asbm 0.1.4.dev3__tar.gz

asbm-0.1.4.dev3/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

asbm-0.1.4.dev3/.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot[bot]
+      - pre-commit-ci[bot]

asbm-0.1.4.dev3/.github/workflows/check-julia.yml

@@ -0,0 +1,48 @@
+name: check-julia
+
+on:
+  push:
+    paths:
+      - 'bindings/julia/**'
+      - 'src/**'
+      - '.github/workflows/check-julia.yml'
+  pull_request:
+    paths:
+      - 'bindings/julia/**'
+      - 'src/**'
+      - '.github/workflows/check-julia.yml'
+
+jobs:
+  julia-test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14, windows-latest]
+        julia-version: ['1.10']
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: julia-actions/setup-julia@v3
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - name: Build native library
+        shell: bash
+        run: |
+          cmake -B bindings/julia/deps/cmake_build \
+                -S bindings/julia \
+                -DCMAKE_BUILD_TYPE=Release
+          cmake --build bindings/julia/deps/cmake_build --config Release
+          cmake --install bindings/julia/deps/cmake_build \
+                --prefix bindings/julia/deps \
+                --config Release \
+                --component julia_binding
+
+      - name: Instantiate Julia dependencies
+        run: julia --project=bindings/julia -e "using Pkg; Pkg.instantiate()"
+
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          project: bindings/julia

asbm-0.1.4.dev3/.github/workflows/check-r.yml

@@ -0,0 +1,49 @@
+name: check-r
+
+on:
+  push:
+    paths:
+      - bindings/r/**
+      - src/**
+      - .github/workflows/check-r.yml
+  pull_request:
+    paths:
+      - bindings/r/**
+      - src/**
+      - .github/workflows/check-r.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  R-CMD-check:
+    name: Check on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: bindings/r
+          extra-packages: |
+            any::rcmdcheck
+            any::igraph
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: bindings/r
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'

asbm-0.1.4.dev3/.github/workflows/release.yml

@@ -0,0 +1,78 @@
+name: release
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  pull_request:
+    paths:
+      - .github/workflows/release.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-14, ubuntu-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.20
+
+      - name: Build wheels
+        env:
+          CIBW_ARCHS_WINDOWS: AMD64
+        run: cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  upload_all:
+    needs: [build_wheels, make_sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

asbm-0.1.4.dev3/.gitignore

@@ -0,0 +1,78 @@
+# Build directories
+/build/
+/build/*
+
+# CMake build files
+/CMakeFiles/
+/CMakeCache.txt
+/cmake_install.cmake
+/Makefile
+
+# Catch2 / external subbuilds
+/build/_deps/
+
+# Compiled objects and libraries
+*.o
+*.obj
+*.a
+*.lib
+*.so
+*.dylib
+*.dll
+
+# Python artifacts
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+*.pyi
+*.pyc
+
+# Virtual environments
+/.venv/
+venv/
+env/
+venvs/
+
+# pip / build outputs
+/dist/
+/build/
+*.egg-info/
+pip-wheel-metadata/
+
+# pytest cache
+.pytest_cache/
+
+# coverage
+.coverage
+coverage.xml
+
+# IDE/editor
+.vscode/
+.idea/
+*.sublime-project
+*.sublime-workspace
+
+# macOS
+.DS_Store
+
+# logs
+.log
+
+# temporary files
+*.tmp
+*.swp
+
+# packaging metadata
+*.egg
+
+# Python compiled extension produced by CMake during local builds (placed into python/asbm/src/asbm)
+python/asbm/src/asbm/*.so
+python/asbm/src/asbm/*.pyd
+
+# Version file generated by setuptools_scm — never commit, always regenerated from git tags
+python/asbm/src/asbm/_version.py
+
+# test and build artifacts
+build/cpp/
+build/tests/

asbm-0.1.4.dev3/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --group docs
+    - uv run python -m sphinx -T -b html -d docs/_build/doctrees -D language=en
+      docs $READTHEDOCS_OUTPUT/html

asbm-0.1.4.dev3/CMakeLists.txt

@@ -0,0 +1,62 @@
+cmake_minimum_required(VERSION 3.15...3.26)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+option(BUILD_TESTING "Build Catch2-based native tests" OFF)
+
+set(PYBIND11_FINDPYTHON ON)
+find_package(pybind11 CONFIG REQUIRED)
+
+# Build a reusable core library so other language bindings can reuse it
+add_library(asbm_core STATIC
+    src/MCMC_core.cpp
+    src/MCMC_proposals.cpp
+    src/MCMC_bookkeeping.cpp
+    src/helpers.cpp
+    src/fit_result.cpp)
+target_include_directories(asbm_core PUBLIC ${CMAKE_SOURCE_DIR}/src)
+set_target_properties(asbm_core PROPERTIES POSITION_INDEPENDENT_CODE ON)
+target_compile_definitions(asbm_core PRIVATE MCMC_CORE_NO_PYBIND $<$<CXX_COMPILER_ID:MSVC>:_USE_MATH_DEFINES>)
+target_compile_features(asbm_core PUBLIC cxx_std_17)
+
+# Python bindings: build a small pybind11 module that links to the core
+pybind11_add_module(_asbm MODULE bindings/python/bindings.cpp)
+target_link_libraries(_asbm PRIVATE asbm_core)
+target_include_directories(_asbm PRIVATE ${CMAKE_SOURCE_DIR}/src)
+target_compile_features(_asbm PRIVATE cxx_std_17)
+set_target_properties(
+  _asbm PROPERTIES LIBRARY_OUTPUT_DIRECTORY
+                         ${CMAKE_SOURCE_DIR}/python/asbm/src/asbm)
+install(TARGETS _asbm LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+
+if(BUILD_TESTING)
+  enable_testing()
+
+  find_package(Catch2 3 QUIET)
+  if(NOT Catch2_FOUND)
+    include(FetchContent)
+    FetchContent_Declare(
+      Catch2
+      GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+      GIT_TAG v3.7.1
+      GIT_SHALLOW TRUE
+    )
+    FetchContent_MakeAvailable(Catch2)
+    list(APPEND CMAKE_MODULE_PATH "${catch2_SOURCE_DIR}/extras")
+  endif()
+
+  add_executable(mcmc_core_test
+    tests/mcmc_core_test.cpp
+    src/MCMC_core.cpp
+    src/MCMC_proposals.cpp
+    src/MCMC_bookkeeping.cpp
+    src/helpers.cpp
+  )
+  target_compile_definitions(mcmc_core_test PRIVATE MCMC_CORE_NO_PYBIND)
+  target_include_directories(mcmc_core_test PRIVATE tests src)
+  target_compile_features(mcmc_core_test PRIVATE cxx_std_17)
+  target_compile_options(mcmc_core_test PRIVATE -Wall -Wextra)
+  target_link_libraries(mcmc_core_test PRIVATE Catch2::Catch2WithMain)
+
+  include(CTest)
+  add_test(NAME mcmc_core_test COMMAND mcmc_core_test)
+endif()

asbm-0.1.4.dev3/LICENSE

@@ -0,0 +1,19 @@
+Copyright 2025 Maximilian Jerdee
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.