tissue-tile-quality-filter 0.1.0__tar.gz

tissue_tile_quality_filter-0.1.0/.dockerignore

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+# Git
+.git/
+.gitignore
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+.venv/
+.env
+*.egg-info/
+dist/
+build/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.ruff_cache/
+
+# IDE
+.vscode/
+.history/
+
+# Project-specific
+example_tiles/
+kaggle_results/
+test_results/
+demo_results/
+test_output/
+kaggle_test_output/
+results/
+
+# Documentation
+docs/
+
+# CI/CD
+.github/
+
+# OS
+.DS_Store
+*.swp
+*.swo

tissue_tile_quality_filter-0.1.0/.github/copilot-instructions.md

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+# Tissue Tile Quality Filter Copilot Instructions
+
+## Critical Rules - Git Operations
+
+### 🚫 ABSOLUTE RESTRICTION
+- **ONLY** allowed git command: `git status` (read-only, informational)
+- **NEVER** run without explicit user permission:
+  - `git add`
+  - `git commit`
+  - `git push`
+  - `git pull`
+  - `git reset`
+  - `git branch`
+  - Any other git command that modifies the repository
+
+### ⚠️ Protocol
+- **Always ask the user first** before executing ANY git command except `git status`
+- Wait for explicit approval before proceeding
+- Example: "Should I enable this feature? Permission to run `git add`?"
+
+## Stack
+-⁠  ⁠uv for dependency management, ruff for linting
+
+## Key rules
+- ⁠All new dependencies go through ⁠ uv add ⁠
+- ⁠Follow ruff formatting rules
+- Add type hints to all functions and variables where possible
+- Write docstrings for all functions and classes
+- Full logging and error handling for all operations
+- Never put import statements inside functions; all imports must be at the top of the file
+- Remove basic examples from docstrings to keep them concise; focus on describing parameters, return values, and behavior instead
+- Do not add icons unless explicitly requested
+
+
+

tissue_tile_quality_filter-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        run: pip install --no-cache-dir uv
+
+      - name: Build package
+        run: |
+          uv pip install --system build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

tissue_tile_quality_filter-0.1.0/.github/workflows/test.yml

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+name: Tests & Linting
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: pip install --no-cache-dir uv
+
+      - name: Sync dependencies
+        run: uv sync
+
+      - name: Run pytest
+        run: uv run pytest tests/ -v --cov=src --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+
+      - name: Type check with Pylance
+        run: uv run ty check
+
+      - name: Lint with ruff
+        run: uv run ruff check

tissue_tile_quality_filter-0.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# Environment
+.env
+
+# custom
+.DS_Store
+
+# backups and logs
+.history/
+*.log
+
+# Ruff
+.ruff_cache/
+
+# Testing and Coverage
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+.hypothesis/
+
+# Generated outputs (DO NOT commit)
+kaggle_results/
+test_results/
+demo_results/
+test_output/
+kaggle_test_output/
+docker_results/
+results/

