Merge branch 'release-0.13.1'

.github/workflows/ci.yaml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Run the test suite
       run: |

.github/workflows/ci_python_compatibility.yaml

@@ -6,19 +6,19 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - name: Check out the source code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache Tox
-      uses: actions/cache@v1
+      uses: actions/cache@v4
       with:
         path: ${{ github.workspace }}/.tox
         key: python-compatibility-${{ matrix.python-version }}-tox

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

CHANGELOG.rst

@@ -5,6 +5,26 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+0.13.1
+******
+
+Added
+-----
+
+- Support for Python 3.12
+- Show incorrect Identifier in the error message
+
+Changed
+-------
+
+- Replace ruamel.yaml with PyYAML dependency via YAtiML update
+
+Removed
+-------
+
+- Support for Python 3.7
+
+
 0.13.0
 ******
 

README.rst

@@ -48,6 +48,6 @@ Legal
 *****
 
 ymmsl_python is Copyright 2018-2023 Netherlands eScience Center and University
-of Amsterdam, and Copyright 2022-2023 ITER Organisation. Licensed under the
-Apache 2.0 license.
+of Amsterdam, Copyright 2022-2023 The ITER Organisation, and Copyright 2024
+Netherlands eScience Center. Licensed under the Apache 2.0 license.
 

docs/conf.py

@@ -61,9 +61,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.13.0'
+version = u'0.13.1'
 # The full version, including alpha/beta/rc tags.
-release = u'0.13.0'
+release = u'0.13.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx-rtd-theme
+yatiml

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name='ymmsl',
-    version='0.13.0',
+    version='0.13.1',
     description="Python bindings for the YAML version of the Multiscale Modeling and Simulation Language",
     long_description=readme + '\n\n',
     author="Lourens Veen",
@@ -33,11 +33,12 @@
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     python_requires='>=3.7, <4',
     test_suite='tests',
     install_requires=[
-        'ruamel.yaml<=0.17.21,!=0.17.5',
-        'yatiml>=0.10.0,<0.11.0'
+        'yatiml>=0.11.1,<0.12.0'
     ],
 )

tests/conftest.py

@@ -421,7 +421,7 @@ def test_yaml8() -> str:
             '    keeps_state_for_next_use: helpful\n'
             '  micro2_fortran:\n'
             '    executable: bin/micro2\n'
-            '    keeps_state_for_next_use: no\n'
+            '    keeps_state_for_next_use: \'no\'\n'
             'resources:\n'
             '  macro:\n'
             '    threads: 1\n'

tests/test_configuration.py

@@ -232,8 +232,9 @@ def test_check_consistent(test_config6: Configuration) -> None:
             ExecutionModel.OPENMPI)
     test_config6.resources[Reference('singlethreaded')] = MPICoresResReq(
             Reference('singlethreaded'), 16, 8)
-    with pytest.raises(RuntimeError):
-        test_config6.check_consistent()
+    # singlethreaded is started with a script, for which we allow either
+    # MPICoresResReq or ThreadedResReq
+    test_config6.check_consistent()
 
 
 def test_load_nil_settings() -> None:

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py37, py38, py39, py310, py311
+envlist = py38, py39, py310, py311, py312
 skip_missing_interpreters = true
 
 [testenv]
@@ -8,19 +8,20 @@ deps =
     flake8
     pytest
     pytest-cov
+    types-PyYAML
 
 commands =
     mypy
-    pytest
+    pytest {posargs}
     flake8 ymmsl
 
 [gh-actions]
 python =
-    3.7: py37
     3.8: py38
     3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [pycodestyle]
 max-doc-length = 80

ymmsl/__init__.py

@@ -17,7 +17,7 @@
 from ymmsl.model import Conduit, Model, ModelReference
 
 
-__version__ = '0.13.0'
+__version__ = '0.13.1'
 __author__ = 'Lourens Veen'
 __email__ = '[email protected]'
 

ymmsl/checkpoint.py

@@ -2,7 +2,7 @@
 
 from typing import List, Optional, Union
 
-from ruamel import yaml
+import yaml
 import yatiml
 
 

ymmsl/component.py

@@ -5,7 +5,7 @@
 from typing import Dict     # noqa: F401
 from typing import Iterable, List, Optional, Union
 
-import ruamel.yaml as yaml
+import yaml
 import yatiml
 
 from ymmsl.identity import Identifier, Reference
@@ -308,5 +308,5 @@ def _yatiml_sweeten(cls, node: yatiml.Node) -> None:
             node.set_attribute('multiplicity', items[0].get_value())
 
         ports_node = node.get_attribute('ports').yaml_node
-        if len(ports_node.value) == 0:
+        if ports_node.tag == 'tag:yaml.org,2002:null':
             node.remove_attribute('ports')

ymmsl/configuration.py

@@ -7,7 +7,7 @@
         Dict, List, MutableMapping, Optional, Sequence, Union, cast)
 
 import yatiml
-from ruamel import yaml
+import yaml
 
 from ymmsl.checkpoint import Checkpoints
 from ymmsl.document import Document
@@ -322,7 +322,9 @@ def check_consistent(self) -> None:
             impl = self.implementations[comp.implementation]
             res = self.resources[comp.name]
             if impl.execution_model == ExecutionModel.DIRECT:
-                if not isinstance(res, ThreadedResReq):
+                if not isinstance(res, ThreadedResReq) and impl.script is None:
+                    # Assume that people know what they're doing if they use
+                    # script for specifying an implementation.
                     raise RuntimeError((
                         'Model component {}\'s implementation does not'
                         ' specify MPI, but mpi_processes are specified in its'

ymmsl/execution.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import cast, Dict, List, Optional, Union
 
-from ruamel import yaml
+import yaml
 import yatiml
 
 from ymmsl.identity import Reference
@@ -207,8 +207,8 @@ def __init__(
     @classmethod
     def _yatiml_recognize(cls, node: yatiml.UnknownNode) -> None:
         # There's no ambiguity, and we want to allow some leeway
-        # and savorize things, so disable recognition.
-        pass
+        # and savorize things, so only require that the node is a mapping.
+        node.require_mapping()
 
     @classmethod
     def _yatiml_savorize(cls, node: yatiml.Node) -> None:

ymmsl/identity.py

@@ -31,7 +31,8 @@ def __init__(self, seq: Any) -> None:
             raise ValueError('Identifiers must consist only of'
                              ' lower- and uppercase letters, digits and'
                              ' underscores, must start with a letter or'
-                             ' an underscore, and must not be empty.')
+                             ' an underscore, and must not be empty.'
+                             ' "{}" is therefore invalid.'.format(self.data))
 
 
 ReferencePart = Union[Identifier, int]

ymmsl/settings.py

@@ -41,10 +41,13 @@ def __init__(
                 self[key] = deepcopy(value)
 
     def __eq__(self, other: Any) -> bool:
-        """Returns whether keys and values are identical."""
+        """Returns whether keys and values are identical.
+
+        The comparison ignores the order of the settings.
+        """
         if not isinstance(other, Settings):
             return NotImplemented
-        return self._store == other._store
+        return dict(self._store.items()) == dict(other._store.items())
 
     def __str__(self) -> str:
         """Represent as a string."""