From 3bf380c3e9f8e4fbba72d67368a337c26a25491e Mon Sep 17 00:00:00 2001 From: Richard Eckart de Castilho Date: Sat, 4 May 2024 20:53:48 +0200 Subject: [PATCH 1/2] #314 - Switch to poetry - Remove setup.py - Switch to pyproject.toml - Update GitHub actions to use poetry - Clean up code a bit according to feedback from flake8 - Update release guide --- .coveragerc | 2 - .github/workflows/publish_to_pypi.yml | 9 +- .github/workflows/run_tests.yml | 15 +- Makefile | 47 +- README.rst | 5 +- cassis/__version__.py | 1 - cassis/cas.py | 4 +- cassis/xmi.py | 4 +- poetry.lock | 1018 +++++++++++++++++++++++++ pyproject.toml | 70 ++ setup.py | 127 --- tests/test_cas.py | 8 +- tests/test_json.py | 2 +- tests/test_typesystem.py | 11 +- tests/test_util.py | 2 - tests/test_xmi.py | 33 +- 16 files changed, 1173 insertions(+), 185 deletions(-) delete mode 100644 cassis/__version__.py create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/.coveragerc b/.coveragerc index 4be8c55..af167bc 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,8 +1,6 @@ [run] source=cassis omit= - setup.py cassis/__init__.py - cassis/__version__.py tests/* docs/* diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml index db28dfa..90c710e 100644 --- a/.github/workflows/publish_to_pypi.yml +++ b/.github/workflows/publish_to_pypi.yml @@ -15,13 +15,12 @@ jobs: python-version: '3.11' - name: Install dependencies run: | - pip install --upgrade -e .[test] + pip install poetry + make dependencies - name: Run tests - run: | - pytest + run: make unit-tests - name: Build package - run: | - python setup.py sdist + run: make build - name: Publish package to TestPyPI if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 30844f5..59bdb45 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -22,17 +22,14 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - pip install --upgrade -e .[test] - pip install flake8 + pip install poetry + make dependencies + - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + run: make lint + - name: Run tests - run: | - pytest --cov=./ --cov-report=xml + run: make coverage - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 diff --git a/Makefile b/Makefile index d5528c4..04d6bf0 100644 --- a/Makefile +++ b/Makefile @@ -1,13 +1,50 @@ +.PHONY: docs tests PYTHON_FILES = cassis tests -test: - python -m pytest -m "not performance" tests/ +# Dependencies +dependencies: + poetry install +# Tests +unit-tests: + poetry run py.test --cov=cassis --cov-branch --cov-fail-under=90 tests + +tests: unit-tests integ-tests + +coverage: + poetry run py.test --cov=cassis --cov-branch --cov-fail-under=90 --cov-report=xml:coverage.xml -m "not performance" tests + +# Static analysis/linting format: - black -l 120 cassis/ - black -l 120 tests/ + black cassis/ + black tests/ isort --profile black $(PYTHON_FILES) --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=120 +lint: + # stop the build if there are Python syntax errors or undefined names + poetry run flake8 --select=E9,F63,F7,F82 --show-source $(PYTHON_FILES) + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + poetry run flake8 --exit-zero $(PYTHON_FILES) + +# Docs +docs: + poetry run mkdocs serve html: - cd docs && make html \ No newline at end of file + cd docs && make html + +# Building and publishing +build: unit-tests lint + poetry build + +publish: build + poetry publish + +# CI + +ci-publish: + poetry publish --build --username "${PYPI_USERNAME}" --password "${PYPI_PASSWORD}" --no-interaction + +ci-bump-version: + poetry run bump2version patch diff --git a/README.rst b/README.rst