fastremap 1.14.0__tar.gz → 1.14.2__tar.gz

{fastremap-1.14.0 → fastremap-1.14.2}/.github/workflows/build_wheel.yml

@@ -6,7 +6,7 @@ on:
     tags:
       - '*'
 env:
-  CIBW_SKIP: cp27-* cp33-* cp34-* cp35-* pp27* pp36* pp37* pp38* pp39* pp310* *-musllinux*
+  CIBW_SKIP: cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp* *-musllinux* cp312-manylinux_i686
 
 jobs:
   build_wheels:
@@ -14,25 +14,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-2019]
         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' }}
         uses: docker/setup-qemu-action@v1
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.19.1
         # 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 numpy setuptools wheel cython 
 
       - uses: actions/upload-artifact@v2
         with:

{fastremap-1.14.0 → fastremap-1.14.2}/ChangeLog

@@ -1,6 +1,31 @@
 CHANGES
 =======
 
+1.14.2
+------
+
+* install: bump python to 3.8, add cnp.import\_array()
+* ci: re-add macos, remove travis, appveyor
+* ci: use numpy without qualification
+* ci: properly specify numpy 2.0 and use working artifact uploader
+* ci: switch to compiling with numpy 2.0
+* ci: use non-buggy version of cibuildwheel
+* refactor: remove COUNT\_T
+* redesign: remove \_\_version\_\_ attribute
+* perf: reduce memory usage during finaly copy for unique\_via\_sort
+* fix: unique supports large arrays for the counts
+* fix: accurate unique counts for large arrays
+* build: more modernizations
+
+1.14.1
+------
+
+* build: temporarily exclude macos until ecosystem fixes itself
+* chore: ignore fastremap.cpp
+* chore: ignore fastremap.cpp
+* build: update for py312
+* build: update build
+
 1.14.0
 ------
 

{fastremap-1.14.0 → fastremap-1.14.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fastremap
-Version: 1.14.0
+Version: 1.14.2
 Summary: Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
 Home-page: https://github.com/seung-lab/fastremap/
 Author: William Silversmith
@@ -214,5 +214,5 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Utilities
-Requires-Python: >=3.7,<4.0
+Requires-Python: >=3.8,<4.0
 Description-Content-Type: text/markdown

{fastremap-1.14.0 → fastremap-1.14.2}/fastremap.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fastremap
-Version: 1.14.0
+Version: 1.14.2
 Summary: Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
 Home-page: https://github.com/seung-lab/fastremap/
 Author: William Silversmith
@@ -214,5 +214,5 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Utilities
-Requires-Python: >=3.7,<4.0
+Requires-Python: >=3.8,<4.0
 Description-Content-Type: text/markdown

{fastremap-1.14.0 → fastremap-1.14.2}/fastremap.egg-info/SOURCES.txt

@@ -1,13 +1,10 @@
 .dockerignore
-.travis.yml
 AUTHORS
 ChangeLog
 LICENSE
 README.md
-appveyor.yml
 automated_test.py
 build_linux.sh
-fastremap.cpp
 fastremap.pxd
 fastremap.pyx
 ipt.hpp

fastremap-1.14.2/fastremap.egg-info/pbr.json

@@ -0,0 +1 @@
+{"git_version": "9b0e91f", "is_release": true}

{fastremap-1.14.0 → fastremap-1.14.2}/fastremap.pyx

@@ -29,9 +29,9 @@ import operator
 
 import numpy as np
 cimport numpy as cnp
+cnp.import_array()
 
-__version__ = '1.14.0'
-__VERSION__ = __version__
+from libcpp.vector cimport vector
 
 ctypedef fused UINT:
   uint8_t
@@ -746,6 +746,7 @@ def _pixel_pairs(cnp.ndarray[ALLINT, ndim=1] labels):
 
   return pairs
 
+@cython.binding(True)
 def unique(labels, return_index=False, return_inverse=False, return_counts=False, axis=None):
   """
   Compute the sorted set of unique labels in the input array.
@@ -853,42 +854,42 @@ def unique_via_sort(cnp.ndarray[ALLINT, ndim=1] labels):
 
   cdef size_t voxels = labels.size  
 
-  cdef cnp.ndarray[ALLINT, ndim=1] uniq = np.zeros((voxels,), dtype=labels.dtype)
-  cdef cnp.ndarray[uint32_t, ndim=1] counts = np.zeros((voxels,), dtype=np.uint32)
+  cdef vector[ALLINT] uniq
+  uniq.reserve(100)
+
+  cdef vector[uint64_t] counts
+  counts.reserve(100)
 
   cdef size_t i = 0
-  cdef size_t j = 0
 
   cdef ALLINT cur = labels[0]
-  cdef size_t accum = 1
+  cdef uint64_t accum = 1
   for i in range(1, voxels):
     if cur == labels[i]:
       accum += 1
     else:
-      uniq[j] = cur
-      counts[j] = accum
+      uniq.push_back(cur)
+      counts.push_back(accum)
       accum = 1
       cur = labels[i]
-      j += 1
 
-  uniq[j] = cur
-  counts[j] = accum
+  uniq.push_back(cur)
+  counts.push_back(accum)
+
+  del labels
 
-  return uniq[:j+1], counts[:j+1]
+  return np.array(uniq), np.array(counts)
 
