Update versions and add default_signalling

c-core/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.20.2 FATAL_ERROR)
-project(deciphon VERSION 0.15.9 LANGUAGES C)
+project(deciphon VERSION 0.15.10 LANGUAGES C)
 
 include(cmake/warnings.cmake)
 include(cmake/sanitizers.cmake)

c-core/viterbi.c

@@ -33,40 +33,40 @@ typedef float    f32;
 #define STEP_LANE_OFFSET 24
 #define STEP_DATA_OFFSET 0
 
-#define STEP_NAME_MASK 0xF0000000
-#define STEP_LANE_MASK 0x0F000000
-#define STEP_DATA_MASK 0x00FFFFFF
+#define STEP_NAME_MASK 0xF0000000u
+#define STEP_LANE_MASK 0x0F000000u
+#define STEP_DATA_MASK 0x00FFFFFFu
 
-#define STEP_SN (0x1 << STEP_NAME_OFFSET)
-#define STEP_NN (0x2 << STEP_NAME_OFFSET)
+#define STEP_SN (0x1u << STEP_NAME_OFFSET)
+#define STEP_NN (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_SB (0x1 << STEP_NAME_OFFSET)
-#define STEP_NB (0x2 << STEP_NAME_OFFSET)
-#define STEP_EB (0x4 << STEP_NAME_OFFSET)
-#define STEP_JB (0x8 << STEP_NAME_OFFSET)
+#define STEP_SB (0x1u << STEP_NAME_OFFSET)
+#define STEP_NB (0x2u << STEP_NAME_OFFSET)
+#define STEP_EB (0x4u << STEP_NAME_OFFSET)
+#define STEP_JB (0x8u << STEP_NAME_OFFSET)
 
-#define STEP_EJ (0x1 << STEP_NAME_OFFSET)
-#define STEP_JJ (0x2 << STEP_NAME_OFFSET)
+#define STEP_EJ (0x1u << STEP_NAME_OFFSET)
+#define STEP_JJ (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_EC (0x1 << STEP_NAME_OFFSET)
-#define STEP_CC (0x2 << STEP_NAME_OFFSET)
+#define STEP_EC (0x1u << STEP_NAME_OFFSET)
+#define STEP_CC (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_ET (0x1 << STEP_NAME_OFFSET)
-#define STEP_CT (0x2 << STEP_NAME_OFFSET)
+#define STEP_ET (0x1u << STEP_NAME_OFFSET)
+#define STEP_CT (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_BM (0x1 << STEP_NAME_OFFSET)
-#define STEP_MM (0x2 << STEP_NAME_OFFSET)
-#define STEP_IM (0x4 << STEP_NAME_OFFSET)
-#define STEP_DM (0x8 << STEP_NAME_OFFSET)
+#define STEP_BM (0x1u << STEP_NAME_OFFSET)
+#define STEP_MM (0x2u << STEP_NAME_OFFSET)
+#define STEP_IM (0x4u << STEP_NAME_OFFSET)
+#define STEP_DM (0x8u << STEP_NAME_OFFSET)
 
-#define STEP_MI (0x1 << STEP_NAME_OFFSET)
-#define STEP_II (0x2 << STEP_NAME_OFFSET)
+#define STEP_MI (0x1u << STEP_NAME_OFFSET)
+#define STEP_II (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_MD (0x1 << STEP_NAME_OFFSET)
-#define STEP_DD (0x2 << STEP_NAME_OFFSET)
+#define STEP_MD (0x1u << STEP_NAME_OFFSET)
+#define STEP_DD (0x2u << STEP_NAME_OFFSET)
 
-#define STEP_ME (0x1 << STEP_NAME_OFFSET)
-#define STEP_DE (0x2 << STEP_NAME_OFFSET)
+#define STEP_ME (0x1u << STEP_NAME_OFFSET)
+#define STEP_DE (0x2u << STEP_NAME_OFFSET)
 
 INLINE u32 step(u32 n, int x)
 {

cli/deciphon/cli.py

@@ -15,6 +15,7 @@
 from typer import Argument, BadParameter, Exit, Option, Typer, echo
 
 from deciphon.catch_validation import catch_validation
+from deciphon.default_signalling import default_signalling
 from deciphon.gencode import gencodes
 from deciphon.h3daemon import H3Daemon
 from deciphon.hmmer_press import hmmer_press
@@ -131,7 +132,8 @@ def scan(
                 scan.dial(daemon.port)
                 for seq in sequences:
                     scan.add(seq)
-                scan.run(snap)
+                with default_signalling():
+                    scan.run(snap)
         if scan.interrupted():
             raise Exit(1)
         echo("Scan has finished successfully and " f"results stored in '{snap.path}'.")

cli/deciphon/default_signalling.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+import signal
+from signal import SIGINT, SIGTERM, Signals, SIG_DFL
+from typing import List
+
+__all__ = ["default_signalling"]
+
+
+class default_signalling:
+    def __init__(self, signals: List[Signals] = [SIGTERM, SIGINT]):
+        self._signals = signals
+        self._handlers: List[signal._HANDLER] = []
+
+    def __enter__(self):
+        for x in self._signals:
+            self._handlers.append(signal.getsignal(x))
+            signal.signal(x, SIG_DFL)
+        return self
+
+    def __exit__(self, *_):
+        for x, y in zip(self._signals, self._handlers):
+            signal.signal(x, y)

cli/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "deciphon"
-version = "0.11.4"
+version = "0.11.5"
 description = "Individually annotate long, error-prone nucleotide sequences into proteins"
 authors = ["Danilo Horta <[email protected]>"]
 license = "MIT"
@@ -10,7 +10,7 @@ packages = [{ include = "deciphon" }]
 [tool.poetry.dependencies]
 python = "^3.9"
 cffi = "^1.15.1"
-deciphon-core = ">=0.20.12"
+deciphon-core = ">=0.20.14"
 deciphon-snap = ">=0.8.2"
 fasta-reader = "^3"
 h3daemon = ">=0.13.8"