Merge branch 'main' into fix-issue-288

.github/workflows/deploy.yml

@@ -79,19 +79,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest]
         include:
           - os: macos-11
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-2019
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: ubuntu-20.04
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - name: Checkout source

.github/workflows/test.yml

@@ -50,19 +50,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest]
         include:
           - os: macos-11
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-2019
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: ubuntu-20.04
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v3
@@ -87,7 +87,9 @@ jobs:
         run: python -m pip install tox tox-gh-actions
 
       - name: Test with tox
-        run: tox
+        run: tox run
+        env:
+            OS: ${{ matrix.os }}
 
       - name: Coverage
         uses: codecov/codecov-action@v3

.gitignore

@@ -55,8 +55,7 @@ instance
 lib
 lib64
 local_settings.py
-models/MDCK_*
-models/test_config.json
+models
 nosetests.xml
 notebooks
 parts

.napari-hub/DESCRIPTION.md

@@ -44,5 +44,5 @@ If working on Apple Silicon make sure to also install the following
 packages from `conda-forge`.
 
 ```sh
-conda install -c conda-forge cvxopt pyqt
+conda install -c conda-forge pyqt
 ```

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.262
+      rev: v0.0.278
       hooks:
         - id: ruff
     - repo: https://github.com/Lucas-C/pre-commit-hooks
-      rev: v1.5.1
+      rev: v1.5.3
       hooks:
         - id: remove-tabs
           exclude: Makefile|docs/Makefile|\.bat$
@@ -22,15 +22,15 @@ repos:
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.7.0
       hooks:
           - id: black
     - repo: https://github.com/pappasam/toml-sort
-      rev: v0.23.0
+      rev: v0.23.1
       hooks:
         - id: toml-sort-fix
     - repo: https://github.com/pre-commit/mirrors-clang-format
-      rev: v15.0.7
+      rev: v16.0.6
       hooks:
       - id: clang-format
         types_or: [c++, c, cuda]

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Optionally declare the Python requirements required to build your docs
 python:

MANIFEST.in

@@ -1 +1,5 @@
 graft btrack/libs
+prune docs
+prune tests
+prune models
+prune examples

Makefile

@@ -18,15 +18,15 @@ ifeq ($(UNAME), Darwin)
 	# do something OSX
 	CXX = clang++ -arch x86_64 -arch arm64
 	EXT = dylib
-	XLD_FLAGS = -arch x86_64 -arch arm64
+	XLDFLAGS =
 endif
 
 NVCC = nvcc
 
-# If your compiler is a bit older you may need to change -std=c++17 to -std=c++0x
+# If your compiler is a bit older you may need to change -std=c++11 to -std=c++0x
 #-I/usr/include/python2.7 -L/usr/lib/python2.7 # -O3
 LLDBFLAGS =
-CXXFLAGS = -c -std=c++17 -m64 -fPIC -I"./btrack/include" \
+CXXFLAGS = -c -std=c++11 -m64 -fPIC -I"./btrack/include" \
 	       -DDEBUG=false -DBUILD_SHARED_LIB
 OPTFLAGS = -O3
 LDFLAGS = -shared $(XLDFLAGS)

