Update build pipeline and switch to pytest

.github/workflows/ismrmrd_python_conda.yml

@@ -1,10 +1,10 @@
 on:
+  push:
+    branches: [master]
+    tags: ["v*.*.*"]
   pull_request:
-    branches:    
-      - master
-  release:
-    types:
-      - created
+    branches: [master]
+  workflow_dispatch:
 
 jobs:
   build-conda-packages:
@@ -13,12 +13,13 @@ jobs:
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
-      - uses: conda-incubator/setup-miniconda@e81abac10ce2c37423b54eae5af93aa3b4d3475c
+      - uses: actions/checkout@v5
+      - uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-version: latest
           activate-environment: ismrmrd-python-build
           environment-file: conda/environment.yml
-          python-version: 3.9
+          python-version: 3.12
           auto-activate-base: false
       - name: Build conda package
         shell: bash -l {0}

.github/workflows/python-publish.yml

@@ -1,56 +1,53 @@
 name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
 
-on: 
-  release:
-    types:
-      - created
+on:
+  push:
+    branches: [master]
+    tags: ["v*.*.*"]
+  pull_request:
+    branches: [master]
   workflow_dispatch:
 
 jobs:
   build:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v5
+    - name: Set up Python 3.x
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.12
+    - name: Install runtime dependencies
+      run: python -m pip install -r requirements.txt --user
+    - name: Perform editable installation to generate the schema subpackage
+      run: python -m pip install -e .
+    - name: Run all tests
+      run: python -m pytest
     - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
+      run: python -m pip install build --user
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
+      run: python -m build --sdist --wheel --outdir dist/ .
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
 
   publish-to-pypi:
-    name: >-
-      Publish Python 🐍 distribution 📦 to PyPI
-    if: startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch'   # only publish to PyPI on tag pushes or  manual trigger
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    if: github.event_name == 'workflow_dispatch' || github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs:
     - build
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/ismrmrmd 
+      url: https://pypi.org/p/ismrmrmd
     permissions:
       id-token: write
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v5
       with:
         name: python-package-distributions
         path: dist/

conda/conda_build_config.yaml

@@ -1,3 +1,3 @@
 python:
-    - 3.9
-    - 3.10
+    - 3.10
+    - 3.12

conda/meta.yaml

@@ -10,12 +10,10 @@ source:
 requirements:
   build:
     - python {{ python }}
-    - xsdata >=24.0
+    - xsdata>=24.0
     - setuptools
-    - wheel
-    - jinja2 >=2.11.0
     - pip
-    
+
   run:
     - python
     - numpy>=1.22.0
@@ -29,10 +27,10 @@ test:
     - tests
   commands:
     - pip check
-    - nosetests
+    - pytest
   requires:
     - pip
-    - nose
+    - pytest
 
 about:
   home: https://github.com/ismrmrd/ismrmrd-python

conda/run_test.sh

@@ -2,6 +2,4 @@
 
 set -euo pipefail
 
-cd tests
-nosetests
-
+pytest

ismrmrd/xsd/__init__.py

@@ -1,2 +1,2 @@
-from .pyxb_compat import (CreateFromDocument, ToXML, ToDOM)
-from .ismrmrdschema import * 
+from .pyxb_compat import CreateFromDocument, ToXML, ToDOM
+from .ismrmrdschema import *

pyproject.toml

@@ -1,3 +1,29 @@
 [build-system]
-requires = ["setuptools","wheel","xsdata[cli]","jinja2 >= 2.11.0"]
-build-backend = "setuptools.build_meta"
+requires = ["setuptools", "xsdata[cli]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ismrmrd"
+dynamic = ["version"]
+dependencies = ["h5py>=2.3", "numpy>=1.22.0", "xsdata>=22.12"]
+requires-python = ">=3.9"
+
+authors = [{name = "ISMRMRD Developers"}]
+
+description = "Python implementation of ISMRMRD"
+readme = "README.md"
+license-files = ["LICENSE"]
+license = "LicenseRef-IsmrmrdSoftwareLicense"
+keywords = ["ismrmrd"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
+]
+
+[project.urls]
+Homepage = "https://github.com/ismrmrd/ismrmrd-python"
+Documentation = "https://github.com/ismrmrd/ismrmrd-python"
+Repository = "https://github.com/ismrmrd/ismrmrd-python"

requirements.txt

@@ -1,6 +1,4 @@
-h5py==2.9.0
-nose==1.3.7
-numpy==1.22.0
-PyXB==1.2.6
-six==1.12.0
-xsdata==24.4
+h5py==3.14.0
+pytest==8.4.1
+numpy==2.3.2
+xsdata==25.7

setup.py

@@ -1,81 +1,75 @@
 import os
-from setuptools import setup, find_packages
-from distutils.command.build import build
-from distutils.command.build_py import build_py
+from setuptools import setup, find_packages, Command
 
