Merge pull request #9 from pravirkr/master

Improved numbits

.clang-format

@@ -0,0 +1,5 @@
+---
+Language: Cpp
+BasedOnStyle:  LLVM
+ColumnLimit:     80
+---

.github/workflows/tests.yaml → .github/workflows/ci.yaml

@@ -1,30 +1,35 @@
-name: tests
+name: GitHub CI
 
-on: [push]
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}.
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies.
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install .[test] -v
         pip install numpy
         pip install pytest pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Run tests for numbits.
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
-        make install
-        make tests
+        python -m pytest --cov=./ --cov-report=xml

.gitignore

@@ -1,16 +1,242 @@
-dist
-build
-.egg
-.tox
-.vscode
-.coverage
-__pycache__
-.mypy_cache
-.pytest_cache
-.ipynb_checkpoints
+# Created by https://www.toptal.com/developers/gitignore/api/c++,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=c++,python
 
-*.py[cod]
+### C++ ###
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
 *.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
 *.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
 *.egg
-*.egg-info
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+# End of https://www.toptal.com/developers/gitignore/api/c++,python

CMakeLists.txt

@@ -0,0 +1,37 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+
+# Scikit-build-core sets these values for you, or you can just hard-code the
+# name and version.
+project(
+  ${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG -march=native -ffast-math")
+
+# Find the module development requirements (requires FindPython from 3.17 or
+# scikit-build-core's built-in backport)
+set(PYBIND11_NEWPYTHON ON)
+find_package(OpenMP)
+find_package(pybind11 CONFIG REQUIRED)
+pybind11_add_module(numbits src/numbits.cpp)
+
+target_link_libraries(numbits PRIVATE pybind11::pybind11)
+
+# Check if OpenMP was found
+if(OpenMP_CXX_FOUND)
+    target_link_libraries(numbits PRIVATE OpenMP::OpenMP_CXX)
+    target_compile_definitions(numbits PRIVATE USE_OPENMP)
+endif()
+
+# This is passing in the version as a define just as an example
+target_compile_definitions(numbits PRIVATE VERSION_INFO=${PROJECT_VERSION})
+
+# The install directory is the output (wheel) directory
+install(TARGETS numbits DESTINATION .)

README.md

@@ -42,18 +42,26 @@ or you can:
     python setup.py install
     ```
 
-### Test call
+### Usage
 
 ```python
 import numpy as np
 import numbits
 a = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8], dtype='uint8')
-b = numbits.unpack(a, nbits=2)
+b = numbits.unpack(a, nbits=2, bitorder="big", parallel=False)
 
 >>> array([0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 3, 0, 0, 1, 0, 0, 0,
            1, 1, 0, 0, 1, 2, 0, 0, 1, 3, 0, 0, 2, 0], dtype=uint8)
 ```
 
+### Benchmarks
+|           |           |
+| --------- | --------- |
+| ![](tests/benchmarks/benchmark_unpack_1bit_little.png) | ![](tests/benchmarks/benchmark_unpack_1bit_big.png) |
+| ![](tests/benchmarks/benchmark_pack_1bit_little.png) | ![](tests/benchmarks/benchmark_pack_1bit_big.png) |
+
+
+
 [tests]: https://github.com/telegraphic/numbits/actions/workflows/tests.yaml/badge.svg
 [pybind]: https://github.com/pybind/pybind11
 [sigpyproc]: https://github.com/FRBs/sigpyproc3