From 981969cda43c612e9b7fd4f1e465531892de39c7 Mon Sep 17 00:00:00 2001 From: Sebastian Tramp Date: Thu, 1 Feb 2024 14:49:54 +0100 Subject: [PATCH 1/4] update template to v6.0.1 --- .copier-answers.yml | 4 +- .flake8 | 4 - .github/workflows/check.yml | 17 +- .github/workflows/publish.yml | 2 +- .gitlab-ci.yml | 32 +- .pre-commit-config.yaml | 46 +- .python-version | 1 + README.md | 2 +- Taskfile.yaml | 135 +-- cmem_plugin_databus/__init__.py | 1 + poetry.lock | 1468 +++++++++++-------------------- pyproject.toml | 67 +- tests/__init__.py | 1 + tests/test_databus.py | 34 - tests/utils.py | 10 +- 15 files changed, 697 insertions(+), 1127 deletions(-) delete mode 100644 .flake8 create mode 100644 .python-version delete mode 100644 tests/test_databus.py diff --git a/.copier-answers.yml b/.copier-answers.yml index 0028412..4f7cce3 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,10 +1,10 @@ # Changes here will be overwritten by Copier -_commit: v5.0.2 +_commit: v6.0.1 _src_path: gh:eccenca/cmem-plugin-template author_mail: streitmatter@informatik.uni-leipzig.de author_name: Denis Streitmatter github_page: https://github.com/dbpedia/cmem-plugin-databus project_description: Load and publish datasets from a DBpedia databus service. project_slug: databus -pypi: false +pypi: true diff --git a/.flake8 b/.flake8 deleted file mode 100644 index ffd12bc..0000000 --- a/.flake8 +++ /dev/null @@ -1,4 +0,0 @@ -# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8 -[flake8] -max-line-length = 88 -extend-ignore = E203 diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index f510917..d5bd94d 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -16,10 +16,11 @@ jobs: check: runs-on: ubuntu-latest + concurrency: testing_environment steps: - name: Check out repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Task uses: arduino/setup-task@v1 @@ -41,21 +42,13 @@ jobs: run: | poetry self add "poetry-dynamic-versioning[plugin]" - - name: bandit - run: | - task check:bandit - - - name: flake8 - run: | - task check:flake8 - - name: mypy run: | task check:mypy - - name: pylint + - name: ruff run: | - task check:pylint + task check:ruff - name: pytest env: @@ -69,7 +62,7 @@ jobs: task check:safety - name: Publish Test Report in Action - uses: mikepenz/action-junit-report@v3 + uses: mikepenz/action-junit-report@v4 if: always() # always run even if the previous step fails with: report_paths: dist/junit-*.xml diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index f873e83..664ec5e 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -17,7 +17,7 @@ jobs: steps: - name: Check out repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Task uses: arduino/setup-task@v1 diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index cde0edb..13f67e9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -19,25 +19,15 @@ stages: - build - publish -bandit: +ruff: stage: test script: - - task check:bandit + - task check:ruff artifacts: when: always reports: junit: - - dist/junit-bandit.xml - -flake8: - stage: test - script: - - task check:flake8 - artifacts: - when: always - reports: - junit: - - dist/junit-flake8.xml + - dist/junit-ruff.xml mypy: stage: test @@ -49,16 +39,6 @@ mypy: junit: - dist/junit-mypy.xml -pylint: - stage: test - script: - - task check:pylint - artifacts: - when: always - reports: - junit: - - dist/junit-pylint.xml - pytest: stage: test coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/' @@ -70,6 +50,8 @@ pytest: coverage_report: coverage_format: cobertura path: