Consistently use flock and not the sometimes-non-interacting fcntl locks

BOTS.md

@@ -0,0 +1,27 @@
+# Notes for AI Assistants
+
+## Development Environment
+
+The Python virtual environment is likely located at `./venv`, but this is just a guess - the user may have it elsewhere or may have already activated a virtualenv. If commands like `python` or `pytest` work directly, the environment is probably already active.
+
+If you need to use the venv explicitly:
+
+```bash
+./venv/bin/python -m pytest src/toil/test/path/to/test.py -v
+./venv/bin/python -c "import toil; print(toil.__version__)"
+```
+
+## Running Tests
+
+Tests use pytest. Example commands:
+
+```bash
+# Run a specific test file
+./venv/bin/python -m pytest src/toil/test/server/safeFileTest.py -v
+
+# Run a specific test
+./venv/bin/python -m pytest src/toil/test/server/safeFileTest.py::TestSafeFileInterleaving::test_reader_blocked_while_writer_holds_lock -v
+
+# Run tests with a keyword filter
+./venv/bin/python -m pytest src/toil/test -k "safe" -v
+```

CLAUDE.md

@@ -0,0 +1 @@
+BOTS.md

src/toil/server/utils.py

@@ -117,7 +117,7 @@ def safe_read_file(file: str) -> str | None:
 
     try:
         # acquire a shared lock on the state file, which is blocking until we can lock it
-        fcntl.lockf(file_obj.fileno(), fcntl.LOCK_SH)
+        fcntl.flock(file_obj.fileno(), fcntl.LOCK_SH)
 
         try:
             return file_obj.read()