soft7 0.2.0__tar.gz → 0.2.2__tar.gz

{soft7-0.2.0 → soft7-0.2.2}/.github/workflows/cd_docs.yml

@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - 'main'
+      - 'push-action/**'  # For the CasperWA/push-protected action
 
   # Run for every new release
   release:
@@ -61,7 +62,7 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
 
-    if: github.event_name != 'pull_request'
+    if: github.event_name != 'pull_request' && ( ! startsWith(github.ref_name, 'push-action/') )
 
     needs: build
 

{soft7-0.2.0 → soft7-0.2.2}/.github/workflows/cd_publish.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   build:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.2
+    uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.3
     if: github.repository == 'SINTEF/soft7' && startsWith(github.ref, 'refs/tags/v')
     with:
       # General

{soft7-0.2.0 → soft7-0.2.2}/.github/workflows/ci_tests.yml

@@ -5,11 +5,12 @@ on:
   push:
     branches:
       - 'main'
+      - 'push-action/**'  # For the CasperWA/push-protected action
 
 jobs:
   basics:
     name: External
-    uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.2
+    uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.3
     with:
       # General
       install_extras: '[dev]'
@@ -42,6 +43,7 @@ jobs:
     runs-on: ubuntu-latest
 
     strategy:
+      fail-fast: false
       matrix:
         # Supported Python versions (according to pyproject.toml)
         python-version: ['3.9', '3.10', '3.11', '3.12']
@@ -62,11 +64,11 @@ jobs:
         pip install -e .[testing]
 
     - name: Run pytest
-      run: pytest -v -rs --cov=s7 --cov-report=xml --cov-report=term-missing
+      run: pytest -v -rs --cov=s7 --cov-report=xml --cov-report=term-missing --color=yes
 
     - name: Upload code coverage report
       if: github.repository == 'SINTEF/soft7'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

{soft7-0.2.0 → soft7-0.2.2}/.pre-commit-config.yaml

@@ -14,7 +14,7 @@ ci:
 # hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     - id: end-of-file-fixer
     - id: debug-statements
@@ -26,18 +26,18 @@ repos:
       args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.19.0
     hooks:
     - id: pyupgrade
       args: ["--py39-plus", "--keep-runtime-typing"]
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
     - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    rev: v0.8.0
     hooks:
     - id: ruff
       args:
@@ -47,14 +47,14 @@ repos:
       - "--no-unsafe-fixes"
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.9
+    rev: 1.7.10
     hooks:
     - id: bandit
       args: ["-r"]
       files: ^s7/.*$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
     - id: mypy
       exclude: ^tests/.*$

{soft7-0.2.0 → soft7-0.2.2}/CHANGELOG.md

@@ -2,15 +2,68 @@
 
 ## [Unreleased](https://github.com/SINTEF/soft7/tree/HEAD)
 
-[Full Changelog](https://github.com/SINTEF/soft7/compare/v0.2.0...HEAD)
+[Full Changelog](https://github.com/SINTEF/soft7/compare/v0.2.2...HEAD)
 
-## Support different SOFT flavors
+# Fix issue with pydantic v2.10
 
-Implement support for different SOFT flavors, specifically, support the [DLite](https://github.com/SINTEF/dlite) flavor of SOFT entities.
+There are some issues with pydantic's v2.10 concerning `Url` models.
+Since we use the pydantic version specified by `oteapi-core`, we make sure to at least use v0.7.0.dev6, since this ensure v2.10.0 and v2.10.1 is not installed.
+When v2.10.2 comes out, it can be tested on `oteapi-core` before a new release is done.
 
-### DX
+All other dependencies and dev tools have also been updated.
+
+## [v0.2.2](https://github.com/SINTEF/soft7/tree/v0.2.2) (2024-11-25)
+
+[Full Changelog](https://github.com/SINTEF/soft7/compare/v0.2.1...v0.2.2)
+
+# Fix issue with pydantic v2.10
 
