refactor(build): change setup.py to pyproject.toml and supress cython warning

.github/workflows/regression.yml

@@ -17,24 +17,30 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.6'
+        python-version: '3.7'
 
-    - name: Install numpy
-      run: |
-        python3 -m pip install numpy
+    - name: git version
+      run: git --version
 
-    - name: Install dependencies
+    - name: Install hdf5 & netcdf & numpy
       run: |
-        python3 -m pip install -r requirements.txt
+          sudo apt-get update
+          sudo apt-get install libhdf5-dev libnetcdf-dev
+          # This is a build time dependency of pygacode
+          # that it assumes to be installed
+          python3 -m pip install numpy
 
-    - name: Install OMAS
+    - name: Build & Install OMAS
       run: |
-        python3 -m pip install .[machine]
+        python3 -m pip install build
+        python3 -m build --sdist 
+        # TODO do not hard code version here
+        python3 -m pip install "./dist/omas-0.93.0.tar.gz[machine]"
 
     - name: Move to root and try importing OMAS
       run: |
@@ -43,4 +49,7 @@ jobs:
 
     - name: Run OMAS tests
       run: |
+        # TODO the tests pickup omas from the python files in the directory not the installed version
+        # so to make that work we run an editable install to create the omas_cython lib in the right place.
+        python3 -m pip install -e
         make test

.github/workflows/regression_no_munittest.yml

@@ -19,14 +19,6 @@ jobs:
       with:
         python-version: '3.x'
 
-    - name: Install numpy
-      run: |
-        python3 -m pip install numpy
-
-    - name: Install dependencies
-      run: |
-        python3 -m pip install -r requirements.txt
-
     - name: Install OMAS
       run: |
         python3 -m pip install .[machine]

Makefile

@@ -87,7 +87,7 @@ tag:
 
 sdist:
 	rm -rf dist
-	python3 setup.py sdist
+	python3 -m build --sdist
 
 pypi: sdist
 	python3 -m twine upload --repository pypi dist/omas-$(VERSION).tar.gz

omas/omas_plot.py

@@ -800,7 +800,7 @@ def get2d(contour_quantity):
             z = scipy.ndimage.zoom(z, sf)
             value_2d = scipy.ndimage.zoom(value_2d, sf)
 
-        cs = ax.contour(r, z, value_2d, levels, **kw)
+        cs = ax.contour(r, z, value_2d, levels=levels, **kw)
 
         if label_contours or ((label_contours is None) and (contour_quantity == 'q')):
             ax.clabel(cs)

omas/omas_utils.py

@@ -5,6 +5,7 @@
 
 from .omas_setup import *
 from .omas_setup import __version__
+from .omas_cython import *
 import sys
 
 # --------------------------------------------
@@ -864,23 +865,6 @@ def omas_global_quantities(imas_version=omas_rcparams['default_imas_version']):
     return _global_quantities[imas_version]
 
 
-# only attempt cython if effective user owns this copy of omas
-# disabled for Windows: need to add check for file ownership under Windows
-if os.name == 'nt' or os.geteuid() != os.stat(__file__).st_uid:
-    with open(os.path.split(__file__)[0] + os.sep + 'omas_cython.pyx', 'r') as f:
-        exec(f.read(), globals())
-else:
-    try:
-        import pyximport
-
-        pyximport.install(language_level=3)
-        from .omas_cython import *
-    except Exception as _excp:
-        warnings.warn('omas cython failed: ' + str(_excp))
-        with open(os.path.split(__file__)[0] + os.sep + 'omas_cython.pyx', 'r') as f:
-            exec(f.read(), globals())
-
-
 def l2ut(path):
     """
     Formats IMAS time lists ['bla',0,'time_slice',5,'quantity'] with universal ODS path 'bla.0.time_slice.:.quantity'

pyproject.toml

@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools", "Cython"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["sphinx*"]
+
+[tool.setuptools.package-data]
+"*" = ["*.json", "*.dat"]
+"omas.samples" = ["*"]
+"omas"=["*.pyx"]
+
+[tool.setuptools.dynamic]
+version = {file = "omas/version"}
+
+[project]
+name = 'omas'
+dynamic = ["version"]
+description = 'Ordered Multidimensional Array Structures'
+authors = [
+    {name = 'Orso Meneghini', email = '[email protected]'},
+]
+classifiers = [
+    'Development Status :: 5 - Production/Stable',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3 :: Only',
+    'License :: OSI Approved :: MIT License',
+]
+keywords = ["integrated modeling",  "OMFIT", "IMAS",  "ITER"]
+
+requires-python = '>=3.7'
+dependencies = [
+    'numpy>=1.16.1',
+    'uncertainties',
+    'pint',
+    'netCDF4',
+    'boto3',
+    'matplotlib',
+    'scipy',
+    'h5py',
+    'pymongo',
+    'dnspython',
+    'xmltodict',
+    'xarray',
+    'tqdm',
+]
+readme="README.md"
+
+[project.urls]
+Homepage = 'https://gafusion.github.io/omas'
+Source = 'https://github.com/gafusion/omas'
+
+[project.optional-dependencies]
+machine = [
+        'omfit_classes',
+        'pexpect',
+        'fortranformat',
+        'pygacode',
+]
+hdc = ['pyhdc']
+imas = ['imas']
+uda = ['pyuda']
+build_sdist = ['build']
+build_structures = ['bs4']
+build_documentation = ['Sphinx', 'sphinx-bootstrap-theme', 'sphinx-gallery', 'Pillow']