index 288f32f..bac2d79 100644 --- a/README.rst +++ b/README.rst @@ -489,9 +489,8 @@ Release - Make sure all issues for the milestone are completed, otherwise move them to the next - Checkout the ``main`` branch -- Bump the version in ``cassis/__version__.py`` to a stable one, e.g. ``__version__ = "0.6.0"``, commit and push, wait until the build completed. An example commit message would be ``No issue. Release 0.6.0`` +- Bump the version in ``pyproject.toml`` to a stable one, e.g. ``__version__ = "0.6.0"``, commit and push, wait until the build completed. An example commit message would be ``No issue. Release 0.6.0`` - Create a tag for that version via e.g. ``git tag v0.6.0`` and push the tags via ``git push --tags``. Pushing a tag triggers the release to pypi -- Bump the version in ``cassis/__version__.py`` to the next development version, e.g. ``0.7.0-dev``, commit and push that. An example commit message would be ``No issue. Bump version after release`` +- Bump the version in ``pyproject.toml`` to the next development version, e.g. ``0.7.0-dev``, commit and push that. An example commit message would be ``No issue. Bump version after release`` - Once the build has completed and pypi accepted the new version, go to the Github release and write the changelog based on the issues in the respective milestone - Create a new milestone for the next version - diff --git a/cassis/__version__.py b/cassis/__version__.py deleted file mode 100644 index 2aceaf4..0000000 --- a/cassis/__version__.py +++ /dev/null @@ -1 +0,0 @@ -__version__ = "0.10.0-dev" diff --git a/cassis/cas.py b/cassis/cas.py index a6206ff..1125abc 100644 --- a/cassis/cas.py +++ b/cassis/cas.py @@ -13,6 +13,8 @@ from cassis.typesystem import ( FEATURE_BASE_NAME_HEAD, + FEATURE_BASE_NAME_LANGUAGE, + TYPE_NAME_DOCUMENT_ANNOTATION, TYPE_NAME_FS_ARRAY, TYPE_NAME_FS_LIST, TYPE_NAME_SOFA, @@ -21,8 +23,6 @@ TypeCheckError, TypeSystem, TypeSystemMode, - TYPE_NAME_DOCUMENT_ANNOTATION, - FEATURE_BASE_NAME_LANGUAGE, ) _validator_optional_string = validators.optional(validators.instance_of(str)) diff --git a/cassis/xmi.py b/cassis/xmi.py index d9d7b35..2e1bfe2 100644 --- a/cassis/xmi.py +++ b/cassis/xmi.py @@ -12,7 +12,6 @@ from cassis.typesystem import ( _LIST_TYPES, _PRIMITIVE_ARRAY_TYPES, - _PRIMITIVE_LIST_TYPES, FEATURE_BASE_NAME_BEGIN, FEATURE_BASE_NAME_END, FEATURE_BASE_NAME_HEAD, @@ -295,7 +294,8 @@ def deserialize(self, source: Union[IO, str], typesystem: TypeSystem, lenient: b else: view = cas.create_view(sofa.sofaID, xmiID=sofa.xmiID, sofaNum=sofa.sofaNum) - # Directly set the sofaString and offsetConverter for the sofa to avoid recomputing the offset convertion (slow!) when using the setter + # Directly set the sofaString and offsetConverter for the sofa to avoid recomputing the offset convertion + # (slow!) when using the setter view.get_sofa()._sofaString = sofa.sofaString view.get_sofa()._offset_converter = sofa._offset_converter view.sofa_mime = sofa.mimeType diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..71295b5 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1018 @@ +# This file is 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functionality of this file, you must: -# $ pip install twine - -import io -import os -import sys -from shutil import rmtree - -from setuptools import setup, Command, find_packages - -# Package meta-data. -NAME = "dkpro-cassis" -DESCRIPTION = "UIMA CAS processing library in Python" -HOMEPAGE = "https://dkpro.github.io" -EMAIL = "dkpro-core-user@googlegroups.com" -AUTHOR = "The DKPro cassis team" -REQUIRES_PYTHON = ">=3.7.0" - -install_requires = [ - "lxml~=4.9.1", - "attrs>=21.2,<24", - "sortedcontainers==2.4.