diff --git a/.coveragerc b/.coveragerc deleted file mode 100644 index 93f7360d..00000000 --- a/.coveragerc +++ /dev/null @@ -1,28 +0,0 @@ -# .coveragerc to control coverage.py -[run] -branch = True -source = osw -# omit = bad_file.py - -[paths] -source = - src/ - */site-packages/ - -[report] -# Regexes for lines to exclude from consideration -exclude_lines = - # Have to re-enable the standard pragma - pragma: no cover - - # Don't complain about missing debug-only code: - def __repr__ - if self\.debug - - # Don't complain if tests don't hit defensive assertion code: - raise AssertionError - raise NotImplementedError - - # Don't complain if non-runnable code isn't run: - if 0: - if __name__ == .__main__.: diff --git a/.github/actions/setup-python-env/action.yml b/.github/actions/setup-python-env/action.yml new file mode 100644 index 00000000..e757f26f --- /dev/null +++ b/.github/actions/setup-python-env/action.yml @@ -0,0 +1,30 @@ +name: "Setup Python Environment" +description: "Set up Python and uv, then install the locked dependencies" + +inputs: + python-version: + description: "Python version to use" + required: true + default: "3.12" + uv-version: + description: "uv version to use" + required: true + default: "0.9.9" + +runs: + using: "composite" + steps: + - uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python-version }} + + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + version: ${{ inputs.uv-version }} + enable-cache: true + cache-suffix: ${{ matrix.python-version }} + + - name: Install Python dependencies + run: uv sync --frozen + shell: bash diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 33b4bfaf..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,120 +0,0 @@ -# GitHub Actions configuration **EXAMPLE**, -# MODIFY IT ACCORDING TO YOUR NEEDS! -# Reference: https://docs.github.com/en/actions - -name: tests - -on: - push: - # Avoid using all the resources/limits available by checking only - # relevant branches and tags. Other branches can be checked via PRs. - branches: [main] - tags: ['v[0-9]*', '[0-9]+.[0-9]+*'] # Match tags that resemble a version - pull_request: # Run in every PR - workflow_dispatch: # Allow manually triggering the workflow - schedule: - # Run roughly every 15 days at 00:00 UTC - # (useful to check if updates on dependencies break the package) - - cron: '0 0 1,16 * *' - -concurrency: - group: >- - ${{ github.workflow }}-${{ github.ref_type }}- - ${{ github.event.pull_request.number || github.sha }} - cancel-in-progress: true - -jobs: - prepare: - runs-on: ubuntu-latest - outputs: - wheel-distribution: ${{ steps.wheel-distribution.outputs.path }} - steps: - - uses: actions/checkout@v4 - with: {fetch-depth: 0} # deep clone for setuptools-scm - - uses: actions/setup-python@v5 - with: {python-version: "3.12"} - - name: Run static analysis and format checkers - run: pipx run pre-commit run --all-files --show-diff-on-failure - - name: Build package distribution files - run: pipx run tox -e clean,build - - name: Record the path of wheel distribution - id: wheel-distribution - run: echo "::set-output name=path::$(ls dist/*.whl)" - - name: Store the distribution files for use in other stages - # `tests` and `publish` will use the same pre-built distributions, - # so we make sure to release the exact same package that was tested - uses: actions/upload-artifact@v4 - with: - name: python-distribution-files - path: dist/ - retention-days: 1 - - test: - needs: prepare - strategy: - matrix: - python: - - "3.10" # oldest Python supported by PSF - - "3.13" # newest Python that is stable - platform: - - ubuntu-latest - - macos-latest - - windows-latest - runs-on: ${{ matrix.platform }} - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - id: setup-python - with: - python-version: ${{ matrix.python }} - - name: Retrieve pre-built distribution files - uses: actions/download-artifact@v4 - with: {name: python-distribution-files, path: dist/} - - name: Run tests - run: >- - pipx run --python '${{ steps.setup-python.outputs.python-path }}' - tox -e test --installpkg '${{ needs.prepare.outputs.wheel-distribution }}' - -- -rFEx --durations 10 --color yes - --wiki_domain "${{ secrets.INTEGR_TEST_WIKI_DOMAIN }}" - --wiki_username "${{ secrets.INTEGR_TEST_WIKI_USERNAME }}" - --wiki_password "${{ secrets.INTEGR_TEST_WIKI_PASSWORD }}" - - name: Generate coverage report - run: pipx run coverage lcov -o coverage.lcov - - name: Upload partial coverage report - uses: coverallsapp/github-action@master - with: - path-to-lcov: coverage.lcov - github-token: ${{ secrets.github_token }} - flag-name: ${{ matrix.platform }} - py${{ matrix.python }} - parallel: true - - finalize: - needs: test - runs-on: ubuntu-latest - steps: - - name: Finalize coverage report - uses: coverallsapp/github-action@master - with: - github-token: ${{ secrets.GITHUB_TOKEN }} - parallel-finished: true - - publish: - needs: finalize - if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }} - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: {python-version: "3.12"} - - name: Retrieve pre-built distribution files - uses: actions/download-artifact@v4 - with: {name: python-distribution-files, path: dist/} - - name: Publish Package - env: - # TODO: Set your PYPI_TOKEN as a secret using GitHub UI - # - https://pypi.org/help/#apitoken - # - https://docs.github.com/en/actions/security-guides/encrypted-secrets - TWINE_REPOSITORY: pypi - TWINE_USERNAME: __token__ - TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} - run: pipx run tox -e publish diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4ac5bfce..6a02351d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,31 +1,41 @@ -# This is a basic workflow to help you get started with Actions +# Deploys the documentation with mike (versioned docs on the gh-pages +# branch; repo setting: Pages source = "Deploy from a branch: gh-pages"). +# +# push to main -> version "dev" +# tag vX.Y.Z -> version "X.Y.Z" + "latest" alias (on-release-main.yml) name: Docs -# Controls when the workflow will run on: - # Triggers the workflow on push or pull request events but only for the master branch push: - branches: [ main ] - - # Allows you to run this workflow manually from the Actions tab + branches: [main] workflow_dispatch: -# A workflow run is made up of one or more jobs that can run sequentially or in parallel +permissions: + # mike commits the built site to the gh-pages branch + contents: write + +concurrency: + group: pages + cancel-in-progress: false + jobs: - # This workflow contains a single job called "build" - build: - # The type of runner that the job will run on + deploy-docs: runs-on: ubuntu-latest - - # Steps represent a sequence of tasks that will be executed as part of the job steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - name: Check out + uses: actions/checkout@v4 with: + # deep clone incl. tags: hatch-vcs needs them and mike needs gh-pages fetch-depth: 0 - - uses: actions/setup-python@v2 - - run: pip install --upgrade pip && pip install mkdocs mkdocs-gen-files "mkdocstrings[python]" mkdocs-material - - run: git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com' - - name: Publish docs - run: mkdocs gh-deploy + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Configure git identity + run: | + git config user.name 'github-actions[bot]' + git config user.email 'github-actions[bot]@users.noreply.github.com' + + - name: Deploy dev documentation + run: uv run mike deploy --push dev diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml new file mode 100644 index 00000000..3f643845 --- /dev/null +++ b/.github/workflows/integration.yml @@ -0,0 +1,35 @@ +# Integration tests against a live test wiki. Credentials come from the +# INTEGR_TEST_* secrets; where they are unavailable (e.g. forks), the +# credential fixtures make the tests skip instead of fail. + +name: Integration + +on: + push: + branches: [main] + workflow_dispatch: + +concurrency: + # runs mutate the shared test wiki, so never run two in parallel + group: integration + cancel-in-progress: false + +jobs: + integration-tests: + runs-on: ubuntu-latest + steps: + - name: Check out + uses: actions/checkout@v4 + with: + # deep clone incl. tags so hatch-vcs can derive the version + fetch-depth: 0 + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Run integration tests + env: + WIKI_DOMAIN: ${{ secrets.INTEGR_TEST_WIKI_DOMAIN }} + WIKI_USERNAME: ${{ secrets.INTEGR_TEST_WIKI_USERNAME }} + WIKI_PASSWORD: ${{ secrets.INTEGR_TEST_WIKI_PASSWORD }} + run: make test-integration diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..bda7a907 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,96 @@ +name: Main + +on: + push: + branches: [main] + pull_request: + types: [opened, synchronize, reopened, ready_for_review] + workflow_dispatch: + +concurrency: + group: >- + ${{ github.workflow }}-${{ github.ref_type }}- + ${{ github.event.pull_request.number || github.sha }} + cancel-in-progress: true + +jobs: + quality: + runs-on: ubuntu-latest + steps: + - name: Check out + uses: actions/checkout@v4 + with: + # deep clone incl. tags so hatch-vcs can derive the version + fetch-depth: 0 + + - uses: actions/cache@v4 + with: + path: ~/.cache/pre-commit + key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Run checks + run: make check + + tests-and-type-check: + runs-on: ${{ matrix.os }} + strategy: + matrix: + # full python range on ubuntu; boundary versions cross-platform + # (preserves the coverage of the previous CI matrix) + os: [ubuntu-latest] + python-version: ["3.10", "3.11", "3.12", "3.13"] + include: + - os: macos-latest + python-version: "3.10" + - os: macos-latest + python-version: "3.13" + - os: windows-latest + python-version: "3.10" + - os: windows-latest + python-version: "3.13" + fail-fast: false + defaults: + run: + shell: bash + steps: + - name: Check out + uses: actions/checkout@v4 + with: + # deep clone incl. tags so hatch-vcs can derive the version + fetch-depth: 0 + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + with: + python-version: ${{ matrix.python-version }} + + # no `make` on the windows runners, so invoke the tools directly + - name: Run tests + run: uv run python -m pytest --cov --cov-config=pyproject.toml --cov-report=xml + + - name: Check typing + run: uv run ty check + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v4 + if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' }} + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + + check-docs: + runs-on: ubuntu-latest + steps: + - name: Check out + uses: actions/checkout@v4 + with: + # deep clone incl. tags so hatch-vcs can derive the version + fetch-depth: 0 + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Check if documentation can be built + run: uv run zensical build -s diff --git a/.github/workflows/on-release-main.yml b/.github/workflows/on-release-main.yml new file mode 100644 index 00000000..90794f20 --- /dev/null +++ b/.github/workflows/on-release-main.yml @@ -0,0 +1,116 @@ +# Automated release: python-semantic-release analyzes the conventional +# commits on main, and when a release is due it updates CHANGELOG.md, +# commits, tags vX.Y.Z, pushes and creates the GitHub release. hatch-vcs +# derives the package version from that tag, so no version file is bumped. +# Publishing happens in this same run: pushes made with GITHUB_TOKEN do +# not retrigger workflows, so a tag-triggered publish would never fire. +# +# Filename and environment name are load-bearing: the PyPI trusted +# publisher (OIDC) references workflow "on-release-main.yml" and +# environment "pypi". + +name: release-main + +on: + push: + branches: [main] + workflow_dispatch: + +# One release run at a time: python-semantic-release pushes commits/tags +# to main, so overlapping runs would race each other. +concurrency: + group: release + cancel-in-progress: false + +jobs: + release: + runs-on: ubuntu-latest + environment: + name: pypi + permissions: + # required for PyPI trusted publishing (OIDC) + id-token: write + # push the release commit/tag and create the GitHub release (PSR) + contents: write + outputs: + released: ${{ steps.psr.outputs.released }} + version: ${{ steps.psr.outputs.version }} + steps: + - name: Check out + uses: actions/checkout@v4 + with: + # full history: PSR analyzes commits, hatch-vcs needs the tags + fetch-depth: 0 + # latest main, not the triggering SHA: runs queued behind the + # concurrency group must include release commits pushed by the + # previous run, or their own push is rejected + ref: main + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Version, tag and changelog with python-semantic-release + id: psr + env: + GH_TOKEN: ${{ github.token }} + run: | + git config user.name "github-actions[bot]" + git config user.email "41898282+github-actions[bot]@users.noreply.github.com" + before=$(git rev-parse HEAD) + uv run semantic-release version + after=$(git rev-parse HEAD) + if [ "$before" != "$after" ]; then + ver=$(git tag --points-at HEAD | grep -E '^v[0-9]' | head -1) + echo "released=true" >> "$GITHUB_OUTPUT" + echo "version=${ver#v}" >> "$GITHUB_OUTPUT" + echo "released $ver" + else + echo "released=" >> "$GITHUB_OUTPUT" + echo "no release necessary" + fi + + - name: Build package distribution files + if: steps.psr.outputs.released != '' + run: uv build + + - name: Check package metadata + if: steps.psr.outputs.released != '' + run: uvx twine check dist/* + + - name: Publish package + if: steps.psr.outputs.released != '' + run: uv publish --trusted-publishing always + + deploy-docs: + needs: release + if: needs.release.outputs.released != '' + runs-on: ubuntu-latest + permissions: + # mike commits the built site to the gh-pages branch + contents: write + concurrency: + group: pages + cancel-in-progress: false + steps: + - uses: actions/checkout@v4 + with: + # deep clone incl. the release commit and tags pushed by PSR + fetch-depth: 0 + ref: main + + - name: Set up the environment + uses: ./.github/actions/setup-python-env + + - name: Configure git identity + run: | + git config user.name 'github-actions[bot]' + git config user.email '41898282+github-actions[bot]@users.noreply.github.com' + + - name: Deploy versioned documentation + env: + VERSION: ${{ needs.release.outputs.version }} + run: | + # --alias-type=copy keeps /latest/ a real directory instead of a + # redirect, so machine-readable files stay fetchable there + uv run mike deploy --push --alias-type=copy --update-aliases "$VERSION" latest + uv run mike set-default --push latest diff --git a/.github/workflows/validate-codecov-config.yml b/.github/workflows/validate-codecov-config.yml new file mode 100644 index 00000000..0a43f506 --- /dev/null +++ b/.github/workflows/validate-codecov-config.yml @@ -0,0 +1,15 @@ +name: validate-codecov-config + +on: + pull_request: + paths: [codecov.yaml] + push: + branches: [main] + +jobs: + validate-codecov-config: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Validate codecov configuration + run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate diff --git a/.gitignore b/.gitignore index 7040c331..33f6ebf9 100644 --- a/.gitignore +++ b/.gitignore @@ -42,9 +42,6 @@ coverage.xml build/* dist/* sdist/* -docs/api/* -docs/_rst/* -docs/_build/* cover/* MANIFEST site @@ -68,3 +65,5 @@ playground */osw_files/* */accounts.pwd.yaml +.ign +.claude diff --git a/.isort.cfg b/.isort.cfg deleted file mode 100644 index 90d20e39..00000000 --- a/.isort.cfg +++ /dev/null @@ -1,3 +0,0 @@ -[settings] -profile = black -known_first_party = osw diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 200f2342..c2b27953 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,55 +1,26 @@ -exclude: '^docs/conf.py' - minimum_pre_commit_version: 3.2.0 repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 - hooks: - - id: trailing-whitespace - - id: check-added-large-files - - id: check-ast - - id: check-json - - id: check-merge-conflict - - id: check-xml - - id: check-yaml - - id: debug-statements - - id: end-of-file-fixer - - id: requirements-txt-fixer - - id: mixed-line-ending - args: ['--fix=auto'] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows - -# If you want to avoid flake8 errors due to unused vars or imports: -- repo: https://github.com/myint/autoflake - rev: v2.3.1 - hooks: - - id: autoflake - args: [ - --in-place, - --remove-all-unused-imports, - --remove-unused-variables, - ] - -- repo: https://github.com/pycqa/isort - rev: 5.13.2 - hooks: - - id: isort - -- repo: https://github.com/psf/black - rev: 24.10.0 - hooks: - - id: black - language_version: python3 - -## If like to embrace black styles even in the docs: -# - repo: https://github.com/asottile/blacken-docs -# rev: v1.12.0 -# hooks: -# - id: blacken-docs -# additional_dependencies: [black] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 + hooks: + - id: trailing-whitespace + - id: check-added-large-files + - id: check-ast + - id: check-case-conflict + - id: check-json + - id: check-merge-conflict + - id: check-toml + - id: check-xml + - id: check-yaml + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + args: ['--fix=auto'] -- repo: https://github.com/PyCQA/flake8 - rev: 7.1.1 - hooks: - - id: flake8 - ## You can add flake8 plugins via `additional_dependencies`: - additional_dependencies: [flake8-bugbear] + # ruff replaces autoflake, isort, black and flake8(+bugbear) + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.7 + hooks: + - id: ruff-check + args: [--exit-non-zero-on-fix] + - id: ruff-format diff --git a/.readthedocs.yml b/.readthedocs.yml deleted file mode 100644 index 21b08145..00000000 --- a/.readthedocs.yml +++ /dev/null @@ -1,23 +0,0 @@ -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -# Required -version: 2 - -# Build documentation in the docs/ directory with Sphinx -sphinx: - configuration: docs/conf.py - -# Build documentation with MkDocs -#mkdocs: -# configuration: mkdocs.yml - -# Optionally build your docs in additional formats such as PDF -formats: - - pdf - -python: - version: 3.8 - install: - - requirements: docs/requirements.txt - - {path: ., method: pip} diff --git a/AUTHORS.md b/AUTHORS.md deleted file mode 100644 index 4cb1827e..00000000 --- a/AUTHORS.md +++ /dev/null @@ -1,6 +0,0 @@ -# Contributors - -* Simon Stier [simon.stier@isc.fraunhofer.de](mailto:simon.stier@isc.fraunhofer.de) -* Lukas Gold -* Andreas Räder -* Matthias Popp diff --git a/CHANGELOG.md b/CHANGELOG.md index d8dd1599..a6a9c6d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,23 +1,36 @@ # Changelog +> **Note:** From here on this file is generated by +> [python-semantic-release](https://python-semantic-release.readthedocs.io/) +> from the conventional commit history; do not edit release sections +> manually. Changes between v0.12.0 and the first generated entry are +> tracked in the +> [GitHub Releases](https://github.com/OpenSemanticLab/osw-python/releases). +> The historical entries at the bottom are preserved for reference. + + + ## Version v0.12.0 - - rework ontology import (BREAKING, see examples/ontology_import.py) - - add in-memory credentials in CredentialManager - - fix: 'value is not a valid enumeration member' errors - - improve namespace detection - - parallelize get_page + +- rework ontology import (BREAKING, see examples/ontology_import.py) +- add in-memory credentials in CredentialManager +- fix: 'value is not a valid enumeration member' errors +- improve namespace detection +- parallelize get_page ## Version v0.11.0 - - fix code generator for Statement - - parallelize page operations - - add legacy file page migration script - - refactor search function in wiki_tools - - add file info to utils - - refactor WtSite to work directly with CredentialManager + +- fix code generator for Statement +- parallelize page operations +- add legacy file page migration script +- refactor search function in wiki_tools +- add file info to utils +- refactor WtSite to work directly with CredentialManager ## Version v0.10.0 - - refactor PagePackage creation - - add requiredExtensions, requiredPackages + +- refactor PagePackage creation +- add requiredExtensions, requiredPackages ## Version v0.9.0 @@ -73,13 +86,11 @@ - add local slot edit feature - ## Version v0.2.0 - rename OSL to OSW - add page package feature - ## Version v0.1.0 - create package diff --git a/CITATION.cff b/CITATION.cff index f141a335..ef929aa1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,4 +7,7 @@ authors: - family-names: Gold given-names: Lukas orcid: https://orcid.org/0000-0001-7444-2969 + - family-names: Räder + given-names: Andreas + orcid: https://orcid.org/0000-0002-2673-0832 title: OpenSemanticWorld Python Package (osw-python) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c1d68b19..0ff9593c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,371 +1,42 @@ -```{todo} THIS IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS! - - The document assumes you are using a source repository service that promotes a - contribution model similar to [GitHub's fork and pull request workflow]. - While this is true for the majority of services (like GitHub, GitLab, - BitBucket), it might not be the case for private repositories (e.g., when - using Gerrit). - - Also notice that the code examples might refer to GitHub URLs or the text - might use GitHub specific terminology (e.g., *Pull Request* instead of *Merge - Request*). - - Please make sure to check the document having these assumptions in mind - and update things accordingly. -``` - -```{todo} Provide the correct links/replacements at the bottom of the document. -``` - -```{todo} You might want to have a look on [PyScaffold's contributor's guide], - - especially if your project