Build and upload to pypa

.github/workflows/main.yml

@@ -0,0 +1,93 @@
+name: main
+
+
+# Automatically cancel a previous run.
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+      branches:
+        - master
+  release:
+    types: [published]
+
+jobs:
+
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Build SDist
+      run: pipx run build --sdist
+
+    - name: Check metadata
+      run: pipx run twine check dist/*
+
+    - uses: actions/upload-artifact@v3
+      with:
+        path: dist/*.tar.gz
+
+  build_wheel:
+    name: Build wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest']
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS_MACOS: x86_64 arm64
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+
+
+  upload_test:
+    name: Upload if test release
+    needs: [build_sdist, build_wheel]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/test_release'
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          name: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+  upload:
+    name: Upload if new release
+    needs: [build_sdist, build_wheel]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

MANIFEST.in

@@ -0,0 +1,9 @@
+include LICENSE.md
+include README.md
+include ompy/decomposition.pyx
+include ompy/rebin.pyx
+include ompy/gauss_smoothing.pyx
+include ompy/stats/stats.cpp
+include ompy/stats/erfinv.hpp
+include ompy/examples/Dy164_raw.m
+include ompy/examples/Si28_raw_matrix_compressed.m

ompy/examples.py → ompy/examples/__init__.py

@@ -1,12 +1,13 @@
 import os
 from typing import Tuple, List
-from .matrix import Matrix
+from ..matrix import Matrix
 import numpy as np
 
-EXAMPLES = {'dy164': {'raw': "../../example_data/Dy164_raw.m",
+
+EXAMPLES = {'dy164': {'raw': "../Dy164_raw.m",
                       # 'response': "../../data/Dy164_response_matrix.m"
                       },
-            'si28': {'raw': "../../example_data/Si28_raw_matrix_compressed.m"}
+            'si28': {'raw': "../Si28_raw_matrix_compressed.m"}
             }
 DATAPATH = os.path.abspath(__file__)
 

ompy/spinfunctions.py

@@ -180,7 +180,7 @@ def gDisc_and_EB05(self, mass: int, NLDa: float, Eshift: float, Sn: float,
         sigma2_Sn = self.gEB05(mass, NLDa, Eshift, Ex=Sn)
         sigma2_EB05 = lambda Ex: self.gEB05(mass, NLDa, Eshift, Ex=Ex)  # noqa
         x = [sigma2_disc[0], Sn]
-        y = [sigma2_disc[1], sigma2_EB05(Sn)]
+        y = [sigma2_disc[1], float(sigma2_EB05(Sn))]
         sigma2 = interp1d(x, y,
                           bounds_error=False,
                           fill_value=(sigma2_disc[1], sigma2_Sn))

src/stats.cpp → ompy/stats/stats.cpp

@@ -1,11 +1,10 @@
 
 #include <pybind11/pybind11.h>
 #include <pybind11/numpy.h>
-#include <cmath>
-
 #include "erfinv.hpp"
 
 
+
 namespace py = pybind11;
 constexpr double sqrt2 = 1.41421356237309504880168872420969807856967187;
 

pyproject.toml

@@ -1,8 +1,71 @@
 [build-system]
-requires = [
-"setuptools",
-"numpy>=1.20.0",
-"cython",
-"pybind11>=2.6.0",
-"wheel"]
+requires = ["setuptools", "numpy>=1.20.0", "cython", "pybind11>=2.6.0", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "OMpy"
+version = "1.1.0"
+authors = [
+    {name="Jørgen Eriksson Midtbø", email="[email protected]"},
+    {name="Fabio Zeiser", email="[email protected]"},
+    {name="Erlend Lima", email="[email protected]"}
+]
+maintainers = [
+    {name="Erlend Lima", email="[email protected]"},
+    {name="Vetle Wegner Ingeberg", email="[email protected]"}
+]
+
+dependencies = [
+"cython", "numpy>=1.20.0", "pandas", "matplotlib", "termtables",
+"pymultinest", "scipy", "uncertainties>=3.0.3", "tqdm", "pathos", "pybind11>=2.6.0"]
+
+description = "A python implementation of the Oslo method"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Physics",
+    ]
+
+[project.urls]
+"Homepage" = "https://github.com/oslocyclotronlab/ompy"
+"Bug Tracker" = "https://github.com/oslocyclotronlab/ompy/issues"
+
+[tool.cibuildwheel]
+build = ["cp310-manylinux_x86_64",
+         "cp311-manylinux_x86_64",
+         "cp310-macosx_x86_64",
+         "cp311-macosx_x86_64",
+         "cp310-macosx_arm64",
+         "cp311-macosx_arm64"]
+
+skip = ["cp36-*", "cp37-*", "cp38-*", "cp39-*", "*-musllinux-*", "pp*"]
+test-requires = "pytest"
+test-command = "pytest {project}/tests"
+test-skip = ["*-macosx_arm64, *-macosx_universal2:arm64", "*-*linux_{aarch64,ppc64le,s390x}"]
+
+[tool.cibuildwheel.macos]
+before-all = [
+    "git clone https://github.com/JohannesBuchner/MultiNest",
+    "cd MultiNest/build",
+    "cmake ..",
+    "make"
+]
+environment = {LD_LIBRARY_PATH="/home/runner/work/ompy/ompy/MultiNest/lib", MACOSX_DEPLOYMENT_TARGET="10.14", FC="/usr/local/bin/gfortran-11"}
+
+[tool.cibuildwheel.linux]
+before-all = [
+    "yum -y install blas-devel lapack-devel",
+    "git clone https://github.com/JohannesBuchner/MultiNest",
+    "cd MultiNest/build",
+    "cmake ..",
+    "make install"
+]
+environment = {LD_LIBRARY_PATH="/usr/local/lib"}

