PartSegCore-compiled-backend 0.15.1__tar.gz → 0.15.4__tar.gz

{PartSegCore_compiled_backend-0.15.1 → PartSegCore_compiled_backend-0.15.4}/.github/workflows/wheels.yml

@@ -2,7 +2,7 @@ name: Wheels
 
 on:
   push:
-    branch:
+    branches:
       - master
     tags:
       - '*'
@@ -10,6 +10,9 @@ on:
     branches:
       - '**'
 
+concurrency:
+  group: wheel-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   test:
@@ -19,17 +22,25 @@ jobs:
         fail-fast: false
         matrix:
           os: [windows-latest, macos-latest, ubuntu-latest]
-          python_version: ['3.8', '3.9' , '3.10', '3.11']
+          python_version: ['3.9' , '3.10', '3.11', '3.12']
       steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         name: Install Python ${{ matrix.python_version }}
         with:
           python-version: ${{ matrix.python_version }}
+      - name: install openbls
+        if: runner.os == 'macOS'
+        run: brew install libomp
       - name: Install tox
         run: pip install tox numpy tox-gh-actions
-      - name: Test PartSeg
+      - name: Test Backend
+        run: OPENBLAS="$(brew --prefix openblas)" OMP="$(brew --prefix libomp)" tox
+        if: runner.os == 'macOS'
+      - name: Test Backend
         run: tox
+        if: runner.os != 'macOS'
+
 
   build_wheels:
     needs: test
@@ -49,7 +60,7 @@ jobs:
         run: brew install openblas
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.4
+        uses: pypa/cibuildwheel@v2.16.2
         env:
           OPENBLAS: "$(brew --prefix openblas)"
 
@@ -73,8 +84,8 @@ jobs:
 
       - name: Build sdist
         run: |
-          pip install numpy
-          python setup.py sdist
+          pip install build
+          python -m build --sdist .
 
       - uses: actions/upload-artifact@v3
         with:
@@ -83,18 +94,20 @@ jobs:
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/PartSegCore-compiled-backend
+    permissions:
+        id-token: write  # IMPORTANT: mandatory for trusted publishing
     # upload to PyPI on every tag starting with 'v'
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          # To test: repository_url: https://test.pypi.org/legacy/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

{PartSegCore_compiled_backend-0.15.1 → PartSegCore_compiled_backend-0.15.4}/.gitignore

@@ -1,5 +1,7 @@
 *.cpp
 src/PartSegCore_compiled_backend/version.py
+src/**.html
+*.html
 
 # Created by https://www.toptal.com/developers/gitignore/api/pycharm+all,jupyternotebooks,python,code,vim,macos,linux,windows
 # Edit at https://www.toptal.com/developers/gitignore?templates=pycharm+all,jupyternotebooks,python,code,vim,macos,linux,windows

PartSegCore_compiled_backend-0.15.4/.readthedocs.yaml

@@ -0,0 +1,35 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+     - method: pip
+       path: .
+       extra_requirements:
+         - docs