is open source. The text should be very similar to - this template, but there are a few extra contents that you might decide to - also include, like mentioning labels of your issue tracker or automated - releases. -``` - # Contributing -Welcome to `osw` contributor's guide. - -This document focuses on getting any potential contributor familiarized with -the development processes, but [other kinds of contributions] are also appreciated. - -If you are new to using [git] or have never collaborated in a project previously, -please have a look at [contribution-guide.org]. Other resources are also -listed in the excellent [guide created by FreeCodeCamp] [^contrib1]. - -Please notice, all users and contributors are expected to be **open, -considerate, reasonable, and respectful**. When in doubt, -[Python Software Foundation's Code of Conduct] is a good reference in terms of -behavior guidelines. - -## Issue Reports - -If you experience bugs or general issues with `osw`, please have a look -on the [issue tracker]. -If you don't see anything useful there, please feel free to fire an issue report. - -:::{tip} -Please don't forget to include the closed issues in your search. -Sometimes a solution was already reported, and the problem is considered -**solved**. -::: - -New issue reports should include information about your programming environment -(e.g., operating system, Python version) and steps to reproduce the problem. -Please try also to simplify the reproduction steps to a very minimal example -that still illustrates the problem you are facing. By removing other factors, -you help us to identify the root cause of the issue. - -## Documentation Improvements - -You can help improve `osw` docs by making them more readable and coherent, or -by adding missing information and correcting mistakes. - -`osw` documentation uses [Sphinx] as its main documentation compiler. -This means that the docs are kept in the same repository as the project code, and -that any documentation update is done in the same way was a code contribution. - -```{todo} Don't forget to mention which markup language you are using. - - e.g., [reStructuredText] or [CommonMark] with [MyST] extensions. -``` - -```{todo} If your project is hosted on GitHub, you can also mention the following tip: - - :::{tip} - Please notice that the [GitHub web interface] provides a quick way of - propose changes in `osw`'s files. While this mechanism can - be tricky for normal code contributions, it works perfectly fine for - contributing to the docs, and can be quite handy. - - If you are interested in trying this method out, please navigate to - the `docs` folder in the source [repository], find which file you - would like to propose changes and click in the little pencil icon at the - top, to open [GitHub's code editor]. Once you finish editing the file, - please write a message in the form at the bottom of the page describing - which changes have you made and what are the motivations behind them and - submit your proposal. - ::: -``` - -When working on documentation changes in your local machine, you can -compile them using [tox] : - -``` -tox -e docs -``` - -and use Python's built-in web server for a preview in your web browser -(`http://localhost:8000`): - -``` -python3 -m http.server --directory 'docs/_build/html' -``` - -## Code Contributions - -```{todo} Please include a reference or explanation about the internals of the project. - - An architecture description, design principles or at least a summary of the - main concepts will make it easy for potential contributors to get started - quickly. -``` - -### Submit an issue - -Before you work on any non-trivial code contribution it's best to first create -a report in the [issue tracker] to start a discussion on the subject. -This often provides additional considerations and avoids unnecessary work. - -### Create an environment - -Before you start coding, we recommend creating an isolated [virtual environment] -to avoid any problems with your installed Python packages. -This can easily be done via either [virtualenv]: - -``` -virtualenv -source /bin/activate -``` - -or [Miniconda]: - -``` -conda create -n osw python=3 six virtualenv pytest pytest-cov -conda activate osw -``` - -### Clone the repository - -1. Create an user account on GitHub if you do not already have one. +Contributions are welcome! File issues and pull requests at +[github.com/OpenSemanticLab/osw-python](https://github.com/OpenSemanticLab/osw-python). -2. Fork the project [repository]: click on the *Fork* button near the top of the - page. This creates a copy of the code under your account on GitHub. +## Workflow -3. Clone this copy to your local disk: +Requires [uv](https://docs.astral.sh/uv/) and `git`. - ``` - git clone git@github.com:YourLogin/osw.git - cd osw - ``` - -4. You should run: - - ``` - pip install -U pip setuptools -e . - ``` - - to be able to import the package under development in the Python REPL. - - ```{todo} if you are not using pre-commit, please remove the following item: - ``` - -5. Install [pre-commit]: - - ``` - pip install pre-commit - pre-commit install - ``` - - `osw` comes with a lot of hooks configured to automatically help the - developer to check the code being written. - -### Implement your changes - -1. Create a branch to hold your changes: - - ``` - git checkout -b my-feature - ``` - - and start making changes. Never work on the main branch! - -2. Start your work on this branch. Don't forget to add [docstrings] to new - functions, modules and classes, especially if they are part of public APIs. - -3. Add yourself to the list of contributors in `AUTHORS.rst`. - -4. When you’re done editing, do: - - ``` - git add - git commit - ``` - - to record your changes in [git]. - - ```{todo} if you are not using pre-commit, please remove the following item: - ``` - - Please make sure to see the validation messages from [pre-commit] and fix - any eventual issues. - This should automatically use [flake8]/[black] to check/fix the code style - in a way that is compatible with the project. - - :::{important} - Don't forget to add unit tests and documentation in case your - contribution adds an additional feature and is not just a bugfix. - - Moreover, writing a [descriptive commit message] is highly recommended. - In case of doubt, you can check the commit history with: - - ``` - git log --graph --decorate --pretty=oneline --abbrev-commit --all - ``` - - to look for recurring communication patterns. - ::: - -5. Please check that your changes don't break any unit tests with: - - ``` - tox - ``` - - (after having installed [tox] with `pip install tox` or `pipx`). - - You can also use [tox] to run several other pre-configured tasks in the - repository. Try `tox -av` to see a list of the available checks. - -### Submit your contribution - -1. If everything works fine, push your local branch to the remote server with: - - ``` - git push -u origin my-feature - ``` - -2. Go to the web page of your fork and click "Create pull request" - to send your changes for review. - - ```{todo} if you are using GitHub, you can uncomment the following paragraph - - Find more detailed information in [creating a PR]. You might also want to open - the PR as a draft first and mark it as ready for review after the feedbacks - from the continuous integration (CI) system or any required fixes. - - ``` - -### Troubleshooting - -The following tips can be used when facing problems to build or test the -package: - -1. Make sure to fetch all the tags from the upstream [repository]. - The command `git describe --abbrev=0 --tags` should return the version you - are expecting. If you are trying to run CI scripts in a fork repository, - make sure to push all the tags. - You can also try to remove all the egg files or the complete egg folder, i.e., - `.eggs`, as well as the `*.egg-info` folders in the `src` folder or - potentially in the root of your project. - -2. Sometimes [tox] misses out when new dependencies are added, especially to - `setup.cfg` and `docs/requirements.txt`. If you find any problems with - missing dependencies when running a command with [tox], try to recreate the - `tox` environment using the `-r` flag. For example, instead of: - - ``` - tox -e docs - ``` - - Try running: - - ``` - tox -r -e docs - ``` - -3. Make sure to have a reliable [tox] installation that uses the correct - Python version (e.g., 3.7+). When in doubt you can run: - - ``` - tox --version - # OR - which tox - ``` - - If you have trouble and are seeing weird errors upon running [tox], you can - also try to create a dedicated [virtual environment] with a [tox] binary - freshly installed. For example: - - ``` - virtualenv .venv - source .venv/bin/activate - .venv/bin/pip install tox - .venv/bin/tox -e all - ``` - -4. [Pytest can drop you] in an interactive session in the case an error occurs. - In order to do that you need to pass a `--pdb` option (for example by - running `tox -- -k --pdb`). - You can also setup breakpoints manually instead of using the `--pdb` option. - -## Maintainer tasks - -### Releases - -```{todo} This section assumes you are using PyPI to publicly release your package. - - If instead you are using a different/private package index, please update - the instructions accordingly. +```bash +git clone git@github.com:YOUR_NAME/osw-python.git +cd osw-python +make install # environment + pre-commit hooks ``` -If you are part of the group of maintainers and have correct user permissions -on [PyPI], the following steps can be used to release a new version for -`osw`: +1. Create a branch: `git checkout -b name-of-your-fix` +2. Make your changes and add tests in `tests/` +3. Run `make check` (lint, type-check, dependency audit) and `make test` +4. Commit, push and open a pull request -1. Make sure all unit tests are successful. -2. Tag the current commit on the main branch with a release tag, e.g., `v1.2.3`. -3. Push the new tag to the upstream [repository], - e.g., `git push upstream v1.2.3` -4. Clean up the `dist` and `build` folders with `tox -e clean` - (or `rm -rf dist build`) - to avoid confusion with old builds and Sphinx docs. -5. Run `tox -e build` and check that the files in `dist` have - the correct version (no `.dirty` or [git] hash) according to the [git] tag. - Also check the sizes of the distributions, if they are too big (e.g., > - 500KB), unwanted clutter may have been accidentally included. -6. Run `tox -e publish -- --repository pypi` and check that everything was - uploaded to [PyPI] correctly. +`make help` lists all targets; the +[development guide](https://opensemanticlab.github.io/osw-python/dev/) +covers details such as running the integration tests and serving the docs +locally. -[^contrib1]: Even though, these resources focus on open source projects and - communities, the general ideas behind collaborating with other developers - to collectively create software are general and can be applied to all sorts - of environments, including private companies and proprietary code bases. +## Releasing +Releases are fully automated with +[python-semantic-release](https://python-semantic-release.readthedocs.io/): +every push to `main` is analyzed, and conventional commits decide the +outcome. `fix:` commits trigger a patch release, `feat:` a minor release +and a `BREAKING CHANGE:` footer (or `!` after the type) a major release; +other types (`chore:`, `docs:`, `ci:`, ...) release nothing. CI then +updates the changelog, tags, builds, publishes to PyPI via trusted +publishing and deploys the versioned docs. No manual version bumping or +tagging. -[black]: https://pypi.org/project/black/ -[commonmark]: https://commonmark.org/ -[contribution-guide.org]: http://www.contribution-guide.org/ -[creating a pr]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request -[descriptive commit message]: https://chris.beams.io/posts/git-commit -[docstrings]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html -[first-contributions tutorial]: https://github.com/firstcontributions/first-contributions -[flake8]: https://flake8.pycqa.org/en/stable/ -[git]: https://git-scm.com -[github web interface]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository -[github's code editor]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository -[github's fork and pull request workflow]: https://guides.github.com/activities/forking/ -[guide created by freecodecamp]: https://github.com/freecodecamp/how-to-contribute-to-open-source -[miniconda]: https://docs.conda.io/en/latest/miniconda.html -[myst]: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html -[other kinds of contributions]: https://opensource.guide/how-to-contribute -[pre-commit]: https://pre-commit.com/ -[pypi]: https://pypi.org/ -[pyscaffold's contributor's guide]: https://pyscaffold.org/en/stable/contributing.html -[pytest can drop you]: https://docs.pytest.org/en/stable/usage.html#dropping-to-pdb-python-debugger-at-the-start-of-a-test -[python software foundation's code of conduct]: https://www.python.org/psf/conduct/ -[restructuredtext]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/ -[sphinx]: https://www.sphinx-doc.org/en/master/ -[tox]: https://tox.readthedocs.io/en/stable/ -[virtual environment]: https://realpython.com/python-virtual-environments-a-primer/ -[virtualenv]: https://virtualenv.pypa.io/en/stable/ - - -```{todo} Please review and change the following definitions: -``` +## AI Guidelines -[repository]: https://github.com//osw -[issue tracker]: https://github.com//osw/issues +AI tools may be used to assist development, but a human developer is always +the author: carefully review all generated content for correctness, quality +and license compliance before submitting it. diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..784d9c51 --- /dev/null +++ b/Makefile @@ -0,0 +1,61 @@ +.DEFAULT_GOAL := help + +.PHONY: install +install: ## Install the virtual environment and pre-commit hooks + @echo ">> Creating virtual environment using uv" + @uv sync + @uv run pre-commit install + +.PHONY: check +check: ## Run code quality tools + @echo ">> Checking lock file consistency with 'pyproject.toml'" + @uv lock --locked + @echo ">> Linting code: Running pre-commit" + @uv run pre-commit run -a + @echo ">> Static type checking: Running ty" + @uv run ty check + @echo ">> Checking for obsolete dependencies: Running deptry" + @uv run deptry src + +.PHONY: test +test: ## Test the code with pytest (integration tests excluded, see pyproject.toml) + @echo ">> Testing code: Running pytest" + @uv run python -m pytest --cov --cov-config=pyproject.toml --cov-report=xml + +.PHONY: test-integration +test-integration: ## Run integration tests (set WIKI_DOMAIN, WIKI_USERNAME, WIKI_PASSWORD [, DB_USERNAME, DB_PASSWORD]; tests skip where credentials are missing) + @echo ">> Testing code: Running pytest on tests/integration" + @uv run python -m pytest tests/integration -o addopts="" \ + $(if $(WIKI_DOMAIN),--wiki_domain "$(WIKI_DOMAIN)") \ + $(if $(WIKI_USERNAME),--wiki_username "$(WIKI_USERNAME)") \ + $(if $(WIKI_PASSWORD),--wiki_password "$(WIKI_PASSWORD)") \ + $(if $(DB_USERNAME),--db_username "$(DB_USERNAME)") \ + $(if $(DB_PASSWORD),--db_password "$(DB_PASSWORD)") + +.PHONY: build +build: clean-build ## Build wheel and sdist + @echo ">> Creating wheel and sdist files" + @uv build + +.PHONY: clean-build +clean-build: ## Remove build artifacts + @echo ">> Removing build artifacts" + @uv run python -c "import shutil; shutil.rmtree('dist', ignore_errors=True)" + +.PHONY: publish +publish: ## Publish a release to PyPI (CI-only via OIDC trusted publishing) + @echo "Publishing happens in CI via OIDC trusted publishing (on-release-main.yml)." + @echo "Releases are cut automatically by python-semantic-release from the" + @echo "conventional commits on main; no manual tagging." + +.PHONY: docs +docs: ## Build and serve the documentation locally + @uv run zensical serve + +.PHONY: docs-test +docs-test: ## Test if documentation can be built without warnings or errors + @uv run zensical build -s + +.PHONY: help +help: + @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}' diff --git a/README.md b/README.md index b4acc1af..40bad964 100644 --- a/README.md +++ b/README.md @@ -1,88 +1,55 @@ [![PyPI-Server](https://img.shields.io/pypi/v/osw.svg)](https://pypi.org/project/osw/) [![DOI](https://zenodo.org/badge/458130867.svg)](https://zenodo.org/badge/latestdoi/458130867) -[![Coveralls](https://img.shields.io/coveralls/github/OpenSemanticLab/osw-python/main.svg)](https://coveralls.io/r/OpenSemanticLab/osw) -[![docs](xx.xx)](https://opensemanticlab.github.io/osw-python/) +[![Codecov](https://codecov.io/gh/OpenSemanticLab/osw-python/graph/badge.svg)](https://codecov.io/gh/OpenSemanticLab/osw-python) +[![docs](https://img.shields.io/badge/docs-online-blue)](https://opensemanticlab.github.io/osw-python/) ![license](https://img.shields.io/github/license/OpenSemanticLab/osw-python.svg) - -[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/) # osw -Python toolset for data processing, queries, wikicode generation and page manipulation within OpenSemanticLab. +Python toolset for data processing, queries, wikicode generation and page +manipulation within [OpenSemanticLab](https://github.com/OpenSemanticLab). -General features for object-oriented interaction with knowledge graphs are planned to be moved to a standalone package: -[oold-python](https://github.com/OpenSemanticWorld/oold-python) +Work with OpenSemanticLab instances the way you work with Python objects: +load pages as typed pydantic entities, query with semantic search, generate +models from the schemas stored in the wiki, and write changes back. -## Installation -``` -pip install osw -``` +**Documentation: ** -### Variants -| Variant | Description | -| -- | -- | -`osw[wikitext]` | Additional functions in `wiki_tools` to transform mediawiki markup / templates -`osw[DB]` | interact with SQL databases per DatabaseController -`osw[S3]` | Interact with S3 Stores per S3FileController -`osw[dataimport]` | Additional tools to import data -`osw[UI]` | To use a helper UI to work with entity slots +## Installation -To install multiple optional/extra dependencies run -``` -pip install osw[opt1, opt2, ...] +```bash +pip install osw ``` -To install all optional/extra dependencies run -``` -pip install osw[all] -``` +Optional extras (`osw[wikitext]`, `osw[DB]`, `osw[S3]`, `osw[dataimport]`, +`osw[UI]`, `osw[all]`) are described in the +[Get Started guide](https://opensemanticlab.github.io/osw-python/get-started/). -## Getting started -You can find examples in the tutorial folder, e.g. [entity creation](https://github.com/OpenSemanticLab/osw-python/blob/main/examples/create_entity.py), [entity manipulaton](https://github.com/OpenSemanticLab/osw-python/blob/main/examples/store_entity.py), [querying](https://github.com/OpenSemanticLab/osw-python/blob/main/examples/query_minimal.py), and [file downloads](https://github.com/OpenSemanticLab/osw-python/blob/main/examples/file_download_minimal.py) +## Quickstart -## Troubleshooting +```python +from osw.express import OswExpress -### `Error: datamodel-codegen not found` -make sure datamodel-codegen is installed and included in PATH, e. g. on jupyterlab: -``` -os.environ["PATH"] += os.pathsep + "/home/jovyan/.local/bin" +osw = OswExpress(domain="wiki-dev.open-semantic-lab.org") +instances = osw.site.semantic_search("[[Category:Item]]") +print(instances) ``` -## Documentation - -https://opensemanticlab.github.io/osw-python/ +More runnable scripts live in [examples/](examples/), and the +[Basics tutorial](docs/tutorials/basics.ipynb) walks through the +OpenSemanticLab data model. -### Tutorials +## Contributing -Tutorials can be found at [tutorials](docs/tutorials/) -- [Basics](docs/tutorials/basics.md) - a description of the data model of OpenSemanticLab and how to interact with it +Contributions are welcome, see [CONTRIBUTING.md](CONTRIBUTING.md). +Development setup, checks and tests are one command each: `make install`, +`make check`, `make test`. -## Development - -Dev install -```bash -pip install -e . [dev,testing] -``` - -Activate pre-commit hooks (in git console) -``` -pre-commit install -``` - -Run tests -```bash -tox -e test -``` - -Run integration tests (tests are skipped if login params are not provided) -```bash -tox -e test -- --wiki_domain "" --wiki_username "<(bot)login>" --wiki_password "" --db_username "" --db_password "" -``` +## Related projects - +General features for object-oriented interaction with knowledge graphs live +in the standalone package [oold-python](https://github.com/OO-LD/oold-python). -## Note +## License -This project has been set up using PyScaffold 4.3.1. For details and usage -information on PyScaffold see https://pyscaffold.org/. +AGPL-3.0-or-later, see [LICENSE.txt](LICENSE.txt). diff --git a/__init__.py b/__init__.py deleted file mode 100644 index 60890872..00000000 --- a/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# This file is required to make Python treat directories containing the file as packages. diff --git a/codecov.yaml b/codecov.yaml new file mode 100644 index 00000000..b29cd8cb --- /dev/null +++ b/codecov.yaml @@ -0,0 +1,14 @@ +# Coverage starts at the legacy baseline (~22 %), so statuses are +# informational for now: reports and PR comments without failing CI. +# Tighten targets as coverage grows. +coverage: + range: 20..80 + round: down + precision: 1 + status: + project: + default: + informational: true + patch: + default: + informational: true diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 31655dd9..00000000 --- a/docs/Makefile +++ /dev/null @@ -1,29 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build -AUTODOCDIR = api - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1) -$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/") -endif - -.PHONY: help clean Makefile - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -clean: - rm -rf $(BUILDDIR)/* $(AUTODOCDIR) - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_static/.gitignore b/docs/_static/.gitignore deleted file mode 100644 index 3c963632..00000000 --- a/docs/_static/.gitignore +++ /dev/null @@ -1 +0,0 @@ -# Empty directory diff --git a/docs/about.md b/docs/about.md new file mode 100644 index 00000000..cd8b82d0 --- /dev/null +++ b/docs/about.md @@ -0,0 +1,39 @@ +# About + +**osw-python** is the Python toolset for +[OpenSemanticLab](https://github.com/OpenSemanticLab): data processing, +semantic queries, wikicode generation and page manipulation, all against the +knowledge graph of an OpenSemanticLab / OpenSemanticWorld instance. + +[![PyPI-Server](https://img.shields.io/pypi/v/osw.svg)](https://pypi.org/project/osw/) +[![DOI](https://zenodo.org/badge/458130867.svg)](https://zenodo.org/badge/latestdoi/458130867) +[![Codecov](https://codecov.io/gh/OpenSemanticLab/osw-python/graph/badge.svg)](https://codecov.io/gh/OpenSemanticLab/osw-python) +[![License](https://img.shields.io/github/license/OpenSemanticLab/osw-python.svg)](https://github.com/OpenSemanticLab/osw-python/blob/main/LICENSE.txt) + +## Why osw-python? + +- **Typed entities** - pages are loaded as pydantic models generated from + the JSON schemas stored in the wiki itself +- **Semantic queries** - run semantic search and SPARQL queries from Python +- **Full page control** - read and write structured data, wikitext and + files on any page slot +- **Controller pattern** - attach runtime behavior (databases, S3 stores, + file handling) to entities without polluting the data model +- **Express mode** - one-liner site access with credential handling built in + +General features for object-oriented interaction with knowledge graphs live +in the standalone package [oold-python](https://github.com/OO-LD/oold-python), +which osw-python builds on. + +## Ecosystem + +| Project | Role | +| ------- | ---- | +| [OpenSemanticLab](https://github.com/OpenSemanticLab) | The platform osw-python talks to | +| [oold-python](https://github.com/OO-LD/oold-python) | Object-oriented linked data foundation | +| [opensemantic.core](https://github.com/OpenSemanticWorld-Packages/opensemantic.core-python) | Generated core data model | + +## License + +AGPL-3.0-or-later, see +[LICENSE.txt](https://github.com/OpenSemanticLab/osw-python/blob/main/LICENSE.txt). diff --git a/docs/api/auth.md b/docs/api/auth.md new file mode 100644 index 00000000..3239f791 --- /dev/null +++ b/docs/api/auth.md @@ -0,0 +1,14 @@ +# Authentication + +Credential handling for wiki and service logins. Credentials are resolved +in this order and held in memory only: + +1. Credentials added programmatically (`add_credential`) +2. An existing credentials file (read-only, if one is configured) +3. The environment variables `OSW_USERNAME` / `OSW_PASSWORD` + (`OSL_*` variants work too), e.g. loaded from a `.env` file +4. An interactive prompt (fallback `ask`) + +The library never writes credentials to disk on its own. + +::: osw.auth.CredentialManager diff --git a/docs/api/controller.md b/docs/api/controller.md new file mode 100644 index 00000000..77648bae --- /dev/null +++ b/docs/api/controller.md @@ -0,0 +1,11 @@ +# Controllers + +A controller extends a model class with functions. + +## Entity + +::: osw.controller.Entity + +## DatabaseController + +::: osw.controller.DatabaseController diff --git a/docs/api/core.md b/docs/api/core.md new file mode 100644 index 00000000..f1cbc122 --- /dev/null +++ b/docs/api/core.md @@ -0,0 +1,5 @@ +# OSW + +The central class for interacting with an OpenSemanticWorld instance. + +::: osw.core.OSW diff --git a/docs/api/index.md b/docs/api/index.md new file mode 100644 index 00000000..1d5082c8 --- /dev/null +++ b/docs/api/index.md @@ -0,0 +1,11 @@ +# API Reference + +The most important entry points of the package: + +| Page | Contents | +| ---- | -------- | +| [OSW](core.md) | The central `OSW` class: load, store and query entities | +| [Wiki Tools](wiki-tools.md) | Helper functions for pages, queries and wikitext | +| [Authentication](auth.md) | `CredentialManager` for logins and tokens | +| [Controllers](controller.md) | Runtime behavior attached to entities | +| [Model](model.md) | The generated data model | diff --git a/docs/api/model.md b/docs/api/model.md new file mode 100644 index 00000000..595edbdc --- /dev/null +++ b/docs/api/model.md @@ -0,0 +1,6 @@ +# Model + +The data model is generated from the JSON schemas of the wiki. The core +model is maintained in +[opensemantic.core-python](https://github.com/OpenSemanticWorld-Packages/opensemantic.core-python/blob/main/src/opensemantic/core/v1/_model.py) +and extended dynamically at runtime via `OSW.fetch_schema`. diff --git a/docs/api/wiki-tools.md b/docs/api/wiki-tools.md new file mode 100644 index 00000000..e147f2ad --- /dev/null +++ b/docs/api/wiki-tools.md @@ -0,0 +1,5 @@ +# Wiki Tools + +Collection of helper functions for pages, queries and wikitext. + +::: osw.wiki_tools diff --git a/docs/auth.md b/docs/auth.md deleted file mode 100644 index 4a4fc53f..00000000 --- a/docs/auth.md +++ /dev/null @@ -1,4 +0,0 @@ -Authentication - -# CredentialManager -::: osw.auth.CredentialManager diff --git a/docs/authors.md b/docs/authors.md deleted file mode 100644 index ced47d0e..00000000 --- a/docs/authors.md +++ /dev/null @@ -1,4 +0,0 @@ -```{include} ../AUTHORS.md -:relative-docs: docs/ -:relative-images: -``` diff --git a/docs/changelog.md b/docs/changelog.md deleted file mode 100644 index 6e2f0fb1..00000000 --- a/docs/changelog.md +++ /dev/null @@ -1,4 +0,0 @@ -```{include} ../CHANGELOG.md -:relative-docs: docs/ -:relative-images: -``` diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 969f2c4c..00000000 --- a/docs/conf.py +++ /dev/null @@ -1,304 +0,0 @@ -# This file is execfile()d with the current directory set to its containing dir. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import os -import sys -import shutil - -# -- Path setup -------------------------------------------------------------- - -__location__ = os.path.dirname(__file__) - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.insert(0, os.path.join(__location__, "../src")) - -# -- Run sphinx-apidoc ------------------------------------------------------- -# This hack is necessary since RTD does not issue `sphinx-apidoc` before running -# `sphinx-build -b html . _build/html`. See Issue: -# https://github.com/readthedocs/readthedocs.org/issues/1139 -# DON'T FORGET: Check the box "Install your project inside a virtualenv using -# setup.py install" in the RTD Advanced Settings. -# Additionally it helps us to avoid running apidoc manually - -try: # for Sphinx >= 1.7 - from sphinx.ext import apidoc -except ImportError: - from sphinx import apidoc - -output_dir = os.path.join(__location__, "api") -module_dir = os.path.join(__location__, "../src/osw") -try: - shutil.rmtree(output_dir) -except FileNotFoundError: - pass - -try: - import sphinx - - cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}" - - args = cmd_line.split(" ") - if tuple(sphinx.__version__.split(".")) >= ("1", "7"): - # This is a rudimentary parse_version to avoid external dependencies - args = args[1:] - - apidoc.main(args) -except Exception as e: - print("Running `sphinx-apidoc` failed!\n{}".format(e)) - -# -- General configuration --------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.intersphinx", - "sphinx.ext.todo", - "sphinx.ext.autosummary", - "sphinx.ext.viewcode", - "sphinx.ext.coverage", - "sphinx.ext.doctest", - "sphinx.ext.ifconfig", - "sphinx.ext.mathjax", - "sphinx.ext.napoleon", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - - -# Enable markdown -extensions.append("myst_parser") - -# Configure MyST-Parser -myst_enable_extensions = [ - "amsmath", - "colon_fence", - "deflist", - "dollarmath", - "html_image", - "linkify", - "replacements", - "smartquotes", - "substitution", - "tasklist", -] - -# The suffix of source filenames. -source_suffix = [".rst", ".md"] - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = "index" - -# General information about the project. -project = "osw" -copyright = "2023, SimonStier" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# version: The short X.Y version. -# release: The full version, including alpha/beta/rc tags. -# If you don’t need the separation provided between version and release, -# just set them both to the same value. -try: - from osw import __version__ as version -except ImportError: - version = "" - -if not version or version.lower() == "unknown": - version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD - -release = version - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If this is True, todo emits a warning for each TODO entries. The default is False. -todo_emit_warnings = True - - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = "alabaster" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -html_theme_options = { - "sidebar_width": "300px", - "page_width": "1200px" -} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = "" - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = "osw-doc" - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ("letterpaper" or "a4paper"). - # "papersize": "letterpaper", - # The font size ("10pt", "11pt" or "12pt"). - # "pointsize": "10pt", - # Additional stuff for the LaTeX preamble. - # "preamble": "", -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ("index", "user_guide.tex", "osw Documentation", "SimonStier", "manual") -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = "" - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - -# -- External mapping -------------------------------------------------------- -python_version = ".".join(map(str, sys.version_info[0:2])) -intersphinx_mapping = { - "sphinx": ("https://www.sphinx-doc.org/en/master", None), - "python": ("https://docs.python.org/" + python_version, None), - "matplotlib": ("https://matplotlib.org", None), - "numpy": ("https://numpy.org/doc/stable", None), - "sklearn": ("https://scikit-learn.org/stable", None), - "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None), - "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), - "setuptools": ("https://setuptools.pypa.io/en/stable/", None), - "pyscaffold": ("https://pyscaffold.org/en/stable", None), -} - -print(f"loading configurations for {project} {version} ...", file=sys.stderr) \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md deleted file mode 100644 index fc1b2138..00000000 --- a/docs/contributing.md +++ /dev/null @@ -1,4 +0,0 @@ -```{include} ../CONTRIBUTING.md -:relative-docs: docs/ -:relative-images: -``` diff --git a/docs/controller.md b/docs/controller.md deleted file mode 100644 index 591c1179..00000000 --- a/docs/controller.md +++ /dev/null @@ -1,9 +0,0 @@ -# OpenSematicLab Controller - -A controller extents a model class with functions - -## Entity -### ::: osw.controller.Entity - -## DatabaseController -### ::: osw.controller.DatabaseController diff --git a/docs/dev.md b/docs/dev.md index 7e3c6ff4..4e673fba 100644 --- a/docs/dev.md +++ b/docs/dev.md @@ -1,24 +1,131 @@ -# Setup -1. create a virtual environment -```bash -python -m venv .venv -``` + -1. install requirements + extras -```bash -pip install -e .[dev,testing] -``` +# Development +Everything you need to work on osw-python. Each step comes as a `make` +one-liner or as the underlying commands, pick your style with the tabs. -# Testing +## Setup -1. Create new test (file name test_*.py) under /tests +Requires [uv](https://docs.astral.sh/uv/) and `git`. + +=== "make" + + ```bash + make install + ``` + +=== "manual" + + ```bash + uv sync + uv run pre-commit install + ``` + +## Quality checks + +Lock consistency, linting and formatting (pre-commit incl. ruff), static +type checking (ty) and dependency audit (deptry) in one go: + +=== "make" + + ```bash + make check + ``` + +=== "manual" + + ```bash + uv lock --locked + uv run pre-commit run -a + uv run ty check + uv run deptry src + ``` + +## Testing + +Add new tests as `test_*.py` under `tests/`. Integration tests are +excluded by default: + +=== "make" + + ```bash + make test + ``` + +=== "manual" + + ```bash + uv run python -m pytest --cov --cov-config=pyproject.toml --cov-report=xml + ``` + +### Integration tests + +Integration tests run against a live wiki and need credentials; tests +whose credentials are missing skip instead of fail. CI runs them on +every push to `main` (workflow `integration.yml`). + +=== "make" + + ```bash + WIKI_DOMAIN="" WIKI_USERNAME="" WIKI_PASSWORD="" \ + make test-integration + ``` + +=== "manual" + + ```bash + uv run pytest tests/integration -o addopts="" \ + --wiki_domain "" \ + --wiki_username "" \ + --wiki_password "" + ``` + +## Documentation + +Serve locally with live reload at `http://localhost:8000`, or run the +strict build that fails on any warning: + +=== "make" + + ```bash + make docs # serve with live reload + make docs-test # strict build + ``` + +=== "manual" + + ```bash + uv run zensical serve + uv run zensical build -s + ``` + +## Building + +=== "make" + + ```bash + make build + ``` + +=== "manual" + + ```bash + uv build + ``` + +## Releasing + +Releases are fully automated +([python-semantic-release](https://python-semantic-release.readthedocs.io/)): +conventional commits on `main` decide the version bump (`fix:` patch, +`feat:` minor, `BREAKING CHANGE:`/`!` major), CI updates the changelog, +tags `vX.Y.Z`, builds, publishes to PyPI via trusted publishing and +deploys the versioned docs. The package version is derived from the tag +by `hatch-vcs`; nothing is bumped manually. + +To preview what the next release would be: -1. Run pytest in the project root dir -```bash -tox -e test -``` -1. To run integration test with credentials, run ```bash -tox -e test -- --wiki_domain "" --wiki_username "" --wiki_password "" +uv run semantic-release --noop version ``` diff --git a/docs/get-started.md b/docs/get-started.md new file mode 100644 index 00000000..0d1292d8 --- /dev/null +++ b/docs/get-started.md @@ -0,0 +1,84 @@ + + +# Get Started + +## Prerequisites + +- Python **3.10 to 3.13** +- `pip` or [`uv`](https://docs.astral.sh/uv/) (recommended) + +## Installation + +=== "uv (recommended)" + + ```bash + uv add osw + ``` + +=== "pip" + + ```bash + pip install osw + ``` + +### Optional extras + +| Extra | Description | +| ----- | ----------- | +| `osw[wikitext]` | Additional functions in `wiki_tools` to transform mediawiki markup / templates | +| `osw[DB]` | Interact with SQL databases per DatabaseController | +| `osw[S3]` | Interact with S3 stores per S3FileController | +| `osw[dataimport]` | Additional tools to import data | +| `osw[UI]` | To use a helper UI to work with entity slots | +| `osw[all]` | All of the above | + +Install multiple extras with `pip install osw[opt1,opt2]`. + +## First steps + +Create a typed entity locally with the generated data model: + +```python +import osw.model.entity as model + +my_entity = model.Item( + label=[model.Label(text="MyItem")], + statements=[model.DataStatement(property="IsA", value="Category:Item")], +) +print(my_entity.json()) +``` + +Connect to an instance and run a semantic query with +[OswExpress](api/core.md): + +```python +from osw.express import OswExpress + +osw = OswExpress(domain="wiki-dev.open-semantic-lab.org") +instances = osw.site.semantic_search("[[Category:Item]]") +print(instances) +``` + +Credentials are resolved from the environment variables `OSW_USERNAME` / +`OSW_PASSWORD` (e.g. loaded from a `.env` file), from an existing +credentials file, or via an interactive prompt - and are held in memory +only, never written to disk; see [Authentication](api/auth.md). + +## Examples and tutorials + +- Runnable scripts in + [examples/](https://github.com/OpenSemanticLab/osw-python/tree/main/examples), + e.g. entity creation, entity manipulation, querying and file downloads +- The [Basics tutorial notebook](https://github.com/OpenSemanticLab/osw-python/blob/main/docs/tutorials/basics.ipynb) + describes the OpenSemanticLab data model and how to interact with it + +## Troubleshooting + +### `Error: datamodel-codegen not found` + +Make sure `datamodel-codegen` is installed and included in `PATH`, e.g. on +jupyterlab: + +```python +os.environ["PATH"] += os.pathsep + "/home/jovyan/.local/bin" +``` diff --git a/docs/index.md b/docs/index.md index 132d1910..4796e7d9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,39 +1,30 @@ -# osw +--- +title: OpenSemanticWorld Python +hide: + - navigation + - toc +--- -Python toolset for data processing, queries, wikicode generation and page manipulation + +
-## Note + -> This is the main page of your project's [Sphinx] documentation. It is -> formatted in [Markdown]. Add additional pages by creating md-files in -> `docs` or rst-files (formatted in [reStructuredText]) and adding links to -> them in the `Contents` section below. -> -> Please check [Sphinx] and [MyST] for more information -> about how to document your project and how to configure your preferences. +

osw-python

+

Typed Python access to OpenSemanticLab knowledge graphs.

-## Contents +

+Work with OpenSemanticLab instances the way you work with Python objects: +load pages as typed pydantic entities, query with semantic search, generate +models from the schemas stored in the wiki, and write changes back - files, +wikitext and structured data included. +

-```{toctree} -:maxdepth: 2 +

+[Get started](get-started.md){ .md-button .md-button--primary } +[Learn more](about.md){ .md-button } +

-Overview -Contributions & Help -License -Authors -Changelog -Module Reference -``` - -## Indices and tables - -* {ref}`genindex` -* {ref}`modindex` -* {ref}`search` - -[Sphinx]: http://www.sphinx-doc.org/ -[Markdown]: https://daringfireball.net/projects/markdown/ -[reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html -[MyST]: https://myst-parser.readthedocs.io/en/latest/ +
diff --git a/docs/license.md b/docs/license.md deleted file mode 100644 index b231201e..00000000 --- a/docs/license.md +++ /dev/null @@ -1,5 +0,0 @@ -# License - -```{literalinclude} ../LICENSE.txt -:language: text -``` diff --git a/docs/model.md b/docs/model.md deleted file mode 100644 index f6de467c..00000000 --- a/docs/model.md +++ /dev/null @@ -1,3 +0,0 @@ -OpenSematicLab Model - -see [opensemantic.core-python](https://github.com/OpenSemanticWorld-Packages/opensemantic.core-python/blob/main/src/opensemantic/core/v1/_model.py) diff --git a/docs/osw.md b/docs/osw.md deleted file mode 100644 index 3e725da3..00000000 --- a/docs/osw.md +++ /dev/null @@ -1,4 +0,0 @@ -OpenSematicWorld Class - -# OSW -::: osw.core.OSW diff --git a/docs/readme.md b/docs/readme.md deleted file mode 100644 index 2cb706b3..00000000 --- a/docs/readme.md +++ /dev/null @@ -1,4 +0,0 @@ -```{include} ../README.md -:relative-docs: docs/ -:relative-images: -``` diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 5c7a058b..00000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,11 +0,0 @@ - -mkdocs -mkdocs-gen-files -mkdocs-material -mkdocstrings[python] -# Requirements file for ReadTheDocs, check .readthedocs.yml. -# To build the module reference correctly, make sure every external package -# under `install_requires` in `setup.cfg` is also listed here! -# sphinx_rtd_theme -myst-parser[linkify] -sphinx>=3.2.1 diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 00000000..c506ca73 --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,102 @@ +/* ---------------------------------------------------------------------------- + osw landing hero (docs/index.md) + Full-bleed, centered hero: logo + headline + short text passage + + call-to-action buttons over a soft accent gradient. + Adapted from the OO-LD/oold-python docs. +---------------------------------------------------------------------------- */ + +.osw-hero { + padding: 4.5rem 1rem 5rem; + text-align: center; +} + +.osw-hero__logo { + width: 160px; + max-width: 45%; + height: auto; + border-radius: 16%; + filter: drop-shadow(0 10px 28px rgba(0, 0, 0, 0.18)); +} + +.osw-hero__title { + margin: 1.4rem 0 0.3rem; + font-size: 2.6rem; + font-weight: 700; + line-height: 1.15; +} + +.osw-hero__tagline { + margin: 0 auto 1.2rem; + font-size: 1.25rem; + font-weight: 500; + color: var(--md-default-fg-color--light); +} + +.osw-hero__text { + max-width: 42rem; + margin: 0 auto 2rem; + font-size: 1.02rem; + line-height: 1.7; + color: var(--md-default-fg-color--light); +} + +.osw-hero__actions .md-button { + margin: 0.35rem 0.4rem; +} + +/* The landing page is a short hero with no scrolling, so don't reserve the + scrollbar gutter (the theme sets `scrollbar-gutter: stable` globally). */ +html:has(.osw-hero) { + scrollbar-gutter: auto; +} + +/* Accent color (matches the theme's deep-orange accent) + gradient end. */ +body:has(.osw-hero) { + --osw-hero-accent: #ff6f00; + --osw-hero-end: color-mix(in srgb, var(--osw-hero-accent) 35%, var(--md-default-bg-color)); +} + +/* One continuous gradient on the full-height content region: page background + at the top, fading to the accent at the very bottom. Scoped to .md-main so + the header, tabs and footer keep their own colors. */ +body:has(.osw-hero) .md-main { + background: + radial-gradient( + 70% 55% at 50% 100%, + color-mix(in srgb, var(--osw-hero-accent) 25%, transparent), + transparent 72% + ), + linear-gradient( + 180deg, + var(--md-default-bg-color) 