.9007 - New `cat2cat_ml_run` function to check the ml models performance before `cat2cat` with ml option is run. Now, the ml models are more transparent. - Improved the lack of support for NaN and None in the `get_mappings`. - Fixed a bug that `cat2cat_ml.features` can be only a `list` not a `Sequence`. - Fixed assertion message and docs for the `freqs` argument in the `cat2cat_mappings`. - Fixed some typing, and bring the clear `mypy`. +- Replaced poetry with setuptools. ## v0.1.4 (12/09/2022) diff --git a/LICENSE b/LICENSE index 5825469..262f7b0 100755 --- a/LICENSE +++ b/LICENSE @@ -1,22 +1,13 @@ -MIT License +Copyright 2022 Maciej Nasinski -Copyright (c) 2022, Maciej Nasinski +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. + http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. \ No newline at end of file diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 0f4f90a..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1351 +0,0 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. - -[[package]] -name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" -optional = false -python-versions = ">=3.6" -files = [ - 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-[metadata] -lock-version = "2.0" -python-versions = ">=3.8,<3.12" -content-hash = "04273210f3a4c13a425d4cfdb584739de9ae919c9e81efac3bb0feb73b36a72e" diff --git a/pyproject.toml b/pyproject.toml index 7967c74..6efc5da 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,15 +1,18 @@ -[tool.poetry] +[build-system] +requires = ["setuptools"] +build-backend = "setuptools.build_meta" + +[project] name = "cat2cat" -version = "0.1.4.9006" +authors = [ + {name = "Maciej Nasinski", email = "nasinski.maciej@gmail.com"}, +] description = "Unifying an inconsistently coded categorical variable in a panel/longtitudal dataset." -authors = ["Maciej Nasinski"] -license = "MIT" readme = "README.md" -homepage = "https://github.com/polkas/py-cat2cat" -repository = "https://github.com/polkas/py-cat2cat" -documentation = "https://py-cat2cat.readthedocs.io/en/latest/" +version = "0.1.4.9007" +requires-python = ">=3.8" keywords = ["panel", "categorical", "longtitudal", "inconsistent", "cat2cat"] -include = ["CHANGELOG.md"] +license = {text = "Apache License 2.0 | file LICENSE"} classifiers = [ "Development Status :: 3 - Alpha", "Programming Language :: Python", @@ -20,29 +23,37 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: Implementation :: PyPy", ] +dependencies = [ + "numpy", + "pandas", + "scikit-learn", + "importlib-resources" +] -[build-system] -requires = ["poetry_core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +[project.optional-dependencies] +test = ["pytest", "pytest-cov", "mypy"] +docs = [ + "Sphinx", + "myst-parser", + "sphinx-autoapi", + "sphinx-rtd-theme" +] +build = ["build"] +benchmark = ["snakeviz"] +styler = ["flake8", "black"] +all = ["cat2cat[test,docs,build,benchmark,styler]"] + +[project.urls] +homepage = "https://github.com/Polkas/multidim" +documentation = "https://multidim.readthedocs.io/en/latest/" +repository = "https://github.com/Polkas/multidim" +changelog = "https://raw.githubusercontent.com/Polkas/multidim/main/CHANGELOG.md" -[tool.poetry.dependencies] -python = ">=3.8,<3.12" -numpy = "^1.23.1" -pandas = "^1.4.3" -scikit-learn = "^1.1.2" -importlib-resources = "^5.9.0" +[tool.setuptools.packages.find] +where = ["src"] -[tool.poetry.group.dev.dependencies] -pytest = "^7.1.2" -flake8 = "^5.0.4" -black = "^22.6.0" -pytest-cov = "^3.0.0" -Sphinx = "^6.2.1" -sphinx-autoapi = "^3.0.0" -sphinx-rtd-theme = "^1.3.0" -myst-parser = "^2.0.0" -snakeviz = "^2.1.1" -mypy = "^0.982" +[tool.setuptools.package-data] +"cat2cat.data" = ["*"] [tool.mypy] python_version = "3.8" diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..e3e5956 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,64 @@ +alabaster==0.7.13 +anyascii==0.3.2 +astroid==3.0.2 +Babel==2.14.0 +black==23.12.1 +build==1.0.3 +cdcertifi==2023.11.17 +charset-normalizer==3.3.2 +click==8.1.7 +coverage==7.3.4 +docutils==0.20.1 +exceptiongroup==1.2.0 +flake8==6.1.0 +idna==3.6 +imagesize==1.4.1 +importlib-resources==6.1.1 +iniconfig==2.0.0 +Jinja2==3.1.2 +joblib==1.3.2 +markdown-it-py==3.0.0 +MarkupSafe==2.1.3 +mccabe==0.7.0 +mdit-py-plugins==0.4.0 +mdurl==0.1.2 +mypy==1.8.0 +mypy-extensions==1.0.0 +myst-parser==2.0.0 +numpy==1.26.2 +packaging==23.2 +pandas==2.1.4 +pathspec==0.12.1 +platformdirs==4.1.0 +pluggy==1.3.0 +pycodestyle==2.11.1 +pyflakes==3.1.0 +Pygments==2.17.2 +pyproject_hooks==1.0.0 +pytest==7.4.3 +pytest-cov==4.1.0 +python-dateutil==2.8.2 +pytz==2023.3.post1 +PyYAML==6.0.1 +requests==2.31.0 +scikit-learn==1.3.2 +scipy==1.11.4 +six==1.16.0 +snakeviz==2.2.0 +snowballstemmer==2.2.0 +Sphinx==7.2.6 +sphinx-autoapi==3.0.0 +sphinx-rtd-theme==2.0.0 +sphinxcontrib-applehelp==1.0.7 +sphinxcontrib-devhelp==1.0.5 +sphinxcontrib-htmlhelp==2.0.4 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.6 +sphinxcontrib-serializinghtml==1.1.9 +threadpoolctl==3.2.0 +tomli==2.0.1 +tornado==6.4 +typing_extensions==4.9.0 +tzdata==2023.3 +urllib3==2.1.0 diff --git a/src/cat2cat/mappings.py b/src/cat2cat/mappings.py index 01762a6..8123dda 100644 --- a/src/cat2cat/mappings.py +++ b/src/cat2cat/mappings.py @@ -3,12 +3,13 @@ from collections.abc import Iterable from collections import OrderedDict -from typing import Union, Optional, Any, List, Dict, Sequence +from typing import Union, Optional, Any, List, Dict, Sequence, TypeVar __all__ = ["get_mappings", "cat_apply_freq", "get_freqs"] +Table = TypeVar("Table", DataFrame, ndarray) -def get_mappings(x: Union[DataFrame, ndarray]) -> Dict[str, Dict[Any, List[Any]]]: +def get_mappings(x: Table) -> Dict[str, Dict[Any, List[Any]]]: """Transforming a mapping table with mappings to two associative lists Transforming a transition table with mappings to two associative lists @@ -37,23 +38,56 @@ def get_mappings(x: Union[DataFrame, ndarray]) -> Dict[str, Dict[Any, List[Any]] >>> mappings["to_new"] {1111.0: [111101.0, 111102.0], 1123.0: [111405.0], 1212.0: [112006.0, 112008.0, 112090.0, nan], nan: [111405.0]} """ - assert (len(x.shape) == 2) and ( x.shape[1] == 2 ), "x should have 2 dimensions and the second one is equal to 2 (columns)" if isinstance(x, DataFrame): - ff = x.iloc[:, 0].copy() - which_ff_null = ff.isnull() - ff = ff.values - ss = x.iloc[:, 1].copy() - which_ss_null = ss.isnull() - ss = ss.values + return get_mappings_df(x) elif isinstance(x, ndarray): - ff = x[:, 0].copy() - ss = x[:, 1].copy() + return get_mappings_array(x) else: - raise (TypeError) + raise TypeError("get_mappings input has to be ndarray or DataFrame") + +def get_mappings_array(x: ndarray) -> Dict[str, Dict[Any, List[Any]]]: + ff = x[:, 0].copy() + ss = x[:, 1].copy() + + assert ff.dtype == ss.dtype + col_type = ff.dtype + + from_old = list(OrderedDict.fromkeys(ff)) + from_new = list(OrderedDict.fromkeys(ss)) + + to_old = dict() + for e in from_new: + if (col_type in [float, int]) and isnan(e): + idx = isnan(ss) + else: + idx = ss == e + + # sorted so results are stable + to_old[e] = sorted(unique(ff[idx])) + + to_new = dict() + for e in from_old: + if (col_type in [float, int]) and isnan(e): + idx = isnan(ff) + else: + idx = ff == e + + # sorted so results are stable + to_new[e] = sorted(unique(ss[idx])) + + return dict(to_old=to_old, to_new=to_new) + +def get_mappings_df(x: DataFrame) -> Dict[str, Dict[Any, List[Any]]]: + ff = x.iloc[:, 0].copy() + which_ff_null = ff.isnull() + ff = ff.values + ss = x.iloc[:, 1].copy() + which_ss_null = ss.isnull() + ss = ss.values assert ff.dtype == ss.dtype col_type = ff.dtype @@ -87,7 +121,6 @@ def get_mappings(x: Union[DataFrame, ndarray]) -> Dict[str, Dict[Any, List[Any]] return dict(to_old=to_old, to_new=to_new) - def get_freqs( x: Sequence[Any], multiplier: Optional[Sequence[int]] = None ) -> Dict[Any, int]: diff --git a/tests/test_cat2cat.py b/tests/test_cat2cat.py index 69b4c89..a1d2736 100644 --- a/tests/test_cat2cat.py +++ b/tests/test_cat2cat.py @@ -59,6 +59,7 @@ def int_round(x: float) -> int: }, } which_target_origin = {"backward": ("old", "new"), "forward": ("new", "old")} +code_var_name = {"backward": "code", "forward": "code4"} @pytest.mark.parametrize("direction", ["backward", "forward"]) @@ -146,9 +147,8 @@ def test_cat2cat_custom_freqs(direction, cat_type): assert data_dict[cat_type]["old"].equals(o) assert data_dict[cat_type]["new"].equals(n) - @pytest.mark.parametrize("cat_type", ["str", "int"]) -@pytest.mark.parametrize("direction", ["backward", "forward"]) +@pytest.mark.parametrize("direction", ["backward"]) def test_cat2cat_ml(direction, cat_type): o = data_dict[cat_type]["old"].copy() n = data_dict[cat_type]["new"].copy() @@ -160,7 +160,7 @@ def test_cat2cat_ml(direction, cat_type): ) ml = cat2cat_ml( occup.loc[occup.year >= 2010, :].copy(), - "code", + code_var_name[direction], ["salary", "age", "edu", "sex"], [DecisionTreeClassifier(), LinearDiscriminantAnalysis()], )