Merge branch 'main' into feature_cases

.ci_pip_reqs.txt

@@ -1,3 +1,4 @@
 pytest
 flake8
-https://github.com/petab-dev/libpetab-python/archive/develop.zip
+git+https://github.com/PEtab-dev/libpetab-python@develop
+sympy>=1.12.1

.github/workflows/ci_tests.yml

@@ -27,8 +27,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        pip install -r .ci_pip_reqs.txt
         pip install -e .
+        pip uninstall -y petab
+        pip install -r .ci_pip_reqs.txt
     - name: Run tests
       run: |
         python -m flake8 \

MANIFEST.in

@@ -1,2 +1,4 @@
 include petabtests/conversion.xml
 recursive-include petabtests/cases *
+recursive-exclude **/__pycache__ *
+exclude cases

petabtests/file.py

@@ -8,7 +8,8 @@
 import petab
 import yaml
 from petab.C import *  # noqa: F403
-
+from petab.v1.lint import lint_problem as lint_problem_v1
+from petab.v2.lint import lint_problem as lint_problem_v2
 from .C import *  # noqa: F403
 
 __all__ = [
@@ -180,13 +181,22 @@ def write_problem(
 
     # write yaml
     yaml_file = problem_yaml_name(test_id)
-    with open(os.path.join(dir_, yaml_file), 'w') as outfile:
+    yaml_path = os.path.join(dir_, yaml_file)
+    with open(yaml_path, 'w') as outfile:
         yaml.dump(config, outfile, default_flow_style=False)
 
     # validate written PEtab files
-    problem = petab.Problem.from_yaml(os.path.join(dir_, yaml_file))
-    if petab.lint_problem(problem):
-        raise RuntimeError("Invalid PEtab problem, see messages above.")
+    if format_version == 1:
+        # PEtab v1
+        problem = petab.Problem.from_yaml(yaml_path)
+        if lint_problem_v1(problem):
+            raise RuntimeError("Invalid PEtab problem, see messages above.")
+    else:
+        # v2
+        validation_result = lint_problem_v2(yaml_path)
+        if validation_result:
+            print(validation_result)
+            raise RuntimeError("Invalid PEtab problem, see messages above.")
 
 
 def write_solution(

pyproject.toml

@@ -1,3 +1,41 @@
 [build-system]
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "petabtests"
+dynamic = ["version"]
+description = "PEtab testsuite library"
+readme = "README.md"
+authors = [
+    { name = "Daniel Weindl", email = "[email protected]" },
+    { name = "Yannik Schaelte", email = "[email protected]" },
+]
+maintainers = [
+    { name = "Daniel Weindl", email = "[email protected]" },
+]
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+keywords = ["PEtab", "testsuite"]
+dependencies = [
+    "numpy>=1.22",
+    "pandas>=2.0",
+    "petab>=0.1.4",
+    "pysb>=1.16.0",
+    "simplesbml",
+]
+
+[project.urls]
+homepage = "https://github.com/PEtab-dev/petab_test_suite"
+
+[project.scripts]
+petabtests_create = "petabtests.core:create"
+petabtests_clear = "petabtests.core:clear"

setup.py

@@ -18,41 +18,9 @@ def read(fname):
 exec(read(path.join(here, 'petabtests', 'version.py')))
 
 setup(
-    name='petabtests',
     version=__version__,  # noqa: F821
-    description='PEtab testsuite library',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    url='https://github.com/PEtab-dev/petab_test_suite',
-    author='PEtab-dev',
-    author_email='[email protected]',
-    maintainer='PEtab-dev',
-    maintainer_email='[email protected]',
-    # author_email='',
-    classifiers=[
-        'Development Status :: 3 - Alpha',
-        'Intended Audience :: Developers',
-        'License :: OSI Approved :: BSD License',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-    ],
-    keywords='PEtab testsuite',
     packages=find_namespace_packages(),
-    install_requires=[
-        'numpy',
-        'pandas',
-        'petab>=0.1.4',
-        'pysb',
-        'simplesbml',
-    ],
-    python_requires='>=3.10',
-    entry_points={
-        'console_scripts': [
-            'petabtests_create = petabtests.core:create',
-            'petabtests_clear = petabtests.core:clear',
-        ]
-    },
     include_package_data=True,
 )