30%, + var(--osw-hero-end) 100% + ); +} + +/* Landing page: hero starts flush under the tabs bar and spans full width. */ +body:has(.osw-hero) .md-main__inner { + margin-top: 0; + max-width: none; +} + +body:has(.osw-hero) .md-content__inner { + margin: 0; + padding: 0; +} + +/* Hide the footer on the landing page only. */ +body:has(.osw-hero) .md-footer { + display: none; +} + +@media screen and (max-width: 44.9375em) { + .osw-hero { + padding: 3rem 1rem 3.5rem; + } + .osw-hero__title { + font-size: 2rem; + } + .osw-hero__tagline { + font-size: 1.1rem; + } +} diff --git a/docs/tools.md b/docs/tools.md deleted file mode 100644 index ab8ceac5..00000000 --- a/docs/tools.md +++ /dev/null @@ -1,3 +0,0 @@ -Collection of helper functions - -::: osw.wiki_tools diff --git a/examples/controller_logic.py b/examples/controller_logic.py index 22c9a4b4..10c33c5a 100644 --- a/examples/controller_logic.py +++ b/examples/controller_logic.py @@ -18,7 +18,7 @@ osw_obj.fetch_schema( fetchSchemaParam=OswExpress.FetchSchemaParam(schema_title="Category:Hardware") ) -from osw.model.entity import Hardware # noqa: E402 +from osw.model.entity import Hardware title = "Item:OSW7d7193567ea14e4e89b74de88983b718" # title = "Item:OSWe02213b6c4664d04834355dc8eb08b99" diff --git a/examples/database_access.py b/examples/database_access.py index 9ba7d54b..fe76ddfe 100644 --- a/examples/database_access.py +++ b/examples/database_access.py @@ -23,7 +23,7 @@ osw_obj.install_dependencies(DEPENDENCIES, mode="append") # Make sure to import controllers after updating the model (ignore linter warning) -import osw.controller as controller # noqa: E402 +import osw.controller as controller # Load database definition db = osw_obj.load_entity("Item:OSWb8cc7705e17c47b19331fdb045bfbca8") # postgres diff --git a/examples/file_upload_download.py b/examples/file_upload_download.py index bfd20ef0..463c3943 100644 --- a/examples/file_upload_download.py +++ b/examples/file_upload_download.py @@ -30,11 +30,11 @@ # Import the controller modules # Note: since they depend on the data classes, they must be imported after the schemas # are loaded -from osw.controller.file.local import ( # noqa (ignore flake8 warning) +from osw.controller.file.local import ( LocalFileController, ) -from osw.controller.file.s3 import S3FileController # noqa (ignore flake8 warning) -from osw.controller.file.wiki import WikiFileController # noqa (ignore flake8 warning) +from osw.controller.file.s3 import S3FileController +from osw.controller.file.wiki import WikiFileController def video_file(): diff --git a/examples/get_page_content.py b/examples/get_page_content.py index f27f9037..e9f85e44 100644 --- a/examples/get_page_content.py +++ b/examples/get_page_content.py @@ -19,7 +19,8 @@ # getting the page content from the main slot (without info box...) page_content = ( - osw.site.get_page(GetPageParam(titles=[fullpagetitle_to_download])) + osw.site + .get_page(GetPageParam(titles=[fullpagetitle_to_download])) .pages[0] .get_slot_content("main") ) diff --git a/examples/gui_local_slot_editing.py b/examples/gui_local_slot_editing.py index 52a20bcf..0d8a0c37 100644 --- a/examples/gui_local_slot_editing.py +++ b/examples/gui_local_slot_editing.py @@ -47,7 +47,7 @@ # Definition of functions def str_or_none(value): if str(value) == "" or value is None: - return str("None") + return "None" else: return str(value) @@ -139,7 +139,7 @@ def save_as_page_package( # Predefining some variables before execution settings_file_path = SETTINGS_FILE_PATH_DEFAULT if os.path.exists(settings_file_path): - with open(settings_file_path, "r") as f: + with open(settings_file_path) as f: settings = json.load(f) settings_read_from_file = True else: @@ -182,54 +182,48 @@ def save_as_page_package( settings_layout = [ [psg.Text("Settings", font=("Helvetica", 20))], [ - psg.Column( + psg.Column([ [ - [ - psg.Text("Settings file"), - ], - [ - psg.Text("Credentials file"), - ], - [ - psg.Text("Local working directory"), - ], - ] - ), - psg.Column( + psg.Text("Settings file"), + ], [ - [ - psg.In( - size=(50, 1), - enable_events=True, - key="-SETTINGS-", - default_text=settings["settings_file_path"], - ), - psg.FileBrowse(button_text="Browse", key="-BROWSE_SETTINGS-"), - psg.Button("Load", key="-LOAD_SETTINGS-"), - psg.Button("Save", key="-SAVE_SETTINGS-"), - ], - [ - psg.In( - size=(50, 1), - enable_events=True, - key="-CREDENTIALS-", - default_text=settings["cred_filepath"], - ), - psg.FileBrowse( - button_text="Browse", key="-BROWSE_CREDENTIALS-" - ), - ], - [ - psg.In( - size=(50, 1), - enable_events=True, - key="-LWD-", - default_text=settings["local_working_directory"], - ), - psg.FolderBrowse(button_text="Browse", key="-BROWSE_LWD-"), - ], - ] - ), + psg.Text("Credentials file"), + ], + [ + psg.Text("Local working directory"), + ], + ]), + psg.Column([ + [ + psg.In( + size=(50, 1), + enable_events=True, + key="-SETTINGS-", + default_text=settings["settings_file_path"], + ), + psg.FileBrowse(button_text="Browse", key="-BROWSE_SETTINGS-"), + psg.Button("Load", key="-LOAD_SETTINGS-"), + psg.Button("Save", key="-SAVE_SETTINGS-"), + ], + [ + psg.In( + size=(50, 1), + enable_events=True, + key="-CREDENTIALS-", + default_text=settings["cred_filepath"], + ), + psg.FileBrowse(button_text="Browse", key="-BROWSE_CREDENTIALS-"), + ], + [ + psg.In( + size=(50, 1), + enable_events=True, + key="-LWD-", + default_text=settings["local_working_directory"], + ), + psg.FolderBrowse(button_text="Browse", key="-BROWSE_LWD-"), + ], + ]), ], [psg.HSeparator()], ] @@ -244,28 +238,24 @@ def save_as_page_package( # Target page [psg.Text("Target page", font=("Helvetica", 16))], [ - psg.Column( + psg.Column([ + [psg.Text("Address, within selected OSW instance")], + [psg.Text("First label of the OSW page:")], + ]), + psg.Column([ [ - [psg.Text("Address, within selected OSW instance")], - [psg.Text("First label of the OSW page:")], - ] - ), - psg.Column( + psg.InputText( + size=(50, 1), + default_text=settings["target_page"], + key="-ADDRESS-", + ), + psg.Button("Load page"), + ], [ - [ - psg.InputText( - size=(50, 1), - default_text=settings["target_page"], - key="-ADDRESS-", - ), - psg.Button("Load page"), - ], - [ - # A display element that will show the label of the OSW page - psg.Multiline(size=(50, 1), key="-LABEL-", no_scrollbar=True) - ], - ] - ), + # A display element that will show the label of the OSW page + psg.Multiline(size=(50, 1), key="-LABEL-", no_scrollbar=True) + ], + ]), ], # [ # psg.HSeparator() @@ -273,30 +263,28 @@ def save_as_page_package( # Slots to download [psg.Text("Slots to download", font=("Helvetica", 16))], [ - psg.Column( + psg.Column([ + [ + psg.Radio( + "Include empty slots", + group_id="-RADIO1-", + default=settings["dump_empty_slots"], + key="-INC_EMPTY-", + enable_events=True, + ) + ], [ - [ - psg.Radio( - "Include empty slots", - group_id="-RADIO1-", - default=settings["dump_empty_slots"], - key="-INC_EMPTY-", - enable_events=True, - ) - ], - [ - psg.Radio( - "Exclude empty slots", - group_id="-RADIO1-", - default=(not settings["dump_empty_slots"]), - key="-EXC_EMPTY-", - enable_events=True, - ) - ], - [psg.Button("Download selected", key="-DL-")], - [psg.Multiline(size=(20, 1), key="-DL_RES-", no_scrollbar=True)], - ] - ), + psg.Radio( + "Exclude empty slots", + group_id="-RADIO1-", + default=(not settings["dump_empty_slots"]), + key="-EXC_EMPTY-", + enable_events=True, + ) + ], + [psg.Button("Download selected", key="-DL-")], + [psg.Multiline(size=(20, 1), key="-DL_RES-", no_scrollbar=True)], + ]), ], # [ # psg.HSeparator() @@ -304,24 +292,22 @@ def save_as_page_package( # Slots to upload [psg.Text("Slots to upload", font=("Helvetica", 16))], [ - psg.Column( + psg.Column([ + [psg.Button("(De)Select all", key="-UL_SEL-")], [ - [psg.Button("(De)Select all", key="-UL_SEL-")], - [ - psg.Listbox( - values=SLOTS.keys(), - default_values=settings["slots_to_upload"], - size=(20, 10), - key="-UL_LIST-", - select_mode=psg.LISTBOX_SELECT_MODE_MULTIPLE, - enable_events=True, - no_scrollbar=True, - ) - ], - [psg.Button("Upload selected", key="-UL-")], - [psg.Multiline(size=(20, 1), key="-UL_RES-", no_scrollbar=True)], - ] - ) + psg.Listbox( + values=SLOTS.keys(), + default_values=settings["slots_to_upload"], + size=(20, 10), + key="-UL_LIST-", + select_mode=psg.LISTBOX_SELECT_MODE_MULTIPLE, + enable_events=True, + no_scrollbar=True, + ) + ], + [psg.Button("Upload selected", key="-UL-")], + [psg.Multiline(size=(20, 1), key="-UL_RES-", no_scrollbar=True)], + ]) ], ] output_layout = [ @@ -347,7 +333,7 @@ def save_as_page_package( settings["settings_file_path"] = values["-SETTINGS-"] elif event == "-LOAD_SETTINGS-": # update settings - with open(settings["settings_file_path"], "r") as f: + with open(settings["settings_file_path"]) as f: settings = json.load(f) # update GUI window["-CREDENTIALS-"].update(settings["cred_filepath"]) @@ -474,13 +460,11 @@ def save_as_page_package( # Some debugging output functionality if DEBUG: - values_str = "\n".join( - [ - f"{key}: {str_or_none(value)}" - for key, value in values.items() - if key != "-OUTPUT-" - ] - ) + values_str = "\n".join([ + f"{key}: {str_or_none(value)}" + for key, value in values.items() + if key != "-OUTPUT-" + ]) listbox_selected_items_str = "\n".join(settings["slots_to_upload"]) window["-OUTPUT-"].update( diff --git a/examples/inter_osw_copy_page.py b/examples/inter_osw_copy_page.py index e04340de..55213eeb 100644 --- a/examples/inter_osw_copy_page.py +++ b/examples/inter_osw_copy_page.py @@ -70,7 +70,7 @@ def set_single_page_content( changed_slots = [] for slot in SLOTS: remote_content = wtpage.get_slot_content(slot) - if remote_content != content_dict.get(slot, None): + if remote_content != content_dict.get(slot): changed_slots.append(slot) if len(changed_slots) == 0: print( diff --git a/examples/page_manipulation.py b/examples/page_manipulation.py index 5d1a940a..3d97f06a 100644 --- a/examples/page_manipulation.py +++ b/examples/page_manipulation.py @@ -89,11 +89,12 @@ def mass_page_edit(): wtsite.modify_search_results( "semantic", "[[Category:labNote]]", - lambda wtpage: - # print("Lambda")#wtpage.title) - wtpage.set_value( - "*.'OslTemplate:ELN/Entry/Header'", {"id": [wtpage.title.split(":")[1]]} - ).update_content(), + lambda wtpage: ( + # print("Lambda")#wtpage.title) + wtpage.set_value( + "*.'OslTemplate:ELN/Entry/Header'", {"id": [wtpage.title.split(":")[1]]} + ).update_content() + ), limit=1, comment="[bot] set id from title", log=True, diff --git a/examples/use_express_functions.py b/examples/use_express_functions.py index 9b662dbd..2befde51 100644 --- a/examples/use_express_functions.py +++ b/examples/use_express_functions.py @@ -3,7 +3,7 @@ import dotenv -from osw.express import OswExpress, osw_download_file, osw_upload_file # noqa: E402 +from osw.express import OswExpress, osw_download_file, osw_upload_file # Best practise load environment variables from .env file dotenv.load_dotenv() # will look for a .env file in CWD and above diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index 64097b65..00000000 --- a/mkdocs.yml +++ /dev/null @@ -1,24 +0,0 @@ -site_name: OpenSemanticWorld Python Package (osw) -site_url: https://OpenSemanticLab.github.io/Tools/ - -plugins: -- search -- autorefs -- mkdocstrings: - handlers: - python: - paths: [src] # search packages in the src folder - options: - docstring_style: numpy - -nav: - - Home: index.md - - tools.md - - auth.md - - osw.md - - model.md - - controller.md - - Development: dev.md - -theme: - name: "material" diff --git a/pyproject.toml b/pyproject.toml index 89a5bedf..d5cf55f6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,354 @@ +[project] +name = "osw" +description = "Python toolset for data processing, queries, wikicode generation and page manipulation" +authors = [{ name = "OpenSemanticWorld", email = "team@opensemantic.world" }] +readme = "README.md" +license = "AGPL-3.0-or-later" +license-files = ["LICENSE.txt"] +requires-python = ">=3.10,<3.14" +dynamic = ["version"] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Developers", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Topic :: Software Development :: Libraries :: Python Modules", +] +dependencies = [ + "oold>=0.15.0", + "opensemantic", + "opensemantic.core>=0.57.4", + "opensemantic.base>=0.42.7", + "pydantic[email]>=1.10.17", + "datamodel-code-generator==0.51.0", + "black", + "isort", + "mwclient>=0.11.0", + # imported directly in src but previously only available transitively, + # surfaced by deptry during the migration + "requests", + "httpx", + "rdflib", + "PyLD", + "SPARQLWrapper", + "jsonpath-ng", + "numpy", + "pyyaml", + "typing_extensions", + # used in custom_types.py on py3.10; was missing before (latent + # ImportError on 3.10), surfaced by ty/deptry during the migration + 'backports.strenum; python_version < "3.11"', + "dask", + "tqdm", + "pybars3-wheel", +] + +[project.urls] +Homepage = "https://github.com/OpenSemanticLab/osw-python" +Documentation = "https://opensemanticlab.github.io/osw-python/" +Source = "https://github.com/OpenSemanticLab/osw-python" +Changelog = "https://github.com/OpenSemanticLab/osw-python/blob/main/CHANGELOG.md" +Download = "https://pypi.org/project/osw/#files" + +[project.optional-dependencies] +wikitext = ["mwparserfromhell"] +DB = [ + "psycopg2", + "sqlalchemy", +] +S3 = ["boto3"] +dataimport = [ + "geopy", + "deepl", + "openpyxl", +] +UI = ["pysimplegui"] +workflow = [ + "prefect>=2.20.25,<3.0", + # prefect 2.20.25 is the final 2.x release (no backports). Its + # GatherTaskGroup subclasses anyio's TaskGroup but doesn't implement + # create_task, which newer anyio 4.x made abstract (broken on 4.14, + # verified good on 4.6.2); hold anyio to the last verified-good 4.6 line + # so the prefect-2.x flow engine can still instantiate task groups. + "anyio>=4.4.0,<4.7", +] +tutorial = ["osw[dataimport]"] +all = ["osw[dataimport,DB,UI,S3,wikitext]"] + [build-system] -# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD! -requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"] -build-backend = "setuptools.build_meta" - -[tool.setuptools_scm] -# For smarter version schemes and other configuration options, -# check out https://github.com/pypa/setuptools_scm -version_scheme = "no-guess-dev" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[tool.hatch.version] +source = "vcs" +# Preserve the setuptools-scm scheme the project used previously so tag-derived +# versions are identical (e.g. 1.1.2.post1.dev25+g). +raw-options = { version_scheme = "no-guess-dev" } + +[dependency-groups] +dev = [ + # test stack + "pytest", + "pytest-cov", + "pytest-mock", + "pytest-asyncio", + # inherit the capped prefect pin (<3.0); a bare "prefect" here resolved to + # 3.x in CI, whose server API breaks the prefect-2.20-targeted tests + "osw[workflow]", + "geopy", + "deepl", + "sqlalchemy", + "psycopg2-binary", # see: https://www.psycopg.org/docs/install.html#psycopg-vs-psycopg-binary + "mwparserfromhell", + "jsondiff", + # tooling + # (tox-uv omitted: it needs packaging>=26, conflicting with the + # prefect-2.x test stack; tox is revisited in the cleanup phase) + "pre-commit>=4.0.0", + "ruff>=0.15.7", + "ty>=0.0.24", + "deptry>=0.25.1", + # optional-extra backends installed in dev so their modules type-check + "boto3", + # installed unconditionally (runtime dep is <3.11 only) so ty resolves + # the version-guarded import in custom_types.py on every python version + "backports.strenum", + # docs + "zensical>=0.0.46", + "mkdocstrings-python>=1.0.3", + # docs versioning: zensical-compatible mike fork (same pin as OO-LD/oold-schema) + "mike @ git+https://github.com/squidfunk/mike.git@2.2.0+zensical-0.1.0", + # automated releases + changelog from conventional commits + "python-semantic-release>=10.0.0", +] + +[tool.hatch.build.targets.wheel] +packages = ["src/osw"] + +[tool.pytest.ini_options] +testpaths = ["tests"] +# Integration tests need wiki/db credentials (see conftest.py pytest_addoption) +# and are excluded by default. Run them explicitly with: +# uv run pytest tests/integration -o addopts="" --wiki_domain=... --wiki_username=... --wiki_password=... +addopts = "--cov --cov-config=pyproject.toml --cov-report=term-missing --ignore=tests/integration" +norecursedirs = ["dist", "build", ".tox"] +asyncio_default_fixture_loop_scope = "function" +# Third-party warnings that are not actionable in this repo. Everything +# emitted by our own code is either fixed or explicitly expected via +# per-test filterwarnings markers. +# KNOWN RESIDUAL: a handful of pydantic class-based-config deprecations +# from oold/prefect are emitted at import time under state that no pytest +# or interpreter filter reaches; they still show up in the summary. +filterwarnings = [ + # oold still uses pydantic-v1-style class-based Config (pydantic v2 deprecation) + "ignore:Support for class-based `config` is deprecated:DeprecationWarning", + # prefect 2.x internals: pydantic v2 deprecations and vendored starlette + "ignore:The `__fields__` attribute is deprecated:DeprecationWarning", + "ignore:The `__fields_set__` attribute is deprecated:DeprecationWarning", + "ignore:The private method `_iter` will be removed:DeprecationWarning", + "ignore:Please use `import python_multipart` instead:PendingDeprecationWarning", + # sqlalchemy reflection notes from the prefect test harness + "ignore:Skipped unsupported reflection", + # datamodel-code-generator does not know OSW's custom JSON-schema formats + "ignore:format of '.*' not understood:UserWarning", + # rdflib internals + "ignore:Dataset.default_context is deprecated:DeprecationWarning", + "ignore:ConjunctiveGraph is deprecated:DeprecationWarning", +] + +[tool.coverage.run] +branch = true +source = ["osw"] + +[tool.coverage.paths] +source = ["src/", "*/site-packages/"] + +[tool.coverage.report] +# Regexes for lines to exclude from consideration +exclude_lines = [ + # Have to re-enable the standard pragma + "pragma: no cover", + # Don't complain about missing debug-only code: + "def __repr__", + "if self\\.debug", + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", + # Don't complain if non-runnable code isn't run: + "if 0:", + "if __name__ == .__main__.:", +] + +[tool.ruff] +target-version = "py310" +line-length = 88 # kept from the previous black configuration +fix = true +extend-exclude = [ + "src/osw/model/entity.py", # autogenerated + "*.ipynb", # tutorial notebooks were never lint targets +] + +[tool.ruff.lint] +select = [ + # flake8-2020 + "YTT", + # flake8-bandit + "S", + # flake8-bugbear + "B", + # flake8-builtins + "A", + # flake8-comprehensions + "C4", + # flake8-debugger + "T10", + # flake8-simplify + "SIM", + # isort + "I", + # mccabe + "C90", + # pycodestyle + "E", "W", + # pyflakes + "F", + # pygrep-hooks + "PGH", + # pyupgrade + "UP", + # ruff + "RUF", + # tryceratops + "TRY", +] +ignore = [ + # -- aligned with oold-python ------------------------------------------ + # LineTooLong (formatter handles wrapping) + "E501", + # DoNotAssignLambda + "E731", + # complex-structure (was effectively off in the old flake8 setup too) + "C901", + # raise-vanilla-args + "TRY003", + # mutable-class-default (pydantic-style class attributes) + "RUF012", + # builtin shadowing in APIs kept for backwards compatibility + "A001", "A002", + # -- legacy debt: pre-existing findings, to be removed incrementally ---- + # pre-PEP-585/604 annotations (Optional[X], List[...]); mass-rewriting + # annotations in this pydantic-heavy codebase deserves its own PR + "UP006", "UP007", "UP035", "UP045", + # implicit Optional in defaults + "RUF013", + # style simplifications with many pre-existing hits + "SIM101", "SIM102", "SIM105", "SIM108", "SIM118", + "C408", "C416", + # warnings without stacklevel / zip without strict + "B028", "B905", + # exception-handling style (changes semantics/tracebacks; own PR) + "B904", "TRY002", "TRY004", "TRY300", "TRY301", "TRY400", + # blanket noqa directives from the flake8 era + "PGH004", + # try-except-pass + "S110", +] + +[tool.ruff.lint.per-file-ignores] +"__init__.py" = ["F401"] # re-exports (kept from the old flake8 config) +"tests/**" = ["S", "SIM117"] # bandit rules and nested with-statements in tests +"examples/**" = ["S", "E402", "F401", "SIM115"] # illustrative scripts +"scripts/**" = ["S"] + +[tool.ruff.format] +preview = true + +[tool.semantic_release] +# No version_toml/version_variables: the package version is derived from +# the git tag by hatch-vcs, so semantic-release only computes the next +# version from the conventional commits, updates the changelog, commits, +# tags (vX.Y.Z) and creates the GitHub release. Publishing to PyPI happens +# in the same workflow run (on-release-main.yml). +commit_parser = "conventional" +tag_format = "v{version}" +commit_message = "chore(release): v{version} [skip ci]" +# our history starts at v0.x; without this, PSR would jump a 0.x baseline +# straight to 1.0.0 (moot at >=1.0.0, kept for copy-paste safety) +allow_zero_version = true +exclude_commit_patterns = ['''chore\(release\):.