README.md

@@ -38,15 +38,6 @@ it is now built against `C++=17`.
 pip install btrack
 ```
 
-#### Installing on Apple Silicon
-
-Run the above command with `pip` and then also install the following with
-[conda](https://github.com/conda-forge/miniforge).
-
-```sh
-conda install -c conda-forge cvxopt
-```
-
 ## Usage examples
 
 Visit [btrack documentation](https://btrack.readthedocs.io) to learn how to use it and see other examples.

btrack/btypes.py

@@ -17,7 +17,7 @@
 
 import ctypes
 from collections import OrderedDict
-from typing import Any, NamedTuple, Optional
+from typing import Any, ClassVar, NamedTuple, Optional
 
 import numpy as np
 
@@ -86,7 +86,7 @@ class PyTrackObject(ctypes.Structure):
 
     """
 
-    _fields_ = [
+    _fields_: ClassVar[list] = [
         ("ID", ctypes.c_long),
         ("x", ctypes.c_double),
         ("y", ctypes.c_double),
@@ -109,9 +109,7 @@ def __init__(self):
 
     @property
     def properties(self) -> dict[str, Any]:
-        if self.dummy:
-            return {}
-        return self._properties
+        return {} if self.dummy else self._properties
 
     @properties.setter
     def properties(self, properties: dict[str, Any]):
@@ -129,10 +127,8 @@ def set_features(self, keys: list[str]) -> None:
             self.n_features = 0
             return
 
-        if not all(k in self.properties for k in keys):
-            missing_features = list(
-                set(keys).difference(set(self.properties.keys()))
-            )
+        if any(k not in self.properties for k in keys):
+            missing_features = list(set(keys).difference(set(self.properties.keys())))
             raise KeyError(f"Feature(s) missing: {missing_features}.")
 
         # store a reference to the numpy array so that Python maintains
@@ -153,7 +149,7 @@ def to_dict(self) -> dict[str, Any]:
             for k, _ in PyTrackObject._fields_
             if k not in ("features", "n_features")
         }
-        node.update(self.properties)
+        node |= self.properties
         return node
 
     @staticmethod
@@ -174,9 +170,7 @@ def from_dict(properties: dict[str, Any]) -> PyTrackObject:
                 setattr(obj, key, float(new_data))
 
         # we can add any extra details to the properties dictionary
-        obj.properties = {
-            k: v for k, v in properties.items() if k not in fields.keys()
-        }
+        obj.properties = {k: v for k, v in properties.items() if k not in fields}
         return obj
 
     def __repr__(self):
@@ -221,7 +215,7 @@ class PyTrackingInfo(ctypes.Structure):
 
     """
 
-    _fields_ = [
+    _fields_: ClassVar[list] = [
         ("error", ctypes.c_uint),
         ("n_tracks", ctypes.c_uint),
         ("n_active", ctypes.c_uint),
@@ -239,8 +233,7 @@ def to_dict(self) -> dict[str, Any]:
         """Return a dictionary of the statistics"""
         # TODO(arl): make this more readable by converting seconds, ms
         # and interpreting error messages?
-        stats = {k: getattr(self, k) for k, typ in PyTrackingInfo._fields_}
-        return stats
+        return {k: getattr(self, k) for k, typ in PyTrackingInfo._fields_}
 
     @property
     def tracker_active(self) -> bool:
@@ -269,7 +262,7 @@ class PyGraphEdge(ctypes.Structure):
     source timestamp, we just assume that the tracker has done it's job.
     """
 
-    _fields_ = [
+    _fields_: ClassVar[list] = [
         ("source", ctypes.c_long),
         ("target", ctypes.c_long),
         ("score", ctypes.c_double),
@@ -278,8 +271,7 @@ class PyGraphEdge(ctypes.Structure):
 
     def to_dict(self) -> dict[str, Any]:
         """Return a dictionary describing the edge."""
-        edge = {k: getattr(self, k) for k, _ in PyGraphEdge._fields_}
-        return edge
+        return {k: getattr(self, k) for k, _ in PyGraphEdge._fields_}
 
 
 class Tracklet:
@@ -353,7 +345,7 @@ class Tracklet:
     x values.
     """
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         ID: int,
         data: list[PyTrackObject],
@@ -397,11 +389,7 @@ def properties(self) -> dict[str, np.ndarray]:
         # this to fill the properties array with NaN for dummy objects
         property_shapes = {
             k: next(
-                (
-                    np.asarray(o.properties[k]).shape
-                    for o in self._data
-                    if not o.dummy
-                ),
+                (np.asarray(o.properties[k]).shape for o in self._data if not o.dummy),
                 None,
             )
             for k in keys
@@ -489,9 +477,7 @@ def softmax(self) -> list:
 
     @property
     def is_root(self) -> bool:
-        return (
-            self.parent == 0 or self.parent is None or self.parent == self.ID
-        )
+        return self.parent == 0 or self.parent is None or self.parent == self.ID
 
     @property
     def is_leaf(self) -> bool:
@@ -526,9 +512,9 @@ def to_dict(
         """Return a dictionary of the tracklet which can be used for JSON
         export. This is an ordered dictionary for nicer JSON output.
         """
-        trk_tuple = tuple([(p, getattr(self, p)) for p in properties])
+        trk_tuple = tuple((p, getattr(self, p)) for p in properties)
         data = OrderedDict(trk_tuple)
-        data.update(self.properties)
+        data |= self.properties
         return data
 
     def to_array(
@@ -576,8 +562,7 @@ def _pandas_html_repr(obj):
         import pandas as pd
     except ImportError:
         return (
-            "<b>Install pandas for nicer, tabular rendering.</b> <br>"
-            + obj.__repr__()
+            "<b>Install pandas for nicer, tabular rendering.</b> <br>" + obj.__repr__()
         )
 
     obj_as_dict = obj.to_dict()

btrack/config.py

@@ -2,7 +2,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import Optional
+from typing import ClassVar, Optional
 
 import numpy as np
 from pydantic import BaseModel, conlist, validator
@@ -95,25 +95,22 @@ class TrackerConfig(BaseModel):
 
     @validator("volume", pre=True, always=True)
     def _parse_volume(cls, v):
-        if isinstance(v, tuple):
-            return ImagingVolume(*v)
-        return v
+        return ImagingVolume(*v) if isinstance(v, tuple) else v
 
     @validator("tracking_updates", pre=True, always=True)
     def _parse_tracking_updates(cls, v):
         _tracking_updates = v
         if all(isinstance(k, str) for k in _tracking_updates):
             _tracking_updates = [
-                constants.BayesianUpdateFeatures[k.upper()]
-                for k in _tracking_updates
+                constants.BayesianUpdateFeatures[k.upper()] for k in _tracking_updates
             ]
         _tracking_updates = list(set(_tracking_updates))
         return _tracking_updates
 
     class Config:
         arbitrary_types_allowed = True
         validate_assignment = True
-        json_encoders = {
+        json_encoders: ClassVar[dict] = {
             np.ndarray: lambda x: x.ravel().tolist(),
         }