odrpack 0.1.0__tar.gz

odrpack-0.1.0/.github/workflows/build-wheels.yml

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+name: Build and upload to PyPI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+        
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Fortran
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          version: 13 # 14 not supported yet in Windows
+
+      # This can't be placed in the cibuildwheel action
+      # Without it, the wheel repair fails
+      - name: Set macOS deployment target
+        if: runner.os == 'macOS'
+        run: |
+          echo "MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | cut -d '.' -f 1-2)" >> $GITHUB_ENV
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.22.0
+        env:
+          # All cibuildwheel options are here (nothing "hidden" in pyproject.toml)
+          CIBW_SKIP: "*-win32 *i686 pp3*"
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_COMMAND: "pytest {project}/tests"
+          CIBW_BEFORE_BUILD_WINDOWS: |
+            bash {project}/cibw-scripts/cibw_before_build_windows.sh {project}
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: |
+            bash ./cibw-scripts/cibw_repair_wheel_command_windows.sh {wheel} {dest_dir}
+           
+      - name: Upload wheels 
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: Upload wheels 
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    name: Publish to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    if: ${{ github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, 'publish-pypi') }}
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+          
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  upload_test_pypi:
+    name: Publish to TestPyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/odrpack
+    permissions:
+      id-token: write
+    if: ${{ github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, 'publish-testpypi') }}
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

odrpack-0.1.0/.github/workflows/test-linux.yml

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+name: Test Linux
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    name: Ubuntu / ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Ubuntu-build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libopenblas-dev
+          gfortran --version
+          gcc --version
+          
+      - name: Install PyPi-build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-build.txt 
+      
+      - name: Build package
+        run: |
+          pip install -e . --no-build-isolation
+          
+      - name: Run tests and collect coverage
+        run: |
+          pytest --cov -v -s --cov-report=xml --junitxml=junit.xml -o junit_family=legacy
+          coverage report
+
+      - name: Run example
+        run: |
+          python ./tests/example5.py
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.python-version == '3.10' }}
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: false
+          
+      - name: Upload test results to Codecov
+        if: ${{ matrix.python-version == '3.10' && !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

odrpack-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# PyPI configuration file
+.pypirc

odrpack-0.1.0/.gitmodules

@@ -0,0 +1,6 @@
+[submodule "extern/pybind11"]
+	path = extern/pybind11
+	url = https://github.com/pybind/pybind11
+[submodule "extern/odrpack95"]
+	path = extern/odrpack95
+	url = https://github.com/HugoMVale/odrpack95

odrpack-0.1.0/.vscode/c_cpp_properties.json

@@ -0,0 +1,21 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${workspaceFolder}/extern/pybind11/include/pybind11",
+                "${workspaceFolder}/extern/odrpack95/c/include/odrpack",
+                //"${workspaceFolder}/extern/nanobind/include/nanobind",
+                "/usr/include/python3.10"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64",
+            "configurationProvider": "mesonbuild.mesonbuild"
+        }
+    ],
+    "version": 4
+}

odrpack-0.1.0/.vscode/settings.json

@@ -0,0 +1,77 @@
+{
+    "files.associations": {
+        "complex": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "bit": "cpp",
+        "*.tcc": "cpp",
+        "cctype": "cpp",
+        "chrono": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "codecvt": "cpp",
+        "compare": "cpp",
+        "concepts": "cpp",
+        "condition_variable": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "deque": "cpp",
+        "forward_list": "cpp",
+        "list": "cpp",
+        "map": "cpp",
+        "set": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "optional": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "fstream": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "semaphore": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "stop_token": "cpp",
+        "streambuf": "cpp",
+        "thread": "cpp",
+        "cinttypes": "cpp",
+        "typeindex": "cpp",
+        "typeinfo": "cpp",
+        "valarray": "cpp",
+        "variant": "cpp",
+        "ranges": "cpp"
+    },
+    "autopep8.args": [
+        "--max-line-length=90"
+    ],
+    "C_Cpp.vcFormat.newLine.beforeOpenBrace.block": "sameLine"
+}

odrpack-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 HugoMVale
+
+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.

