Support for binseq CBQ io incorporating #95

.github/workflows/release-pypi.yaml

@@ -21,7 +21,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       # portable SIMD floor (x86-64-v3/AVX2, apple-m1) - never target-cpu=native for wheels
       - name: Use portable cargo config
@@ -45,7 +45,7 @@ jobs:
   sdist:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:

.github/workflows/release.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - uses: dtolnay/rust-toolchain@stable
       - uses: Swatinem/rust-cache@v2
       - name: Build & test & rename
@@ -65,7 +65,7 @@ jobs:
     # Skip prerelease tags (SemVer prereleases contain a hyphen, e.g. 0.17.0-rc.1).
     if: ${{ !contains(github.ref_name, '-') }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - uses: dtolnay/rust-toolchain@stable
       - name: Publish deacon to crates.io
         run: cargo publish -p deacon

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
         os: [ubuntu-24.04, ubuntu-24.04-arm, macos-15]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install Rust toolchain
         uses: dtolnay/rust-toolchain@stable
       - name: Cache cargo registry
@@ -28,3 +28,27 @@ jobs:
       # Not a default workspace member, so cargo test skips it
       - name: Run deacon-wasm unit tests
         run: cargo test -p deacon-wasm
+
+  python-test:
+    name: Python bindings
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v7
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Cache cargo registry
+        uses: Swatinem/rust-cache@v2
+      - name: Use portable config
+        run: mv .cargo/config-portable.toml .cargo/config.toml
+      - name: Build bindings
+        run: |
+          python -m venv .venv
+          .venv/bin/python -m pip install "maturin>=1.7,<2"
+          .venv/bin/maturin develop -m deacon-py/Cargo.toml
+      - name: Run Python tests
+        run: .venv/bin/python -m unittest discover -s deacon-py/tests -v

CHANGELOG.md

@@ -5,19 +5,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.17.0] - 2026-08-11
+## [0.17.0] - 2026-08-18
 
 ### Added
 
-- `deacon filter --ordered` uses paraseq 0.5.0 order preservation for deterministic output. Also exposed as `ordered` in the Python bindings and JSON summary.
+- `deacon filter --ordered` preserves output order via paraseq 0.5.0.  Arg `ordered` added to Python bindings and JSON summary.
+- `deacon filter` accepts CBQ (BINSEQ) input and writes CBQ when given a `.cbq` path. Single and paired CBQ is supported. Output block size is the greater of `--cbq-block-size` (default 16 MiB) and the input block size given CBQ input. By convention an alternate `.cba` output extension writes CBQ without quality scores, implying `--discard-quality`.
+- Python `Index.filter()` now exposes `check_pairs`, `summary`, and `cbq_block_size`, and accepts path-like objects for all paths.
 
 ### Changed
 
-- Python `Index.filter()` options after `fastq2` are now keyword-only.
+- **Breaking (Python):** index/filter input paths are positional-only; options and all `Index.fetch()` arguments are keyword-only. `filter` also renames `fastq`/`fastq2` to `input`/`input2`.
+- Python filtering rejects `abs_threshold=0`, matching the CLI.
+- Renamed `--fasta` (`-f`)/`output_fasta` to `--discard-quality`/`discard_quality`.
 
 ### Removed
 
-- `deacon filter --rename-random`, and `rename_random` from the JSON summary and Python bindings.
+- Removed `--rename-random` CLI arg and `rename_random` from the JSON summary and Python bindings.
 
 ## [0.16.0] - 2026-08-09