microcafe 0.1.0__tar.gz

microcafe-0.1.0/.vscode/settings.json

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+{
+    "python-envs.defaultEnvManager": "ms-python.python:venv"
+}

microcafe-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: microcafe
+Version: 0.1.0
+Summary: Python SDK for microCafe - AI-powered microbiome analysis
+Project-URL: Homepage, https://microcafe.ai
+Project-URL: Documentation, https://docs.microcafe.ai
+Project-URL: Repository, https://github.com/microcafe/microcafe-python
+Project-URL: Issues, https://github.com/microcafe/microcafe-python/issues
+Author-email: microCafe <support@microcafe.ai>
+License: MIT
+Keywords: 16S,api,bioinformatics,genomics,metagenomics,microbiome
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Requires-Dist: click>=8.0.0
+Requires-Dist: requests>=2.28.0
+Provides-Extra: dev
+Requires-Dist: black>=23.0.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# microCafe Python SDK
+
+Official Python SDK for [microCafe](https://microcafe.ai) — AI-powered microbiome analysis.
+
+## Installation
+
+```bash
+pip install microcafe
+```
+
+## Quick Start
+
+```python
+from microcafe import Client
+
+# Auto-reads API key from env var or ~/.microcafe/config.json
+client = Client()
+
+# Or pass explicitly
+client = Client(api_key="mc_your_key_here")
+
+# Classify a single sequence
+result = client.classify("ATCGATCGATCG...")
+print(result.predictions[0].genus)       # "Bacteroides"
+print(result.predictions[0].confidence)  # 0.95
+
+# Classify a file (submits, polls, returns abundance)
+summary = client.classify_file("sequences.fq")
+print(summary.summary.raw_counts)           # {"Bacteroides": 150, "Prevotella": 80}
+print(summary.summary.relative_abundance)   # {"Bacteroides": 65.2, "Prevotella": 34.8}
+```
+
+## CLI Usage
+
+```bash
+# Save API key (stored in ~/.microcafe/config.json)
+microcafe configure mc_your_key_here
+
+# Classify a single sequence
+microcafe classify "ATCGATCGATCG..."
+microcafe classify "ATCGATCG..." --format json
+
+# Classify a file (submits, shows progress bar, returns abundance)
+microcafe classify-file sequences.fq
+microcafe classify-file sequences.fq --output results.json
+microcafe classify-file sequences.fq --format json
+
+# Check job status
+microcafe status <job_id>
+microcafe status <job_id> --wait       # poll until complete
+
+# Get abundance table
+microcafe abundance <job_id>
+microcafe abundance <job_id> --top 20  # show top 20 genera
+microcafe abundance <job_id> --output abundance.json
+
+# Get per-sequence predictions
+microcafe predictions <job_id>
+microcafe predictions <job_id> --output predictions.json
+```
+
+## Python API Reference
+
+### Client
+
+```python
+from microcafe import Client
+
+# Auto-resolves API key from env var or config file
+client = Client()
+
+# Or configure explicitly
+client = Client(
+    api_key="mc_xxx",           # Optional if env var or config file is set
+    base_url="https://...",     # Optional, default: https://microcafe.ai/api
+    timeout=300                 # Optional, request timeout in seconds
+)
+```
+
+### Single Sequence Classification
+
+```python
+result = client.classify(
+    sequence="ATCGATCG...",
+    top_k=5  # Number of top predictions
+)
+
+print(result.sequence_length)
+for pred in result.predictions:
+    print(f"{pred.genus}: {pred.confidence}")
+```
+
+### File Classification
+
+```python
+# Submits file, polls for progress, returns abundance summary
+summary = client.classify_file(
+    file_path="sequences.fq",
+    top_k=5,
+    poll_interval=2.0,  # Seconds between status checks
+    on_progress=lambda s: print(f"{s.progress}%")  # Optional callback
+)
+
+print(summary.summary.raw_counts)
+print(summary.summary.relative_abundance)
+```
+
+### Job Management
+
+```python
+# Submit file (returns immediately)
+job = client.classify_file_async("sequences.fq")
+print(job.job_id)
+
+# Check status
+status = client.get_job_status(job.job_id)
+print(f"{status.progress}% — {status.sequences_processed}/{status.total_sequences}")
+
+# Wait for completion
+final_status = client.wait_for_job(job.job_id)
+
+# Get results
+abundance = client.get_job_summary(job.job_id)    # abundance table
+predictions = client.get_job_results(job.job_id)   # per-sequence predictions
+```
+
+## Environment Variables
+
+```bash
+export MICROCAFE_API_KEY=mc_your_key_here
+```
+
+```python
+# No need to pass api_key if env var is set
+client = Client()
+```
+
+## Error Handling
+
+```python
+from microcafe import Client, MicroCafeError, RateLimitError, AuthenticationError
+
+try:
+    result = client.classify("ATCG...")
+except RateLimitError as e:
+    print(f"Rate limited. Retry after {e.retry_after} seconds")
+except AuthenticationError:
+    print("Invalid API key")
+except MicroCafeError as e:
+    print(f"Error: {e.message}")
+```
+
+## Supported File Formats
+
+- FASTA (`.fasta`, `.fa`)
+- FASTQ (`.fastq`, `.fq`)
+
+## Links
+
+- [microCafe Website](https://microcafe.ai)
+- [API Documentation](https://microcafe.ai/api/docs)
+- [Get API Key](https://microcafe.ai/dashboard/api-console)
+
+## License
+
+MIT