dist/coverage.xml + junit: + - dist/junit-pytest.xml paths: - dist/badge-coverage.svg - dist/badge-tests.svg @@ -84,7 +66,6 @@ safety: build: stage: build needs: - - bandit - mypy - pytest - safety @@ -100,8 +81,7 @@ pypi: # publishing only available on a tag stage: publish needs: - - flake8 - - pylint + - ruff - build allow_failure: true when: manual diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ee847d7..d117733 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,17 +2,37 @@ repos: - repo: local hooks: - - id: pylint - name: pylint - entry: poetry run pylint - exclude: '^tests/.*$' - language: system - types: [python] - - repo: local - hooks: - - id: forbidden-files - name: forbidden files - entry: found copier update rejection files; review them and remove them - language: fail - files: "\\.rej$" + + - id: ruff + name: check:ruff + entry: task check:ruff + language: python + types_or: [python, pyi] + pass_filenames: false + + - id: poetry-check + name: poetry-check + description: run poetry check to validate config + entry: poetry check + language: python + pass_filenames: false + files: ^(.*/)?pyproject\.toml$ + + - id: poetry-lock + name: poetry-lock + description: run poetry lock to update lock file + entry: poetry lock + language: python + pass_filenames: false + files: ^(.*/)?(poetry\.lock|pyproject\.toml)$ + + - id: poetry-install + name: poetry-install + description: > + run poetry install to install dependencies from the lock file + entry: poetry install + language: python + pass_filenames: false + stages: [post-checkout, post-merge] + always_run: true diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/README.md b/README.md index 4a1f973..d93235e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ Load and publish datasets from a DBpedia databus service. -[![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/dbpedia/cmem-plugin-databus/actions/workflows/check.yml/badge.svg)](https://github.com/dbpedia/cmem-plugin-databus/actions) +[![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/dbpedia/cmem-plugin-databus/actions/workflows/check.yml/badge.svg)](https://github.com/dbpedia/cmem-plugin-databus/actions) [![pypi version](https://img.shields.io/pypi/v/cmem-plugin-databus)](https://pypi.org/project/databus) [![license](https://img.shields.io/pypi/l/cmem-plugin-databus)](https://pypi.org/project/cmem-plugin-databus) ## Development diff --git a/Taskfile.yaml b/Taskfile.yaml index 66d13e7..5578f6a 100644 --- a/Taskfile.yaml +++ b/Taskfile.yaml @@ -12,8 +12,6 @@ dotenv: ['.copier-answers.env', '.env'] vars: PACKAGE: cmem_plugin_$project_slug DIST_DIR: dist - PWD: - sh: pwd includes: custom: @@ -24,21 +22,25 @@ tasks: default: summary: | - Just a list of documented tasks. + Just a list of documented tasks silent: true cmds: - task --list # {{{ preparation tasks check:prepare: + internal: true summary: | prepare check targets by creating appropriate directory run: once cmds: - mkdir -p {{.DIST_DIR}}/coverage - poetry:install: - desc: Install dependencies managed by Poetry. + poetry:check: + internal: true + platforms: [darwin, linux] + summary: | + Check poetry versioning plugin. Currently not under Windows run: once preconditions: - sh: '[[ {{.PDV_VERSION}} > {{.PDV_VERSION_MIN}} ]]' @@ -48,9 +50,6 @@ tasks: You can install it with the following command: poetry self add "poetry-dynamic-versioning[plugin]" - cmds: - - poetry check - - poetry install vars: PDV_VERSION_MIN: 0.20 PDV_VERSION: @@ -58,23 +57,28 @@ tasks: poetry self show --addons