cibuildwheels - Phase 1

.github/workflows/build_wheels.yml

@@ -0,0 +1,35 @@
+name: Build Wheels
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - "**.md"
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        # env:
+        #   CIBW_SOME_OPTION: value
+        #    ...
+        # with:
+        #   package-dir: .
+        #   output-dir: wheelhouse
+        #   config-file: "{package}/pyproject.toml"
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl

.gitignore

@@ -1,11 +1,10 @@
 btrack/include/eigen
-btrack/__pycache__
-btrack/optimise/__pycache__
+__pycache__
 btrack/agents.py
 btrack/render_movie.py
 models/MDCK_*
 examples/napari.png
-examples/.ipynb_checkpoints
+*.ipynb_checkpoints
 models/test_config.json
 notebooks
 deprecated
@@ -25,3 +24,7 @@ docs/api/*
 coverage.xml
 .envrc
 .hypothesis
+*.so
+*.dylib
+*.DLL
+wheelhouse

btrack/include/defs.h

@@ -23,6 +23,15 @@
 #ifndef M_PI
     #define M_PI 3.14159265358979323846
 #endif
+#ifndef VERSION_MAJOR
+    #define VERSION_MAJOR 0
+#endif
+#ifndef VERSION_MINOR
+    #define VERSION_MINOR 0
+#endif
+#ifndef VERSION_BUILD
+    #define VERSION_BUILD 0
+#endif
 
 // store some information about the compilation
 static unsigned int v_major = VERSION_MAJOR;

btrack/include/hypothesis.h

@@ -31,7 +31,7 @@
 #include "pdf.h"
 #include "updates.h"
 #include "bayes.h"
-
+#include <cassert>
 
 
 // Store a hypothesis to return to Python

btrack/include/tracklet.h

@@ -24,6 +24,7 @@
 #include "motion.h"
 #include "inference.h"
 #include "defs.h"
+#include <cassert>
 
 // #define MAX_LOST 5
 

btrack/include/types.h

@@ -23,6 +23,7 @@
 #include <iostream>
 #include <limits>
 #include "defs.h"
+#include <cassert>
 
 
 

btrack/src/tracker.cc

@@ -14,6 +14,9 @@
 --------------------------------------------------------------------------------
 */
 
+#ifndef DEBUG
+    #define DEBUG 0
+#endif
 
 #include "tracker.h"
 
@@ -519,7 +522,7 @@ void BayesianTracker::cost_EXACT(
 
   // set up some variables for Bayesian updates
   double uniform_prior = 1. / (n_objects+1);
-  double prior_assign, PrDP, posterior, update, safe_update;
+  double prior_assign, posterior, safe_update;
 
   // start by intializing the belief matrix with a uniform prior
   if (use_uniform_prior) {
@@ -586,7 +589,7 @@ void BayesianTracker::cost_APPROXIMATE(
   std::clock_t t_update_start = std::clock();
 
   // set up some variables for Bayesian updates
-  double prior_assign, PrDP, posterior, safe_update;
+  double prior_assign, posterior, safe_update;
 
   // Posterior is a misnoma here because it is initially the prior, but
   // becomes the posterior

build.sh

@@ -9,12 +9,3 @@ if [ ! -e ./btrack/include/eigen/signature_of_eigen3_matrix_library ]
 then
   git clone https://gitlab.com/libeigen/eigen.git ./btrack/include/eigen
 fi
-
-# build the tracker
-echo "Compiling btrack from source..."
-make clean
-make
-
-# run the installation
-echo "Installing btrack python package..."
-pip install -e .

pyproject.toml

@@ -71,6 +71,23 @@ exclude = '''
 line-length = 79
 target-version = ["py38", "py39", "py310"]
 
+[tool.cibuildwheel]
+before-all = [
+    "bash build.sh",
+]
+test-command = "pytest {project}"
+test-extras = [
+    "napari",
+]
+test-requires = [
+    "dask",
+    "pytest",
+]
+linux.before-all = [
+    "yum install -y fontconfig",
+    "bash build.sh",
+]
+
 [tool.coverage]
 report = {skip_covered = true, sort = "cover"}
 run = {branch = true, parallel = true, source = ["btrack"]}

setup.py

@@ -0,0 +1,12 @@
+from setuptools import Extension, setup
+
+setup(
+    ext_modules=[
+        Extension(
+            "libtracker",
+            ["btrack/src/tracker.cc"],
+            include_dirs=["btrack/include"],
+            extra_compile_args=["-c", "-std=c++17", "-m64", "-fPIC"],
+        ),
+    ],
+)