microcafe-0.1.0/README.md

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+# microCafe Python SDK
+
+Official Python SDK for [microCafe](https://microcafe.ai) — AI-powered microbiome analysis.
+
+## Installation
+
+```bash
+pip install microcafe
+```
+
+## Quick Start
+
+```python
+from microcafe import Client
+
+# Auto-reads API key from env var or ~/.microcafe/config.json
+client = Client()
+
+# Or pass explicitly
+client = Client(api_key="mc_your_key_here")
+
+# Classify a single sequence
+result = client.classify("ATCGATCGATCG...")
+print(result.predictions[0].genus)       # "Bacteroides"
+print(result.predictions[0].confidence)  # 0.95
+
+# Classify a file (submits, polls, returns abundance)
+summary = client.classify_file("sequences.fq")
+print(summary.summary.raw_counts)           # {"Bacteroides": 150, "Prevotella": 80}
+print(summary.summary.relative_abundance)   # {"Bacteroides": 65.2, "Prevotella": 34.8}
+```
+
+## CLI Usage
+
+```bash
+# Save API key (stored in ~/.microcafe/config.json)
+microcafe configure mc_your_key_here
+
+# Classify a single sequence
+microcafe classify "ATCGATCGATCG..."
+microcafe classify "ATCGATCG..." --format json
+
+# Classify a file (submits, shows progress bar, returns abundance)
+microcafe classify-file sequences.fq
+microcafe classify-file sequences.fq --output results.json
+microcafe classify-file sequences.fq --format json
+
+# Check job status
+microcafe status <job_id>
+microcafe status <job_id> --wait       # poll until complete
+
+# Get abundance table
+microcafe abundance <job_id>
+microcafe abundance <job_id> --top 20  # show top 20 genera
+microcafe abundance <job_id> --output abundance.json
+
+# Get per-sequence predictions
+microcafe predictions <job_id>
+microcafe predictions <job_id> --output predictions.json
+```
+
+## Python API Reference
+
+### Client
+
+```python
+from microcafe import Client
+
+# Auto-resolves API key from env var or config file
+client = Client()
+
+# Or configure explicitly
+client = Client(
+    api_key="mc_xxx",           # Optional if env var or config file is set
+    base_url="https://...",     # Optional, default: https://microcafe.ai/api
+    timeout=300                 # Optional, request timeout in seconds
+)
+```
+
+### Single Sequence Classification
+
+```python
+result = client.classify(
+    sequence="ATCGATCG...",
+    top_k=5  # Number of top predictions
+)
+
+print(result.sequence_length)
+for pred in result.predictions:
+    print(f"{pred.genus}: {pred.confidence}")
+```
+
+### File Classification
+
+```python
+# Submits file, polls for progress, returns abundance summary
+summary = client.classify_file(
+    file_path="sequences.fq",
+    top_k=5,
+    poll_interval=2.0,  # Seconds between status checks
+    on_progress=lambda s: print(f"{s.progress}%")  # Optional callback
+)
+
+print(summary.summary.raw_counts)
+print(summary.summary.relative_abundance)
+```
+
+### Job Management
+
+```python
+# Submit file (returns immediately)
+job = client.classify_file_async("sequences.fq")
+print(job.job_id)
+
+# Check status
+status = client.get_job_status(job.job_id)
+print(f"{status.progress}% — {status.sequences_processed}/{status.total_sequences}")
+
+# Wait for completion
+final_status = client.wait_for_job(job.job_id)
+
+# Get results
+abundance = client.get_job_summary(job.job_id)    # abundance table
+predictions = client.get_job_results(job.job_id)   # per-sequence predictions
+```
+
+## Environment Variables
+
+```bash
+export MICROCAFE_API_KEY=mc_your_key_here
+```
+
+```python
+# No need to pass api_key if env var is set
+client = Client()
+```
+
+## Error Handling
+
+```python
+from microcafe import Client, MicroCafeError, RateLimitError, AuthenticationError
+
+try:
+    result = client.classify("ATCG...")
+except RateLimitError as e:
+    print(f"Rate limited. Retry after {e.retry_after} seconds")
+except AuthenticationError:
+    print("Invalid API key")
+except MicroCafeError as e:
+    print(f"Error: {e.message}")
+```
+
+## Supported File Formats
+
+- FASTA (`.fasta`, `.fa`)
+- FASTQ (`.fastq`, `.fq`)
+
+## Links
+
+- [microCafe Website](https://microcafe.ai)
+- [API Documentation](https://microcafe.ai/api/docs)
+- [Get API Key](https://microcafe.ai/dashboard/api-console)
+
+## License
+
+MIT