*'''] + +[tool.semantic_release.changelog] +# prepend new versions at the insertion flag, keep the manual history below +mode = "update" +insertion_flag = "" + +[tool.semantic_release.changelog.default_templates] +changelog_file = "CHANGELOG.md" + +[tool.ty.environment] +python = "./.venv" +python-version = "3.10" + +[tool.ty.src] +# Excluded from type checking: +# - src/osw/model/entity.py: generated (datamodel-code-generator) models +# - examples, scripts: illustrative/maintenance code, not part of the package +# - tests: not yet type-clean, tightened in a follow-up +exclude = [ + "src/osw/model/entity.py", + "examples", + "scripts", + "tests", + "docs", +] + +[tool.ty.rules] +# First-time ty adoption on a codebase with heavy pydantic-v1-style +# metaprogramming: the rules below have hundreds of pre-existing findings +# and are downgraded to "ignore" for now. Tighten incrementally by +# removing entries from this list and fixing what surfaces. +unresolved-attribute = "ignore" +invalid-argument-type = "ignore" +invalid-parameter-default = "ignore" +invalid-assignment = "ignore" +unsupported-operator = "ignore" +not-subscriptable = "ignore" +invalid-return-type = "ignore" +not-iterable = "ignore" +no-matching-overload = "ignore" +missing-argument = "ignore" +deprecated = "ignore" +call-non-callable = "ignore" +possibly-missing-submodule = "ignore" +invalid-method-override = "ignore" +unused-awaitable = "ignore" +unknown-argument = "ignore" + +[tool.deptry] +extend_exclude = ["examples", "scripts", "docs"] + +[tool.deptry.package_module_name_map] +opensemantic-core = "opensemantic" +opensemantic-base = "opensemantic" +pybars3-wheel = "pybars" +"backports.strenum" = "backports" +# extras packages not installed in the dev env, mapped explicitly so +# deptry does not have to guess ("Assuming ..." warnings) +psycopg2 = "psycopg2" +openpyxl = "openpyxl" +pysimplegui = "PySimpleGUI" + +[tool.deptry.per_rule_ignores] +# DEP002: declared but not imported anywhere in src +# (extras packages are not imported by the package itself) +DEP002 = [ + "psycopg2", + "openpyxl", + "pysimplegui", + "anyio", + "osw", +] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index c9a3bc47..00000000 --- a/setup.cfg +++ /dev/null @@ -1,211 +0,0 @@ -# This file is used to configure your project. -# Read more about the various options under: -# https://setuptools.pypa.io/en/latest/userguide/declarative_config.html -# https://setuptools.pypa.io/en/latest/references/keywords.html - -[metadata] -name = osw -description = Python toolset for data processing, queries, wikicode generation and page manipulation -author = OpenSemanticWorld -author_email = team@opensemantic.world -license = AGPL-3.0-or-later -license_files = LICENSE.txt -long_description = file: README.md -long_description_content_type = text/markdown; charset=UTF-8; variant=GFM -url = https://github.com/OpenSemanticLab/osw-python -# Add here related links, for example: -project_urls = - Documentation = https://opensemanticlab.github.io/osw-python/ - Source = https://github.com/OpenSemanticLab/osw-python - Changelog = https://github.com/OpenSemanticLab/osw-python/blob/main/CHANGELOG.md -# Tracker = https://github.com/pyscaffold/pyscaffold/issues -# Conda-Forge = https://anaconda.org/conda-forge/pyscaffold - Download = https://pypi.org/project/osw/#files -# Twitter = https://twitter.com/PyScaffold - -# Change if running only on Windows, Mac or Linux (comma-separated) -platforms = any - -# Add here all kinds of additional classifiers as defined under -# https://pypi.org/classifiers/ -classifiers = - Development Status :: 3 - Alpha - Programming Language :: Python - - -[options] -zip_safe = False -packages = find_namespace: -include_package_data = True -package_dir = - =src - -# Require a min/specific Python version (comma-separated conditions) -python_requires = >=3.10, <3.14 - -# Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0. -# Version specifiers like >=2.2,<3.0 avoid problems due to API changes in -# new major versions. This works if the required packages follow Semantic Versioning. -# For more information, check out https://semver.org/. -install_requires = - oold>=0.15.0 - opensemantic - opensemantic.core>=0.57.4 - opensemantic.base>=0.42.7 - pydantic[email]>=1.10.17 - datamodel-code-generator==0.51.0 - black - isort - ruamel.yaml<0.19.0 - mwclient>=0.11.0 - rdflib - PyLD - SPARQLWrapper - jsonpath-ng - numpy - pyyaml - pandas - typing_extensions - pathlib - sphinx - chardet - matplotlib - scipy - dask - asyncio - tqdm - pybars3-wheel - -[options.packages.find] -where = src -exclude = - tests - -[options.extras_require] -# Add here additional requirements for extra features, to install with: -# `pip install osw[PDF]` like: -# PDF = ReportLab; RXP -wikitext = - mwparserfromhell -DB = - psycopg2 - sqlalchemy -S3 = - boto3 -dataimport = - geopy - deepl - openpyxl -UI = - pysimplegui -workflow = - prefect>=2.20.25,<3.0 - # prefect 2.20.25 is the final 2.x release (no backports). Its - # GatherTaskGroup subclasses anyio's TaskGroup but doesn't implement - # create_task, which newer anyio 4.x made abstract (broken on 4.14, - # verified good on 4.6.2); hold anyio to the last verified-good 4.6 line - # so the prefect-2.x flow engine can still instantiate task groups. - anyio>=4.4.0,<4.7 -tutorial = - %(dataimport)s -all = - %(dataimport)s - %(DB)s - %(UI)s - %(S3)s - %(wikitext)s - - -# Add here dev requirements (semicolon/line-separated) -dev = - pre-commit>=3.2.0 - tox - -# Add here test requirements (semicolon/line-separated) -testing = - pytest-asyncio - # inherit the capped prefect pin (<3.0); a bare "prefect" here resolved to - # 3.x in CI, whose server API breaks the prefect-2.20-targeted tests - %(workflow)s - setuptools - pytest - pytest-cov - pytest-mock - geopy - deepl - sqlalchemy - psycopg2-binary # see: https://www.psycopg.org/docs/install.html#psycopg-vs-psycopg-binary - mwparserfromhell - jsondiff - -[options.entry_points] -# Add here console scripts like: -# console_scripts = -# script_name = osw.module:function -# For example: -# console_scripts = -# fibonacci = osw.skeleton:run -# And any other entry points, for example: -# pyscaffold.cli = -# awesome = pyscaffoldext.awesome.extension:AwesomeExtension - -[tool:pytest] -# Specify command line options as you would do when invoking pytest directly. -# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml -# in order to write a coverage file that can be read by Jenkins. -# CAUTION: --cov flags may prohibit setting breakpoints while debugging. -# Comment those flags to avoid this pytest issue. -addopts = - --cov osw --cov-report term-missing - --verbose -norecursedirs = - dist - build - .tox -testpaths = tests -asyncio_default_fixture_loop_scope = function - -# Use pytest markers to select/deselect specific tests -# markers = -# slow: mark tests as slow (deselect with '-m "not slow"') -# system: mark end-to-end system tests - -[devpi:upload] -# Options for the devpi: PyPI server and packaging tool -# VCS export must be deactivated since we are using setuptools-scm -no_vcs = 1 -formats = bdist_wheel - -[tool.black] -line-length = 88 - -[flake8] -# Some sane defaults for the code style checker flake8 -# 79 characters is the default line length according to PEP8 -# 88 is the option recommended by black -max_line_length = 88 -select = C,E,F,W,B,B950 -extend_ignore = E203, E501, W503 -# ^ Black-compatible -# E203 and W503 have edge cases handled by black -# E501 allows a line length of 79 only -exclude = - .tox - build - dist - .eggs - docs/conf.py - src/osw/model/entity.py #autogenerated -per-file-ignores = - __init__.py:F401 - -[pyscaffold] -# PyScaffold's parameters when the project was created. -# This will be used when updating. Do not change! -version = 4.3.1 -package = osw -extensions = - github_actions - markdown - no_skeleton - pre_commit diff --git a/setup.py b/setup.py deleted file mode 100644 index 4187093f..00000000 --- a/setup.py +++ /dev/null @@ -1,22 +0,0 @@ -""" - Setup file for osw. - Use setup.cfg to configure your project. - - This file was generated with PyScaffold 4.3.1. - PyScaffold helps you to put up the scaffold of your new Python project. - Learn more under: https://pyscaffold.org/ -""" - -from setuptools import setup - -if __name__ == "__main__": - try: - setup(use_scm_version={"version_scheme": "no-guess-dev"}) - except: # noqa - print( - "\n\nAn error occurred while building the project, " - "please ensure you have the most updated version of setuptools, " - "setuptools_scm and wheel with:\n" - " pip install -U setuptools setuptools_scm wheel\n\n" - ) - raise diff --git a/src/osw/auth.py b/src/osw/auth.py index 04134a9d..8408cd35 100644 --- a/src/osw/auth.py +++ b/src/osw/auth.py @@ -1,6 +1,8 @@ from __future__ import annotations import getpass +import os +import warnings from enum import Enum from pathlib import Path from typing import List, Optional, Union @@ -160,6 +162,17 @@ def get_credential(self, config: CredentialConfig) -> BaseCredential: return match return self._oold_to_osw(match) + # Environment variables (e.g. loaded from a .env file) come before + # any interactive fallback; credentials are kept in memory only. + username = os.getenv("OSW_USERNAME") or os.getenv("OSL_USERNAME") + password = os.getenv("OSW_PASSWORD") or os.getenv("OSL_PASSWORD") + if username is not None and password is not None: + cred = CredentialManager.UserPwdCredential( + username=username, password=password, iri=config.iri + ) + self.add_credential(cred) + return cred + if config.fallback is CredentialManager.CredentialFallback.ask: if self.cred_filepath: filepath_str = "', '".join([str(fp) for fp in self.cred_filepath]) @@ -172,9 +185,9 @@ def get_credential(self, config: CredentialConfig) -> BaseCredential: cred = CredentialManager.UserPwdCredential( username=username, password=password, iri=config.iri ) + # kept in memory only; persisting credentials to a file happens + # exclusively through an explicit save_credentials_to_file() call self.add_credential(cred) - if self.cred_filepath: - self.save_credentials_to_file() return cred return None @@ -202,10 +215,7 @@ def iri_in_credentials(self, iri: str) -> bool: bool True if a credential exists for the given iri """ - for cred in self._credentials: - if cred.iri == iri: - return True - return False + return any(cred.iri == iri for cred in self._credentials) def iri_in_file(self, iri: str) -> bool: """checks if a credential for a given iri exists in the file @@ -224,7 +234,7 @@ def iri_in_file(self, iri: str) -> bool: for fp in self.cred_filepath: if fp != "": if Path(fp).exists(): - with open(fp, "r", encoding="utf-8") as stream: + with open(fp, encoding="utf-8") as stream: try: accounts = yaml.safe_load(stream) if accounts is None: @@ -253,6 +263,13 @@ def save_credentials_to_file( If True, the cred_filepath is set to the given filepath. If False, the cred_filepath of the CredentialManager is not changed. """ + warnings.warn( + "save_credentials_to_file() writes credentials to disk in clear " + "text and is deprecated. Prefer environment variables (e.g. via " + "a .env file) or in-memory credentials.", + DeprecationWarning, + stacklevel=2, + ) cred_filepaths = [filepath] if filepath is None: cred_filepaths = self.cred_filepath @@ -279,65 +296,5 @@ def save_credentials_to_file( else: print(f"Credentials file created at '{fp.resolve()}'.") - # Creating or updating .gitignore file in the working directory - cwd = Path.cwd() - potential_fp = [ - cwd / ".gitignore", - cwd.parent / ".gitignore", - ] - gitignore_fp = potential_fp[0] - # Stops if a .gitignore file is found - for fp in potential_fp: - if fp.exists(): - gitignore_fp = fp - break - # Creates a .gitignore file if none is found - if not gitignore_fp.exists(): - if not gitignore_fp.parent.exists(): - gitignore_fp.parent.mkdir(parents=True) - gitignore_fp.touch() - # Reads the .gitignore file - with open(gitignore_fp, "r") as stream: - content = stream.read() - comment_set = False - osw_dir_added = False - # For every file path in the list of credentials file paths - for _ii, fp in enumerate(cred_filepaths): - if default_paths.osw_files_dir in fp.parents and not osw_dir_added: - msg = ( - f"Adding '{default_paths.osw_files_dir}' to gitignore file " - f"'{gitignore_fp}'." - ) - containing_gitignore = gitignore_fp.parent.absolute() - if containing_gitignore in default_paths.osw_files_dir.parents: - # If the default_path.osw_files_dir is a subdirectory of the directory - # containing the .gitignore file, add the relative path to the - # .gitignore file - rel = default_paths.osw_files_dir.relative_to(containing_gitignore) - to_add = f"\n*/{str(rel.as_posix())}/*" - else: - # Test if the default_path.osw_files_dir is a subdirectory of the - # directory containing the .gitignore file - to_add = ( - f"\n*/{default_paths.osw_files_dir.absolute().as_posix()}/*" - ) - osw_dir_added = True - else: - msg = f"Adding '{fp.name}' to gitignore file '{gitignore_fp}'." - to_add = f"\n*/{fp.name}" - if not to_add or to_add in content: - continue - print(msg) - with open(gitignore_fp, "a") as stream: - # Only add comment if not already set - comment = ( - "\n# Automatically added by osw.auth.CredentialManager." - "save_credentials_to_file:" - ) - if not comment_set and comment not in content: - stream.write(comment) - comment_set = True - stream.write(to_add) - CredentialManager.CredentialConfig.update_forward_refs() diff --git a/src/osw/controller/__init__.py b/src/osw/controller/__init__.py index c4b5aa7a..c27549a9 100644 --- a/src/osw/controller/__init__.py +++ b/src/osw/controller/__init__.py @@ -9,11 +9,11 @@ # imports of controllers for always present models # note: to keep this import auto-removal per pre-commit hook is disabled -from osw.controller.entity import Entity # noqa: F401 +from osw.controller.entity import Entity # conditional imports # Note: does not work if the module is imported before the model is loaded models = [m[0] for m in inspect.getmembers(model)] if "Database" in models: - from osw.controller.database import DatabaseController # noqa: F401 + from osw.controller.database import DatabaseController diff --git a/src/osw/controller/entity.py b/src/osw/controller/entity.py index 50dd9a0b..3ab43577 100644 --- a/src/osw/controller/entity.py +++ b/src/osw/controller/entity.py @@ -3,7 +3,7 @@ class Entity(model.Entity): def explain(self): - print(f"Entity with label '{str(self.label[0].text)}'") + print(f"Entity with label '{self.label[0].text!s}'") # model.Entity = Entity diff --git a/src/osw/controller/file/wiki.py b/src/osw/controller/file/wiki.py index 19e76439..8a032291 100644 --- a/src/osw/controller/file/wiki.py +++ b/src/osw/controller/file/wiki.py @@ -130,8 +130,7 @@ def put(self, file: IO, **kwargs: Dict[str, Any]): if key in OSW.StoreEntityParam.__fields__ and value is not None } for key in ["entities", "namespace"]: - if key in se_params: - del se_params[key] # avoid duplicated kwargs + se_params.pop(key, None) # avoid duplicated kwargs self.osw.store_entity( OSW.StoreEntityParam( entities=[self.cast(model.WikiFile, **wf_params)], @@ -194,9 +193,7 @@ def _init(self, name=None, suffix=None): if self.namespace is None: self.namespace = get_namespace(self) # update meta information - if not hasattr(self, "meta"): - self.meta = model.Meta() - elif self.meta is None: + if not hasattr(self, "meta") or self.meta is None: self.meta = model.Meta() if not hasattr(self.meta, "wiki_page") or self.meta.wiki_page is None: self.meta.wiki_page = model.WikiPage() diff --git a/src/osw/controller/page_package.py b/src/osw/controller/page_package.py index 9fce6958..da827120 100644 --- a/src/osw/controller/page_package.py +++ b/src/osw/controller/page_package.py @@ -222,7 +222,7 @@ def read_package_info_file( ) else: package_info_fp = matching_files_in_dir[0] - with open(package_info_fp, "r") as package_info_fp: + with open(package_info_fp) as package_info_fp: package_info = json.load(package_info_fp) return package_info @@ -301,7 +301,7 @@ def get_required_pages_from_file(fp: Union[str, Path]) -> List[str]: pre_suffix = ".slot_main" slot_name = pre_suffix.split(".slot_")[-1] - with open(fp, "r", encoding="utf-8") as f: + with open(fp, encoding="utf-8") as f: content = f.read() if not PATTERNS_PER_SLOT.get(slot_name): return required_pages @@ -321,32 +321,28 @@ def get_required_pages_from_file(fp: Union[str, Path]) -> List[str]: intermediate = [] if "-" in res: intermediate.append(res.split("-")[-1]) - elif "." or ":" in res: + elif True: intermediate.extend(res.split(".")) # intermediate.extend(res.split(":")) else: intermediate.append(res) - required_pages.extend( - [ - "Property:" + s - for s in intermediate - if not s.startswith("Property:") - and not check_for_exceptions(s) - # only here to catch exceptions early - ] - ) - elif "template" in pattern.group_keys: - for match in match_res: - required_pages.append(match) - elif "item" in pattern.group_keys: - for match in match_res: - required_pages.append(match) - elif "file" in pattern.group_keys: + required_pages.extend([ + "Property:" + s + for s in intermediate + if not s.startswith("Property:") + and not check_for_exceptions(s) + # only here to catch exceptions early + ]) + elif ( + "template" in pattern.group_keys + or "item" in pattern.group_keys + or "file" in pattern.group_keys + ): for match in match_res: required_pages.append(match) - return_obj = list( - set(entry for entry in required_pages if not check_for_exceptions(entry)) - ) + return_obj = list({ + entry for entry in required_pages if not check_for_exceptions(entry) + }) return_obj.sort() return return_obj @@ -572,7 +568,7 @@ def get_required_pages( ) required_pages_dict = {} if required_pages_path.exists() and not params.direct_call: - with open(required_pages_path, "r") as f: + with open(required_pages_path) as f: self.requiredPages = json.load(f)["list"] else: self.requiredPages = [] @@ -791,18 +787,18 @@ def recursive( ) prev_missing_page_labels = {} if missing_pages_labeled_fp.exists(): - with open(missing_pages_labeled_fp, "r", encoding="utf-8") as f: + with open(missing_pages_labeled_fp, encoding="utf-8") as f: prev_missing_page_labels = json.load(f) # Create a new dict for the labels of missing pages to avoid unwanted # migration of "old" keys missing_pages_labeled = {} # Only query pages that are not yet labeled pages_to_query = list( - set(missing_pages) - set(list(prev_missing_page_labels.keys())) + set(missing_pages) - set(prev_missing_page_labels.keys()) ) # pages that are not yet labeled found_pages = {} - if not len(pages_to_query) == 0: + if len(pages_to_query) != 0: # Get the labels of the missing pages from the OSW wtsite_obj = WtSite( WtSite.WtSiteConfig( diff --git a/src/osw/core.py b/src/osw/core.py index cc1a3a9e..b2b83212 100644 --- a/src/osw/core.py +++ b/src/osw/core.py @@ -124,12 +124,12 @@ def __init__(self, **data: Any): # implement resolver backend with osw.load_entity class OswDefaultBackend(Backend): - # oold.backend.interface is pydantic v2, so we cannot use # our v1 OSW model as attribute directly osw_obj: Any - def resolve_iris(self, iris: List[str]) -> dict[str, dict]: + # stub satisfying the oold Backend interface; resolve() does the work + def resolve_iris(self, iris: List[str]) -> dict[str, dict]: # ty: ignore[empty-body] pass def resolve(self, request: ResolveParam): @@ -338,9 +338,9 @@ def register_schema(self, schema_registration: SchemaRegistration): if "allOf" not in schema: schema["allOf"] = [] for base in schema_registration.schema_bases: - schema["allOf"].append( - {"$ref": f"/wiki/{base}?action=raw&slot=jsonschema"} - ) + schema["allOf"].append({ + "$ref": f"/wiki/{base}?action=raw&slot=jsonschema" + }) page.set_slot_content("jsonschema", schema) else: @@ -758,7 +758,7 @@ def _fetch_schema( # with the same content content = "" - with open(temp_model_path, "r", encoding="utf-8") as f: + with open(temp_model_path, encoding="utf-8") as f: content = f.read() os.remove(temp_model_path) @@ -792,21 +792,19 @@ def _fetch_schema( # Pattern to match empty subclasses # Matches: class SubClass(BaseClass): # followed by optional whitespace/docstring and pass - pattern = "".join( - ( - r"class\s+", # 'class' keyword - r"(\w+)", # capture subclass name - r"\s*\(\s*", # opening parenthesis - r"(\w+)", # capture base class name - r"\s*\)\s*:", # closing parenthesis and colon - r"\s*", # optional whitespace - r'(?:\n\s*(?:""".*?"""|\'\'\'.*?\'\'\')' - # optional docstring (triple quotes) - r"\s*)?", # end optional docstring - r"\n\s*pass\s*", # pass statement - r"(?:\n|$)", # newline or end of string - ) - ) + pattern = "".join(( + r"class\s+", # 'class' keyword + r"(\w+)", # capture subclass name + r"\s*\(\s*", # opening parenthesis + r"(\w+)", # capture base class name + r"\s*\)\s*:", # closing parenthesis and colon + r"\s*", # optional whitespace + r'(?:\n\s*(?:""".*?"""|\'\'\'.*?\'\'\')' + # optional docstring (triple quotes) + r"\s*)?", # end optional docstring + r"\n\s*pass\s*", # pass statement + r"(?:\n|$)", # newline or end of string + )) # Find all empty subclasses matches = list(re.finditer(pattern, content, re.MULTILINE | re.DOTALL)) @@ -849,7 +847,6 @@ def _fetch_schema( content = re.sub(pattern_replace, base_class_name, content) if fetchSchemaParam.mode == "replace": - header = "from uuid import uuid4\n" # if target path is default model/entity.py, we need to add imports @@ -901,7 +898,7 @@ def _fetch_schema( if fetchSchemaParam.mode == "append": org_content = "" - with open(result_model_path, "r", encoding="utf-8") as f: + with open(result_model_path, encoding="utf-8") as f: org_content = f.read() pattern = re.compile( @@ -1185,7 +1182,8 @@ def load_entity( if jsondata: for category in jsondata["type"]: schema = ( - self.site.get_page( + self.site + .get_page( WtSite.GetPageParam( titles=[category], offline_pages=param.offline_pages ) @@ -1236,7 +1234,8 @@ def load_entity( entity: model.Entity = cls(**jsondata) except Exception as e: _logger.error(f"Error creating entity from page {page.title}: {e}") - entity = None + # legacy: `entity` is annotated as OswBaseModel and Entity above + entity = None # ty: ignore[conflicting-declarations] if entity is not None: # make sure we do not override existing metadata @@ -1301,13 +1300,7 @@ def __setattr__(self, key, value): field_name: value.get(field_name, self.overwrite) for field_name in self.model.