tissue_tile_quality_filter-0.1.0/.python-version

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+3.11

tissue_tile_quality_filter-0.1.0/DOCKER.md

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+# Docker Usage Guide
+
+This document explains how to build and run the Tissue Tile Quality Filter using Docker.
+
+## Why Docker?
+
+- **Reproducibility**: Same environment across all machines
+- **Isolation**: No dependency conflicts with your system
+- **Portability**: Run on any machine with Docker installed
+- **Scalability**: Easy to run multiple containers in parallel
+
+## Quick Start
+
+### 1. Build the image
+
+```bash
+docker build -t tissue-tile-quality-filter:v0.1.0 .
+```
+
+### 2. Run with Docker
+
+Process tiles from the `example_tiles/synthetic_tiles` directory:
+
+```bash
+docker run --rm \
+  -v ./example_tiles/synthetic_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  tissue-tile-quality-filter:v0.1.0 \
+  process /input --output /output --verbose
+```
+
+### 3. Check the results
+
+Results are saved to `./docker_results/`:
+```bash
+ls -la docker_results/
+```
+
+## Docker Commands Reference
+
+### Show help
+```bash
+docker run --rm tissue-tile-quality-filter:v0.1.0 --help
+```
+
+### Display package info
+```bash
+docker run --rm tissue-tile-quality-filter:v0.1.0 info
+```
+
+### Process with custom options
+```bash
+docker run --rm \
+  -v ./example_tiles/kaggle_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  tissue-tile-quality-filter:v0.1.0 \
+  process /input \
+    --batch-id my_batch \
+    --threshold high \
+    --output /output \
+    --workers 4 \
+    --verbose
+```
+
+## Using Docker Compose
+
+For convenience, use `docker-compose.yml`:
+
+### Build and run
+```bash
+docker-compose up --build
+```
+
+### Override the command
+```bash
+docker-compose run --rm tissue-tile-quality-filter \
+  process /data/input/kaggle_tiles --threshold high --output /data/output --verbose
+```
+
+## Volume Mounting Explanation
+
+- `-v ./example_tiles/synthetic_tiles:/input:ro` 
+  - Host directory: `./example_tiles/synthetic_tiles` (your local tiles)
+  - Container path: `/input` (where the container sees them)
+  - `:ro` = read-only (prevents accidental modification)
+
+- `-v ./docker_results:/output:rw`
+  - Host directory: `./docker_results` (created if it doesn't exist)
+  - Container path: `/output` (where results are written)
+  - `:rw` = read-write
+
+## Image Details
+
+### Base Image
+- `python:3.11-slim` - Official Python 3.11 slim image (~150MB)
+
+### Multi-stage Build
+- **Stage 1 (Builder)**: Compiles dependencies in isolation
+- **Stage 2 (Runtime)**: Contains only runtime files, minimal size (~800MB)
+
+### Security
+- Non-root user (`appuser`, UID 1000)
+- Read-only filesystem where possible
+- No unnecessary packages
+

tissue_tile_quality_filter-0.1.0/Dockerfile

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+# Multi-stage Dockerfile for Tissue Tile Quality Filter
+# Version: 0.1.0
+
+# Stage 1: Build stage
+FROM python:3.11-slim AS builder
+
+# Install uv package manager
+RUN pip install --no-cache-dir uv
+
+WORKDIR /build
+
+# Copy dependency files and README (required by pyproject.toml for build system)
+COPY pyproject.toml README.md ./
+
+# Copy source code
+COPY src/ ./src/
+
+# Create venv and install dependencies
+RUN uv venv /opt/venv && \
+    uv pip install --python /opt/venv/bin/python .
+
+# Stage 2: Runtime stage
+FROM python:3.11-slim
+
+# Install runtime dependencies (OpenCV needs some system packages)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libsm6 \
+    libxext6 \
+    libxrender-dev \
+    libgl1 \
+    libglib2.0-0 \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+# Copy virtual environment from builder
+COPY --from=builder /opt/venv /opt/venv
+
+# Copy application source code
+COPY src/ ./src/
+
+# Set environment variables
+ENV PATH="/opt/venv/bin:$PATH" \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+# Create a non-root user for security
+RUN useradd -m -u 1000 appuser && \
+    chown -R appuser:appuser /app
+
+LABEL org.opencontainers.image.title="Tissue Tile Quality Filter" \
+      org.opencontainers.image.version="0.1.0" \
+      org.opencontainers.image.description="Production-grade histology tile quality assessment pipeline"
+
+# Set the CLI as the entrypoint
+ENTRYPOINT ["python", "-m", "tissue_tile_quality_filter"]
+
+USER appuser