microcafe-0.1.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "microcafe"
+version = "0.1.0"
+description = "Python SDK for microCafe - AI-powered microbiome analysis"
+readme = "README.md"
+license = {text = "MIT"}
+requires-python = ">=3.8"
+authors = [
+    {name = "microCafe", email = "support@microcafe.ai"}
+]
+keywords = ["microbiome", "bioinformatics", "genomics", "16S", "metagenomics", "api"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "requests>=2.28.0",
+    "click>=8.0.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "black>=23.0.0",
+    "ruff>=0.1.0",
+]
+
+[project.scripts]
+microcafe = "microcafe.cli:main"
+
+[project.urls]
+Homepage = "https://microcafe.ai"
+Documentation = "https://docs.microcafe.ai"
+Repository = "https://github.com/microcafe/microcafe-python"
+Issues = "https://github.com/microcafe/microcafe-python/issues"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/microcafe"]
+
+[tool.black]
+line-length = 100
+target-version = ["py38"]
+
+[tool.ruff]
+line-length = 100
+select = ["E", "F", "I"]

microcafe-0.1.0/src/microcafe/__init__.py

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+# src/microcafe/__init__.py
+"""
+microCafe Python SDK - AI-powered microbiome analysis.
+
+Usage:
+    from microcafe import Client
+    
+    client = Client(api_key="mc_your_key_here")
+    
+    # Single sequence
+    result = client.classify("ATCGATCG...")
+    print(result.predictions[0].genus)
+    
+    # File classification
+    summary = client.classify_file("sequences.fq")
+    print(summary.summary.raw_counts)
+"""
+
+from .client import Client
+from .exceptions import (
+    MicroCafeError,
+    AuthenticationError,
+    RateLimitError,
+    ValidationError,
+    JobNotFoundError,
+    JobNotCompletedError,
+    ServerError,
+)
+from .models import (
+    Prediction,
+    ClassificationResult,
+    Summary,
+    JobStatus,
+    JobResults,
+    JobSummary,
+)
+
+__version__ = "0.1.0"
+__all__ = [
+    "Client",
+    "MicroCafeError",
+    "AuthenticationError",
+    "RateLimitError",
+    "ValidationError",
+    "JobNotFoundError",
+    "JobNotCompletedError",
+    "ServerError",
+    "Prediction",
+    "ClassificationResult",
+    "Summary",
+    "JobStatus",
+    "JobResults",
+    "JobSummary",
+]