__fields__.keys() } - elif key == "overwrite": - if self.per_property is not None: - self._per_property = { - field_name: self.per_property.get(field_name, self.overwrite) - for field_name in self.model.__fields__.keys() - } - elif key == "model": + elif key == "overwrite" or key == "model": if self.per_property is not None: self._per_property = { field_name: self.per_property.get(field_name, self.overwrite) @@ -1399,7 +1392,7 @@ def _apply_overwrite_policy(param: OSW._ApplyOverwriteParam) -> WtPage: def set_content(content_to_set: dict) -> None: if param.debug: - print(f"content_to_set: {str(content_to_set)}") + print(f"content_to_set: {content_to_set!s}") for slot_ in content_to_set.keys(): page.set_slot_content(slot_, content_to_set[slot_]) @@ -1458,7 +1451,7 @@ def set_content(content_to_set: dict) -> None: if remote_content["footer"]: new_content["footer"] = remote_content["footer"] if param.debug: - print(f"'remote_content': {str(remote_content)}") + print(f"'remote_content': {remote_content!s}") # Get the local content # Properties that are not set in the local content will be set to None # We want those not to be listed as keys @@ -1466,7 +1459,7 @@ def set_content(content_to_set: dict) -> None: if param.remove_empty: remove_empty(local_content["jsondata"]) if param.debug: - print(f"'local_content': {str(local_content)}") + print(f"'local_content': {local_content!s}") # Apply the overwrite logic # a) If there is a key in the remote content that is not in the local # content, we have to keep it @@ -1479,53 +1472,44 @@ def set_content(content_to_set: dict) -> None: # if key not in local_content["jsondata"].keys() # } if param.debug: - print(f"'New content' after 'remote' update: {str(new_content)}") + print(f"'New content' after 'remote' update: {new_content!s}") # b) If there is a key in the local content that is not in the remote # content, we have to keep it - new_content["jsondata"].update( - { - key: value - for (key, value) in local_content["jsondata"].items() - if key not in remote_content["jsondata"].keys() - } - ) + new_content["jsondata"].update({ + key: value + for (key, value) in local_content["jsondata"].items() + if key not in remote_content["jsondata"].keys() + }) if param.debug: - print(f"'New content' after 'local' update: {str(new_content)}") + print(f"'New content' after 'local' update: {new_content!s}") # c) If there is a key in both contents, we have to apply the overwrite # logic # todo: include logic for hidden and read_only properties! - new_content["jsondata"].update( - { - key: value - for (key, value) in local_content["jsondata"].items() - if param.policy.get_overwrite_setting(key) == OverwriteOptions.true - } - ) + new_content["jsondata"].update({ + key: value + for (key, value) in local_content["jsondata"].items() + if param.policy.get_overwrite_setting(key) == OverwriteOptions.true + }) if param.debug: - print(f"'New content' after 'True' update: {str(new_content)}") - new_content["jsondata"].update( - { - key: value - for (key, value) in remote_content["jsondata"].items() - if param.policy.get_overwrite_setting(key) == OverwriteOptions.false - } - ) + print(f"'New content' after 'True' update: {new_content!s}") + new_content["jsondata"].update({ + key: value + for (key, value) in remote_content["jsondata"].items() + if param.policy.get_overwrite_setting(key) == OverwriteOptions.false + }) if param.debug: - print(f"'New content' after 'False' update: {str(new_content)}") - new_content["jsondata"].update( - { - key: value - for (key, value) in local_content["jsondata"].items() - if ( - param.policy.get_overwrite_setting(key) - == OverwriteOptions.only_empty - and is_empty(remote_content["jsondata"].get(key)) - ) - } - ) + print(f"'New content' after 'False' update: {new_content!s}") + new_content["jsondata"].update({ + key: value + for (key, value) in local_content["jsondata"].items() + if ( + param.policy.get_overwrite_setting(key) == OverwriteOptions.only_empty + and is_empty(remote_content["jsondata"].get(key)) + ) + }) if param.debug: - print(f"'New content' after 'only empty' update: {str(new_content)}") - print(f"'New content' to be stored: {str(new_content)}") + print(f"'New content' after 'only empty' update: {new_content!s}") + print(f"'New content' to be stored: {new_content!s}") set_content(new_content) return page # Guard clause --> exit function @@ -1912,12 +1896,12 @@ class QueryInstancesParam(OswBaseModel): @staticmethod def get_full_page_name_parts( - category_: Union[str, Type[OswBaseModel]] + category_: Union[str, Type[OswBaseModel]], ) -> Dict[str, str]: error_msg = ( f"Category must be a string like 'Category:' or a " f"dataclass subclass with a 'type' attribute. This error occurred on " - f"'{str(category_)}'" + f"'{category_!s}'" ) if isinstance(category_, str): string_to_split = category_ diff --git a/src/osw/custom_types.py b/src/osw/custom_types.py index 03e520df..970255b3 100644 --- a/src/osw/custom_types.py +++ b/src/osw/custom_types.py @@ -1,15 +1,12 @@ import sys from pathlib import Path +from types import NoneType # noqa: F401 from pydantic.v1.types import FilePath as PydanticFilePath from pydantic.v1.validators import path_validator # , path_exists_validator -if sys.version_info < (3, 10): - NoneType = type(None) -else: - from types import NoneType # noqa: F401 if sys.version_info < (3, 11): - from backports.strenum import StrEnum # noqa: F401 + from backports.strenum import StrEnum else: from enum import StrEnum # noqa: F401 diff --git a/src/osw/data/import_utility.py b/src/osw/data/import_utility.py index 6730513c..fb78c89f 100644 --- a/src/osw/data/import_utility.py +++ b/src/osw/data/import_utility.py @@ -302,9 +302,7 @@ def isclass(obj, cls): obj_type.sort() if isinstance(cls_type, list): cls_type.sort() - if obj_type == cls_type and obj_type is not None: - return True - return False + return bool(obj_type == cls_type and obj_type is not None) def flatten_list(nested_list): @@ -412,7 +410,7 @@ def jsonpath_search_and_return_list( result = jp_parse.find(search_tar[str(cls_type)]) except Exception as e: warnings.warn( - f"jsonpath_search_and_return_list() threw and " f"exception:\n{str(e)}", + f"jsonpath_search_and_return_list() threw and exception:\n{e!s}", stacklevel=2, ) result = jp_parse.find(search_tar) @@ -424,9 +422,7 @@ def jsonpath_search_and_return_list( res_type = res.value["type"] res_type.sort() append = False - if class_to_match is None: - append = True - elif isclass(res.value, class_to_match): + if class_to_match is None or isclass(res.value, class_to_match): append = True if append: if val_key is None: @@ -481,14 +477,9 @@ def nan_empty_or_none(inp: Any) -> bool: result """ if isinstance(inp, str): - if inp == "nan" or inp == "": - return True - return False + return bool(inp == "nan" or inp == "") elif isinstance(inp, list): - for ele in inp: - if not nan_empty_or_none(ele): - return False - return True + return all(nan_empty_or_none(ele) for ele in inp) elif inp is None: return True else: @@ -800,9 +791,7 @@ def test_if_empty_list_or_none(obj) -> bool: if obj is None: return True elif isinstance(obj, list): - if len(obj) == 0: - return True - elif len([item for item in obj if item is not None]) == 0: + if len(obj) == 0 or len([item for item in obj if item is not None]) == 0: return True return False @@ -905,7 +894,7 @@ def translate_list_with_deepl( cred_filepath = default_paths.cred_filepath if translations is None: translations = {} - domains, accounts = wt.read_domains_from_credentials_file(cred_filepath) + _domains, accounts = wt.read_domains_from_credentials_file(cred_filepath) domain = "api-free.deepl.com" auth = accounts[domain]["password"] translator = deepl.Translator(auth) diff --git a/src/osw/defaults.py b/src/osw/defaults.py index 56352bd1..8fdac59b 100644 --- a/src/osw/defaults.py +++ b/src/osw/defaults.py @@ -120,9 +120,10 @@ def update_attr(set_attr, to_update, old_val, new_val): old_rel_path = getattr(self, attr_name).relative_to(old_val) new_rel_path = new_val / old_rel_path setattr(self, attr_name, new_rel_path) + cls_name = type(self).__name__ print( - f"Following the setting of {self.__name__}.{set_attr}, " - f"{self.__name__}.{attr_name} was updated to {new_rel_path}." + f"Following the setting of {cls_name}.{set_attr}, " + f"{cls_name}.{attr_name} was updated to {new_rel_path}." ) if attr_name == "base": @@ -156,7 +157,7 @@ class Params(Defaults): @validator("wiki_domain") def validate_wiki_domain(cls, v): pattern = r"^(?!-)[A-Za-z0-9.-]{1,63}(? TextIO: mode = self.mode kwargs["mode"] = mode if self.file_io is None or self.file_io.closed: - self.file_io = open(self.path, **kwargs) + self.file_io = open(self.path, **kwargs) # noqa: SIM115 handle kept as instance state return self.file_io def close(self) -> None: - """Close the file, if not already closed.""" - if self.file_io is None or self.file_io.closed: - warn("File already closed or not opened.") - else: + """Close the file. Like io streams, closing an already closed (or + never opened) file is a silent no-op.""" + if self.file_io is not None and not self.file_io.closed: self.file_io.close() def read(self, n: int = -1) -> AnyStr: @@ -736,7 +709,7 @@ def __init__( data["meta"] = model.Meta(wiki_page=wiki_page) data["title"] = title # Set change_id to existing meta - for meta in [data.get("meta"), getattr(data["source_file_controller"], "meta")]: + for meta in [data.get("meta"), data["source_file_controller"].meta]: if meta is not None: if getattr(meta, "change_id", None) is None: meta.change_id = [data["change_id"]] diff --git a/src/osw/ontology.py b/src/osw/ontology.py index 9652750c..f3380f95 100644 --- a/src/osw/ontology.py +++ b/src/osw/ontology.py @@ -8,7 +8,6 @@ from pydantic.v1 import PrivateAttr from pyld import jsonld from rdflib import Graph -from typing_extensions import deprecated from osw.core import OSW, model from osw.utils.strings import camel_case, pascal_case @@ -607,12 +606,10 @@ def _apply_osw_structure(self): "de", ]: # ToDo: Support all/more languages - print( - ( - "Warning: remove value with unsupported language: ", - f"{node[key]['lang']}", - ) - ) + print(( + "Warning: remove value with unsupported language: ", + f"{node[key]['lang']}", + )) del node[key] continue elif isinstance(node[key], list): @@ -626,20 +623,16 @@ def _apply_osw_structure(self): "lang" ] not in ["en", "de"]: # ToDo: Support all/more languages - print( - ( - "Warning: remove value with unsupported language: ", - f"{node[key][i]['lang']}", - ) - ) + print(( + "Warning: remove value with unsupported language: ", + f"{node[key][i]['lang']}", + )) del node[key][i] continue else: print( - ( - "Warning: remove invalide multilang value: " - f"{node[key][i]}" - ) + "Warning: remove invalide multilang value: " + f"{node[key][i]}" ) del node[key][i] else: @@ -762,7 +755,6 @@ def _create_entities(self): if counter < limit: if "rdf_type" in node and "label" in node: - e = None try: if "owl:Class" in node["rdf_type"]: @@ -839,7 +831,6 @@ def _store_ontology(self, param: StoreOntologyParam): ) ) - @deprecated("use ontology.OntologyImporter.StoreOntologiesParam instead") class StoreOntologiesParam(model.OswBaseModel): entities: Optional[List[model.OswBaseModel]] """If we use model.Entity here, all instances are casted to model.Entity diff --git a/src/osw/params.py b/src/osw/params.py index 6be389f9..1baef4fc 100644 --- a/src/osw/params.py +++ b/src/osw/params.py @@ -1,4 +1,4 @@ -from osw.auth import CredentialManager # noqa: F401 +from osw.auth import CredentialManager from osw.core import ( # noqa: F401 OSW, OVERWRITE_CLASS_OPTIONS, @@ -7,7 +7,7 @@ ) from osw.express import DataModel, OswExpress # noqa: F401 from osw.wiki_tools import SearchParam # noqa: F401 -from osw.wtsite import WtPage, WtSite # noqa: F401 +from osw.wtsite import WtPage, WtSite # From osw.auth.CredentialManager: diff --git a/src/osw/sparql_client_smw.py b/src/osw/sparql_client_smw.py index 69b6a2cb..c2cbbd26 100644 --- a/src/osw/sparql_client_smw.py +++ b/src/osw/sparql_client_smw.py @@ -89,9 +89,7 @@ def __init__(self, endpoint, domain, auth="none", user="", password=""): zip(self.smw_encoding_lists["in"], self.smw_encoding_lists["out"]) ) self.encoding_dict = {} - self.encoding_dict_inv = dict( - (self.encoding_dict[k], k) for k in self.encoding_dict - ) + self.encoding_dict_inv = {self.encoding_dict[k]: k for k in self.encoding_dict} def create_sparql_client(self, endpoint, auth="none", user="", password=""): self.sparql = SPARQLWrapper(endpoint) @@ -158,9 +156,8 @@ def get_sparql_triplets( } } LIMIT {{{limit}}} - """.replace( - "{{{select_statement}}}", select_statement - ) + """ + .replace("{{{select_statement}}}", select_statement) .replace("{{{where_statement}}}", where_statement) .replace("{{{inner_where_statement}}}", inner_where_statement) .replace("{{{limit}}}", str(limit)) diff --git a/src/osw/utils/regex.py b/src/osw/utils/regex.py index 422ca71f..e5598ecc 100644 --- a/src/osw/utils/regex.py +++ b/src/osw/utils/regex.py @@ -110,10 +110,7 @@ def validate_group_keys(cls, group_keys, values) -> List[str]: def test_pattern(self) -> bool: """Test the pattern by asserting self.example_match.groups.values()) == self.expected_groups""" - if list(self.example_match.groups.values()) == self.expected_groups: - return True - else: - return False + return list(self.example_match.groups.values()) == self.expected_groups class MatchResult(OswBaseModel): @@ -353,9 +350,9 @@ def test_regex_pattern( } former_matches.extend(previously_unmatched) - coverage["Accumulative coverage"] = sum( - [len(result["Matching strings"]) for result in matching_results] - ) / len(strings) + coverage["Accumulative coverage"] = sum([ + len(result["Matching strings"]) for result in matching_results + ]) / len(strings) total_coverage = len(former_matches) / len(strings) coverage["Total coverage"] = total_coverage coverage["Not covered"] = 1 - total_coverage diff --git a/src/osw/utils/regex_pattern.py b/src/osw/utils/regex_pattern.py index fa3926fc..ba35c74e 100644 --- a/src/osw/utils/regex_pattern.py +++ b/src/osw/utils/regex_pattern.py @@ -73,8 +73,7 @@ expected_groups=["211104-sist-0003", "n stamped 20211116080457", ".pdf.ots"], ), RegExPatternExtended( - description="File page full page title (old format) with ISC-ID and " - "one suffix", + description="File page full page title (old format) with ISC-ID and one suffix", pattern=r"File:([A-Za-z0-9\-]+[\- ]{1}[0-9]{4})[\- ]{1}(.*)" r"(\.[a-zA-Z0-9]*[a-zA-Z]+[a-zA-Z0-9]*)", group_keys=["ISC-ID", "Label", "Suffix(es)"], diff --git a/src/osw/utils/util.py b/src/osw/utils/util.py index ba8f1588..49b8c3af 100644 --- a/src/osw/utils/util.py +++ b/src/osw/utils/util.py @@ -108,7 +108,7 @@ def flush(self): def redirect_print( - file_like: Union[IO, Path, MessageBuffer, AsyncMessageBuffer] + file_like: Union[IO, Path, MessageBuffer, AsyncMessageBuffer], ) -> Callable: def decorator(func_: Callable) -> Callable: """ @@ -315,7 +315,7 @@ def parallelize( async def _run_tasks(): loop = asyncio.get_event_loop() # ToDo: handle IO-bound different from CPU-bound tasks - # see https://docs.python.org/3/library/asyncio-eventloop.html#asyncio.loop.run_in_executor # noqa + # see https://docs.python.org/3/library/asyncio-eventloop.html#asyncio.loop.run_in_executor # None => ThreadPoolExecutor for IO-bound tasks tasks = [ loop.run_in_executor(None, functools.partial(func, item, **kwargs)) @@ -419,7 +419,7 @@ async def inner(func_, iterable_, **kwargs_): return asyncio.run(inner(func, iterable, **kwargs)) -class RedirectStdout(object): +class RedirectStdout: """Can be used as a decorator or context manager to temporarily redirect stdout to a buffer. @@ -464,7 +464,7 @@ def wrapped_function(*args, **kwargs): print("Redirecting print messages to a buffer.") message_buffer = MessageBuffer() io_buffer = StringIO() - file_as_buffer = open("xx.txt", "w") + file_as_buffer = open("xx.txt", "w") # noqa: SIM115 buffer handed to caller def prepend_timestamp(line): return f"{datetime.now().isoformat()}: {line}" @@ -611,6 +611,6 @@ def print_lines_3(num_lines): message_buffer.flush() file_as_buffer.close() print("Messages from the file buffer:") - with open("xx.txt", "r") as f: + with open("xx.txt") as f: for line_ in f.readlines(): print(line_, end="") diff --git a/src/osw/utils/wikitext.py b/src/osw/utils/wikitext.py index 180698d5..64c60fb8 100644 --- a/src/osw/utils/wikitext.py +++ b/src/osw/utils/wikitext.py @@ -78,9 +78,9 @@ def update_template_within_wikitext( # this will cleanup empty lines within the template code (wanted), but also within # the wiki text around it (unwanted) if remove_empty_lines: - new_text = "\n".join( - [ll.rstrip() for ll in str(new_text).splitlines() if ll.strip()] - ) + new_text = "\n".join([ + ll.rstrip() for ll in str(new_text).splitlines() if ll.strip() + ]) return new_text @@ -151,9 +151,9 @@ def merge_wiki_page_text( r1string += "\r\n " + str(rel1) t1.add(subtemplate_param, r1string) # print("Tmerged: " + str(t1)) - non_empty_lines = "\n".join( - [ll.rstrip() for ll in str(t1).splitlines() if ll.strip()] - ) + non_empty_lines = "\n".join([ + ll.rstrip() for ll in str(t1).splitlines() if ll.strip() + ]) return non_empty_lines @@ -214,11 +214,11 @@ def create_flat_content_structure_from_wikitext( if t_count == 0: res = text values = str(text).strip().split(";") - if array_mode == "force": - res = values - elif array_mode == "only_multiple" and len(values) > 1: - res = values - elif array_mode == "separator_present" and ";" in text: + if ( + array_mode == "force" + or (array_mode == "only_multiple" and len(values) > 1) + or (array_mode == "separator_present" and ";" in text) + ): res = values return res @@ -241,10 +241,10 @@ def find_dependencies(wikitext, debug=False): for template in code.filter_templates(recursive=True): if template.name.split(":")[0].isupper(): if debug: - print("MagicWord: {}".format(template.name)) + print(f"MagicWord: {template.name}") elif template.name[0] == "#": if debug: - print("ParserFunction: {}".format(template.name)) + print(f"ParserFunction: {template.name}") if "#set:" in template.name or "#declare:" in template.name: if ( "=" in template.name.split(":")[1] @@ -252,41 +252,41 @@ def find_dependencies(wikitext, debug=False): property_ = "Property:" + template.name.split(":")[1].split("=")[0] dependencies.append(property_) if debug: - print("=> {}".format(property_)) + print(f"=> {property_}") for param in template.params: property_ = "Property:" + param.split("=")[0] dependencies.append(property_) if debug: - print("=> {}".format(property_)) + print(f"=> {property_}") else: if debug: - print("Template: {}".format(template.name)) + print(f"Template: {template.name}") template_name = str(template.name) if ":" not in template.name: template_name = "Template:" + template_name dependencies.append(template_name) if debug: - print("=> {}".format(template_name)) + print(f"=> {template_name}") # for tag in code.filter_tags(recursive=True): # if (debug): print("Tag: {}".format(tag)) for link in code.filter_wikilinks(recursive=True): if "::" in link: if debug: - print("Annotation: {}".format(link)) + print(f"Annotation: {link}") property_ = "Property:" + link.split("::")[0].split("[[")[-1] dependencies.append(property_) if debug: - print("=> {}".format(property_)) + print(f"=> {property_}") if "Category:" in link: if debug: - print("Category: {}".format(link)) + print(f"Category: {link}") category = link.replace("[[", "").replace("]]", "") dependencies.append(str(category)) if debug: - print("=> {}".format(category)) + print(f"=> {category}") else: if debug: - print("Link: {}".format(link)) + print(f"Link: {link}") dependencies = np.unique(dependencies).tolist() # remove duplicates filtered_dependencies = [] # do not manipulate the iterated object for dependency in dependencies: @@ -297,9 +297,7 @@ def find_dependencies(wikitext, debug=False): # see https://www.semantic-mediawiki.org/wiki/Help:Special_properties if "Property:" in dependency and (" " in dependency or "_" in dependency): if debug: - print( - "Info: Remove presumptive built-in property {}".format(dependency) - ) + print(f"Info: Remove presumptive built-in property {dependency}") else: filtered_dependencies.append(dependency) return filtered_dependencies @@ -333,7 +331,7 @@ def find_dependencies_recursively(title, site, dependencies=None, debug=False): if dependency not in dependencies: # for circular dependencies dependencies.append(dependency) if debug: - print("Scan nested {}".format(dependency)) + print(f"Scan nested {dependency}") find_dependencies_recursively( dependency, site, dependencies=dependencies, debug=debug ) @@ -390,7 +388,7 @@ def get_wikitext_from_flat_content_dict(d: dict) -> str: wt += "\n}}" elif isinstance(value, list): # print("list") - wt += "\n|{}=".format(key) + wt += f"\n|{key}=" string_index = 0 for index, element in enumerate(value): if isinstance(element, dict): @@ -410,7 +408,7 @@ def get_wikitext_from_flat_content_dict(d: dict) -> str: string_index += 1 else: # print("literal") - wt += "\n|{}={}".format(key, value) + wt += f"\n|{key}={value}" return wt @@ -437,11 +435,7 @@ def get_wikitext_from_flat_content_structure(content): elif isinstance(content_element, str): wt += content_element # "\n" + content_element else: - print( - "Error: content element is not dict or string: {}".format( - content_element - ) - ) + print(f"Error: content element is not dict or string: {content_element}") return wt @@ -548,7 +542,8 @@ def wikiJson2SchemaJsonRecursion(schema: dict, wikiJson: dict, footerWikiJson=No "osl_template" in value and "osl_template" in schemaJson and