tissue_tile_quality_filter-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tissue-tile-quality-filter
+Version: 0.1.0
+Summary: A Python pipeline for histology image tile quality filtering with blur detection and tissue coverage analysis
+Requires-Python: >=3.11
+Requires-Dist: click>=8.0.0
+Requires-Dist: opencv-python>=4.8.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pillow>=10.0.0
+Requires-Dist: pyarrow>=14.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: python-dotenv>=1.0.0
+Description-Content-Type: text/markdown
+
+# Tissue Tile Quality Filter Pipeline
+
+A production-grade Python pipeline for automated quality assessment of histology image tiles. Detects blur, tissue coverage, and filters tiles based on configurable quality thresholds.
+
+---
+
+## Installation
+
+### From PyPI (recommended)
+```bash
+pip install tissue-tile-quality-filter
+```
+
+### From source (development)
+```bash
+git clone https://github.com/sinemdemirkayabudak/tissue-tile-quality-filter.git
+cd tissue-tile-quality-filter
+uv sync
+```
+
+---
+
+## Usage
+
+There are two ways to use this package: **CLI** for quick batch processing, or **Python API** for integration into your own code.
+
+### CLI Usage
+
+Process a directory of tiles from the command line:
+
+```bash
+# Basic usage (installed via pip)
+tissue-tile-quality-filter process ./tiles
+
+# With options
+tissue-tile-quality-filter process ./tiles \
+  --batch-id my_batch \
+  --threshold high \
+  --output ./results \
+  --workers 4 \
+  --verbose
+
+# View quality thresholds
+tissue-tile-quality-filter info
+```
+
+If running from source (development):
+```bash
+# Development usage (with uv)
+uv run tissue-tile-quality-filter process ./tiles --verbose
+```
+
+**Options:**
+- `--output, -o`: Output directory (default: `./results`)
+- `--batch-id, -b`: Batch identifier (default: `batch_001`)
+- `--threshold, -t`: Quality threshold: `high`, `medium`, `low` (default: `medium`)
+- `--workers, -w`: Number of parallel workers (default: auto-detect CPU count)
+- `--verbose, -v`: Enable verbose output
+
+### Python API Usage
+
+Integrate the pipeline into your own Python code:
+
+```python
+from pathlib import Path
+from tissue_tile_quality_filter import TileQualityFilterPipeline, export_to_csv
+
+# Initialize pipeline
+pipeline = TileQualityFilterPipeline(
+    batch_id="my_batch",
+    pass_threshold="medium",
+    max_workers=4  # Parallel processing
+)
+
+# Process directory
+batch_report = pipeline.process_directory(Path("./tiles"))
+
+# Export results
+export_to_csv(batch_report, Path("./results/tiles.csv"))
+
+# Access batch statistics
+print(f"Passed: {batch_report.passed_tiles}/{batch_report.total_tiles}")
+print(f"Pass rate: {batch_report.pass_rate:.1f}%")
+```
+
+See [docs/python_api_usage.py](docs/python_api_usage.py) for complete examples.
+
+---
+
+## Docker
+
+Run the pipeline in a containerized environment for reproducibility and portability.
+
+### Using pre-built image (recommended)
+```bash
+# Pull from Docker registry
+docker pull sinembudak/tissue-tile-quality-filter:v0.1.0
+
+# Process tiles using volume mount
+docker run --rm \
+  -v ./example_tiles/synthetic_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  sinembudak/tissue-tile-quality-filter:v0.1.0 \
+  process /input --output /output --verbose
+
+# View available commands
+docker run --rm sinembudak/tissue-tile-quality-filter:v0.1.0 --help
+```
+
+### Building from source
+```bash
+# Build the image locally
+docker build -t tissue-tile-quality-filter:v0.1.0 .
+
+# Run the local build
+docker run --rm \
+  -v ./example_tiles/synthetic_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  tissue-tile-quality-filter:v0.1.0 \
+  process /input --output /output --verbose
+```
+
+See [DOCKER.md](DOCKER.md) for complete Docker documentation.