release_note.md

@@ -12,6 +12,8 @@ Changed:
 - Fixed a bug where the `std` attribute of `Vector` was not saved to file.
 - Reimplemented PPF for normal distribution and truncated normal distribution in C++ for improved performance (about 300% faster than the SciPy implementation!).
 - Fixed a potential bug where `units` attribute is set erroniously when reading the discrete level density from file (`load_levels_discrete` and `load_levels_discrete_smooth`).
+- Moved example data to the source folder such that they are distributed with the package and avalible regardless of if OMpy is installed with `-e` option or not.
+- Source code for the `ompy.stats` sublibrary now lives in the `ompy` folder.
 
 Deprecated:
 - `shape` argument of Matrix for creation of a matrix filled with zeros. Use `ZerosMatrix` instead.

setup.py

@@ -9,6 +9,11 @@
 from ctypes.util import find_library
 from pybind11.setup_helpers import Pybind11Extension
 
+try:
+    import wheel.bdist_wheel
+except ImportError:
+    wheel = None
+
 try:
     from Cython.Build import cythonize
     from Cython.Distutils import build_ext
@@ -108,10 +113,15 @@ def write_version_py(filename='ompy/version_setup.py'):
                        'git_revision': GIT_REVISION})
     finally:
         a.close()
-write_version_py()
+try:
+    write_version_py()
+except:
+    pass
 
 # If macOS, use ctypes.util.find_library to determine if OpenMP is avalible.
 openmp = os.getenv("ompy_OpenMP")
+if wheel is not None:  # We do not build with OpenMP if wheel
+    openmp = False
 if openmp is None and platform.system() == 'Darwin':  # Check if macOS
     if find_library("omp") != None:
         openmp = True
@@ -131,7 +141,7 @@ def write_version_py(filename='ompy/version_setup.py'):
 if os.path.exists(fname):
     os.remove(fname)
 
-extra_compile_args = ["-O3", "-ffast-math", "-march=native"]
+extra_compile_args = ["-O3"]
 extra_link_args = []
 if openmp and platform.system() == 'Darwin':
     extra_compile_args.insert(-1, "-Xpreprocessor -fopenmp")
@@ -144,8 +154,8 @@ def write_version_py(filename='ompy/version_setup.py'):
         Extension("ompy.decomposition",
                   ["ompy/decomposition.pyx"],
                   # on MacOS the clang compiler pretends not to support OpenMP, but in fact it does so
-                  extra_compile_args=extra_compile_args,
-                  extra_link_args=extra_link_args,
+                  #extra_compile_args=extra_compile_args,
+                  #extra_link_args=extra_link_args,
                   include_dirs=[numpy.get_include()]
                   ),
         Extension("ompy.rebin", ["ompy/rebin.pyx"], include_dirs=[numpy.get_include()]),
@@ -154,7 +164,7 @@ def write_version_py(filename='ompy/version_setup.py'):
 
 ext_modules_pybind11 = [
         Pybind11Extension("ompy.stats",
-                          ["src/stats.cpp"],
+                          ["ompy/stats/stats.cpp"],
                           cxx_std=20,
                           extra_compile_args=["-O3"]),
         Pybind11Extension("ompy.rhosigchi",
@@ -177,20 +187,42 @@ def write_version_py(filename='ompy/version_setup.py'):
  "pybind11>=2.6.0"
 ]
 
-setup(name='OMpy',
-      version=get_version_info()[0],
+def read_version():
+    try:
+        with open("ompy/version_setup.py") as f:
+            ns = {}
+            exec(f.read(), ns)
+            version = ns["full_version"]
+        return version
+    except FileNotFoundError:
+        return VERSION
+
+try:
+    version = get_version_info()[0]
+except:
+    version = read_version()
+
+
+setup(name='ompy',
+      version=version,
       author="Jørgen Eriksson Midtbø, Fabio Zeiser, Erlend Lima",
       author_email=("[email protected], "
                     "[email protected], "
                     "[email protected]"),
       url="https://github.com/oslocyclotronlab/ompy",
-      packages=find_packages(),
+      python_requires=">= 3.8",
+      packages=['ompy', 'ompy.examples', 'ompy.stats', 'ompy.introspection'],
+      package_data={
+          "ompy": ["decomposition.pyx", "rebin.pyx", "gauss_smoothing.pyx"],
+          "ompy.stats": ['*.hpp'],
+          "ompy.examples": ['*.m']
+      },
       ext_modules=cythonize(ext_modules,
                             compiler_directives={'language_level': "3",
                                                  'embedsignature': True},
                             compile_time_env={"OPENMP": openmp}
                             )+ext_modules_pybind11,
       zip_safe=False,
-      install_requires=install_requires
+      setup_requires=["cython", "numpy>=1.20.0", "pybind11>=2.6.0"]
       )