sep-x 1.5.0__tar.gz

sep_x-1.5.0/.clang-format

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+# SPDX-License-Identifier: MIT
+#
+# Copyright (c) 2023 Intercreate, Inc.
+# Author: J.P. Hutchins <jp@intercreate.io>
+#
+# Python(black)-inspired .clang-format for C repositories
+#
+# Includes Zephyr and Arm macro compatibility
+
+---
+BasedOnStyle: Google
+
+AlignAfterOpenBracket: BlockIndent
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Never
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+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
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+  - __syscall
+  - __syscall_always_inline
+  - __subsystem
+BinPackArguments: false
+BinPackParameters: false
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+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Custom
+BreakStringLiterals: true
+ColumnLimit: 88
+DerivePointerAlignment: false
+ForEachMacros:
+  - 'FOR_EACH'
+  - 'FOR_EACH_FIXED_ARG'
+  - 'FOR_EACH_IDX'
+  - 'FOR_EACH_IDX_FIXED_ARG'
+  - 'FOR_EACH_NONEMPTY_TERM'
+  - 'RB_FOR_EACH'
+  - 'RB_FOR_EACH_CONTAINER'
+  - 'SYS_DLIST_FOR_EACH_CONTAINER'
+  - 'SYS_DLIST_FOR_EACH_CONTAINER_SAFE'
+  - 'SYS_DLIST_FOR_EACH_NODE'
+  - 'SYS_DLIST_FOR_EACH_NODE_SAFE'
+  - 'SYS_SFLIST_FOR_EACH_CONTAINER'
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+  - 'SYS_SFLIST_FOR_EACH_NODE_SAFE'
+  - 'SYS_SLIST_FOR_EACH_CONTAINER'
+  - 'SYS_SLIST_FOR_EACH_CONTAINER_SAFE'
+  - 'SYS_SLIST_FOR_EACH_NODE'
+  - 'SYS_SLIST_FOR_EACH_NODE_SAFE'
+  - '_WAIT_Q_FOR_EACH'
+  - 'Z_FOR_EACH'
+  - 'Z_FOR_EACH_ENGINE'
+  - 'Z_FOR_EACH_EXEC'
+  - 'Z_FOR_EACH_FIXED_ARG'
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+  - 'TYPE_SECTION_FOREACH'
+IncludeBlocks: Preserve
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+  - 'CHECKIF'
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+SortIncludes: CaseSensitive
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+WhitespaceSensitiveMacros:
+  - STRINGIFY
+  - Z_STRINGIFY

sep_x-1.5.0/.github/workflows/build-wheels-upload-pypi.yml

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+# GitHub action for building the distribution and wheels of the sep package
+# and uploading them to the PyPI package index.
+
+name: build-wheels-upload-pypi
+
+on: [push, workflow_dispatch]
+  # push:
+  #   # Run this action on the trigger event when *any* tag is pushed
+  #   tags:
+  #      - '*'
+
+jobs:
+
+  # This action is split into three jobs:
+  # - Building the source distribution
+  # - Building the wheels for the distribution
+  # - Uploading the artifacts to PyPI package
+  # The first and second job run in parallel.
+  # The uploading jos needs to have the other two finished without error.
+
+  # From now on, we run the tests before continuing with these jobs.
+
+  run_tests:
+    uses: ./.github/workflows/python-package-tox.yml
+
+  build_sdist:
+    needs: [run_tests]
+
+    # First the source distribution is done on ubuntu. This is not related
+    # to any operating system, so we could do it on the default os.
+
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: install_python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      # For the build, sep needs numpy and cython and we add twine and wheel
+      # for better testing and checking.
+
+      - name: Install dependencies
+        run: python -m pip install setuptools twine numpy wheel build
+
+      - name: Build sdist
+        run: python -m build --sdist
+
+      - name: Show files
+        run: ls -lh dist
+        shell: bash
+
+      - name: Check metadata
+        run: twine check dist/*
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    needs: [run_tests]
+
+    # Second the wheels are build for different OS and python versions. This is
+    # done with the help of the `cibuildwheel` package.
+    #
+    # The wheels are built for Windows, Linux and MacOS and the python versions
+    # 3.9 - 3.13.
+    #
+    # The three operating system could be done in parallel.
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CIBW_ARCHS_MACOS: "x86_64 universal2 arm64"
+
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.12"]
+        os: [windows-latest, macos-latest, ubuntu-24.04, ubuntu-24.04-arm]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+          CIBW_MANYLINUX_I686_IMAGE: manylinux_2_28
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_SKIP: '*-musllinux_*'
+          CIBW_ARCHS_LINUX: "auto"
+
+      - name: Show files
+        run: ls -lh wheelhouse
+        shell: bash
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  upload_to_pypi:
+
+    # Finally we collect all out data from the artifacts and put them back to
+    # dist directory for upload. The final step waits for the other jobs to be
+    # finished and starts only if the trigger event of the action was a push
+    # of a tag starting with <v> as version separation. All other jobs run
+    # without heading <v>
+
+    runs-on: [ubuntu-latest]
+    needs: [build_wheels, build_sdist]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sep-x
+    permissions:
+      id-token: write
+
+    # upload to PyPI on every tag starting with 'v'
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+
+    steps:
+    - uses: actions/setup-python@v5
+
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: dist*
+        merge-multiple: true
+        path: dist
+
+    - name: upload_to_pypi
+      uses: pypa/gh-action-pypi-publish@release/v1
+      # with:
+      #   repository-url: https://test.pypi.org/legacy/