odrpack-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: odrpack
+Version: 0.1.0
+Summary: Package for weighted orthogonal distance regression (ODR).
+Keywords: regression,statistics,mathematics
+Author-Email: Hugo Vale <57530119+HugoMVale@users.noreply.github.com>
+License: MIT License
+         
+         Copyright (c) 2025 HugoMVale
+         
+         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.
+         
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Project-URL: Repository, https://github.com/HugoMVale/odrpack-python
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Description-Content-Type: text/markdown
+
+# odrpack (-python)
+
+[![Test-Linux](https://github.com/HugoMVale/odrpack-python/actions/workflows/test-linux.yml/badge.svg)](https://github.com/HugoMVale/odrpack-python/actions)
+[![codecov](https://codecov.io/gh/HugoMVale/odrpack-python/graph/badge.svg?token=B9sFyJiweC)](https://codecov.io/gh/HugoMVale/odrpack-python)
+[![Latest Commit](https://img.shields.io/github/last-commit/HugoMVale/odrpack-python)](https://img.shields.io/github/last-commit/HugoMVale/odrpack-python)
+
+## Description
+
+This Python package provides bindings for the well-known weighted orthogonal distance regression
+(ODR) solver [odrpack95]. This design ensures that users benefit from the performance and reliability
+of the original Fortran implementation, while working within the modern Python ecosystem.  
+
+ODR, also known as [errors-in-variables regression], is designed primarily for instances when both
+the explanatory and response variables have significant errors. 
+
+<p align="center">
+  <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/8/81/Total_least_squares.svg/220px-Total_least_squares.svg.png" width="200" alt="Deming regression; special case of ODR.">
+</p>
+
+[errors-in-variables regression]: https://en.wikipedia.org/wiki/Errors-in-variables_models
+[odrpack95]: https://github.com/HugoMVale/odrpack95
+
+
+## Installation
+
+You can install the package via pip:
+
+```bash
+pip install odrpack
+```
+
+## Usage
+
+```py
+from odrpack import odr
+import numpy as np
+
+beta0 = np.array([2., 0.5])
+lower = np.array([0., 0.])
+upper = np.array([10., 0.9])
+x = np.array([0.982, 1.998, 4.978, 6.01])
+y = np.array([2.7, 7.4, 148.0, 403.0])
+
+
+def f(beta: np.ndarray, x: np.ndarray) -> np.ndarray:
+    "Model function."
+    return beta[0] * np.exp(beta[1]*x)
+
+
+sol = odr(f, beta0, y, x, lower=lower, upper=upper, iprint=1001)
+
+print("\n beta:", sol.beta)
+print("\n delta:", sol.delta)
+```
+
+```sh
+beta: [1.63337057 0.9       ]
+delta: [-0.36885787 -0.31272733  0.02928942  0.11031791]
+```

odrpack-0.1.0/README.md

@@ -0,0 +1,59 @@
+# odrpack (-python)
+
+[![Test-Linux](https://github.com/HugoMVale/odrpack-python/actions/workflows/test-linux.yml/badge.svg)](https://github.com/HugoMVale/odrpack-python/actions)
+[![codecov](https://codecov.io/gh/HugoMVale/odrpack-python/graph/badge.svg?token=B9sFyJiweC)](https://codecov.io/gh/HugoMVale/odrpack-python)
+[![Latest Commit](https://img.shields.io/github/last-commit/HugoMVale/odrpack-python)](https://img.shields.io/github/last-commit/HugoMVale/odrpack-python)
+
+## Description
+
+This Python package provides bindings for the well-known weighted orthogonal distance regression
+(ODR) solver [odrpack95]. This design ensures that users benefit from the performance and reliability
+of the original Fortran implementation, while working within the modern Python ecosystem.  
+
+ODR, also known as [errors-in-variables regression], is designed primarily for instances when both
+the explanatory and response variables have significant errors. 
+
+<p align="center">
+  <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/8/81/Total_least_squares.svg/220px-Total_least_squares.svg.png" width="200" alt="Deming regression; special case of ODR.">
+</p>
+
+[errors-in-variables regression]: https://en.wikipedia.org/wiki/Errors-in-variables_models
+[odrpack95]: https://github.com/HugoMVale/odrpack95
+
+
+## Installation
+
+You can install the package via pip:
+
+```bash
+pip install odrpack
+```
+
+## Usage
+
+```py
+from odrpack import odr
+import numpy as np
+
+beta0 = np.array([2., 0.5])
+lower = np.array([0., 0.])
+upper = np.array([10., 0.9])
+x = np.array([0.982, 1.998, 4.978, 6.01])
+y = np.array([2.7, 7.4, 148.0, 403.0])
+
+
+def f(beta: np.ndarray, x: np.ndarray) -> np.ndarray:
+    "Model function."
+    return beta[0] * np.exp(beta[1]*x)
+
+
+sol = odr(f, beta0, y, x, lower=lower, upper=upper, iprint=1001)
+
+print("\n beta:", sol.beta)
+print("\n delta:", sol.delta)
+```
+
+```sh
+beta: [1.63337057 0.9       ]
+delta: [-0.36885787 -0.31272733  0.02928942  0.11031791]
+```