Refactor HMMER daemon and update dependencies 🚀

- Refactored `hmmer.py` to replace `SchedContext` with `h3daemon` for spawning
and managing the daemon.
- Updated the method for shutdown to leverage `h3daemon`.
- Renamed test functions in `test_hmmer.py` and `test_press.py`.
- Updated `h3daemon` dependency version in `pyproject.toml`.

This refactor improves the codebase by utilizing the latest `h3daemon` API, which simplifies the HMMER daemon's spawn and shutdown processes, leading to cleaner and more maintainable code. Also, renaming test functions aligns with the simplified process, enhancing readability. 📊✨

worker/deciphon_worker/hmmer.py

@@ -2,7 +2,7 @@
 from typing import Any
 
 from deciphon_schema import HMMFile
-from h3daemon.sched import SchedContext
+import h3daemon
 from loguru import logger
 
 from deciphon_worker.thread import launch_thread
@@ -12,22 +12,17 @@
 
 class HMMER:
     def __init__(self, hmmfile: HMMFile, stdout: Any, stderr: Any):
-        info("starting hmmer daemon")
-        h3file = HMMFile(path=hmmfile.path)
-        stdout = stdout
-        stderr = stderr
-        self._sched_ctx = SchedContext(h3file, stdout=stdout, stderr=stderr)
-        self._sched = self._sched_ctx.__enter__()
-
-    def shutdown(self):
-        info("stopping hmmer daemon")
-        if self._sched_ctx is not None:
-            self._sched_ctx.__exit__()
-            self._sched_ctx = None
+        pidfile = h3daemon.spawn(
+            hmmfile, stdout=stdout, stderr=stderr, detach=False, force=True
+        )
+        self._manager = h3daemon.possess(pidfile)
+
+    def shutdown(self, force=False):
+        self._manager.shutdown(force=force)
 
     @property
     def port(self):
-        return self._sched.get_cport()
+        return self._manager.port()
 
 
 def launch_hmmer(hmmfile: HMMFile, stdout: Any = None, stderr: Any = None):

worker/deciphon_worker/scanner.py

@@ -45,8 +45,8 @@ def __init__(
         stdout: Any = None,
         stderr: Any = None,
     ):
-        h3file = HMMFile(path=dbfile.hmmpath.path)
-        self._hmmer: HMMER = launch_hmmer(h3file, stdout, stderr).result()
+        hmmfile = HMMFile(path=dbfile.hmmpath.path)
+        self._hmmer: HMMER = launch_hmmer(hmmfile, stdout, stderr).result()
         info("starting scan daemon")
         self._scan = Scan(
             dbfile,

worker/pyproject.toml

@@ -8,7 +8,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-h3daemon = "^0.14.9"
+h3daemon = "^0.15.0"
 deciphon-core = "^1.0.7"
 loguru = "^0.7.2"
 tenacity = "^9.0.0"

worker/tests/test_hmmer.py

@@ -7,7 +7,7 @@
 from deciphon_worker import launch_hmmer, shutting
 
 
-def test_hmmer_worker(tmp_path, files_path: Path):
+def test_hmmer(tmp_path, files_path: Path):
     os.chdir(tmp_path)
     shutil.copy(files_path / "minifam.hmm", Path("minifam.hmm"))
     hmmfile = HMMFile(path=Path("minifam.hmm"))

worker/tests/test_press.py

@@ -7,7 +7,7 @@
 from deciphon_worker import press
 
 
-def test_press_worker(tmp_path, files_path: Path):
+def test_press(tmp_path, files_path: Path):
     os.chdir(tmp_path)
     shutil.copy(files_path / "minifam.hmm", Path("minifam.hmm"))
     hmmfile = HMMFile(path=Path("minifam.hmm"))