Bump version to 2.0.1

README.md

@@ -178,3 +178,21 @@ diff <(tail -n +2 /tmp/assemblytics_test/human/assemblytics_structural_variants.
 (No `pip install -e .` yet? Run these from inside `public/` instead, replacing `assemblytics` with `python -m assemblytics.cli` and adjusting the `input_examples/`/`output_examples/` paths to `../input_examples/`/`../output_examples/`.)
 
 Each `diff` should print nothing (no differences) followed by the "OK" line. The `tail -n +2` skips the header line, and `sort` makes the comparison order-independent since variant IDs can legitimately be assigned in a different order between runs.
+
+## Cutting a new release
+
+1. **Bump the version** in `pyproject.toml` and `assemblytics/__init__.py`.
+2. **Update `public/worker.js` line 18** to reference the new wheel filename.
+3. **Rebuild the wheel** and copy it into `public/`:
+   ```bash
+   make wheel
+   ```
+4. **Remove the old wheel** from `public/` and commit everything.
+5. **Push to `main`** and merge.
+6. **Fix the GitHub release tag** — if you created the tag before the version bump commit landed on `main`, delete it and recreate it:
+   ```bash
+   git tag -d vX.Y.Z
+   git push origin :refs/tags/vX.Y.Z
+   ```
+   Then create a new release on GitHub targeting the updated `main`. This triggers the **Publish to PyPI** workflow automatically via OIDC Trusted Publishing.
+7. **Update the bioconda recipe** (`packaging/bioconda/meta.yaml`): bump the version and update the `sha256` to match the new PyPI tarball (find it on the PyPI release page or with `pip download assemblytics==X.Y.Z && sha256sum assemblytics-X.Y.Z.tar.gz`).

assemblytics/__init__.py

@@ -1 +1 @@
-__version__ = "2.0.0"
+__version__ = "2.0.1"

public/worker.js

@@ -15,7 +15,7 @@ matplotlib.use('Agg')
 import warnings
 warnings.filterwarnings("ignore", category=UserWarning, module="matplotlib")
 import micropip
-await micropip.install('./assemblytics-2.0.0-py3-none-any.whl')
+await micropip.install('./assemblytics-2.0.1-py3-none-any.whl')
         `);
 
         self.postMessage({ type: 'status', message: 'Environment Ready' });

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "assemblytics"
-version = "2.0.0"
+version = "2.0.1"
 description = "Detect and analyze structural variants from a de novo genome assembly aligned to a reference genome"
 readme = "README.md"
 license = { text = "MIT" }