 @cython.boundscheck(False)
 @cython.wraparound(False)  # turn off negative index wrapping for entire function
 @cython.nonecheck(False)
-def unique_via_array(cnp.ndarray[ALLINT, ndim=1] labels, size_t max_label, return_index=False):
-  """
-  unique(cnp.ndarray[ALLINT, ndim=1] labels, return_counts=False)
-
-  Faster implementation of np.unique that depends
-  on the maximum label in the array being less than
-  the size of the array.
-  """
-  cdef cnp.ndarray[uint32_t, ndim=1] counts = np.zeros( 
-    (max_label+1,), dtype=np.uint32
+def unique_via_array(
+  cnp.ndarray[ALLINT, ndim=1] labels, 
+  size_t max_label, 
+  return_index
+):
+  cdef cnp.ndarray[uint64_t, ndim=1] counts = np.zeros( 
+    (max_label+1,), dtype=np.uint64
   )
   cdef cnp.ndarray[uintptr_t, ndim=1] index
   
@@ -916,8 +917,8 @@ def unique_via_array(cnp.ndarray[ALLINT, ndim=1] labels, size_t max_label, retur
   cdef cnp.ndarray[ALLINT, ndim=1] segids = np.zeros( 
     (real_size,), dtype=labels.dtype
   )
-  cdef cnp.ndarray[uint32_t, ndim=1] cts = np.zeros( 
-    (real_size,), dtype=np.uint32
+  cdef cnp.ndarray[uint64_t, ndim=1] cts = np.zeros( 
+    (real_size,), dtype=np.uint64
   )
   cdef cnp.ndarray[uintptr_t, ndim=1] idx
 

{fastremap-1.14.0 → fastremap-1.14.2}/setup.py

@@ -22,8 +22,8 @@ if sys.platform == 'darwin':
   extra_compile_args += ['-stdlib=libc++', '-mmacosx-version-min=10.9']
 
 setuptools.setup(
-  setup_requires=['pbr', 'numpy'],
-  python_requires=">=3.7,<4.0",
+  setup_requires=['pbr', 'cython', 'numpy'],
+  python_requires=">=3.8,<4.0",
   pbr=True,
   ext_modules=[
     setuptools.Extension(

fastremap-1.14.2/test.py

@@ -0,0 +1,21 @@
+import fastremap
+import numpy as np 
+
+x = np.ones((1700,1700,1700), dtype=np.uint8)
+uniq, cts = fastremap.unique(x, return_counts=True)
+print(uniq, cts)
+
+print(cts[0] / 2**32)
+
+
+# @profile
+# def run():
+#   x = np.ones( (512,512,512), dtype=np.uint32, order='C')
+#   x += 1
+#   print(x.strides, x.flags)
+#   y = np.asfortranarray(x)
+#   print(x.strides, x.flags)
+
+#   print("done.")
+
+# run()

{fastremap-1.14.0 → fastremap-1.14.2}/tox.ini

@@ -1,10 +1,12 @@
 [tox]
-envlist = py38,py38,py310,py311
+envlist = py38,py39,py310,py311,py312
 
 [testenv]
 platform = darwin
 deps = 
 	oldest-supported-numpy
+	setuptools
+	wheel
 	-rrequirements.txt
 	-rrequirements_dev.txt
 

fastremap-1.14.0/.travis.yml

@@ -1,17 +0,0 @@
-language: python
-python:
-- '3.6'
-- '3.7'
-- '3.8'
-- '3.9'
-before_install:
-- sudo apt-get install python3-pip
-install:
-- virtualenv -p python3 venv
-- source venv/bin/activate
-- pip3 install -r requirements.txt -r requirements_dev.txt
-- pip3 install -e .
-- python3 setup.py sdist bdist_wheel --universal
-script:
-- python3 -m pytest -v -x automated_test.py
-

fastremap-1.14.0/appveyor.yml

@@ -1,41 +0,0 @@
-image: Visual Studio 2019
-
-environment:
-  matrix:
-    - PYTHON: "C:\\Python37"
-    - PYTHON: "C:\\Python38"
-    - PYTHON: "C:\\Python39"
-    - PYTHON: "C:\\Python310-x64"
-    - PYTHON: "C:\\Python37-x64"
-    - PYTHON: "C:\\Python38-x64"
-    - PYTHON: "C:\\Python39-x64"
-    - PYTHON: "C:\\Python310-x64"
-
-install:
-  # We need wheel installed to build wheels
-  - "%PYTHON%\\python.exe -m pip install wheel"
-
-build: off
-
-test_script:
-  # Put your test command here.
-  # If you don't need to build C extensions on 64-bit Python 3.3 or 3.4,
-  # you can remove "build.cmd" from the front of the command, as it's
-  # only needed to support those cases.
-  # Note that you must use the environment variable %PYTHON% to refer to
-  # the interpreter you're using - Appveyor does not do anything special
-  # to put the Python version you want to use on PATH.
-  - "%PYTHON%\\python.exe -m pip install -r requirements.txt pytest"
-  - "%PYTHON%\\python.exe -m pip install -e ."
-  - "%PYTHON%\\python.exe -m pytest -v -x automated_test.py"
-
-after_test:
-  # This step builds your wheels.
-  # Again, you only need build.cmd if you're building C extensions for
-  # 64-bit Python 3.3/3.4. And you need to use %PYTHON% to get the correct
-  # interpreter
-  - "%PYTHON%\\python.exe setup.py bdist_wheel"
-
-artifacts:
-  # bdist_wheel puts your built wheel in the dist directory
-  - path: dist\*