remove logger setup (acquire-project#73)

closes acquire-project#71 

I also unexpectedly ran into rust complaining about a misaligned pointer
read. So I fixed that. I can't quite figure out why it manifested now,
but it was quite repeatable.

Cargo.toml

@@ -9,22 +9,22 @@ name = "acquire"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.18", features = [
+pyo3 = { version = "0.19", features = [
     "extension-module",
     "anyhow",
     "abi3-py38",
     "serde",
 ] }
 pyo3-log = "0.8"
-numpy = "0.18"
+numpy = "0.19"
 log = "0.4"
 anyhow = "1.0"
 parking_lot = "0.12"
 serde = { version = "1.0", features = ["derive"] }
-pythonize = "0.18"
+pythonize = "0.19"
 
 [build-dependencies]
-bindgen = "0.65"
+bindgen = "0.66"
 cmake = "0.1"
 http = "0.2"
 json = "0.12"

python/acquire/__init__.py

@@ -1,5 +1,14 @@
 import time
-from typing import TYPE_CHECKING, Any, Generator, List, Literal, Optional, Tuple, Union
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Generator,
+    List,
+    Literal,
+    Optional,
+    Tuple,
+    Union,
+)
 
 import numpy.typing as npt
 
@@ -14,13 +23,6 @@
     import napari  # type: ignore
 
 
-FORMAT: str = (
-    "%(levelname)s %(name)s %(asctime)-15s %(filename)s:%(lineno)d %(message)s"
-)
-logging.basicConfig(format=FORMAT)
-logging.getLogger().setLevel(logging.INFO)
-
-
 g_runtime: Optional[Runtime] = None
 """The global acquire runtime."""
 
@@ -159,7 +161,9 @@ def update_layer(args: Tuple[npt.NDArray[Any], int]) -> None:
             viewer.add_image(new_image, name=layer_key)
 
     @thread_worker(connect={"yielded": update_layer})
-    def do_acquisition() -> Generator[Tuple[npt.NDArray[Any], int], None, None]:
+    def do_acquisition() -> (
+        Generator[Tuple[npt.NDArray[Any], int], None, None]
+    ):
         logging.basicConfig(level=logging.DEBUG)
         logging.getLogger().setLevel(logging.DEBUG)
 
@@ -188,9 +192,13 @@ def next_frame() -> Optional[npt.NDArray[Any]]:
                 if packet := runtime.get_available_data(stream_id):
                     n = packet.get_frame_count()
                     nframes[stream_id] += n
-                    logging.info(f"[stream {stream_id}] frame count: {nframes}")
+                    logging.info(
+                        f"[stream {stream_id}] frame count: {nframes}"
+                    )
                     f = next(packet.frames())
-                    logging.debug(f"stream {stream_id} frame {f.metadata().frame_id}")
+                    logging.debug(
+                        f"stream {stream_id} frame {f.metadata().frame_id}"
+                    )
                     return f.data().squeeze().copy()
             return None
 

python/acquire/__init__.pyi

@@ -4,8 +4,6 @@ import napari  # type: ignore
 
 from .acquire import *
 
-FORMAT: str
-
 def setup(
     runtime: Runtime,
     camera: Union[str, List[str]] = ...,
@@ -17,4 +15,6 @@ def setup_two_streams(runtime: Runtime, frame_count: int) -> Properties: ...
 
 g_runtime: Optional[Runtime]
 
-def gui(viewer: "napari.Viewer", frame_count: int = ..., stream_count: int = ...) -> None: ...
+def gui(
+    viewer: "napari.Viewer", frame_count: int = ..., stream_count: int = ...
+) -> None: ...

src/runtime.rs

@@ -225,7 +225,7 @@ impl RawAvailableData {
             let mut cur = self.beg.as_ptr();
             let end = self.end.as_ptr();
             while cur < end {
-                let frame: &capi::VideoFrame = &*cur;
+                let frame: &capi::VideoFrame = &std::ptr::read_unaligned(cur);
                 log::trace!(
                     "[stream {}] Advancing count for frame {} w size {}",
                     self.stream_id,