sep_x-1.5.0/.github/workflows/python-package-tox.yml

@@ -0,0 +1,31 @@
+# This workflow will install tox and use it to run tests.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: CI
+
+on: [push, workflow_call, workflow_dispatch, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [windows-latest, macos-latest, ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install Tox and any other packages
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+      - name: Run Tox
+        # Run tox using the version of Python in `PATH`, append platform
+        run: tox
+        env:
+          PLATFORM: ${{ matrix.os }}

sep_x-1.5.0/.gitignore

@@ -0,0 +1,59 @@
+# emacs
+*~
+
+# --------------------------------------------
+# C
+
+*.o
+*.os
+*.so
+*.so.*
+*.dylib
+*.dylib.*
+*.a
+ctest/test_image
+
+# generated by tests
+data/sep.cat
+data/sepback.fits
+
+# scons
+.sconsign.dblite
+
+# tarball
+sep-*.tar.gz
+
+# -------------------------------------------
+# Python
+
+__pycache__
+
+docs/_build
+docs/api
+build/
+
+MANIFEST
+*.egg-info
+
+# pytest
+.pytest_cache
+.cache
+
+# generated C file
+sep.c
+
+# PyCharm
+.idea
+.project
+
+# Eclipse
+.pydevproject
+
+# Jupyter
+.ipynb_checkpoints
+
+# tox
+.tox
+
+# version
+*_version.py

sep_x-1.5.0/.pre-commit-config.yaml

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+exclude: "^data/"
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        name: isort (python)
+-   repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+    -   id: black
+        args: [--preview]
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+    -   id: numpydoc-validation
+-   repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: v1.0.0
+    hooks:
+    -   id: sphinx-lint
+        args: [--enable=all, --disable=default-role, --max-line-length=75, -v]
+        files: ^docs\/|^.*\.(rst$|md$)
+-   repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v19.1.4
+    hooks:
+    -   id: clang-format
+        types_or: [c++, c, cuda]

sep_x-1.5.0/.readthedocs.yaml

@@ -0,0 +1,39 @@
+# Read the Docs configuration file for Sphinx projects
+# 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: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# 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:
+    # - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+      - docs

sep_x-1.5.0/AUTHORS.md

@@ -0,0 +1,12 @@
+* Emmanuel Bertin (bertin@iap.fr) : original SExtractor code
+* Kyle Barbary (@kbarbary) : Conversion of SExtractor code to library
+* Kyle Boone (@kboone) : Bugfix, matched filter
+* Thomas Robitaille (@astrofrog) : Exact aperture overlap code
+* Matt Craig (@mwcraig) : Windows & OS X support
+* Curtis McCully (@cmccully): Parameter uncertainties
+* Evert Rol (@evertrol): setup.py fixes
+* Joe Lyman (@lyalpha): Make deblending limit settable
+* Michael Wuertenberger (@mworion): PyPI wheels
+* Ingvar Stepanyan (@rreverser): Build system, public API and thread safety fixes.
+* Gabe Brammer (@gbrammer): Fix memory addressing with large arrays.
+* Peter Watson (@PJ-Watson): Add extraction from existing segmentation map.

