build: update for py312

Author: william-silversmith

.github/workflows/build_wheel.yml

@@ -5,22 +5,22 @@ on:
     tags:
       - '*'
 env:
-  CIBW_SKIP: cp27-* cp33-* cp34-* cp35-* pp27* pp36* pp37* pp38* pp39* pp310* *-musllinux_aarch64
+  CIBW_SKIP: cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp* *-musllinux_aarch64
 
 jobs:
   build_wheels:
     name: Build wheels on ${{matrix.arch}} for ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-latest]
+        os: [ubuntu-latest, windows-2019, macos-latest]
         arch: [auto]
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-latest
             arch: aarch64
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up QEMU
         if:  ${{ matrix.arch == 'aarch64' }}
@@ -31,8 +31,8 @@ jobs:
         # to supply options, put them in 'env', like:
         env:
           CIBW_ARCHS_LINUX: ${{matrix.arch}}
-          CIBW_BEFORE_BUILD: pip install oldest-supported-numpy
+          CIBW_BEFORE_BUILD: pip install oldest-supported-numpy setuptools wheel cython
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl

ChangeLog

@@ -1,6 +1,10 @@
 CHANGES
 =======
 
+2.2.1
+-----
+
+* config: update formatting of setup.cfg
 * build: update build to use pyx and easier numpy install
 * test: py38, 39, 310, 311
 * build: update build for py311

setup.py

@@ -36,7 +36,7 @@ def __repr__(self):
             'compressed_segmentation.pyx'
         )],
         language='c++',
-        include_dirs=[ 'include', NumpyImport() ],
+        include_dirs=[ 'include', str(NumpyImport()) ],
         extra_compile_args=extra_compile_args,
     ),
   ],

src/compressed_segmentation.pyx

@@ -26,6 +26,7 @@ from functools import reduce
 
 from libcpp.vector cimport vector
 
+import cython
 cimport numpy as np
 import numpy as np
 
@@ -56,6 +57,7 @@ DEFAULT_BLOCK_SIZE = (8,8,8)
 class DecodeError(Exception):
   pass
 
+@cython.binding(True)
 def compress(data, block_size=DEFAULT_BLOCK_SIZE, order='C'):
   """
   compress(data, block_size=DEFAULT_BLOCK_SIZE, order='C')
@@ -194,6 +196,7 @@ cdef decompress_helper(
   del output
   return np.frombuffer(buf, dtype=dtype).reshape( volume_size, order=order )
 
+@cython.binding(True)
 def decompress(
     bytes encoded, volume_size, dtype, 
     block_size=DEFAULT_BLOCK_SIZE, order='C'
@@ -222,6 +225,7 @@ def decompress(
   else:
     raise TypeError("dtype ({}) must be one of uint32 or uint64.".format(dtype))
 
+@cython.binding(True)
 def labels(
   bytes encoded, shape, dtype, 
   block_size=DEFAULT_BLOCK_SIZE
@@ -252,6 +256,7 @@ def labels(
 
   return np.unique(labels)
 
+@cython.binding(True)
 def remap(
   bytes encoded, shape, dtype, 
   mapping, preserve_missing_labels=False,