From fb2d72f5e48188a76c0d94d207f9f30545364852 Mon Sep 17 00:00:00 2001
From: Danilo Horta <danilo.horta@pm.me>
Date: Thu, 5 Dec 2024 16:24:09 +0000
Subject: [PATCH] =?UTF-8?q?Refactor=20shutdown=20and=20assert=5Fpeers=5Fhe?=
 =?UTF-8?q?althy=20functions=20=F0=9F=8E=AF?=
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- `daemon.py`: Adjust shutdown order and remove race condition.
- `healthy.py`: Loosen peer health check assertions.
- `pyproject.toml`: Bump version from 0.16.1 to 0.16.2.

Improved shutdown sequence to handle exceptions better. Relaxed peer health
check conditions to support more configurations. Version update reflects
enhancements.
---
 h3daemon/h3daemon/daemon.py  | 13 ++++++-------
 h3daemon/h3daemon/healthy.py |  8 ++++----
 h3daemon/pyproject.toml      |  2 +-
 3 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/h3daemon/h3daemon/daemon.py b/h3daemon/h3daemon/daemon.py
index ef8c5c4..f50ed8d 100644
--- a/h3daemon/h3daemon/daemon.py
+++ b/h3daemon/h3daemon/daemon.py
@@ -21,7 +21,6 @@ def shutdown(x: psutil.Process, force: bool):
     with suppress(psutil.NoSuchProcess):
         if force:
             x.kill()
-            x.wait()
         else:
             x.terminate()
             try:
@@ -71,10 +70,10 @@ def spawn(cls, hmmfile: HMMFile, cport: int = 0, wport: int = 0):
                 assert_peers_healthy(master, worker)
         except Exception as exception:
             debug_exception(exception)
-            if master:
-                shutdown(master.process, force=True)
             if worker:
                 shutdown(worker.process, force=True)
+            if master:
+                shutdown(master.process, force=True)
             raise exception
 
         return cls(master, worker, None)
@@ -100,11 +99,11 @@ def possess(cls, pidfile: PIDLockFile):
         return cls(master, worker, process)
 
     def shutdown(self, force=False):
-        if self._master is not None:
-            shutdown(self._master.process, force)
-
         if self._worker is not None:
-            shutdown(self._worker.process, force)
+            shutdown(self._worker.process, True)
+
+        if self._master is not None:
+            shutdown(self._master.process, True)
 
         if self._process is not None:
             shutdown(self._process, force)
diff --git a/h3daemon/h3daemon/healthy.py b/h3daemon/h3daemon/healthy.py
index 86741c6..6cc7ad0 100644
--- a/h3daemon/h3daemon/healthy.py
+++ b/h3daemon/h3daemon/healthy.py
@@ -11,12 +11,12 @@ def assert_peers_healthy(master: Master, worker: Worker):
     worker_lport = worker.local_established_ports()
     worker_rport = worker.remote_established_ports()
 
-    assert len(master_lport) == 1
+    assert len(master_lport) >= 1
     assert len(worker_rport) == 1
-    assert master_lport[0] == worker_rport[0]
-    assert len(master_rport) == 1
+    assert worker_rport[0] in master_lport
+    assert len(master_rport) >= 1
     assert len(worker_lport) == 1
-    assert master_rport[0] == worker_lport[0]
+    assert worker_lport[0] in master_rport
     assert len(master_listen) == 2
     master_ports = set(master_listen)
     assert len(master_ports) == 2
diff --git a/h3daemon/pyproject.toml b/h3daemon/pyproject.toml
index 00778e8..553f3bc 100644
--- a/h3daemon/pyproject.toml
+++ b/h3daemon/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "h3daemon"
-version = "0.16.1"
+version = "0.16.2"
 description = "HMMER server"
 authors = ["Danilo Horta <horta@ebi.ac.uk>"]
 license = "MIT"