-import logging
 import shutil
 from pathlib import Path
-import re 
-
-logging.basicConfig()
-log_ = logging.getLogger(__name__)
+import re
 
 schema_file = os.path.join('schema','ismrmrd.xsd')
 config_file = os.path.join('schema','.xsdata.xml')
 
-class my_build_py(build_py):
-    def run(self):
-        # honor the --dry-run flag
-        if not self.dry_run:
-            outloc = self.build_lib
-            outloc = os.path.join(outloc,'ismrmrd/xsd/ismrmrdschema')
 
-
-            generate_schema(schema_file, config_file, outloc)
-                    # distutils uses old-style classes, so no super()
-        build_py.run(self)
+import setuptools.command.build
+setuptools.command.build.build.sub_commands.append(("generate_schema", None))
 
+class GenerateSchemaCommand(Command):
+    description = "Generate Python code from ISMRMRD XML schema using xsdata"
+    user_options = []
 
-def fix_init_file(package_name,filepath):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.build_lib = None
+        self.editable_mode = False
 
-    with open(filepath,'r+') as f:
-        text = f.read()
-        text = re.sub(f'from {package_name}.ismrmrd', 'from .ismrmrd',text)
-        f.seek(0)
-        f.write(text)
-        f.truncate()
+    def initialize_options(self):
+        pass
 
+    def finalize_options(self):
+        # # Set build_lib for non-editable installs
+        self.set_undefined_options("build_py", ("build_lib", "build_lib"))
 
+    def run(self):
+        # Use editable_mode if present (PEP 660)
+        if self.editable_mode:
+            outdir = 'ismrmrd/xsd/'
+        else:
+            outdir = os.path.join(self.build_lib, 'ismrmrd/xsd/')
+        self.announce(f'Generating schema to {outdir} (editable_mode={self.editable_mode})', level=3)
+        self.generate_schema(schema_file, config_file, 'ismrmrdschema', outdir)
 
+    def get_source_files(self):
+        return [schema_file, config_file]
 
-def generate_schema(schema_filename, config_filename, outloc  ):
-    def to_uri(filename):
-        return Path(filename).absolute().as_uri()
+    def get_outputs(self):
+        return [
+            "{build_lib}/ismrmrd/xsd/ismrmrdschema/__init__.py",
+            "{build_lib}/ismrmrd/xsd/ismrmrdschema/ismrmrd.py"
+        ]
 
-    import sys 
-    import subprocess
-
-    subpackage_name = 'ismrmrdschema'
-    args = [sys.executable,'-m','xsdata', str(schema_filename), '--config',str(config_filename), '--package',subpackage_name]
-    subprocess.run(args)
-    fix_init_file(subpackage_name,f"{subpackage_name}/__init__.py")
-    shutil.rmtree(os.path.join(outloc,subpackage_name),ignore_errors=True)
-    shutil.move(subpackage_name,outloc)
+    def fix_init_file(self, package_name,filepath):
+        with open(filepath,'r+') as f:
+            text = f.read()
+            text = re.sub(f'from {package_name}.ismrmrd', 'from .ismrmrd',text)
+            f.seek(0)
+            f.write(text)
+            f.truncate()
 
-this_directory = Path(__file__).parent
-long_description = (this_directory / "README").read_text()
+    def generate_schema(self, schema_filename, config_filename, subpackage_name, outdir):
+        import sys
+        import subprocess
+        # subpackage_name = 'ismrmrdschema'
+        args = [sys.executable, '-m', 'xsdata', str(schema_filename), '--config', str(config_filename), '--package', subpackage_name]
+        subprocess.run(args)
+        self.fix_init_file(subpackage_name, f"{subpackage_name}/__init__.py")
+        destination = os.path.join(outdir, subpackage_name)
+        shutil.rmtree(destination, ignore_errors=True)
+        shutil.move(subpackage_name, destination)
+        print(f"JOE: Moved {subpackage_name} to {destination}")
 
 setup(
-    name='ismrmrd',
     version='1.14.1',
-    author='ISMRMRD Developers',
-    description='Python implementation of the ISMRMRD',
-    license='Public Domain',
-    keywords='ismrmrd',
-    url='https://ismrmrd.github.io',
-    long_description = long_description,
-    long_description_content_type='text/markdown',
     packages=find_packages(),
-    classifiers=[
-        'Development Status :: 5 - Production/Stable',
-        'Intended Audience :: Science/Research',
-        'License :: Public Domain',
-        'Operating System :: OS Independent',
-        'Topic :: Scientific/Engineering :: Medical Science Apps.'
-        ],
-    install_requires=['xsdata>=22.12', 'numpy>=1.22.0', 'h5py>=2.3'],
-    setup_requires=['nose>=1.0', 'xsdata[cli]>=22.12', 'jinja2 >= 2.11'],
-    test_suite='nose.collector',
-    cmdclass={'build_py':my_build_py}
+    cmdclass={
+        'generate_schema': GenerateSchemaCommand
+    }
 )