Bump version to 0.4.0a2

- pyproject.toml: version 0.4.0a1 → 0.4.0a2
- docs/installation.md: update alpha version note
- docs/news.md: add v0.4.0a2 release notes

Author: Zikun-Yang

docs/source/installation.md

@@ -31,7 +31,7 @@ Install VAMPIRE using pip:
 $ pip install --pre vampire-tr
 ```
 
-> **Note for preview releases:** VAMPIRE `0.4.x` is currently in alpha (`0.4.0a1`).
+> **Note for preview releases:** VAMPIRE `0.4.x` is currently in alpha (`0.4.0a2`).
 > You must use `--pre` so that pip installs the preview version instead of the
 > latest stable `0.3.x` release.
 :::

docs/source/news.md

@@ -2,6 +2,14 @@
 
 <!-- marker: after prelude -->
 
+## 2026-05-19 — VAMPIRE v0.4.0a2 (preview)
+
+Second alpha release with bug fixes, CI improvements, and relaxed integration tests.
+
+- **Bug fix:** Fixed motif polishing logic that lost unmatched de-novo motifs.
+- **CI:** Removed ruff lint workflow; relaxed exact DataFrame comparison in integration tests.
+- **Tests:** Added `--job` parameter for subprocess isolation between `scan` and `anno`.
+
 ## 2026-05-07 — VAMPIRE v0.4.0a1 (preview)
 
 Preview release of VAMPIRE 0.4.0 with a refactored `scan` / `anno` module split, polars 1.x compatibility, and updated container definition.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "vampire-tr"
-version = "0.4.0a1"
+version = "0.4.0a2"
 readme = "README.md"
 license = "MIT"
 license-files = ["LICENSE"]