-Update dev tools and use [PyPIs Trusted Publishers](https://docs.pypi.org/trusted-publishers/) scheme.
+There are some issues with pydantic's v2.10 concerning `Url` models.
+Since we use the pydantic version specified by `oteapi-core`, we make sure to at least use v0.7.0.dev6, since this ensure v2.10.0 and v2.10.1 is not installed.
+When v2.10.2 comes out, it can be tested on `oteapi-core` before a new release is done.
+
+All other dependencies and dev tools have also been updated.
+
+**Merged pull requests:**
+
+- Update pytest-httpx requirement from ~=0.33.0 to \>=0.33,\<0.35 in the dependencies group [\#82](https://github.com/SINTEF/soft7/pull/82) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#81](https://github.com/SINTEF/soft7/pull/81) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Bump codecov/codecov-action from 4 to 5 in the actions group [\#80](https://github.com/SINTEF/soft7/pull/80) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#79](https://github.com/SINTEF/soft7/pull/79) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#78](https://github.com/SINTEF/soft7/pull/78) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Bump the dependencies group with 2 updates [\#77](https://github.com/SINTEF/soft7/pull/77) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#76](https://github.com/SINTEF/soft7/pull/76) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Update pydata-sphinx-theme requirement from ~=0.15.2 to \>=0.15.2,\<0.17.0 in the dependencies group [\#75](https://github.com/SINTEF/soft7/pull/75) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#74](https://github.com/SINTEF/soft7/pull/74) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Bump SINTEF/ci-cd from 2.8.2 to 2.8.3 in the actions group [\#73](https://github.com/SINTEF/soft7/pull/73) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#72](https://github.com/SINTEF/soft7/pull/72) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#70](https://github.com/SINTEF/soft7/pull/70) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Update pre-commit requirement from ~=3.7 to ~=4.0 in the dependencies group [\#69](https://github.com/SINTEF/soft7/pull/69) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#68](https://github.com/SINTEF/soft7/pull/68) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Update pytest-httpx requirement from ~=0.31.1 to ~=0.32.0 in the dependencies group [\#67](https://github.com/SINTEF/soft7/pull/67) ([dependabot[bot]](https://github.com/apps/dependabot))
+- \[pre-commit.ci\] pre-commit autoupdate [\#66](https://github.com/SINTEF/soft7/pull/66) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Update pytest-httpx requirement from ~=0.30.0 to \>=0.30,\<0.32 in the dependencies group [\#65](https://github.com/SINTEF/soft7/pull/65) ([dependabot[bot]](https://github.com/apps/dependabot))
+
+## [v0.2.1](https://github.com/SINTEF/soft7/tree/v0.2.1) (2024-09-18)
+
+[Full Changelog](https://github.com/SINTEF/soft7/compare/v0.2.0...v0.2.1)
+
+## Remove upper limit for `oteapi-core` dependency
+
+While not recommended, this does make it possible to support the DataSpaces developed at SINTEF.
+In the future a more stringent dependency tree/graph should be implemented for all packages.
+
+**Fixed bugs:**
+
+- Update example OpenAPI specs [\#61](https://github.com/SINTEF/soft7/issues/61)
+- Fix deployment issue [\#57](https://github.com/SINTEF/soft7/issues/57)
+
+**Merged pull requests:**
+
+- Remove upper level version dependency for `oteapi-core` [\#62](https://github.com/SINTEF/soft7/pull/62) ([CasperWA](https://github.com/CasperWA))
+- \[pre-commit.ci\] pre-commit autoupdate [\#60](https://github.com/SINTEF/soft7/pull/60) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- \[pre-commit.ci\] pre-commit autoupdate [\#59](https://github.com/SINTEF/soft7/pull/59) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Ensure CI jobs are run for push-protected action branches [\#58](https://github.com/SINTEF/soft7/pull/58) ([CasperWA](https://github.com/CasperWA))
 