value["osl_template"]["default"] == schemaJson["osl_template"] - or "osl_schema" in value + ) or ( + "osl_schema" in value and "osl_schema" in schemaJson and value["osl_schema"]["default"] == schemaJson["osl_schema"] ): @@ -560,16 +555,18 @@ def wikiJson2SchemaJsonRecursion(schema: dict, wikiJson: dict, footerWikiJson=No if "type" in schema_def[key]: # use schema to resolve types if schema_def[key]["type"] == "integer": schemaJson[key] = int(schemaJson[key]) - elif schema_def[key]["type"] == "float": - schemaJson[key] = float(schemaJson[key]) - elif schema_def[key]["type"] == "number": + elif ( + schema_def[key]["type"] == "float" + or schema_def[key]["type"] == "number" + ): schemaJson[key] = float(schemaJson[key]) elif schema_def[key]["type"] == "string": schemaJson[key] = str(schemaJson[key]) elif schema_def[key]["type"] == "array": - if not isinstance(schemaJson[key], list): - del schemaJson[key] - elif len(schemaJson[key]) == 0: + if ( + not isinstance(schemaJson[key], list) + or len(schemaJson[key]) == 0 + ): del schemaJson[key] else: # assume type==object if isinstance(schemaJson[key], list) and len(schemaJson[key]) == 1: diff --git a/src/osw/utils/workflow.py b/src/osw/utils/workflow.py index bbf70fc1..16712265 100644 --- a/src/osw/utils/workflow.py +++ b/src/osw/utils/workflow.py @@ -250,7 +250,7 @@ async def handle_async_request(self, request: httpx.Request) -> httpx.Response: except Exception: body = "" log.warning( - "ApiGateway returned 403, re-authenticating. " "Response: %s", + "ApiGateway returned 403, re-authenticating. Response: %s", body, ) self._relogin_cb() @@ -364,7 +364,7 @@ def notify_teams( host_url = str(PREFECT_API_URL.value()).replace("/api", "") - _flow_run = f"**🚨Flow Run: [{flow.name} > {flow_run.name}]({host_url}/flow-runs/flow-run/{flow_run.id}) ❗{state.name}❗**\n\n" # noqa + _flow_run = f"**🚨Flow Run: [{flow.name} > {flow_run.name}]({host_url}/flow-runs/flow-run/{flow_run.id}) ❗{state.name}❗**\n\n" if flow_run.deployment_id is not None: # Assigned deployment found @@ -372,14 +372,18 @@ def notify_teams( f"{host_url}/deployments/deployment/{flow_run.deployment_id}" ) if self.deployment_name == "" or self.deployment_name is None: - _deployment = f"🚀 Deployment: _[{flow_run.deployment_id}]({deployment_url})_\n\n" # noqa + _deployment = ( + f"🚀 Deployment: _[{flow_run.deployment_id}]({deployment_url})_\n\n" + ) else: - _deployment = f"🚀 Deployment: _[{self.deployment_name}]({deployment_url})_\n\n" # noqa + _deployment = ( + f"🚀 Deployment: _[{self.deployment_name}]({deployment_url})_\n\n" + ) else: # No deployment assigned _deployment = "🚀 Deployment: _Just flow, no deployment_\n\n" - _ts = f"🕑 Timestamp: _{flow_run.state.timestamp.strftime('%Y-%m-%d %H:%M:%S %Z')}_\n\n" # noqa + _ts = f"🕑 Timestamp: _{flow_run.state.timestamp.strftime('%Y-%m-%d %H:%M:%S %Z')}_\n\n" if flow_run.tags != []: _tags = f"🏷️ Tags: _#{' #'.join(flow_run.tags)}_\n\n" else: diff --git a/src/osw/wiki_tools.py b/src/osw/wiki_tools.py index db20fead..a92bb156 100644 --- a/src/osw/wiki_tools.py +++ b/src/osw/wiki_tools.py @@ -16,9 +16,9 @@ from osw.utils.wikitext import find_dependencies_recursively # noqa from osw.utils.wikitext import get_wikitext_from_flat_content_dict # noqa from osw.utils.wikitext import get_wikitext_from_flat_content_structure # noqa - from osw.utils.wikitext import merge_wiki_page_text # noqa; + from osw.utils.wikitext import merge_wiki_page_text from osw.utils.wikitext import schemaJson2WikiJson # noqa - from osw.utils.wikitext import update_template_within_wikitext # noqa + from osw.utils.wikitext import update_template_within_wikitext from osw.utils.wikitext import wikiJson2SchemaJson # noqa from osw.utils.wikitext import wikiJson2SchemaJsonRecursion # noqa @@ -30,7 +30,7 @@ def read_domains_from_credentials_file( - cred_filepath: Union[str, FilePath] + cred_filepath: Union[str, FilePath], ) -> Tuple[List[str], Dict[str, Dict[str, str]]]: """Reads domains and credentials from a yaml file @@ -43,7 +43,7 @@ def read_domains_from_credentials_file( ------- """ - with open(cred_filepath, "r", encoding="utf-8") as stream_: + with open(cred_filepath, encoding="utf-8") as stream_: try: accounts_dict = yaml.safe_load(stream_) domains_list = list(accounts_dict.keys()) @@ -73,15 +73,15 @@ def read_credentials_from_yaml( contain keys 'username' and 'password'. """ if password_file != "": - with open(password_file, "r") as stream: + with open(password_file) as stream: try: accounts = yaml.safe_load(stream) if domain is not None and domain in accounts.keys(): domain = domain elif len(accounts.keys()) > 0: - domain = list(accounts.keys())[0] + domain = next(iter(accounts.keys())) if len(accounts.keys()) > 0: - domain = list(accounts.keys())[0] + domain = next(iter(accounts.keys())) user = accounts[domain]["username"] password = accounts[domain]["password"] except yaml.YAMLError as exc: @@ -244,7 +244,7 @@ def semantic_search_(single_query): result = site.api("ask", query=single_query, format="json") if query.debug: if len(result["query"]["results"]) == 0: - print("Query '{}' returned no results".format(single_query)) + print(f"Query '{single_query}' returned no results") else: print( "Query '{}' returned {} results".format( diff --git a/src/osw/wtsite.py b/src/osw/wtsite.py index e426c694..7fc8bca6 100644 --- a/src/osw/wtsite.py +++ b/src/osw/wtsite.py @@ -112,7 +112,7 @@ def __init__(self, config: Union[WtSiteConfig, WtSiteLegacyConfig]): self._iri = config.iri site_args = [config.iri] # increase pool_maxsize to improve performance with many requests to the same server - # see: https://stackoverflow.com/questions/18466079/change-the-connection-pool-size-for-pythons-requests-module-when-in-threading # noqa + # see: https://stackoverflow.com/questions/18466079/change-the-connection-pool-size-for-pythons-requests-module-when-in-threading session = requests.Session() adapter = requests.adapters.HTTPAdapter(pool_maxsize=50) session.mount(scheme + "://", adapter) @@ -137,14 +137,12 @@ def __init__(self, config: Union[WtSiteConfig, WtSiteLegacyConfig]): self._site = mwclient.Site(*site_args, **site_kwargs) self._site.login(username=cred.username, password=cred.password) elif isinstance(cred, CredentialManager.OAuth1Credential): - site_kwargs.update( - **{ - "consumer_token": cred.consumer_token, - "consumer_secret": cred.consumer_secret, - "access_token": cred.access_token, - "access_secret": cred.access_secret, - } - ) + site_kwargs.update(**{ + "consumer_token": cred.consumer_token, + "consumer_secret": cred.consumer_secret, + "access_token": cred.access_token, + "access_secret": cred.access_secret, + }) self._site = mwclient.Site(*site_args, **site_kwargs) else: raise ValueError("Unsupported credential type: " + str(type(cred))) @@ -243,7 +241,7 @@ def from_credentials( """ if isinstance(credentials, str) or isinstance(credentials, Path): - domains, accounts = wt.read_domains_from_credentials_file(credentials) + _domains, accounts = wt.read_domains_from_credentials_file(credentials) else: accounts = credentials if isinstance(key, int): @@ -358,9 +356,7 @@ def get_page_(title: str, index: int = None): if not wtpage.exists: if param.raise_warning: warnings.warn( - "WARNING: Page with title '{}' does not exist.".format( - title - ), + f"WARNING: Page with title '{title}' does not exist.", RuntimeWarning, 3, ) @@ -379,7 +375,7 @@ def get_page_(title: str, index: int = None): else: # last entry -> throw exception retry = param.retries if param.raise_exception: - raise e + raise print(msg) self._clear_cookies() return wtpage @@ -621,9 +617,7 @@ def upload_page_(page, index: int = None): if index is None: print(f"Uploaded page to {page.get_url()}.") else: - print( - f"({index + 1}/{max_index}): Uploaded page to " f"{page.get_url()}." - ) + print(f"({index + 1}/{max_index}): Uploaded page to {page.get_url()}.") if param.parallel: _ = parallelize(upload_page_, param.pages, flush_at_end=param.debug) @@ -663,7 +657,7 @@ def copy_pages(self, param: CopyPagesParam): """Copies pages from a source site to this (target) site.""" def copy_single_page(content_dict: dict): - title = list(content_dict.keys())[0] + title = next(iter(content_dict.keys())) wtpage = WtPage(wtSite=self, title=title) return wtpage.copy( config=WtPage.CopyPageConfig( @@ -800,7 +794,7 @@ def create_page_package(self, param: CreatePagePackageParam): shutil.rmtree(config.content_path) except OSError as e: if debug: - print("Error: %s - %s." % (e.filename, e.strerror)) + print(f"Error: {e.filename} - {e.strerror}.") # Create a dump config if dump_config is None: dump_config = WtPage.PageDumpConfig( @@ -826,11 +820,9 @@ def create_page_package(self, param: CreatePagePackageParam): pages = [] if param.offline_pages is not None: pages.extend( - ( - param.offline_pages[title] - for title in added_titles - if title in param.offline_pages - ) + param.offline_pages[title] + for title in added_titles + if title in param.offline_pages ) titles_to_fetch = list( set(titles_to_fetch) - set(param.offline_pages.keys()) @@ -879,11 +871,9 @@ def create_page_package(self, param: CreatePagePackageParam): file_pages = [] if param.offline_pages is not None: file_pages.extend( - ( - param.offline_pages[title] - for title in added_file_titles - if title in param.offline_pages - ) + param.offline_pages[title] + for title in added_file_titles + if title in param.offline_pages ) file_titles_to_fetch = list( set(added_file_titles) - set(param.offline_pages.keys()) @@ -1007,7 +997,7 @@ def read_page_package(self, param: ReadPagePackageParam) -> ReadPagePackageResul f"Error: No JSON files found in '{storage_path}'." ) # Read packages info file - with open(pi_fp, "r", encoding="utf-8") as f: + with open(pi_fp, encoding="utf-8") as f: packages_json = json.load(f) # Assume that the pages files are located in the subdir storage_path_content = ut.list_files_and_directories( @@ -1036,12 +1026,12 @@ def get_slot_content( for pdir in parent_dir: slot_path = pdir / url_path if slot_path in files_in_storage_path: - with open(slot_path, "r", encoding="utf-8") as f: + with open(slot_path, encoding="utf-8") as f: file_content = f.read() # Makes sure not to open an empty file with json if len(file_content) > 0: if url_path.endswith(".json"): - with open(slot_path, "r", encoding="utf-8") as f: + with open(slot_path, encoding="utf-8") as f: slot_data = json.load(f) return slot_data elif url_path.endswith(".wikitext"): @@ -1541,7 +1531,7 @@ def set_slot_content(self, slot_key, content): if the slot_key is not defined in SLOTS """ if slot_key not in self._slots: - slot_dict = SLOTS.get(slot_key, None) + slot_dict = SLOTS.get(slot_key) if slot_dict is None: raise ValueError( f"Error: Slot '{slot_key}' not defined in 'SLOTS'." @@ -1902,8 +1892,7 @@ def copy(self, config: CopyPageConfig) -> PageCopyResult: self.set_slot_content(slot_key=slot, content=slot_contents[slot]) self.edit(comment=config.comment) s2p = ( - f"Page {verb}: " - f"'https://{self.wtSite.mw_site.host}/wiki/{self.title}'." + f"Page {verb}: 'https://{self.wtSite.mw_site.host}/wiki/{self.title}'." ) if verb == "updated": s2p = ( @@ -2216,7 +2205,7 @@ def import_xml(self, config: ImportConfig) -> ImportResult: 'xmlns="http://www.mediawiki.org', '_xmlns="http://www.mediawiki.org' ) print(config.xml) - tree = et.fromstring(config.xml) + tree = et.fromstring(config.xml) # noqa: S314 parses our own exported XML # Replace title and namespace with the requested ones tree.find(".//title").text = self.title.split(":")[1] diff --git a/tests/conftest.py b/tests/conftest.py index c2c23a63..389a3466 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,10 +1,10 @@ """ - Dummy conftest.py for osw. +Dummy conftest.py for osw. - If you don't know what this is for, just leave it empty. - Read more about conftest.py under: - - https://docs.pytest.org/en/stable/fixture.html - - https://docs.pytest.org/en/stable/writing_plugins.html +If you don't know what this is for, just leave it empty. +Read more about conftest.py under: +- https://docs.pytest.org/en/stable/fixture.html +- https://docs.pytest.org/en/stable/writing_plugins.html """ import pytest diff --git a/tests/controller_mixin.py b/tests/controller_mixin.py index afdd7d1e..ce023cba 100644 --- a/tests/controller_mixin.py +++ b/tests/controller_mixin.py @@ -7,7 +7,7 @@ class ControllerTestController(model.Entity): def testfunction(self): - print(f"Entity with label '{str(self.label.text)}'") + print(f"Entity with label '{self.label.text!s}'") def controller_mixin(cls) -> Type: @@ -23,7 +23,7 @@ def controller_mixin(cls) -> Type: # the controller class ctrl_cls = eval(f"{prefix}{cls.__name__}{postfix}") # the patched class inheriting both from the data and the controller class - mixin_cls = create_model(cls.__name__, __base__=tuple([ctrl_cls, cls])) + mixin_cls = create_model(cls.__name__, __base__=(ctrl_cls, cls)) return mixin_cls diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py new file mode 100644 index 00000000..5fc62cbc --- /dev/null +++ b/tests/integration/conftest.py @@ -0,0 +1,53 @@ +"""Working-directory isolation for the integration tests. + +The tests and the library defaults create files relative to the current +working directory - among them credential files in CLEAR TEXT +(accounts.pwd.yaml and domain-named files) and download caches +(osw_files/). Running each test in its own pytest tmp dir keeps all of +that out of the repository tree; pytest cleans its tmp dirs up on its +own. Never rely on .gitignore for credential artifacts. +""" + +from pathlib import Path + +import pytest + +import osw.model.entity +from osw.defaults import paths as default_paths + + +@pytest.fixture(autouse=True, scope="session") +def _restore_entity_model(): + """Snapshot and restore src/osw/model/entity.py around the test session. + + OSW.fetch_schema regenerates the entity model INTO THE INSTALLED + PACKAGE by design, which in an editable install is the source tree. + Restoring the pre-session content keeps the working tree clean after + `make test-integration` without relying on git or .gitignore. + """ + model_file = Path(osw.model.entity.__file__) + snapshot = model_file.read_bytes() + yield + if model_file.read_bytes() != snapshot: + model_file.write_bytes(snapshot) + print(f"\nRestored pre-session state of '{model_file}'.") + + +@pytest.fixture(autouse=True) +def _isolate_working_dir(tmp_path, monkeypatch): + # covers every Path.cwd()-relative write in the tests themselves + monkeypatch.chdir(tmp_path) + # osw.defaults captures Path.cwd() at import time, so the singleton + # still points into the repo; re-base it for the duration of the + # test (setting `base` cascades to the dependent paths) and restore + # the previous values afterwards. + old = { + "base": default_paths.base, + "osw_files_dir": default_paths.osw_files_dir, + "cred_filepath": default_paths.cred_filepath, + "download_dir": default_paths.download_dir, + } + default_paths.base = tmp_path + yield + for name, value in old.items(): + setattr(default_paths, name, value) diff --git a/tests/integration/db_test.py b/tests/integration/db_test.py index 1819bc66..55a28be8 100644 --- a/tests/integration/db_test.py +++ b/tests/integration/db_test.py @@ -5,7 +5,7 @@ from osw.core import OSW from osw.wtsite import WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user # --wiki_password pass --db_username user --db_password pass @@ -13,7 +13,7 @@ def _test_connection_string( wiki_domain, wiki_username, wiki_password, db_username, db_password ): # make sure to import controllers after updating the model (ignore linter warning) - import osw.controller as controller # noqa: E402 + import osw.controller as controller cstr = controller.DatabaseController.ConnectionString( dialect="postgresql", @@ -60,7 +60,7 @@ def test_connect_and_query( # make sure to import controllers after updating the model (ignore linter warning) # the following does not work reliably if module was imported before model was loaded # import osw.controller as controller - from osw.controller.database import DatabaseController # noqa: E402 + from osw.controller.database import DatabaseController # load database definition db = osw.load_entity("Item:OSWb8cc7705e17c47b19331fdb045bfbca8") # postgres diff --git a/tests/integration/file_page_migration_dependencies.py b/tests/integration/file_page_migration_dependencies.py index f484bf5d..5657a6c5 100644 --- a/tests/integration/file_page_migration_dependencies.py +++ b/tests/integration/file_page_migration_dependencies.py @@ -36,7 +36,7 @@ def check_dependencies(): def main(wiki_domain: str, wiki_username: str, wiki_password: str): dependencies_met = check_dependencies() if not dependencies_met: - # For local testing without tox + # For local testing without CLI options if wiki_domain is None or wiki_domain == "None": # Make sure that the password file is available cwd = Path(__file__).parent.absolute() @@ -45,7 +45,7 @@ def main(wiki_domain: str, wiki_username: str, wiki_password: str): domain="wiki-dev.open-semantic-lab.org", password_file=str(pw_fp), ) - # For testing with tox + # For testing with CLI options else: site = mwclient.Site(host=wiki_domain) site.login(username=wiki_username, password=wiki_password) diff --git a/tests/integration/login_test.py b/tests/integration/login_test.py index 042e7b21..c3ef6e24 100644 --- a/tests/integration/login_test.py +++ b/tests/integration/login_test.py @@ -3,7 +3,7 @@ # from osw.core import OSW # from osw.wtsite import WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass def test_login(wiki_domain, wiki_username, wiki_password): diff --git a/tests/integration/ontology_import_test.py b/tests/integration/ontology_import_test.py index 77ad83be..ed544b5a 100644 --- a/tests/integration/ontology_import_test.py +++ b/tests/integration/ontology_import_test.py @@ -8,10 +8,10 @@ from osw.wtsite import WtSite # Run with: -# tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass -def test_ontology_import(wiki_domain, wiki_username, wiki_password): +def test_ontology_import(wiki_domain, wiki_username, wiki_password, tmp_path): cm = CredentialManager() cm.add_credential( CredentialManager.UserPwdCredential( @@ -62,7 +62,8 @@ def test_ontology_import(wiki_domain, wiki_username, wiki_password): base_class=model.OwlClass, base_class_title="Category:OSW725a3cf5458f4daea86615fcbd0029f8", # OwlClass dump_files=True, - dump_path=os.path.dirname(os.path.abspath(__file__)), + # dump into the pytest tmp dir, not the module directory + dump_path=str(tmp_path), dry_run=False, ) diff --git a/tests/integration/store_and_load_test.py b/tests/integration/store_and_load_test.py index e9a365bc..2ba833ef 100644 --- a/tests/integration/store_and_load_test.py +++ b/tests/integration/store_and_load_test.py @@ -14,7 +14,7 @@ from osw.wiki_tools import SearchParam from osw.wtsite import WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass def test_store_and_load(wiki_domain, wiki_username, wiki_password): diff --git a/tests/integration/test_express.py b/tests/integration/test_express.py index 214ddfcc..2c803e53 100644 --- a/tests/integration/test_express.py +++ b/tests/integration/test_express.py @@ -2,7 +2,7 @@ This test can't be run directly (anymore) since calling fixtures directly has been deprecated in pytest 4.0.0. Instead, the test can be run with the following command, which requires pytest-mock to be installed: -tox -e test -- path/to/test_express.py --wiki_domain domain --wiki_username user +uv run pytest tests/integration -o addopts="" tests/integration/test_express.py --wiki_domain domain --wiki_username user --wiki_password pass @@ -23,6 +23,7 @@ """ import os +import uuid from contextlib import contextmanager from pathlib import Path @@ -51,7 +52,7 @@ def create_dummy_file(file_path: Path): @contextmanager def preserve_entity_py_state(): path = Path(__file__).parents[2] / "src" / "osw" / "model" / "entity.py" - with open(path, "r") as file: + with open(path) as file: original_entity = file.read() try: yield None @@ -61,34 +62,44 @@ def preserve_entity_py_state(): def osw_express_and_credentials(osw_express, wiki_domain, wiki_username, wiki_password): + from osw.auth import CredentialManager + assert osw_express.domain == wiki_domain # An error would occur if the connection attempt to the wiki would have failed assert osw_express.site is not None - assert osw_express.cred_filepath is not None - assert osw_express.cred_filepath.exists() - assert osw_express.cred_filepath.is_file() - credentials = yaml.safe_load(osw_express.cred_filepath.open("r")) - assert wiki_domain in credentials - assert credentials[wiki_domain]["username"] == wiki_username - assert credentials[wiki_domain]["password"] == wiki_password + # Credentials are resolvable (in memory or from a caller-provided file); + # the library never writes a credential file on its own. + cred = osw_express.cred_mngr.get_credential( + CredentialManager.CredentialConfig( + iri=wiki_domain, + fallback=CredentialManager.CredentialFallback.none, + ) + ) + assert cred is not None + assert cred.username == wiki_username + assert cred.password == wiki_password + # a credential file is only ever one the caller provided themselves + if osw_express.cred_filepath is not None: + assert osw_express.cred_filepath.exists() return True def test_init_with_domain(wiki_domain, wiki_username, wiki_password, mocker): """Test OswExpress initialization with defined domain, but no cred_filepath nor - cred_mngr. As this is the first test to load the osw.express module, - the installation of the dependencies should be triggered here.""" + cred_mngr. Credentials are prompted for interactively and are kept in + memory only; no credential file is