update project configuration and dependencies

Author: btfranklin

.github/workflows/python-package.yml

@@ -30,10 +30,9 @@ jobs:
             - name: Install dependencies
               run: |
                   pdm install --group dev
-            - name: Lint with flake8
+            - name: Lint with ruff
               run: |
-                  pdm run flake8 src tests --count --select=E9,F63,F7,F82 --show-source --statistics
-                  pdm run flake8 src tests --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+                  pdm run ruff check src tests --statistics
             - name: Test with pytest
               run: |
                   pdm run pytest

.github/workflows/python-publish.yml

@@ -20,6 +20,8 @@ jobs:
 
         steps:
             - uses: actions/[email protected]
+              with:
+                  fetch-depth: 0
             - name: Set up Python
               uses: actions/[email protected]
               with:

AGENTS.md

@@ -7,7 +7,7 @@ The installable package remains under `src/compendiumscribe`. `cli.py` now expos
 - `pdm install --dev` installs runtime and dev dependencies (ensure `PDM_HOME` points to a writable path if running in a sandbox).
 - `pdm run create-compendium "Cell biology"` exercises the CLI; add `--output path.xml`, `--no-background`, or `--max-tool-calls N` as needed.
 - `pdm run pytest` is mandatory before calling work complete. Tests already rely on stubs, so they are fast and offline-capable. If `pdm` cannot write logs, set `PDM_HOME=.pdm_home` and retry.
-- `pdm run flake8 src tests` keeps style and linting consistent; do not treat work as finished until this passes cleanly.
+- `pdm run ruff check src tests` keeps style and linting consistent; do not treat work as finished until this passes cleanly.
 - `pdm build` produces the wheel and sdist when preparing a release.
 
 ## Coding Style & Naming Conventions