sep_x-1.5.0/CHANGES.md

@@ -0,0 +1,90 @@
+Unreleased
+==========
+
+* Add optimal-extraction circular photometry (`sum_circle_optimal`) with
+  auto-grouping for overlapping apertures and configurable grouping radius.
+* Add sigma-clipped annulus statistics (`stats_circann`, `stats_ellipann`)
+  for robust local background estimation.
+* Add sigma-clipped annulus background controls (`clip_sigma`, `clip_iters`)
+  to `sum_circle`, `sum_ellipse`, and `sum_circle_optimal`, with a fast
+  legacy fallback when `clip_iters=0`.
+
+v1.3.7 (8 November 2024)
+========================
+
+* Test against Python 3.13.
+* Update the Makefile to support Semantic Versioning from git tags.
+* Update the C libraries to allow for passing the version as a compiler
+  flag.
+* Update `setup.py` to pass the SCM version to the Cython compiler.
+* Include C tests in the Tox suite (for linux and macos only).
+* Document any and all changes to the C API since forking.
+* Restructure changelog documentation.
+
+v1.3.6 (7 October 2024)
+=======================
+
+* Fix wrong int type in Windows
+  ([#2](https://github.com/PJ-Watson/sep-pjw/issues/2), thanks to
+  @acenko for pointing this out).
+* Update tests to run on multiple operating systems.
+
+v1.3.5 (12 June 2024)
+=====================
+
+* Small fixes and updates to ensure compatibility with NumPy 2.0.
+
+v1.3.4 (21 February 2024)
+========================
+
+* Include .clang-format as a pre-commit hook, to ensure consistent code
+  style (improved readability, easier maintenance).
+* Fixed `make test` to account for the changes in
+  [v1.3.0](https://github.com/PJ-Watson/sep-pjw/releases/tag/v1.3.0).
+* All header files include the correct definitions.
+
+v1.3.3 (7 February 2024)
+========================
+
+* Add changelog to documentation.
+* Add tests for re-running with seg map.
+* Fix array boundary bugs when re-running with seg map.
+* Fix bug with precision loss when calculating threshold.
+* Improve error handling when object pixels exceed pix stack.
+
+v1.3.2 (5 February 2024)
+========================
+
+* Move documentation to new location, fix package names and imports.
+* Add wheels for Python 3.11/3.12.
+* Fix C compilation errors on windows (VLAs).
+* Publish updated version to PyPI under new name.
+
+v1.3.1 (31 January 2024)
+========================
+
+* Formatting changes (follow [black](https://github.com/psf/black)
+  formatting style).
+* Fix `bench.py` and `test.py`, removing deprecated functions.
+* Move metadata into `pyproject.toml`.
+* Add pre-commit hooks for code and docstring validation.
+* Change to dynamic versioning (git tag/commit based).
+
+v1.3.0 (1 December 2023)
+========================
+
+* The `segmentation_map` argument of `sep.extract()` will now accept
+  either an array or boolean. If an existing segmentation map is passed,
+  the object detection stage is skipped, and sources will be individually
+  analysed according to the provided map. This change is
+  backwards-compatible with respect to the Python module.
+
+  Please note that as no deblending is performed, the calculated
+  thresholds (and any dependent parameters) may not be the same as
+  originally derived.
+
+* Use 64-bit integers throughout, to fix memory addressing with large
+  arrays
+  ([#122](https://github.com/kbarbary/sep/issues/122 "Original issue"),
+  inspired by [Gabe Brammer's fork](https://github.com/gbrammer/sep)
+  with additional fixes).