created.""" # A connection is opened with domain already set, so mocking is required for the # username and password only mocked_input = mocker.patch("builtins.input") mocked_getpass = mocker.patch("getpass.getpass") - mocked_input.side_effect = [str(Path(default_paths.cred_filepath)), wiki_username] + mocked_input.side_effect = [wiki_username] mocked_getpass.return_value = wiki_password osw_express = osw.express.OswExpress(domain=wiki_domain) osw_express_and_credentials(osw_express, wiki_domain, wiki_username, wiki_password) - assert osw_express.cred_filepath == Path(osw.express.default_paths.cred_filepath) + # in-memory only: no credential file path is set and none is created + assert osw_express.cred_filepath is None + assert not Path(default_paths.cred_filepath).exists() osw_express.shut_down() - osw_express.cred_filepath.unlink() def test_init_from_env_vars(wiki_domain, wiki_username, wiki_password): @@ -173,8 +184,9 @@ def test_file_upload_download(wiki_domain, wiki_username, wiki_password): assert osw_express_and_credentials( osw_express, wiki_domain, wiki_username, wiki_password ) - # Test file upload - file_path = Path.cwd() / "test_file.txt" + # Test file upload; unique name per run so leftovers on the shared + # test wiki never collide with a re-upload (fileexists-no-change) + file_path = Path.cwd() / f"test_file_{uuid.uuid4().hex[:8]}.txt" create_dummy_file(file_path) # Upload a file to an OSW instance wiki_file = osw.express.osw_upload_file(file_path, osw_express=osw_express) @@ -197,7 +209,7 @@ def test_file_upload_download(wiki_domain, wiki_username, wiki_password): if __name__ == "__main__": cred_filepath_ = Path("accounts.pwd.yaml") - with open(cred_filepath_, "r") as file: + with open(cred_filepath_) as file: accounts = yaml.safe_load(file) wiki_domain_ = "wiki-dev.open-semantic-lab.org" wiki_username_ = accounts[wiki_domain_]["username"] @@ -208,17 +220,15 @@ def test_file_upload_download(wiki_domain, wiki_username, wiki_password): import pytest # Runs all tests - pytest.main( - [ - __file__, - "--wiki_domain", - wiki_domain_, - "--wiki_username", - wiki_username_, - "--wiki_password", - wiki_password_, - ] - ) + pytest.main([ + __file__, + "--wiki_domain", + wiki_domain_, + "--wiki_username", + wiki_username_, + "--wiki_password", + wiki_password_, + ]) else: # Runs tests that can be run directly: test_init_with_cred_filepath(wiki_domain_, wiki_username_, wiki_password_) diff --git a/tests/integration/test_express_init.py b/tests/integration/test_express_init.py index b76c5369..7db2056f 100644 --- a/tests/integration/test_express_init.py +++ b/tests/integration/test_express_init.py @@ -11,7 +11,7 @@ and wiki_password fixtures (passed via CLI args). Run with: - tox -e test -- tests/integration/test_express_init.py + uv run pytest tests/integration -o addopts="" tests/integration/test_express_init.py --wiki_domain --wiki_username --wiki_password Or for unit-style tests only (no live wiki needed): @@ -19,6 +19,7 @@ """ import os +import uuid import warnings from contextlib import contextmanager from pathlib import Path @@ -439,17 +440,19 @@ def test_open_read_close(self, tmp_path): fr.close() assert fio.closed - def test_close_already_closed_warns(self, tmp_path): - """Test that closing an already-closed file emits a warning.""" + def test_close_already_closed_is_noop(self, tmp_path): + """Closing an already-closed (or never opened) file is a silent + no-op, matching io stream semantics.""" fp = tmp_path / "test.txt" fp.write_text("data") fr = FileResult(path=fp) - # Not opened yet - should warn with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") + fr.close() # never opened + fr.open() fr.close() - assert len(w) == 1 - assert "already closed" in str(w[0].message).lower() + fr.close() # already closed + assert len(w) == 0 def test_read_auto_opens(self, tmp_path): """Test that read() auto-opens the file if not opened.""" @@ -518,7 +521,7 @@ def test_open_with_explicit_mode(self, tmp_path): class TestDownloadFileResultValidation: """Test DownloadFileResult __init__ validation paths without live wiki.""" - DOWNLOAD_ENV_VARS = ENV_VARS + ["OSW_DOWNLOAD_DIR", "OSL_DOWNLOAD_DIR"] + DOWNLOAD_ENV_VARS = [*ENV_VARS, "OSW_DOWNLOAD_DIR", "OSL_DOWNLOAD_DIR"] def test_title_without_domain_raises(self): """When url_or_title is a plain title (no URL) and no domain env var @@ -778,6 +781,7 @@ def test_none_to_import_raises(self): with pytest.raises(ValueError, match="to_import"): import_with_fallback(None, {}) + @pytest.mark.filterwarnings("ignore:No 'dependencies' were passed:UserWarning") def test_nonexistent_class_no_deps_raises(self): """When the class doesn't exist and no dependencies or osw_fpt are given, should raise AttributeError.""" @@ -1107,7 +1111,7 @@ def test_invalid_source_type_raises(self, tmp_path): def preserve_entity_py_state(): """Preserve and restore entity.py to avoid test side effects.""" path = Path(__file__).parents[2] / "src" / "osw" / "model" / "entity.py" - with open(path, "r") as file: + with open(path) as file: original_entity = file.read() try: yield None @@ -1130,9 +1134,11 @@ def test_live_upload_download_via_instance( osw_obj = osw.express.OswExpress( domain=wiki_domain, cred_filepath=cred_filepath ) - # Create dummy file - source_file = Path.cwd() / "test_instance_upload.txt" - source_file.write_text("Instance upload test content") + # Create dummy file; unique name/content per run so leftovers + # on the shared test wiki never collide with a re-upload + uid = uuid.uuid4().hex[:8] + source_file = Path.cwd() / f"test_instance_upload_{uid}.txt" + source_file.write_text(f"Instance upload test content {uid}") try: # Upload via instance method @@ -1146,7 +1152,9 @@ def test_live_upload_download_via_instance( overwrite=True, ) assert local_file.path.exists() - assert local_file.path.read_text() == "Instance upload test content" + assert local_file.path.read_text() == ( + f"Instance upload test content {uid}" + ) # Cleanup local_file.close() @@ -1175,14 +1183,22 @@ def test_live_upload_with_target_fpt( osw_obj = osw.express.OswExpress( domain=wiki_domain, cred_filepath=cred_filepath ) - source_file = Path.cwd() / "test_target_fpt_upload.txt" - source_file.write_text("Target FPT test content") - + # Unique name and content per run: the shared test wiki keeps + # pages between runs, and re-uploading identical content raises + # a fileexists-no-change API error. + uid = uuid.uuid4().hex[:8] + content = f"Target FPT test content {uid}" + source_file = Path.cwd() / f"test_target_fpt_upload_{uid}.txt" + source_file.write_text(content) + title = f"File:TestTargetFptUpload{uid}.txt" + + wiki_file = None + local_file = None try: wiki_file = osw_obj.upload_file( source=source_file, - url_or_title="File:TestTargetFptUpload.txt", - target_fpt="File:TestTargetFptUpload.txt", + url_or_title=title, + target_fpt=title, ) assert wiki_file is not None assert wiki_file.change_id is not None @@ -1193,13 +1209,14 @@ def test_live_upload_with_target_fpt( url_or_title=wiki_file.url_or_title, overwrite=True, ) - assert local_file.path.read_text() == "Target FPT test content" - - # Cleanup - local_file.close() - local_file.delete() - wiki_file.delete() + assert local_file.path.read_text() == content finally: + # best-effort cleanup so no state leaks onto the shared wiki + if local_file is not None: + local_file.close() + local_file.delete() + if wiki_file is not None: + wiki_file.delete() if source_file.exists(): source_file.unlink() osw_obj.shut_down() @@ -1211,6 +1228,10 @@ def test_live_upload_with_target_fpt( class TestLiveImportWithFallback: """Test import_with_fallback fallback path with live wiki.""" + @pytest.mark.filterwarnings("ignore:No 'dependencies' were passed:UserWarning") + @pytest.mark.filterwarnings( + "ignore:An exception occurred while loading the module dependencies:UserWarning" + ) def test_live_fallback_fetches_from_wiki( self, wiki_domain, wiki_username, wiki_password ): diff --git a/tests/integration/test_file_controller.py b/tests/integration/test_file_controller.py index bea1ba81..2dbdadb4 100644 --- a/tests/integration/test_file_controller.py +++ b/tests/integration/test_file_controller.py @@ -1,11 +1,13 @@ +from pathlib import Path + from osw.auth import CredentialManager from osw.core import OSW, model from osw.wtsite import WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass -def test_file_controller(wiki_domain, wiki_username, wiki_password): +def test_file_controller(wiki_domain, wiki_username, wiki_password, tmp_path): cm = CredentialManager() cm.add_credential( CredentialManager.UserPwdCredential( @@ -28,8 +30,10 @@ def test_file_controller(wiki_domain, wiki_username, wiki_password): mode = "replace" osw_obj.fetch_schema(OSW.FetchSchemaParam(schema_title=cat, mode=mode)) - run_test(osw_obj, "tests/integration/test.svg", "tests/integration/test2.svg") - run_test(osw_obj, "tests/integration/test.png", "tests/integration/test2.png") + # source assets live next to this module; outputs go to the tmp dir + here = Path(__file__).parent + run_test(osw_obj, here / "test.svg", tmp_path / "test2.svg") + run_test(osw_obj, here / "test.png", tmp_path / "test2.png") def run_test(osw_obj, file_path_1, file_path_2): diff --git a/tests/integration/test_file_page_migration.py b/tests/integration/test_file_page_migration.py index 66dc46e6..2f95f41e 100644 --- a/tests/integration/test_file_page_migration.py +++ b/tests/integration/test_file_page_migration.py @@ -9,8 +9,8 @@ from osw.data.import_utility import uuid_to_full_page_title from osw.wtsite import WtPage, WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass -# run locally with: tox -e test -- --wiki_domain None --wiki_username None --wiki_password None +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass +# run locally with: uv run pytest tests/integration -o addopts="" --wiki_domain None --wiki_username None --wiki_password None # This will trigger the fallback option (and not the skip condition) @@ -40,13 +40,13 @@ def test_file_page_migration(wiki_domain: str, wiki_username: str, wiki_password move_file_pages_and_redirect_references, ) - # For local testing without tox + # For local testing without CLI options if wiki_domain is None or wiki_domain == "None": wtsite = WtSite.from_domain( domain="wiki-dev.open-semantic-lab.org", password_file=str(PWD_FILE_PATH), ) - # For testing with tox + # For testing with CLI options else: site = mwclient.Site(host=wiki_domain) site.login(username=wiki_username, password=wiki_password) @@ -67,7 +67,7 @@ def test_file_page_migration(wiki_domain: str, wiki_username: str, wiki_password file_page = wtsite.get_page(WtSite.GetPageParam(titles=[file_page_name])).pages[0] if file_page.exists: file_page.delete() - with open(path_to_test_file, "r") as file: + with open(path_to_test_file) as file: _ = wtsite.mw_site.upload( file=file, filename=file_page_name, @@ -116,7 +116,7 @@ def test_file_page_migration(wiki_domain: str, wiki_username: str, wiki_password jsondata = new_file_page.get_slot_content("jsondata") if jsondata is None: raise ValueError( - "jsondata is None - meta data was not written to the file " "page!" + "jsondata is None - meta data was not written to the file page!" ) assert jsondata["type"] == WikiFile.__fields__["type"].get_default() modified_using_page = wtsite.get_page( @@ -128,7 +128,7 @@ def test_file_page_migration(wiki_domain: str, wiki_username: str, wiki_password ) content_dict = parsed_content[0] assert bare_file_name in content_dict["Template:Editor/SvgEdit"]["file_name"] - assert "uuid" in list(content_dict.values())[0].keys() + assert "uuid" in next(iter(content_dict.values())).keys() except AssertionError as e: # Assertion Error for now exception = e diff --git a/tests/integration/test_page_export_import.py b/tests/integration/test_page_export_import.py index 4cc7224d..9ad42ad0 100644 --- a/tests/integration/test_page_export_import.py +++ b/tests/integration/test_page_export_import.py @@ -4,7 +4,7 @@ from osw.core import OSW from osw.wtsite import WtPage, WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass def _test_ontology_import(wiki_domain, wiki_username, wiki_password): diff --git a/tests/integration/test_page_package.py b/tests/integration/test_page_package.py index 43febbb0..bf631691 100644 --- a/tests/integration/test_page_package.py +++ b/tests/integration/test_page_package.py @@ -17,7 +17,7 @@ def test_offline_package_from_git(wiki_domain, wiki_username, wiki_password): ) wtsite = WtSite(WtSite.WtSiteConfig(iri=wiki_domain, cred_mngr=cm)) # create OSW instance which auto-registers as a oold backend - osw_obj = OSW(site=wtsite) # noqa: F841 + osw_obj = OSW(site=wtsite) package = "world.opensemantic.core@v0.53.1" package_name, package_version = package.split("@") diff --git a/tests/integration/test_rdf_generation.py b/tests/integration/test_rdf_generation.py index b1be7eb6..b07d5dbc 100644 --- a/tests/integration/test_rdf_generation.py +++ b/tests/integration/test_rdf_generation.py @@ -9,7 +9,7 @@ from osw.wtsite import WtSite -# run with: tox -e test -- --wiki_domain domain --wiki_username user --wiki_password pass +# run with: uv run pytest tests/integration -o addopts="" --wiki_domain domain --wiki_username user --wiki_password pass def test_local_rdf_graph_with_remote_context(wiki_domain, wiki_username, wiki_password): cm = CredentialManager() cm.add_credential( diff --git a/tests/integration/test_wtsite.py b/tests/integration/test_wtsite.py index b3b0dbcb..aad24452 100644 --- a/tests/integration/test_wtsite.py +++ b/tests/integration/test_wtsite.py @@ -12,7 +12,7 @@ pytest tests/integration/test_wtsite.py -k "not Live" -v Run all tests with live wiki: - tox -e test -- tests/integration/test_wtsite.py + uv run pytest tests/integration -o addopts="" tests/integration/test_wtsite.py --wiki_domain --wiki_username --wiki_password """ @@ -401,7 +401,7 @@ def fake_login(**_): raise mwclient.errors.LoginError( mock_mw_site, "Aborted", - "Unable to continue login. Your session most likely " "timed out.", + "Unable to continue login. Your session most likely timed out.", ) mock_mw_site.login.side_effect = fake_login diff --git a/tests/test_osl.py b/tests/test_osl.py index db9449f2..4dd9e376 100644 --- a/tests/test_osl.py +++ b/tests/test_osl.py @@ -153,8 +153,7 @@ def test_apply_overwrite_policy(): ) original_page = OfflineWtPage( # wtSite=OSW.wt_site, # todo: missing - title="Item:" - + OSW.get_osw_id(original_item_local.uuid) + title="Item:" + OSW.get_osw_id(original_item_local.uuid) ) jsondata = json.loads(original_item_local.json(exclude_none=True)) # Emulate the default setting for StoreEntityParam.remove_empty, diff --git a/tests/test_wiki_tools.py b/tests/test_wiki_tools.py index ef63834a..a73b4339 100644 --- a/tests/test_wiki_tools.py +++ b/tests/test_wiki_tools.py @@ -4,7 +4,7 @@ def test_create_flat_content_structure_from_wikitext(): - wikitext = "{{Template" "|param=value" "}}" + wikitext = "{{Template|param=value}}" expected = [{"Template": {"param": ["value"]}}] result = wt.create_flat_content_structure_from_wikitext(wikitext) assert result == expected diff --git a/tests/utils/code_postprocessing_test.py b/tests/utils/code_postprocessing_test.py index 80c27154..d56060e2 100644 --- a/tests/utils/code_postprocessing_test.py +++ b/tests/utils/code_postprocessing_test.py @@ -126,13 +126,13 @@ class Config: Either text or link """ type: list[str] | None = ["Category:OSWccac243b31f94574847861e5d9685b82"] -''' # noqa +''' result = remove_constraints_from_forward_refs(src_code) # Test 1: DataFormat forward references should have min_items removed assert ( - "data_format: list[DataFormat] | None = Field(\n None,\n min_items=1," # noqa + "data_format: list[DataFormat] | None = Field(\n None,\n min_items=1," not in result ) assert ( @@ -150,17 +150,17 @@ class Config: # Test 3: DatasetSchema is NOT a forward ref (defined before Dataset), # so min_items should remain assert ( - "dataset_schema: list[DatasetSchema] | None = Field(\n None,\n min_items=1," # noqa + "dataset_schema: list[DatasetSchema] | None = Field(\n None,\n min_items=1," in result ) # Test 4: Other fields should remain unchanged assert ( - 'distributions: list[Distribution] | None = Field(\n None, title="Distributions / Downloads"\n )' # noqa + 'distributions: list[Distribution] | None = Field(\n None, title="Distributions / Downloads"\n )' in result ) assert ( - 'themes: list[Entity] | None = Field(\n None, range="Category:Entity", title="Themes / Topics"\n )' # noqa + 'themes: list[Entity] | None = Field(\n None, range="Category:Entity", title="Themes / Topics"\n )' in result ) diff --git a/tests/utils/templates_test.py b/tests/utils/templates_test.py index 589adcdf..63bb4b19 100644 --- a/tests/utils/templates_test.py +++ b/tests/utils/templates_test.py @@ -1,4 +1,3 @@ -# flake8: noqa: E501 import json from osw.utils.oold import escape_json_strings @@ -328,7 +327,7 @@ def test_helper_join(): def test_raw_block(): - template = """ + template = r""" { "unit": { "format": "autocomplete", @@ -408,7 +407,7 @@ def test_replace_helper(): def test_metamodel_with_replace_helper(): - template = """ + template = r""" { "title": "{{{name}}}", "defaultProperties": [{{#replace "^[\s]*,+|,+[\s]*$" "" "g"}}{{!-- Trim leading and trailing whitespace + comma --}}{{#if positive_electrode}} diff --git a/tests/utils/workflow_test.py b/tests/utils/workflow_test.py index c3ace144..dd2fe156 100644 --- a/tests/utils/workflow_test.py +++ b/tests/utils/workflow_test.py @@ -76,9 +76,12 @@ def osw_python_test_flow_to_deploy(): @pytest.mark.asyncio +@pytest.mark.filterwarnings("ignore:coroutine '_deploy' was never awaited") async def test_deploy_serve(): """Test of deployment of example flow""" with prefect_test_harness(): + # TODO: deliberately not awaited (a real deployment would need a + # prefect server); only verifies the coroutine can be constructed _deploy(param=deploy_param) diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 1d3aad75..00000000 --- a/tox.ini +++ /dev/null @@ -1,104 +0,0 @@ -# Tox configuration file -# Read more under https://tox.wiki/ -# THIS SCRIPT IS SUPPOSED TO BE AN EXAMPLE. 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a/zensical.toml b/zensical.toml new file mode 100644 index 00000000..50218f41 --- /dev/null +++ b/zensical.toml @@ -0,0 +1,117 @@ +[project] +site_name = "OpenSemanticWorld Python Package (osw)" +repo_url = "https://github.com/OpenSemanticLab/osw-python" +site_url = "https://OpenSemanticLab.github.io/osw-python/" +site_description = "Python toolset for data processing, queries, wikicode generation and page manipulation within OpenSemanticLab." +site_author = "OpenSemanticWorld" +edit_uri = "edit/main/docs/" +repo_name = "OpenSemanticLab/osw-python" +copyright = 'Maintained by OpenSemanticWorld.' + +extra_css = ["stylesheets/extra.css"] + +nav = [ + { "Home" = "index.md" }, + { "About" = "about.md" }, + { "Get Started" = "get-started.md" }, + { "API Reference" = [ + { "Overview" = "api/index.md" }, + { "OSW" = "api/core.md" }, + { "Wiki Tools" = "api/wiki-tools.md" }, + { "Authentication" = "api/auth.md" }, + { "Controllers" = "api/controller.md" }, + { "Model" = "api/model.md" }, + ]}, + { "Development" = "dev.md" }, +] + +[project.plugins.mkdocstrings.handlers.python] +paths = ["src"] + +[project.plugins.mkdocstrings.handlers.python.options] +docstring_style = "numpy" + +[project.theme] +language = "en" +# GitHub org avatar as logo/favicon (no vendored copy to maintain) +logo = "https://github.com/OpenSemanticLab.png" +favicon = "https://github.com/OpenSemanticLab.png" +features = [ + "announce.dismiss", + "content.code.annotate", + "content.action.edit", + "content.action.view", + "content.code.copy", + "content.code.select", + "content.footnote.tooltips", + "content.tabs.link", + "content.tooltips", + "navigation.footer", + "navigation.indexes", + "navigation.tabs", + "navigation.instant", + "navigation.instant.prefetch", + "navigation.path", + "navigation.prune", + "navigation.top", + "navigation.tracking", + "search.highlight", +] + +[project.theme.icon] +previous = "fontawesome/solid/angle-left" +next = "fontawesome/solid/angle-right" +repo = "fontawesome/brands/github" + +[[project.theme.palette]] +media = "(prefers-color-scheme: light)" +scheme = "default" +primary = "white" +accent = "deep orange" +toggle.icon = "material/brightness-7" +toggle.name = "Switch to dark mode" + +[[project.theme.palette]] +media = "(prefers-color-scheme: dark)" +scheme = "slate" +primary = "black" +accent = "deep orange" +toggle.icon = "material/brightness-4" +toggle.name = "Switch to system preference" + +# Docs versioning: version selector fed by mike (versions.json on the +# gh-pages branch). main -> dev, tag vX.Y.Z -> X.Y.Z + latest alias. +[project.extra.version] +provider = "mike" + +[[project.extra.social]] +icon = "fontawesome/brands/github" +link = "https://github.com/OpenSemanticLab/osw-python" + +[[project.extra.social]] +icon = "fontawesome/brands/python" +link = "https://pypi.org/project/osw" + +[project.markdown_extensions.attr_list] + +[project.markdown_extensions.md_in_html] + +[project.markdown_extensions.pymdownx.emoji] +emoji_generator = "zensical.extensions.emoji.to_svg" +emoji_index = "zensical.extensions.emoji.twemoji" + +[project.markdown_extensions.pymdownx.superfences] + +[[project.markdown_extensions.pymdownx.superfences.custom_fences]] +name = "mermaid" +class = "mermaid" +format = "pymdownx.superfences.fence_code_format" + +[project.markdown_extensions.pymdownx.tabbed] +alternate_style = true + +[project.markdown_extensions.pymdownx.arithmatex] +generic = true + +[project.markdown_extensions.toc] +permalink = true