seqa-py 0.1.0__tar.gz

seqa_py-0.1.0/.env.example

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+# Copy to .env and fill in values
+
+# AWS S3
+AWS_ACCESS_KEY_ID=
+AWS_SECRET_ACCESS_KEY=
+AWS_REGION=
+S3_BUCKET=
+
+# Azure Blob
+AZURE_TENANT_ID=
+AZURE_CLIENT_ID=
+AZURE_CLIENT_SECRET=
+AZURE_STORAGE_ACCOUNT=
+AZURE_STORAGE_CONTAINER=
+
+# GCS
+GOOGLE_STORAGE_ACCOUNT=
+GOOGLE_BUCKET=

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

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist
+          manylinux: auto
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  build-macos:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: PyO3/maturin-action@v1
+        with:
+          target: universal2-apple-darwin
+          args: --release --out dist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos
+          path: dist
+
+  build-windows:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: PyO3/maturin-action@v1
+        with:
+          target: x86_64
+          args: --release --out dist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  publish:
+    needs: [build-linux, build-macos, build-windows, sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true
+          path: dist
+      - uses: PyO3/maturin-action@v1
+        with:
+          command: upload
+          args: --non-interactive --skip-existing dist/*
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

seqa_py-0.1.0/.gitignore

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+.venv/
+__pycache__/
+*.pyc
+*.pyo
+.env
+.pytest_cache/
+.ruff_cache/
+dist/
+*.egg-info/
+target
+*.so
+.idea/

seqa_py-0.1.0/.python-version

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+3.12

seqa_py-0.1.0/CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+seqa_py is a Python port of [seqa-rs](../seqa-rs) — a library for querying genomic files (BAM, VCF, GFF, BED, BigWig, BigBed, FASTA) across cloud and local storage backends.
+
+## Build & Test Commands
+
+```bash
+uv sync                                    # Install Python dependencies
+uv run maturin develop                     # Compile Rust extension (required after any src/lib.rs change)
+uv run pytest                              # Run all tests
+uv run pytest tests/test_local.py -v       # Run local tests (no cloud creds needed)
+uv run pytest tests/test_local.py::TestVcfLocal::test_first_line  # Single test
+uv run ruff check .                        # Lint
+uv run ruff format .                       # Format
+```
+
+The Rust extension must be rebuilt (`maturin develop`) any time `src/lib.rs` changes.
+
+## Architecture
+
+### Coordinate System
+
+All genomic formats preserve their native coordinates. Internal canonical format is **0-based half-open** `[begin, end)`. Terminology: always `begin`/`end`, never `start`/`stop`.
+
+| Format | System |
+|--------|--------|
+| BED, BAM, BigWig | 0-based half-open |
+| VCF, GFF, GTF | 1-based closed |
+
+### Extension Layout
+
+- `src/lib.rs` — PyO3 bindings; compiled to `_seqa_py.so` via maturin.
+- `seqa_py/__init__.py` — Python wrapper; imports `query_file` from `._seqa_py` (relative). The `module-name = "seqa_py._seqa_py"` setting in `pyproject.toml` ensures maturin installs the extension inside the `seqa_py` package and creates a `seqa_py.pth` editable pointer.
+- `seqa_core` is referenced via local path `../seqa-rs/seqa_core` in `Cargo.toml`.
+
+### Storage Layer
+
+File access is cloud-agnostic. `StoreService.from_uri()` auto-detects backend from URL scheme (`s3://`, `az://`, `gs://`, `file://`, `http(s)://`).
+
+### Search Pipeline
+
+Per-format search functions (`bam_search`, `tabix_search`, `fasta_search`, `bigwig_search`, `bigbed_search`) each take a `SearchOptions` object and return a `SearchResult`.
+
+## Environment Variables
+
+Cloud storage and database access require environment variables:
+- **S3**: `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, `AWS_REGION`, `S3_BUCKET`
+- **Azure**: `AZURE_TENANT_ID`, `AZURE_CLIENT_ID`, `AZURE_CLIENT_SECRET`, `AZURE_STORAGE_CONTAINER`, `AZURE_STORAGE_ACCOUNT`
+- **GCS**: `GOOGLE_STORAGE_ACCOUNT`, `GOOGLE_BUCKET`
+
+## Test Deletion Policy
+
+**Never delete a failing test** to make CI green. Before removing any test, you must:
+
+1. Identify every assertion and code path exercised by the test.
+2. Find an existing *passing* test that covers each of those cases — not just "similar" functionality, but the same inputs, the same code path, and equivalent assertions.
+3. If full coverage cannot be confirmed, mark the test with `@pytest.mark.skip` and a comment explaining why (e.g., machine-specific path, missing credentials) rather than deleting it.
+4. Prefer moving credential-dependent tests to integration test files over removing them.
+
+Silently dropping tests to unblock CI is not acceptable.