poetry-dynamic-versioning --tree | head -1 | cut -d " " -f 2 | cut -d "." -f 1-2 - python:format: - desc: Format Python files. - <<: *preparation + poetry:install: + internal: true + desc: Install dependencies managed by Poetry + run: once + deps: + - poetry:check cmds: - - poetry run black . + - poetry install - poetry:update: - desc: Update dependencies managed by Poetry to their newest versions. - run: once + format:fix: + desc: Format Python files and fix obvious issues + <<: *preparation cmds: - - poetry update + - poetry run ruff format tests {{.PACKAGE}} + - poetry run ruff check tests {{.PACKAGE}} --fix-only - poetry:shell: - desc: Open a poetry shell. - interactive: true + format:fix-unsafe: + desc: Format Python files and fix 'unsafe' issues + <<: *preparation cmds: - - poetry shell + - poetry run ruff format tests {{.PACKAGE}} + - poetry run ruff check tests {{.PACKAGE}} --fix-only --unsafe-fixes clean: desc: Removes dist, *.pyc and some caches @@ -86,22 +90,40 @@ tasks: # {{{ check tasks check: - desc: Run whole test suite. - deps: - - check:bandit - - check:flake8 - - check:mypy - - check:pylint - - check:pytest - - check:safety + desc: Run whole test suite incl. unit and integration tests + cmds: + - task: check:linters + - task: check:pytest + + check:linters: + desc: Run all linter and static code analysis tests + cmds: + - task: check:ruff + - task: check:mypy + - task: check:safety check:pytest: - desc: Run pytest suite. + desc: Run unit and integration tests + platforms: [darwin, linux, windows] <<: *preparation cmds: - - poetry run pytest --memray --junitxml={{.JUNIT_FILE}} --cov-report term --cov-report xml:{{.COVERAGE_FILE}} --cov-report html:{{.COVERAGE_DIR}} --cov={{.PACKAGE}} - - poetry run genbadge coverage -l -i {{.COVERAGE_FILE}} -o {{.BADGE_COVERAGE}} - - poetry run genbadge tests -l -i {{.JUNIT_FILE}} -o {{.BADGE_TESTS}} + # --memray is not used on windows + - platforms: [windows] + cmd: > + poetry run pytest --junitxml={{.JUNIT_FILE}} + --cov-report term --cov-report xml:{{.COVERAGE_FILE}} + --cov-report html:{{.COVERAGE_DIR}} --cov={{.PACKAGE}} + - platforms: [darwin, linux] + cmd: > + poetry run pytest --memray --junitxml={{.JUNIT_FILE}} + --cov-report term --cov-report xml:{{.COVERAGE_FILE}} + --cov-report html:{{.COVERAGE_DIR}} --cov={{.PACKAGE}} + - cmd: > + poetry run genbadge coverage -l + -i {{.COVERAGE_FILE}} -o {{.BADGE_COVERAGE}} + - cmd: > + poetry run genbadge tests -l + -i {{.JUNIT_FILE}} -o {{.BADGE_TESTS}} vars: JUNIT_FILE: ./{{.DIST_DIR}}/junit-pytest.xml COVERAGE_FILE: ./{{.DIST_DIR}}/coverage.xml @@ -109,19 +131,8 @@ tasks: BADGE_COVERAGE: ./{{.DIST_DIR}}/badge-coverage.svg BADGE_TESTS: ./{{.DIST_DIR}}/badge-tests.svg - check:pylint: - desc: Check source code with pylint. - <<: *preparation - cmds: - - poetry run pylint --exit-zero {{.PACKAGE}} - - poetry run pylint {{.PACKAGE}} {{.XML_PARAMS}} - vars: - FORMAT: --output-format=pylint_junit.JUnitReporter - JUNIT_FILE: ./{{.DIST_DIR}}/junit-pylint.xml - XML_PARAMS: --output={{.JUNIT_FILE}} {{.FORMAT}} - check:mypy: - desc: Check source code with mypy. + desc: Complain about typing errors <<: *preparation cmds: - poetry run mypy -p tests -p {{.PACKAGE}} --junit-xml {{.JUNIT_FILE}} @@ -129,33 +140,23 @@ tasks: JUNIT_FILE: ./{{.DIST_DIR}}/junit-mypy.xml check:safety: - desc: Check source code with safety. + desc: Complain about vulnerabilities in dependencies <<: *preparation cmds: - # ignore 48547 rdflib - json-ld not in use # ignore 51358 safety - dev dependency only - # ignore 52322 