setup.py

@@ -1,128 +1,6 @@
-import os
-import sys
-import glob
-import subprocess
-
-install_requires = [
-    'numpy>=1.16.1',
-    'uncertainties',
-    'pint',
-    'netCDF4',
-    'boto3',
-    'matplotlib',
-    'scipy',
-    'h5py',
-    'pymongo',
-    'dnspython',
-    'xmltodict',
-    'xarray',
-    'setuptools>=41.2',
-    'tqdm',
-    'Cython',
-]
-
-extras_require = {
-    'machine': [
-        'omfit_classes',
-        'pexpect',
-        'fortranformat',
-        'pygacode',
-    ],
-    'hdc': ['pyhdc'],
-    'imas': ['imas'],
-    'uda': ['pyuda'],
-    'build_structures': ['bs4'],
-    'build_documentation': ['Sphinx', 'sphinx-bootstrap-theme', 'sphinx-gallery', 'Pillow'],
-}
-
-# Add .json IMAS structure files to the package
-here = os.path.abspath(os.path.split(__file__)[0]) + os.sep
-
-# Automatically generate requirement.txt file if this is the OMAS repo and requirements.txt is missing
-if os.path.exists(here + '.git') and not os.path.exists(here + 'requirements.txt'):
-    with open(here + 'requirements.txt', 'w') as f:
-        f.write('# Do not edit this file by hand, operate on setup.py instead\n#\n')
-        f.write('# usage: pip install -r requirements.txt\n\n')
-        for item in install_requires:
-            f.write(item.ljust(25) + '# required\n')
-        for requirement in extras_require:
-            f.write('\n')
-            for item in extras_require[requirement]:
-                f.write('# ' + item.ljust(25) + '# %s\n' % requirement)
-
-packages = ['omas', 'omas.examples', 'omas.samples', 'omas.tests', 'omas.utilities']
-package_data = {
-    'omas': ['*.py', '*.pyx', 'version'],
-    'omas.examples': ['*.py'],
-    'omas.samples': ['*'],
-    'omas.tests': ['*.py'],
-    'omas.utilities': ['*.py'],
-}
-
-machine_mappings_dir = here + os.sep + 'omas' + os.sep + 'machine_mappings'
-for item in glob.glob(os.sep.join([here, 'omas', 'imas_structures', '*'])):
-    packages.append('omas.imas_structures.' + os.path.split(item)[1])
-    package_data['omas.imas_structures.' + os.path.split(item)[1]] = ['*.json']
-for retry in [1, 2]:
-    if os.path.exists(here + '.git') and retry == 1:
-        try:
-            tmp = f'pushd {machine_mappings_dir}; git ls-files; popd'
-            machine_mappings_files = subprocess.check_output(tmp, shell=True).decode("utf-8").strip().split('\n')[2:-1]
-            machine_mappings_files = ['omas' + os.sep + 'machine_mappings' + os.sep + k for k in machine_mappings_files]
-        except subprocess.CalledProcessError:
-            pass
-        else:
-            print("setup.py machine_mappings_files based on git")
-            break
-    else:
-        machine_mappings_files = []
-        for root, subdirs, files in os.walk(machine_mappings_dir):
-            root = root[len(machine_mappings_dir) + 1 :]
-            for file in reversed(files):
-                machine_mappings_files.append('omas' + os.sep + 'machine_mappings' + os.sep + root + os.sep + file)
-dirs = {os.path.dirname(file): [] for file in sorted(machine_mappings_files)}
-for file in machine_mappings_files:
-    dirs[os.path.dirname(file)].append(os.path.basename(file))
-for dir in dirs:
-    packages.append(dir.replace('/', '.'))
-    package_data[dir.replace('/', '.')] = dirs[dir]
-
-long_description = '''
-OMAS is a Python library designed to simplify the interface of third-party codes with the `ITER <http://iter.org>`_ Integrated Modeling and Analysis Suite (`IMAS <https://confluence.iter.org/display/IMP>`_).
-
-* It provides a **convenient Python API**
-
-* capable of storing data with **different file/database formats**
-
-* in a form that is **always compatible with the IMAS data model**
-
-Mapping the physics codes I/O to the IMAS data model is done in third party Python codes such as the `OMFIT framework <https://omfit.io>`_.
-'''
-
-print()
-print('INFO: optional dependencies:')
-from pprint import pprint
-
-pprint(extras_require)
-print()
-print('INFO: run the `imports_check.py` script to quickly verify that all Python dependencies for OMAS are installed')
-print()
-
-from setuptools import setup
+from setuptools import Extension, setup
+from Cython.Build import cythonize
 
 setup(
-    name='omas',
-    version=open(here + 'omas/version', 'r').read().strip(),
-    description='Ordered Multidimensional Array Structures',
-    url='https://gafusion.github.io/omas',
-    author='Orso Meneghini',
-    license='MIT',
-    classifiers=['License :: OSI Approved :: MIT License', 'Programming Language :: Python :: 3'],
-    keywords='integrated modeling OMFIT IMAS ITER',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    packages=packages,
-    package_data=package_data,
-    install_requires=install_requires,
-    extras_require=extras_require,
+    ext_modules = cythonize("omas/omas_cython.pyx")
 )