From fee2d2f662cfaaf5127c501d08226c48292b4c20 Mon Sep 17 00:00:00 2001 From: "Jeffrey C. Lerman" Date: Thu, 5 Dec 2024 11:00:41 -0800 Subject: [PATCH] maintenance: (#18) - bump dependencies - add python3.12 support - add flake8 linter - replace use of toml library with tomli or tomllib, depending on python version --- .github/workflows/publish-package.yml | 2 +- .github/workflows/python-package.yml | 4 +- .pre-commit-config.yaml | 10 +- philter_lite/filters/__init__.py | 11 +- philter_lite/filters/filter_db.py | 13 +- poetry.lock | 507 +++++++++++++------------- pyproject.toml | 15 +- tests/test_package_metadata.py | 11 +- tests/test_philter.py | 60 +-- tox.ini | 11 +- 10 files changed, 329 insertions(+), 315 deletions(-) diff --git a/.github/workflows/publish-package.yml b/.github/workflows/publish-package.yml index e6be78b..b194ac0 100644 --- a/.github/workflows/publish-package.yml +++ b/.github/workflows/publish-package.yml @@ -16,7 +16,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install poetry==1.7.1 + pip install poetry==1.8.4 - name: Build and publish env: PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 792ab12..3d7bd69 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v2 @@ -29,4 +29,4 @@ jobs: pip install tox - name: Test and run checks run: | - tox -e py,lint,typing + tox -e py,lint diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e4fd591..58b4950 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,7 @@ --- repos: - repo: https://github.com/psf/black - rev: 23.9.1 + rev: 24.10.0 hooks: - id: black language_version: python3 @@ -12,8 +12,14 @@ repos: - id: isort args: [ --profile, black ] + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.13.0 + hooks: + - id: mypy + exclude: '^tests/' + - repo: https://github.com/pycqa/flake8 - rev: 6.1.0 + rev: 7.1.1 hooks: - id: flake8 language: python diff --git a/philter_lite/filters/__init__.py b/philter_lite/filters/__init__.py index 9639abd..f5a5ed9 100644 --- a/philter_lite/filters/__init__.py +++ b/philter_lite/filters/__init__.py @@ -1,10 +1,14 @@ import os import re +import sys import warnings from dataclasses import dataclass from typing import List, Optional, Pattern, Set -import toml +if sys.version_info < (3, 11): + import tomli as tomllib +else: + import tomllib from philter_lite.filters import filter_db @@ -136,8 +140,9 @@ def load_filters(filter_path) -> List[Filter]: """ if not os.path.exists(filter_path): raise Exception("Filepath does not exist", filter_path) - with open(filter_path, "r") as fil_file: - return [filter_from_dict(x) for x in toml.loads(fil_file.read())["filters"]] + with open(filter_path, "rb") as fil_file: + filters_toml = tomllib.load(fil_file) + return [filter_from_dict(x) for x in filters_toml["filters"]] def _precompile(regex: str) -> Pattern[str]: diff --git a/philter_lite/filters/filter_db.py b/philter_lite/filters/filter_db.py index 8a72363..b571906 100644 --- a/philter_lite/filters/filter_db.py +++ b/philter_lite/filters/filter_db.py @@ -1,21 +1,26 @@ +import sys from importlib import resources from typing import Any, MutableMapping -import toml +if sys.version_info < (3, 11): + import tomli as tomllib +else: + import tomllib + from philter_lite import filters def load_regex_db() -> MutableMapping[str, Any]: - return toml.loads(resources.read_text(filters, "regex.toml")) + return tomllib.loads(resources.read_text(filters, "regex.toml")) def load_regex_context_db() -> MutableMapping[str, Any]: - return toml.loads(resources.read_text(filters, "regex_context.toml")) + return tomllib.loads(resources.read_text(filters, "regex_context.toml")) def load_set_db() -> MutableMapping[str, Any]: - return toml.loads(resources.read_text(filters, "set.toml")) + return tomllib.loads(resources.read_text(filters, "set.toml")) regex_db: