wsidata 0.1.0__tar.gz

wsidata-0.1.0/.github/workflows/build.yaml

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+name: CI
+
+on:
+  push:
+    paths:
+      - '.github/**'
+      - 'wsidata/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+  pull_request:
+    paths:
+      - '.github/**'
+      - 'wsidata/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+
+jobs:
+  Test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3.0.4
+        with:
+          activate-environment: test-env
+          python-version: ${{ matrix.python-version }}
+      - name: Test project installation
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[all,dev]
+          pip install torch torchstain
+      - name: Install OpenSlide
+        if: matrix.os != 'windows-latest'
+        run: |
+          conda install -c conda-forge openslide-python
+      - name: Install scyjava
+        run: |
+          conda install -c conda-forge scyjava
+      - name: Test with pytest
+        run: |
+          pip install pytest
+          pytest tests/
+
+  Upload_to_pypi:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: Install Hatch
+        uses: pypa/hatch@install
+
+      - name: Publish to test pypi
+        env:
+          HATCH_INDEX_REPO: https://test.pypi.org/legacy/
+          HATCH_INDEX_USER: __token__
+          HATCH_INDEX_AUTH: ${{ secrets.PYPI_TEST_TOKEN }}
+        run: |
+          hatch build
+          hatch publish || exit 0
+
+      - name: Publish to pypi
+        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+        env:
+          HATCH_INDEX_REPO: https://upload.pypi.org/legacy/
+          HATCH_INDEX_USER: __token__
+          HATCH_INDEX_AUTH: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          hatch build
+          hatch publish

wsidata-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Ruff cache
+.ruff_cache/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+.DS_Store
+
+data/
+work/
+.nextflow.log*

wsidata-0.1.0/.pre-commit-config.yaml

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+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

wsidata-0.1.0/.readthedocs.yaml

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+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+          - dev

wsidata-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: wsidata
+Version: 0.1.0
+Dynamic: Summary
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.7
+Requires-Dist: opencv-python
+Requires-Dist: openslide-python
+Requires-Dist: rich
+Requires-Dist: spatialdata>=0.2.2
+Requires-Dist: tiffslide
+Provides-Extra: all
+Requires-Dist: torch; extra == 'all'
+Requires-Dist: torchstain; extra == 'all'
+Requires-Dist: torchvision; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: hatchling; extra == 'dev'
+Requires-Dist: myst-nb; extra == 'dev'
+Requires-Dist: numpydoc; extra == 'dev'
+Requires-Dist: pydata-sphinx-theme; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: sphinx; extra == 'dev'
+Requires-Dist: sphinx-copybutton; extra == 'dev'
+Requires-Dist: sphinx-design; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# wsidata
+
+<p align="center">
+    <picture align="center">
+    <img src="https://raw.githubusercontent.com/rendeirolab/wsidata/main/assets/logo.svg" width="100px">
+    </picture>
+</p>
+<p align="center">
+  <i>Efficient data structures and IO for whole slide images analysis</i>
+</p>
+
+
+## Installation
+
+```bash
+pip install wsidata
+```

wsidata-0.1.0/README.md

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+# wsidata
+
+<p align="center">
+    <picture align="center">
+    <img src="https://raw.githubusercontent.com/rendeirolab/wsidata/main/assets/logo.svg" width="100px">
+    </picture>
+</p>
+<p align="center">
+  <i>Efficient data structures and IO for whole slide images analysis</i>
+</p>
+
+
+## Installation
+
+```bash
+pip install wsidata
+```