gitpython - dev dependency only - # ignore 51457 py - dev dependency only - - poetry run safety check -i 48547 -i 51358 -i 52322 -i 51457 + # ignore 61489 pillow - dev dependency only + - poetry run safety check -i 51358 -i 61489 - check:bandit: - desc: Check source code with bandit. + check:ruff: + desc: Complain about everything else <<: *preparation cmds: - - poetry run bandit --exit-zero -r {{.PACKAGE}} - - poetry run bandit --format xml -r {{.PACKAGE}} -o {{.JUNIT_FILE}} + - poetry run ruff check --show-source tests {{.PACKAGE}} + - poetry run ruff check --exit-zero tests {{.PACKAGE}} {{.XML_PARAMS}} + - poetry run ruff format --check tests {{.PACKAGE}} vars: - JUNIT_FILE: ./{{.DIST_DIR}}/junit-bandit.xml - - check:flake8: - desc: Check source code with flake8. - <<: *preparation - cmds: - - poetry run flake8 --exit-zero tests {{.PACKAGE}} {{.XML_PARAMS}} - - poetry run flake8 --show-source tests {{.PACKAGE}} - vars: - JUNIT_FILE: ./{{.DIST_DIR}}/junit-flake8.xml - XML_PARAMS: --format junit-xml --output-file {{.JUNIT_FILE}} + JUNIT_FILE: ./{{.DIST_DIR}}/junit-ruff.xml + XML_PARAMS: --output-format junit --output-file {{.JUNIT_FILE}} # }}} # {{{ build and deploy tasks @@ -163,15 +164,17 @@ tasks: deploy: desc: Install plugin package in Corporate Memory deps: - - clean - build cmds: - cmemc admin workspace python install dist/*.tar.gz - cmemc admin workspace python list-plugins build: - desc: Build tarball and a wheel package. + desc: Build a tarball and a wheel package <<: *preparation + deps: + - clean + - poetry:check cmds: - poetry build diff --git a/cmem_plugin_databus/__init__.py b/cmem_plugin_databus/__init__.py index e69de29..b92b52a 100644 --- a/cmem_plugin_databus/__init__.py +++ b/cmem_plugin_databus/__init__.py @@ -0,0 +1 @@ +"""databus - main package""" diff --git a/poetry.lock b/poetry.lock index 8126b97..ef1fdd5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,180 +1,113 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. - -[[package]] -name = "astroid" -version = "2.15.6" -description = "An abstract syntax tree for Python with inference support." -optional = false -python-versions = ">=3.7.2" -files = [ - {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"}, - 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-[tool.pylint.MASTER] -load-plugins="pylint_junit" - -[tool.pylint.General] -ignore = "version.py" - -[tool.pylint.'MESSAGES CONTROL'] -extension-pkg-whitelist = "pydantic" -disable = "fixme" - -# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#pylint -[tool.pylint.messages_control] -disable = "R0903" - -[tool.pylint.format] -max-line-length = "88" +bump = true [tool.mypy] warn_return_any = true @@ -73,3 +55,30 @@ ignore_missing_imports = true [tool.pytest.ini_options] addopts = "" +[tool.ruff] +line-length = 100 +target-version = "py311" + +[tool.ruff.format] +line-ending = "lf" # Use `\n` line endings for all files + +[tool.ruff.lint] +select = ["ALL"] +ignore = [ + "ANN101", # Missing type annotation for self in method + "ANN204", # Missing return type annotation for special method `__init__` + "COM812", # missing-trailing-comma + "D107", # Missing docstring in __init__ + "D203", # [*] 1 blank line required before class docstring + "D211", # No blank lines allowed before class docstring + "D213", # Multi-line docstring summary should start at the second line + "D400", # First line should end with a period + "D415", # First line should end with a period, question mark, or exclamation point + "EM", # Exception texts - https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + "G004", # Logging statement uses f-string + "ISC001", # single-line-implicit-string-concatenation + "PD", # opinionated linting for pandas code + "S101", # use of assert detected + "TRY003", # Avoid specifying long messages outside the exception class +] + diff --git a/tests/__init__.py b/tests/__init__.py index e69de29..30ea453 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""tests""" diff --git a/tests/test_databus.py b/tests/test_databus.py deleted file mode 100644 index 2ea9cdb..0000000 --- a/tests/test_databus.py +++ /dev/null @@ -1,34 +0,0 @@ -"""Plugin tests.""" -import pytest -from cmem_plugin_databus.utils import DatabusFileAutocomplete - -# def test_plugin(): -# plugin = SimpleDatabusLoadingPlugin( -# "https://d8lr.tools.dbpedia.org/jlareck/migration/stw-thesaurus-for-economics_2/1.0.10-alpha/stw-thesaurus-for-economics_2.ttl" -# ) -# -# plugin.execute() - - -@pytest.mark.skip(reason="need to rewrite") -def test_fetch_results(): - len_mappings = { - "https://d8lr.tools.dbpedia.org": 2, - "https://d8lr.tools.dbpedia.org/jlareck/": 3, - "https://d8lr.tools.dbpedia.org/jlareck/migration/": 4, - "https://d8lr.tools.dbpedia.org/jlareck/migration/omwn-cow_1/": 5, - "https://d8lr.tools.dbpedia.org/jlareck/migration/omwn-cow_1/1.0.10-alpha/": 6, - } - - def assert_correct_result_sizes(databus_uri: str, expected_size: int) -> None: - results = DatabusFileAutocomplete.fetch_results_by_uri(databus_uri) - assert len(results) > 0 - for result in results: - assert len(result.replace("https://", "").split("/")) == expected_size - - for uri, expected_path_size in len_mappings.items(): - assert_correct_result_sizes(uri, expected_path_size) - - -def test_dummy(): - assert 1 == 1 diff --git a/tests/utils.py b/tests/utils.py index 22e7a0d..962c553 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -1,5 +1,6 @@ """Testing utilities.""" import os +from typing import ClassVar import pytest @@ -7,11 +8,11 @@ from cmem.cmempy.api import get_token from cmem.cmempy.config import get_oauth_default_credentials from cmem_plugin_base.dataintegration.context import ( - PluginContext, - UserContext, - TaskContext, ExecutionContext, + PluginContext, ReportContext, + TaskContext, + UserContext, ) needs_cmem = pytest.mark.skipif( @@ -23,7 +24,7 @@ class TestUserContext(UserContext): """dummy user context that can be used in tests""" __test__ = False - default_credential: dict = {} + default_credential: ClassVar[dict] = {} def __init__(self): # get access token from default service account @@ -67,3 +68,4 @@ def __init__(self, project_id: str = "dummyProject", task_id: str = "dummyTask") self.report = ReportContext() self.task = TestTaskContext(project_id=project_id, task_id=task_id) self.user = TestUserContext() + From 70c2031b04ceedf90aa0db52d123306658a5b463 Mon Sep 17 00:00:00 2001 From: Sebastian Tramp Date: Fri, 2 Feb 2024 09:25:52 +0100 Subject: [PATCH 2/4] 50% ruff issues fixed --- .idea/cmem-plugin-databus.iml | 7 +- cmem_plugin_databus/cmem_wrappers.py | 22 ++- cmem_plugin_databus/loader.py | 197 +++++++++--------- cmem_plugin_databus/publisher.py | 81 ++++---- cmem_plugin_databus/utils.py | 85 ++++---- tests/test_loader.py | 285 ++++++++++++++------------- tests/utils.py | 1 - 7 files changed, 335 insertions(+), 343 deletions(-) diff --git a/.idea/cmem-plugin-databus.iml b/.idea/cmem-plugin-databus.iml index 90b3b86..5a0d7bc 100644 --- a/.idea/cmem-plugin-databus.iml +++ b/.idea/cmem-plugin-databus.iml @@ -4,16 +4,15 @@ - - + -