Refactor Daemon context and remove unused files 🛠️

- Updated `__init__.py` to simplify imports and __all__ definition.
- Changed `start` function in `cli.py` for parameter renaming.
- Refactored `daemon.py` to streamline context handling and added new `spawn` function.
- Deleted unused `daemonize.py` and `possess.py` files to clean up the codebase.
- Modified test in `test_daemon.py` to remove unnecessary debug file operations.

h3daemon/h3daemon/__init__.py

@@ -1,6 +1,3 @@
-from h3daemon.daemon import Daemon, daemon_context
-from h3daemon.daemonize import spawn
-from h3daemon.ensure_pressed import ensure_pressed
-from h3daemon.possess import possess
+from h3daemon.daemon import context, possess, spawn
 
-__all__ = ["Daemon", "ensure_pressed", "spawn", "possess", "daemon_context"]
+__all__ = ["spawn", "possess", "context"]

h3daemon/h3daemon/cli.py

@@ -9,7 +9,7 @@
 from typer import echo
 
 from h3daemon.daemon import Daemon
-from h3daemon.daemonize import spawn
+from h3daemon import spawn
 from h3daemon.pidfile import create_pidfile
 from h3daemon import possess
 
@@ -56,7 +56,7 @@ def start(
     ferr = open(stderr, "w+") if stderr else stderr
     spawn(
         hmm,
-        cport=port,
+        port=port,
         stdin=fin,
         stdout=fout,
         stderr=ferr,

h3daemon/h3daemon/daemon.py

@@ -1,18 +1,27 @@
 from contextlib import contextmanager, suppress
+from multiprocessing import Process
+from typing import Any, Optional
 
 import psutil
+from daemon import DaemonContext
 from deciphon_schema import HMMFile
 from pidlockfile import PIDLockFile
 from tenacity import retry, stop_after_delay, wait_exponential
 
 from h3daemon.debug import debug_exception, debug_message
 from h3daemon.ensure_pressed import ensure_pressed
-from h3daemon.errors import ChildNotFoundError, PIDNotFoundError
+from h3daemon.errors import (
+    ChildNotFoundError,
+    DaemonAlreadyRunningError,
+    PIDNotFoundError,
+)
 from h3daemon.master import Master
-from h3daemon.portfile import read_portfile
+from h3daemon.pidfile import create_pidfile
+from h3daemon.port import find_free_port
+from h3daemon.portfile import create_portfile, read_portfile
 from h3daemon.worker import Worker
 
-__all__ = ["Daemon", "daemon_context"]
+__all__ = ["Daemon", "context"]
 
 
 def shutdown(x: psutil.Process, *, force: bool, wait: bool):
@@ -137,10 +146,62 @@ def join(self):
 
 
 @contextmanager
-def daemon_context(hmmfile: HMMFile, cport: int = 0, wport: int = 0):
-    x = Daemon.create(hmmfile, cport, wport)
+def context(hmmfile: HMMFile, port: int = 0):
+    x = Daemon.create(hmmfile, port, find_free_port())
     try:
-        x.wait_for_readiness()
-        yield x
+        yield x.port()
     finally:
         x.shutdown()
+
+
+def daemonize(
+    hmmfile: HMMFile,
+    port: int = 0,
+    stdin: Optional[Any] = None,
+    stdout: Optional[Any] = None,
+    stderr: Optional[Any] = None,
+    detach: Optional[bool] = None,
+):
+    pidfile = create_pidfile(hmmfile)
+    assert pidfile.is_locked() is None
+    with DaemonContext(
+        working_directory=str(hmmfile.path.parent),
+        pidfile=pidfile,
+        detach_process=detach,
+        stdin=stdin,
+        stdout=stdout,
+        stderr=stderr,
+    ):
+        port = find_free_port() if port == 0 else port
+        wport = find_free_port()
+        create_portfile(pidfile, port, wport)
+        x = Daemon.create(hmmfile, port, wport)
+        x.join()
+
+
+def spawn(
+    hmmfile: HMMFile,
+    port: int = 0,
+    stdin: Optional[Any] = None,
+    stdout: Optional[Any] = None,
+    stderr: Optional[Any] = None,
+    detach: Optional[bool] = None,
+    force: Optional[bool] = False,
+):
+    pidfile = create_pidfile(hmmfile)
+    if pidfile.is_locked():
+        if not force:
+            raise DaemonAlreadyRunningError(f"Daemon for {hmmfile} is already running.")
+        x = Daemon.possess(pidfile)
+        x.shutdown(force=force)
+
+    args = (hmmfile, port, stdin, stdout, stderr, detach)
+    p = Process(target=daemonize, args=args, daemon=False)
+    p.start()
+    return pidfile
+
+
+def possess(pidfile: PIDLockFile, wait=True):
+    if wait:
+        return Daemon.possess_wait(pidfile)
+    return Daemon.possess(pidfile)

h3daemon/tests/test_daemon.py

@@ -11,16 +11,8 @@
 @pytest.mark.repeat(30)
 def test_hmmer(tmp_path, files_path: Path):
     os.chdir(tmp_path)
-    debug_file = Path(tmp_path / "h3daemon_debug.txt")
-    debug_file.touch()
-
     shutil.copy(files_path / "minifam.hmm", Path("minifam.hmm"))
-
-    try:
-        hmmfile = HMMFile(path=Path("minifam.hmm"))
-        pidfile = h3daemon.spawn(hmmfile, detach=True, force=True)
-        daemon = h3daemon.possess(pidfile, wait=True)
-        daemon.shutdown()
-    finally:
-        with open(debug_file, "r") as f:
-            print(f.read())
+    hmmfile = HMMFile(path=Path("minifam.hmm"))
+    pidfile = h3daemon.spawn(hmmfile, detach=True, force=True)
+    daemon = h3daemon.possess(pidfile, wait=True)
+    daemon.shutdown()