PartSegCore_compiled_backend-0.15.4/PKG-INFO

@@ -0,0 +1,72 @@
+Metadata-Version: 2.1
+Name: PartSegCore_compiled_backend
+Version: 0.15.4
+Summary: PartSegCore compiled backend,
+Author-email: Grzegorz Bokota <g.bokota@cent.uw.edu.pl>
+License: BSD-3-Clause
+Project-URL: Homepage, https://4dnucleome.cent.uw.edu.pl/PartSeg/
+Project-URL: Documentation, https://partsegcore-compiled-backend.readthedocs.io/en/stable/
+Project-URL: Source Code, https://github.com/4DNucleome/PartSegCore-compiled-backend
+Keywords: bioimaging
+Platform: Linux
+Platform: Windows
+Platform: MacOs
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: License.txt
+Requires-Dist: numpy>=1.25.0
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=5.0.0; extra == "docs"
+
+# PartSegCore_compiled_backend
+
+![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)
+[![Wheels](https://github.com/4DNucleome/PartSegCore-compiled-backend/actions/workflows/wheels.yml/badge.svg?branch=master)](https://github.com/4DNucleome/PartSegCore-compiled-backend/actions/workflows/wheels.yml)
+[![PyPI version](https://badge.fury.io/py/PartSegCore_compiled_backend.svg)](https://pypi.org/project/PartSegCore-compiled-backend/)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/partsegcore-compiled-backend/badges/version.svg)](https://anaconda.org/conda-forge/partsegcore-compiled-backend)
+[![Python Version](https://img.shields.io/pypi/pyversions/partsegcore-compiled-backend.svg)](https://pypi.org/project/partsegcore-compiled-backend)
+[![Documentation Status](https://readthedocs.org/projects/partsegcore-compiled-backend/badge/?version=stable)](https://partsegcore-compiled-backend.readthedocs.io/en/stable/)
+[![Publication DOI](https://img.shields.io/badge/Publication%20DOI-10.1186%2Fs12859--021--03984--1-blue)](https://doi.org/10.1186/s12859-021-03984-1)
+
+This is a package with all cython/c++ backend for ParSeg
+
+Current release extracted from PartSegCore module to avoid building multiple wheels
+for the main package and speedup tests.
+
+This package requires `libomp` for build.
+On linux it can be installed with `apt install libomp-dev` or `yum install libomp-devel`.
+On macOS it can be installed with `brew install libomp`.
+
+As `clang` version created on macOS do not have native openmp `brew` do
+not set `libomp` as default visible.
+If you install `libomp` with `brew` and want to build package
+from source you need to set `OMP` variable to `libomp` location.
+
+For example:
+
+```bash
+export OMP="$(brew --prefix libomp)"
+pip install .
+```
+
+As currently there is no wheel for macOS ARM64
+it is required to build package from source.
+
+## Cite as
+
+Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction
+from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021).
+[https://doi.org/10.1186/s12859-021-03984-1](https://doi.org/10.1186/s12859-021-03984-1)

PartSegCore_compiled_backend-0.15.4/Readme.md

@@ -0,0 +1,39 @@
+# PartSegCore_compiled_backend
+
+![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)
+[![Wheels](https://github.com/4DNucleome/PartSegCore-compiled-backend/actions/workflows/wheels.yml/badge.svg?branch=master)](https://github.com/4DNucleome/PartSegCore-compiled-backend/actions/workflows/wheels.yml)
+[![PyPI version](https://badge.fury.io/py/PartSegCore_compiled_backend.svg)](https://pypi.org/project/PartSegCore-compiled-backend/)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/partsegcore-compiled-backend/badges/version.svg)](https://anaconda.org/conda-forge/partsegcore-compiled-backend)
+[![Python Version](https://img.shields.io/pypi/pyversions/partsegcore-compiled-backend.svg)](https://pypi.org/project/partsegcore-compiled-backend)
+[![Documentation Status](https://readthedocs.org/projects/partsegcore-compiled-backend/badge/?version=stable)](https://partsegcore-compiled-backend.readthedocs.io/en/stable/)
+[![Publication DOI](https://img.shields.io/badge/Publication%20DOI-10.1186%2Fs12859--021--03984--1-blue)](https://doi.org/10.1186/s12859-021-03984-1)
+
+This is a package with all cython/c++ backend for ParSeg
+
+Current release extracted from PartSegCore module to avoid building multiple wheels
+for the main package and speedup tests.
+
+This package requires `libomp` for build.
+On linux it can be installed with `apt install libomp-dev` or `yum install libomp-devel`.
+On macOS it can be installed with `brew install libomp`.
+
+As `clang` version created on macOS do not have native openmp `brew` do
+not set `libomp` as default visible.
+If you install `libomp` with `brew` and want to build package
+from source you need to set `OMP` variable to `libomp` location.
+
+For example:
+
+```bash
+export OMP="$(brew --prefix libomp)"
+pip install .
+```
+
+As currently there is no wheel for macOS ARM64
+it is required to build package from source.
+
+## Cite as
+
+Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction
+from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021).
+[https://doi.org/10.1186/s12859-021-03984-1](https://doi.org/10.1186/s12859-021-03984-1)