*", - "toposort==1.7", - "more-itertools>=8.12,<9", - "deprecation==2.1.*", - "importlib_resources==5.4.*" -] - -test_dependencies = [ - "tox==3.24.*", - "pytest==6.2.*", - "lxml-asserts==0.1.*", - "pytest-lazy-fixture==0.6.*", - "codecov==2.1.*", - "pytest-cov==3.0.*", - "rstcheck==3.3.*" -] - -dev_dependencies = [ - "black==21.12b0", - "isort==5.10.*" -] - -doc_dependencies = [ - "sphinx", - "sphinx-autodoc-typehints", - "sphinx-rtd-theme" -] - -extras = { - "test": test_dependencies, - "dev": dev_dependencies, - "doc": doc_dependencies -} - -# The rest you shouldn"t have to touch too much :) -# ------------------------------------------------ -# Except, perhaps the License and Trove Classifiers! -# If you do change the License, remember to change the Trove Classifier for that! - -here = os.path.abspath(os.path.dirname(__file__)) - -# Import the README and use it as the long-description. -# Note: this will only work if "README.rst" is present in your MANIFEST.in file! -try: - with io.open(os.path.join(here, "README.rst"), encoding="utf-8") as f: - long_description = "\n" + f.read() -except FileNotFoundError: - long_description = DESCRIPTION - -# Load the package"s __version__.py module as a dictionary. -about = {} -with open(os.path.join(here, "cassis", "__version__.py")) as f: - exec(f.read(), about) - - -# Where the magic happens: -setup( - name=NAME, - version=about["__version__"], - description=DESCRIPTION, - long_description=long_description, - long_description_content_type="text/x-rst", - author=AUTHOR, - author_email=EMAIL, - python_requires=REQUIRES_PYTHON, - url=HOMEPAGE, - keywords="uima dkpro cas xmi", - - project_urls={ - "Bug Tracker": "https://github.com/dkpro/dkpro-cassis/issues", - "Documentation": "https://cassis.readthedocs.org/", - "Source Code": "https://github.com/dkpro/dkpro-cassis", - }, - - packages=find_packages(exclude="tests"), - package_data={"cassis": ["resources/*.xml"]}, - - install_requires=install_requires, - test_suite="tests", - - tests_require=test_dependencies, - extras_require=extras, - - include_package_data=True, - license="Apache License 2.0", - classifiers=[ - # Trove classifiers - # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Topic :: Software Development :: Libraries", - "Topic :: Scientific/Engineering :: Human Machine Interfaces", - "Topic :: Text Processing :: Linguistic" - ], -) diff --git a/tests/test_cas.py b/tests/test_cas.py index f09f06d..670db07 100644 --- a/tests/test_cas.py +++ b/tests/test_cas.py @@ -20,8 +20,8 @@ def test_default_typesystem_is_not_shared(): cas1 = Cas() cas2 = Cas() - t1 = cas1.typesystem.create_type(name="test.Type") - t2 = cas2.typesystem.create_type(name="test.Type") + cas1.typesystem.create_type(name="test.Type") + cas2.typesystem.create_type(name="test.Type") def test_default_typesystem_is_not_shared_load_from_xmi(empty_cas_xmi): @@ -29,8 +29,8 @@ def test_default_typesystem_is_not_shared_load_from_xmi(empty_cas_xmi): cas1 = load_cas_from_xmi(empty_cas_xmi) cas2 = load_cas_from_xmi(empty_cas_xmi) - t1 = cas1.typesystem.create_type(name="test.Type") - t2 = cas2.typesystem.create_type(name="test.Type") + cas1.typesystem.create_type(name="test.Type") + cas2.typesystem.create_type(name="test.Type") # View diff --git a/tests/test_json.py b/tests/test_json.py index 1509a5c..810e421 100644 --- a/tests/test_json.py +++ b/tests/test_json.py @@ -1,6 +1,6 @@ import json -from cassis.typesystem import TYPE_NAME_ANNOTATION, TypeSystemMode, TYPE_NAME_DOCUMENT_ANNOTATION +from cassis.typesystem import TYPE_NAME_ANNOTATION, TYPE_NAME_DOCUMENT_ANNOTATION, TypeSystemMode from tests.fixtures import * from tests.test_files.test_cas_generators import MultiFeatureRandomCasGenerator, MultiTypeRandomCasGenerator from tests.util import assert_json_equal diff --git a/tests/test_typesystem.py b/tests/test_typesystem.py index d5a84c8..1f0ecbf 100644 --- a/tests/test_typesystem.py +++ b/tests/test_typesystem.py @@ -10,6 +10,7 @@ TYPE_NAME_ANNOTATION_BASE, TYPE_NAME_ARRAY_BASE, TYPE_NAME_BOOLEAN, + TYPE_NAME_DOCUMENT_ANNOTATION, TYPE_NAME_INTEGER, TYPE_NAME_SOFA, TYPE_NAME_STRING, @@ -17,7 +18,6 @@ TYPE_NAME_TOP, TypeCheckError, is_predefined, - TYPE_NAME_DOCUMENT_ANNOTATION, ) from tests.fixtures import * from tests.util import assert_xml_equal @@ -315,7 +315,6 @@ def test_type_inherits_from_annotation(): ], ) def test_is_predefined(type_name: str, expected: bool): - assert is_predefined(type_name) == expected @@ -498,7 +497,7 @@ def test_is_primitive_collection(type_name: str, expected: bool): ("uima.cas.DoubleArray", True), ], ) -def test_is_primitive_collection(type_name: str, expected: bool): +def test_is_primitive_array(type_name: str, expected: bool): typesystem = TypeSystem() assert typesystem.is_primitive_array(type_name) == expected @@ -883,9 +882,9 @@ def test_that_merging_types_creates_self_contained_type_system(): def test_that_dkpro_core_typeystem_can_be_loaded(): ts = load_dkpro_core_typesystem() - POS = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS") - NamedEntity = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity") - CoreferenceLink = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.coref.type.CoreferenceLink") + assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS") is not None + assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity") is not None + assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.coref.type.CoreferenceLink") is not None # Type checking diff --git a/tests/test_util.py b/tests/test_util.py index 8a2fbd0..3a4a54b 100644 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -1,5 +1,3 @@ -from pathlib import Path - from cassis.typesystem import TYPE_NAME_ANNOTATION, TYPE_NAME_FS_ARRAY from tests.fixtures import * from tests.test_files.test_cas_generators import MultiFeatureRandomCasGenerator, MultiTypeRandomCasGenerator diff --git a/tests/test_xmi.py b/tests/test_xmi.py index f6bb02b..aaf0d9b 100644 --- a/tests/test_xmi.py +++ b/tests/test_xmi.py @@ -65,7 +65,7 @@ def test_deserializing_from_string(small_typesystem_xml): - + """ load_cas_from_xmi(cas_xmi, typesystem=typesystem) @@ -102,7 +102,7 @@ def test_views_are_parsed(small_xmi, small_typesystem_xml): - + """ cas = load_cas_from_xmi(cas_xmi, typesystem=typesystem) @@ -302,11 +302,11 @@ def test_offsets_are_recomputed_when_sofa_string_changes(cas_with_smileys_xmi, d def test_offsets_work_for_empty_sofastring(): xmi = """ - - - - + + + + """ @@ -316,14 +316,15 @@ def test_offsets_work_for_empty_sofastring(): def test_that_invalid_offsets_remain_unmapped_on_import(): xmi = """ - - - - - + + + + + - """ + + """ # assert no exception with warnings.catch_warnings(record=True) as ws: @@ -361,14 +362,14 @@ def test_leniency_type_not_in_typesystem_lenient(cas_with_leniency_xmi, small_ty typesystem = load_typesystem(small_typesystem_xml) with pytest.warns(UserWarning): - cas = load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=True) + load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=True) def test_leniency_type_not_in_typesystem_not_lenient(cas_with_leniency_xmi, small_typesystem_xml): typesystem = load_typesystem(small_typesystem_xml) with pytest.raises(TypeNotFoundError): - cas = load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=False) + load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=False) def test_multiple_references_allowed_true(): From 804540d6cad7caedd8608c1ca8ba17739bfe8a76 Mon Sep 17 00:00:00 2001 From: Richard Eckart de Castilho Date: Sat, 4 May 2024 21:12:40 +0200 Subject: [PATCH 2/2] #314 - Switch to poetry - Use ruff - Address linter issues in json.py --- .github/workflows/run_tests.yml | 2 +- .readthedocs.yml | 13 +- Makefile | 11 +- cassis/json.py | 11 +- poetry.lock | 765 ++++++++++++++++++-------------- pyproject.toml | 25 +- 6 files changed, 461 insertions(+), 366 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 59bdb45..a78e7e3 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] + python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - uses: actions/checkout@v4 diff --git a/.readthedocs.yml b/.readthedocs.yml index 8fd7006..e1743e7 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -4,13 +4,10 @@ build: os: ubuntu-22.04 tools: python: "3.11" - + jobs: + post_create_environment: + - python -m pip install poetry + post_install: + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --only main,docs sphinx: configuration: docs/conf.py - -python: - install: - - method: pip - path: . - extra_requirements: - - doc diff --git a/Makefile b/Makefile index 04d6bf0..0428116 100644 --- a/Makefile +++ b/Makefile @@ -16,22 +16,17 @@ coverage: # Static analysis/linting format: - black cassis/ - black tests/ - isort --profile black $(PYTHON_FILES) --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=120 + poetry run ruff format $(PYTHON_FILES) lint: # stop the build if there are Python syntax errors or undefined names - poetry run flake8 --select=E9,F63,F7,F82 --show-source $(PYTHON_FILES) + poetry run ruff check --select=E9,F63,F7,F82 --output-format=full $(PYTHON_FILES) # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - poetry run flake8 --exit-zero $(PYTHON_FILES) + poetry run ruff check --exit-zero $(PYTHON_FILES) # Docs docs: - poetry run mkdocs serve - -html: cd docs && make html # Building and publishing diff --git a/cassis/json.py b/cassis/json.py index 23cb42e..b3ce2d2 100644 --- a/cassis/json.py +++ b/cassis/json.py @@ -1,12 +1,19 @@ import base64 import json import math -from collections import OrderedDict +from collections import OrderedDict, defaultdict from io import TextIOBase, TextIOWrapper from math import isnan +from typing import Union, IO, Optional, Dict, List +from toposort import toposort_flatten from cassis.cas import NAME_DEFAULT_SOFA, Cas, IdGenerator, Sofa, View -from cassis.typesystem import * +from cassis.typesystem import TYPE_NAME_ANNOTATION, TypeSystem, is_predefined, merge_typesystems, TYPE_NAME_SOFA, \ + FEATURE_BASE_NAME_SOFAARRAY, array_type_name_for_type, FEATURE_BASE_NAME_SOFASTRING, FEATURE_BASE_NAME_SOFAID, \ + FEATURE_BASE_NAME_SOFAMIME, FEATURE_BASE_NAME_SOFANUM, FEATURE_BASE_NAME_SOFAURI, TYPE_NAME_FS_ARRAY, \ + TYPE_NAME_BYTE_ARRAY, TYPE_NAME_FLOAT_ARRAY, TYPE_NAME_DOUBLE_ARRAY, TypeSystemMode, TYPE_NAME_DOCUMENT_ANNOTATION, \ + Type, Feature, TYPE_NAME_TOP, is_primitive_array, TYPE_NAME_FLOAT, TYPE_NAME_DOUBLE, \ + element_type_name_for_array_type, is_primitive, is_array RESERVED_FIELD_PREFIX = "%" REF_FEATURE_PREFIX = "@" diff --git a/poetry.lock b/poetry.lock index 71295b5..5225f3e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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