MutableMapping[str, Any] = load_regex_db() diff --git a/poetry.lock b/poetry.lock index d6c876d..0b1f6a7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "cfgv" @@ -49,24 +49,24 @@ files = [ [[package]] name = "distlib" -version = "0.3.7" +version = "0.3.9" description = "Distribution utilities" optional = false python-versions = "*" files = [ - {file = "distlib-0.3.7-py2.py3-none-any.whl", hash = "sha256:2e24928bc811348f0feb63014e97aaae3037f2cf48712d51ae61df7fd6075057"}, - {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"}, + {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"}, + {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"}, ] [[package]] name = "exceptiongroup" -version = "1.1.3" +version = "1.2.2" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" files = [ - {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = 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managing and maintaining multi-language pre-commit hooks." optional = false python-versions = ">=3.9" files = [ - {file = "pre_commit-3.7.0-py2.py3-none-any.whl", hash = "sha256:5eae9e10c2b5ac51577c3452ec0a490455c45a0533f7960f993a0d01e59decab"}, - {file = "pre_commit-3.7.0.tar.gz", hash = "sha256:e209d61b8acdcf742404408531f0c37d49d2c734fd7cff2d6076083d191cb060"}, + {file = "pre_commit-4.0.1-py2.py3-none-any.whl", hash = "sha256:efde913840816312445dc98787724647c65473daefe420785f885e8ed9a06878"}, + {file = "pre_commit-4.0.1.tar.gz", hash = "sha256:80905ac375958c0444c65e9cebebd948b3cdb518f335a091a670a89d652139d2"}, ] [package.dependencies] @@ -226,13 +222,13 @@ virtualenv = ">=20.10.0" [[package]] name = "pytest" -version = "8.1.1" +version = "8.3.4" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" files = [ - {file = "pytest-8.1.1-py3-none-any.whl", hash = "sha256:2a8386cfc11fa9d2c50ee7b2a57e7d898ef90470a7a34c4b949ff59662bb78b7"}, - 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"sha256:201e7c28bb210e374999d1dde6382923ab0ed1a8a5faeece48ab525b7810a553"}, ] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "53e9d8679e6e3bad3d4d6dd9ffbd2940046aed4bdf11d715ee4e3f0df20f6c32" +content-hash = "aca5dcaa2846ab83962002d990bad5967b86ac557b079270c228108710be7372" diff --git a/pyproject.toml b/pyproject.toml index 6714869..5dedf36 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "philter-lite" -version = "0.5.0" +version = "0.5.1" description = "Open-source PHI-filtering software. A fork of philter-ucsf." readme = "README.md" authors = [ @@ -14,6 +14,7 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", ] @@ -21,19 +22,19 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.9" chardet = "^5.2.0" -nltk = "^3.8.1" -xmltodict = "^0.13.0" -toml = "^0.10.0" +nltk = "^3.9.1" +xmltodict = "^0.14.2" +tomli = {version = "^2.1.0", python = "<3.11"} -[tool.poetry.dev-dependencies] -pre-commit = "^3.7.0" +[tool.poetry.group.dev.dependencies] +pre-commit = "^4.0.1" pytest = "^8.1.1" [tool.poetry.scripts] philter_lite = 'philter_lite.main:main' [build-system] -requires = ["poetry_core>=1.8.1"] +requires = ["poetry_core>=1.9.0"] build-backend = "poetry.core.masonry.api" [tool.black] diff --git a/tests/test_package_metadata.py b/tests/test_package_metadata.py index 28c1d0b..91eb4bc 100644 --- a/tests/test_package_metadata.py +++ b/tests/test_package_metadata.py @@ -1,15 +1,22 @@ """Confirm that project metadata is set correctly.""" + import os +import sys from typing import Any, Mapping -import toml +if sys.version_info < (3, 11): + import tomli as tomllib +else: + import tomllib + import philter_lite TESTS_DIR = os.path.dirname(os.path.abspath(__file__)) PYPROJECT_TOML_PATH = os.path.join(TESTS_DIR, "..", "pyproject.toml") -pyproject_toml: Mapping[str, Any] = toml.load(PYPROJECT_TOML_PATH) +with open(PYPROJECT_TOML_PATH, "rb") as pyproject_file: + pyproject_toml: Mapping[str, Any] = tomllib.load(pyproject_file) def test_version(): diff --git a/tests/test_philter.py b/tests/test_philter.py index 6a944d4..a1a357f 100644 --- a/tests/test_philter.py +++ b/tests/test_philter.py @@ -17,14 +17,14 @@ def test_filter_from_dict(): "phi_type": "SOMETHING", } - filter = filter_from_dict(filter_dict) + my_filter = filter_from_dict(filter_dict) - assert filter.type == "regex" - assert filter.title == "test_city" - assert filter.data is not None - assert filter.exclude == "test_ex" - assert filter.phi_type == "SOMETHING" - assert isinstance(filter, filters.RegexFilter) + assert my_filter.type == "regex" + assert my_filter.title == "test_city" + assert my_filter.data is not None + assert my_filter.exclude == "test_ex" + assert my_filter.phi_type == "SOMETHING" + assert isinstance(my_filter, filters.RegexFilter) filter_dict = { "title": "Find Names 1", @@ -36,15 +36,15 @@ def test_filter_from_dict(): "phi_type": "Something", } - filter = filter_from_dict(filter_dict) + my_filter = filter_from_dict(filter_dict) - assert filter.type == "regex_context" - assert filter.title == "Find Names 1" - assert filter.data is not None - assert filter.exclude is True - assert filter.context == "right" - assert filter.context_filter == "Firstnames Blacklist" - assert isinstance(filter, filters.RegexContextFilter) + assert my_filter.type == "regex_context" + assert my_filter.title == "Find Names 1" + assert my_filter.data is not None + assert my_filter.exclude is True + assert my_filter.context == "right" + assert my_filter.context_filter == "Firstnames Blacklist" + assert isinstance(my_filter, filters.RegexContextFilter) filter_dict = { "title": "Whitelist 1", @@ -55,14 +55,14 @@ def test_filter_from_dict(): "phi_type": "Something", } - filter = filter_from_dict(filter_dict) + my_filter = filter_from_dict(filter_dict) - assert filter.type == "set" - assert filter.title == "Whitelist 1" - assert filter.data is not None - assert filter.exclude is False - assert filter.pos == set() - assert isinstance(filter, filters.SetFilter) + assert my_filter.type == "set" + assert my_filter.title == "Whitelist 1" + assert my_filter.data is not None + assert my_filter.exclude is False + assert my_filter.pos == set() + assert isinstance(my_filter, filters.SetFilter) filter_dict = { "title": "POS MATCHER", @@ -72,13 +72,13 @@ def test_filter_from_dict(): "phi_type": "OTHER", } - filter = filter_from_dict(filter_dict) + my_filter = filter_from_dict(filter_dict) - assert filter.type == "pos_matcher" - assert filter.title == "POS MATCHER" - assert filter.exclude is False - assert filter.pos == ["CD"] - assert isinstance(filter, filters.PosFilter) + assert my_filter.type == "pos_matcher" + assert my_filter.title == "POS MATCHER" + assert my_filter.exclude is False + assert my_filter.pos == ["CD"] + assert isinstance(my_filter, filters.PosFilter) def test_filter_from_dict_missing_phi_type(): @@ -90,8 +90,8 @@ def test_filter_from_dict_missing_phi_type(): "notes": "test_notes", } - filter = filter_from_dict(filter_dict) - assert filter.phi_type == "OTHER" + my_filter = filter_from_dict(filter_dict) + assert my_filter.phi_type == "OTHER" def test_filter_from_dict_missing_file(): diff --git a/tox.ini b/tox.ini index 1bbd585..65b63b4 100644 --- a/tox.ini +++ b/tox.ini @@ -1,22 +1,15 @@ [tox] -envlist = typing,lint,py39,py310,py311 +envlist = lint,py39,py310,py311,py312 isolated_build = True [testenv] deps = pytest commands_pre = - python -c 'import nltk; nltk.download("averaged_perceptron_tagger")' + python -c 'import nltk; nltk.download("averaged_perceptron_tagger_eng")' commands = python -m pytest {posargs} [lint] deps = pre-commit commands = pre-commit run --all-files skip_install = True - - -[typing] -deps = - types-toml - mypy -commands = mypy philter_lite/