tissue_tile_quality_filter-0.1.0/README.md

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+# Tissue Tile Quality Filter Pipeline
+
+A production-grade Python pipeline for automated quality assessment of histology image tiles. Detects blur, tissue coverage, and filters tiles based on configurable quality thresholds.
+
+---
+
+## Installation
+
+### From PyPI (recommended)
+```bash
+pip install tissue-tile-quality-filter
+```
+
+### From source (development)
+```bash
+git clone https://github.com/sinemdemirkayabudak/tissue-tile-quality-filter.git
+cd tissue-tile-quality-filter
+uv sync
+```
+
+---
+
+## Usage
+
+There are two ways to use this package: **CLI** for quick batch processing, or **Python API** for integration into your own code.
+
+### CLI Usage
+
+Process a directory of tiles from the command line:
+
+```bash
+# Basic usage (installed via pip)
+tissue-tile-quality-filter process ./tiles
+
+# With options
+tissue-tile-quality-filter process ./tiles \
+  --batch-id my_batch \
+  --threshold high \
+  --output ./results \
+  --workers 4 \
+  --verbose
+
+# View quality thresholds
+tissue-tile-quality-filter info
+```
+
+If running from source (development):
+```bash
+# Development usage (with uv)
+uv run tissue-tile-quality-filter process ./tiles --verbose
+```
+
+**Options:**
+- `--output, -o`: Output directory (default: `./results`)
+- `--batch-id, -b`: Batch identifier (default: `batch_001`)
+- `--threshold, -t`: Quality threshold: `high`, `medium`, `low` (default: `medium`)
+- `--workers, -w`: Number of parallel workers (default: auto-detect CPU count)
+- `--verbose, -v`: Enable verbose output
+
+### Python API Usage
+
+Integrate the pipeline into your own Python code:
+
+```python
+from pathlib import Path
+from tissue_tile_quality_filter import TileQualityFilterPipeline, export_to_csv
+
+# Initialize pipeline
+pipeline = TileQualityFilterPipeline(
+    batch_id="my_batch",
+    pass_threshold="medium",
+    max_workers=4  # Parallel processing
+)
+
+# Process directory
+batch_report = pipeline.process_directory(Path("./tiles"))
+
+# Export results
+export_to_csv(batch_report, Path("./results/tiles.csv"))
+
+# Access batch statistics
+print(f"Passed: {batch_report.passed_tiles}/{batch_report.total_tiles}")
+print(f"Pass rate: {batch_report.pass_rate:.1f}%")
+```
+
+See [docs/python_api_usage.py](docs/python_api_usage.py) for complete examples.
+
+---
+
+## Docker
+
+Run the pipeline in a containerized environment for reproducibility and portability.
+
+### Using pre-built image (recommended)
+```bash
+# Pull from Docker registry
+docker pull sinembudak/tissue-tile-quality-filter:v0.1.0
+
+# Process tiles using volume mount
+docker run --rm \
+  -v ./example_tiles/synthetic_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  sinembudak/tissue-tile-quality-filter:v0.1.0 \
+  process /input --output /output --verbose
+
+# View available commands
+docker run --rm sinembudak/tissue-tile-quality-filter:v0.1.0 --help
+```
+
+### Building from source
+```bash
+# Build the image locally
+docker build -t tissue-tile-quality-filter:v0.1.0 .
+
+# Run the local build
+docker run --rm \
+  -v ./example_tiles/synthetic_tiles:/input:ro \
+  -v ./docker_results:/output:rw \
+  tissue-tile-quality-filter:v0.1.0 \
+  process /input --output /output --verbose
+```
+
+See [DOCKER.md](DOCKER.md) for complete Docker documentation.

tissue_tile_quality_filter-0.1.0/docker-compose.yml

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+version: '3.8'
+
+services:
+  tissue-tile-quality-filter:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    image: tissue-tile-quality-filter:v0.1.0
+    volumes:
+      # Mount input tiles directory
+      - ./example_tiles:/data/input:ro
+      # Mount output directory
+      - ./docker_results:/data/output:rw
+    environment:
+      - PYTHONUNBUFFERED=1
+    # Example command (override with actual command)
+    command: process /data/input/synthetic_tiles --output /data/output --verbose