PartSegCore_compiled_backend-0.15.4/build_utils/build_libomp.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+build_dir=${DIR}/libs_build
+
+git clone --depth 1 --branch llvmorg-11.1.0 https://github.com/llvm/llvm-project
+pushd llvm-project/openmp
+mkdir build
+cd build
+cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
+make
+make install
+
+popd
+rm -rf llvm-project

PartSegCore_compiled_backend-0.15.4/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

PartSegCore_compiled_backend-0.15.4/docs/calc_bounds.rst

@@ -0,0 +1,5 @@
+PartSegCore_compiled_backend.calc_bounds
+========================================
+
+.. automodule:: PartSegCore_compiled_backend.calc_bounds
+   :members:

PartSegCore_compiled_backend-0.15.4/docs/conf.py

@@ -0,0 +1,52 @@
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+import PartSegCore_compiled_backend
+
+# -- Project information -----------------------------------------------------
+
+project = 'PartSegCore-compiled-backend'
+copyright = '2024, Grzegorz Bokota'
+author = 'Grzegorz Bokota'
+release = PartSegCore_compiled_backend.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'nature'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

PartSegCore_compiled_backend-0.15.4/docs/fast_unique.rst

@@ -0,0 +1,5 @@
+PartSegCore_compiled_backend.fast_unique
+========================================
+
+.. automodule:: PartSegCore_compiled_backend.fast_unique
+   :members:

PartSegCore_compiled_backend-0.15.4/docs/index.rst

@@ -0,0 +1,34 @@
+.. PartSegCore-compiled-backend documentation master file, created by
+   sphinx-quickstart on Sat Jan 20 15:05:13 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root ``toctree`` directive.
+
+Welcome to PartSegCore-compiled-backend's documentation!
+========================================================
+
+The PartSegCore-compiled-backend was created as package for PartSeg project.
+It contains parts of code that needs to be compiled. It was created to simplify
+maintenance of PartSeg project. But maybe you could find here useful functions.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   calc_bounds
+   fast_unique
+   napari_mapping
+   sprawl_utils
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+Cite as
+=======
+
+Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). https://doi.org/10.1186/s12859-021-03984-1

PartSegCore_compiled_backend-0.15.4/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

PartSegCore_compiled_backend-0.15.4/docs/napari_mapping.rst

@@ -0,0 +1,5 @@
+PartSegCore_compiled_backend.napari_mapping
+===========================================
+
+.. automodule:: PartSegCore_compiled_backend.napari_mapping
+   :members:

PartSegCore_compiled_backend-0.15.4/docs/sprawl_utils.rst

@@ -0,0 +1,5 @@
+PartSegCore_compiled_backend.sprawl_utils.find_split
+====================================================
+
+.. automodule:: PartSegCore_compiled_backend.sprawl_utils.find_split
+   :members:

PartSegCore_compiled_backend-0.15.4/notebooks/data_util.py

@@ -0,0 +1,153 @@
+import numpy as np
+from typing import Sequence, Optional, Union, Tuple, Callable
+import itertools
+from skimage import morphology
+
+
+def _generate_ball(radius: int, ndim: int) -> np.ndarray:
+    """Generate a ball of given radius and dimension.
+
+    Parameters
+    ----------
+    radius : int
+        Radius of the ball.
+    ndim : int
+        Dimension of the ball.
+
+    Returns
+    -------
+    ball : ndarray of uint8
+        Binary array of the hyper ball.
+    """
+
+    if ndim == 2:
+        return morphology.disk(radius)
+    if ndim == 3:
+        return morphology.ball(radius)
+    shape = (2 * radius + 1,) * ndim
+    radius_sq = radius**2
+    coords = np.indices(shape) - radius
+    return (np.sum(coords**2, axis=0) <= radius_sq).astype(np.uint8)
+
+
+def _generate_density(radius: int, ndim: int) -> np.ndarray:
+    """Generate gaussian density of given radius and dimension."""
+    shape = (2 * radius + 1,) * ndim
+    coords = np.indices(shape) - radius
+    dist = np.sqrt(np.sum(coords**2 / ((radius / 4) ** 2), axis=0))
+    res = np.exp(-dist)
+    res[res < 0.02] = 0
+    return res
+
+
+def _structure_at_coordinates(
+    shape: Tuple[int],
+    coordinates: np.ndarray,
+    structure: np.ndarray,
+    *,
+    multipliers: Sequence = itertools.repeat(1),
+    dtype=None,
+    reduce_fn: Callable[[np.ndarray, np.ndarray, Optional[np.ndarray]], np.ndarray],
+):
+    """Update data with structure at given coordinates.
+
+    Parameters
+    ----------
+    coordinates : ndarray
+        Coordinates of the points. The structures will be added at these
+        points (center).
+    structure : ndarray
+        Array with encoded structure. For example, ball (boolean) or density
+        (0,1) float.
+    multipliers : ndarray
+        These values are multiplied by the values in the structure before
+        updating the array. Can be used to generate different labels, or to
+        vary the intensity of floating point gaussian densities.
+    reduce_fn : function
+        Function with which to update the array at a particular position. It
+        should take two arrays as input and an optional output array.
+    """
+    radius = (structure.shape[0] - 1) // 2
+    data = np.zeros(shape, dtype=dtype)
+
+    for point, value in zip(coordinates, multipliers):
+        slice_im, slice_ball = _get_slices_at(shape, point, radius)
+        reduce_fn(data[slice_im], value * structure[slice_ball], out=data[slice_im])
+    return data
+
+
+def _get_slices_at(shape, point, radius):
+    slice_im = []
+    slice_ball = []
+    for i, p in enumerate(point):
+        slice_im.append(slice(max(0, p - radius), min(shape[i], p + radius + 1)))
+        ball_start = max(0, radius - p)
+        ball_stop = slice_im[-1].stop - slice_im[-1].start + ball_start
+        slice_ball.append(slice(ball_start, ball_stop))
+    return tuple(slice_im), tuple(slice_ball)
+
+
+def _update_data_with_mask(data, struct, out=None):
+    """Update ``data`` with ``struct`` where ``struct`` is nonzero."""
+    # these branches are needed because np.where does not support
+    # an out= keyword argument
+    if out is None:
+        return np.where(struct, struct, data)
+    else:  # noqa: RET505
+        nz = struct != 0
+        out[nz] = struct[nz]
+        return out
+
+
+def _smallest_dtype(n: int) -> np.dtype:
+    """Find the smallest dtype that can hold n values."""
+    for dtype in [np.uint8, np.uint16, np.uint32, np.uint64]:
+        if np.iinfo(dtype).max >= n:
+            return dtype
+            break
+    else:
+        raise ValueError(f'{n=} is too large for any dtype.')
+
+
+def labeled_particles(
+    shape: Sequence[int],
+    dtype: Optional[np.dtype] = None,
+    n: int = 144,
+    seed: Optional[int] = None,
+    return_density: bool = False,
+) -> Union[np.ndarray, Tuple[np.ndarray, np.ndarray, np.ndarray]]:
+    """Generate labeled blobs of given shape and dtype.
+
+    Parameters
+    ----------
+    shape : Sequence[int]
+        Shape of the resulting array.
+    dtype : Optional[np.dtype]
+        Dtype of the resulting array.
+    n : int
+        Number of blobs to generate.
+    seed : Optional[int]
+        Seed for the random number generator.
+    return_density : bool
+        Whether to return the density array and center coordinates.
+    """
+    if dtype is None:
+        dtype = _smallest_dtype(n)
+    rng = np.random.default_rng(seed)
+    ndim = len(shape)
+    points = rng.integers(shape, size=(n, ndim))
+    values = rng.integers(np.iinfo(dtype).min, np.iinfo(dtype).max, size=n, dtype=dtype)
+    sigma = int(max(shape) / (4.0 * n ** (1 / ndim)))
+    ball = _generate_ball(sigma, ndim)
+
+    labels = _structure_at_coordinates(
+        shape, points, ball, multipliers=values, reduce_fn=_update_data_with_mask, dtype=dtype
+    )
+
+    if return_density:
+        dens = _generate_density(sigma * 2, ndim)
+        densities = _structure_at_coordinates(shape, points, dens, reduce_fn=np.maximum, dtype=np.float32)
+
+        return labels, densities, points
+    else:  # noqa: RET505
+        return labels