sep_x-1.5.0/CMakeLists.txt

@@ -0,0 +1,50 @@
+cmake_minimum_required(VERSION 2.6)
+
+project(sep C)
+
+LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules/")
+include(GNUInstallDirs)
+
+set(SOURCES
+   ${CMAKE_SOURCE_DIR}/src/analyse.c
+   ${CMAKE_SOURCE_DIR}/src/convolve.c
+   ${CMAKE_SOURCE_DIR}/src/deblend.c
+   ${CMAKE_SOURCE_DIR}/src/extract.c
+   ${CMAKE_SOURCE_DIR}/src/lutz.c
+   ${CMAKE_SOURCE_DIR}/src/aperture.c
+   ${CMAKE_SOURCE_DIR}/src/background.c
+   ${CMAKE_SOURCE_DIR}/src/psf.c
+   ${CMAKE_SOURCE_DIR}/src/util.c
+   )
+
+include_directories(${CMAKE_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/src ${CFITSIO_INCLUDE_DIR})
+
+link_directories(${CMAKE_LIBRARY_PATH} ${CMAKE_SOURCE_DIR}/src)
+
+add_library(sep SHARED ${SOURCES})
+set_target_properties(sep PROPERTIES OUTPUT_NAME sep)
+set_target_properties(sep PROPERTIES VERSION 0.6.0 SOVERSION 0)
+set_target_properties(sep PROPERTIES C_VISIBILITY_PRESET hidden)
+
+option(SEP_USE_OPENMP "Enable OpenMP acceleration" ON)
+if (SEP_USE_OPENMP)
+   find_package(OpenMP QUIET)
+   if (OpenMP_C_FOUND)
+      if (OpenMP_C_FLAGS)
+         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+      endif()
+      if (OpenMP_C_LIBRARIES)
+         target_link_libraries(sep ${OpenMP_C_LIBRARIES})
+      endif()
+   endif()
+endif()
+
+if (MSVC)
+   add_definitions(-D_USE_MATH_DEFINES)
+else ()
+   add_compile_options(-Wcast-qual)
+   target_link_libraries(sep m)
+endif()
+
+install(TARGETS sep LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install(FILES ${CMAKE_SOURCE_DIR}/src/sep.h DESTINATION include)

sep_x-1.5.0/FindSEP.cmake

@@ -0,0 +1,52 @@
+# - Try to find SEP
+# Once done this will define
+#
+#  SEP_FOUND - system has SEP
+#  SEP_INCLUDE_DIR - the SEP include directory
+#  SEP_LIBRARIES - Link these to use SEP
+#  SEP_VERSION_STRING - Human readable version number of sep
+#  SEP_VERSION_MAJOR  - Major version number of sep
+#  SEP_VERSION_MINOR  - Minor version number of sep
+
+# Copyright (c) 2017, Ilia Platone, <info@iliaplatone.com>
+# Based on FindLibfacile by Carsten Niehaus, <cniehaus@gmx.de>
+#
+# Redistribution and use is allowed according to the terms of the BSD license.
+# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+
+if (SEP_LIBRARIES)
+
+  # in cache already
+  set(SEP_FOUND TRUE)
+  message(STATUS "Found SEP: ${SEP_LIBRARIES}")
+
+
+else (SEP_LIBRARIES)
+
+  find_library(SEP_LIBRARIES NAMES sep
+    PATHS
+    ${_obLinkDir}
+    ${GNUWIN32_DIR}/lib
+    /usr/local/lib
+  )
+
+  if(SEP_LIBRARIES)
+    set(SEP_FOUND TRUE)
+  else (SEP_LIBRARIES)
+    set(SEP_FOUND FALSE)
+  endif(SEP_LIBRARIES)
+
+
+  if (SEP_FOUND)
+    if (NOT SEP_FIND_QUIETLY)
+      message(STATUS "Found SEP: ${SEP_LIBRARIES}")
+    endif (NOT SEP_FIND_QUIETLY)
+  else (SEP_FOUND)
+    if (SEP_FIND_REQUIRED)
+      message(FATAL_ERROR "SEP not found. Please install libsep-dev")
+    endif (SEP_FIND_REQUIRED)
+  endif (SEP_FOUND)
+
+  mark_as_advanced(SEP_LIBRARIES)
+
+endif (SEP_LIBRARIES)

sep_x-1.5.0/MANIFEST.in

@@ -0,0 +1,10 @@
+include README.md
+include CHANGES.md
+include AUTHORS.md
+include licenses/*
+include pyproject.toml
+
+include src/*.[c,h,i]
+include sep.pyx
+include sep.c
+recursive-include benchmarks *.py *.md