 ## [v0.2.0](https://github.com/SINTEF/soft7/tree/v0.2.0) (2024-08-27)
 

{soft7-0.2.0 → soft7-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: soft7
-Version: 0.2.0
+Version: 0.2.2
 Summary: SOFT7 semantic interoperability framework.
 Keywords: interoperability,semantic
 Author-email: Thomas Fjæstad Hagelien <thomas.f.hagelien@sintef.no>, Casper Welzel Andersen <casper.w.andersen@sintef.no>, Treesa Rose Joseph <treesa.joseph@sintef.no>
@@ -15,22 +15,22 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
-Requires-Dist: httpx~=0.27.0
-Requires-Dist: oteapi-core>=0.7.0.dev2,<1
-Requires-Dist: otelib~=0.5.0.dev0
+Requires-Dist: httpx~=0.27.2
+Requires-Dist: oteapi-core>=0.7.0.dev6
+Requires-Dist: otelib~=0.5.0.dev1
 Requires-Dist: pyyaml~=6.0
 Requires-Dist: typing-extensions~=4.12; python_version < '3.12'
-Requires-Dist: pre-commit~=3.7 ; extra == "dev"
-Requires-Dist: soft7[docs,graph,testing] ; extra == "dev"
+Requires-Dist: pre-commit~=4.0 ; extra == "dev"
+Requires-Dist: soft7[docs, graph, testing] ; extra == "dev"
 Requires-Dist: myst-nb~=1.1 ; extra == "docs"
-Requires-Dist: pydata-sphinx-theme~=0.15.2 ; extra == "docs"
-Requires-Dist: sphinx>=7.3,<9.0 ; extra == "docs"
+Requires-Dist: pydata-sphinx-theme~=0.16.0 ; extra == "docs"
+Requires-Dist: sphinx>=7.4.7,<9 ; extra == "docs"
 Requires-Dist: jinja2~=3.1 ; extra == "graph"
-Requires-Dist: rdflib~=7.0 ; extra == "graph"
+Requires-Dist: rdflib~=7.1 ; extra == "graph"
 Requires-Dist: sparqlwrapper~=2.0 ; extra == "graph"
-Requires-Dist: pytest~=8.2 ; extra == "testing"
-Requires-Dist: pytest-cov~=5.0 ; extra == "testing"
-Requires-Dist: pytest-httpx~=0.30.0 ; extra == "testing"
+Requires-Dist: pytest~=8.3 ; extra == "testing"
+Requires-Dist: pytest-cov~=6.0 ; extra == "testing"
+Requires-Dist: pytest-httpx~=0.34.0 ; extra == "testing"
 Requires-Dist: requests-mock~=1.12 ; extra == "testing"
 Requires-Dist: soft7[graph] ; extra == "testing"
 Project-URL: Changelog, https://github.com/SINTEF/soft7/blob/main/CHANGELOG.md

{soft7-0.2.0 → soft7-0.2.2}/pyproject.toml

@@ -29,9 +29,9 @@ requires-python = "~=3.9"
 dynamic = ["version"]
 
 dependencies = [
-    "httpx~=0.27.0",
-    "oteapi-core>=0.7.0.dev2,<1",
-    "otelib~=0.5.0.dev0",
+    "httpx~=0.27.2",
+    "oteapi-core>=0.7.0.dev6",
+    "otelib~=0.5.0.dev1",
     "pyyaml~=6.0",
     "typing-extensions~=4.12; python_version < '3.12'",
 ]
@@ -42,23 +42,23 @@ dependencies = [
 [project.optional-dependencies]
 docs = [
     "myst-nb~=1.1",
-    "pydata-sphinx-theme~=0.15.2",
-    "sphinx>=7.3,<9.0",
+    "pydata-sphinx-theme~=0.16.0",
+    "sphinx>=7.4.7,<9",  # Allow v7 to support Python 3.9
 ]
 graph = [
     "jinja2~=3.1",
-    "rdflib~=7.0",
+    "rdflib~=7.1",
     "sparqlwrapper~=2.0",
 ]
 testing = [
-    "pytest~=8.2",
-    "pytest-cov~=5.0",
-    "pytest-httpx~=0.30.0",
+    "pytest~=8.3",
+    "pytest-cov~=6.0",
+    "pytest-httpx~=0.34.0",
     "requests-mock~=1.12",
     "soft7[graph]",
 ]
 dev = [
-    "pre-commit~=3.7",
+    "pre-commit~=4.0",
     "soft7[docs,graph,testing]",
 ]
 

{soft7-0.2.0 → soft7-0.2.2}/s7/__init__.py

@@ -7,8 +7,8 @@ import logging
 from .pydantic_models.soft7_entity import SOFT7Entity, SOFT7EntityPropertyType
 from .pydantic_models.soft7_entity import parse_input_entity as get_entity
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"
 
-__all__ = ("__version__", "SOFT7Entity", "SOFT7EntityPropertyType", "get_entity")
+__all__ = ("SOFT7Entity", "SOFT7EntityPropertyType", "__version__", "get_entity")
 
 logging.getLogger("s7").setLevel(logging.DEBUG)

{soft7-0.2.0 → soft7-0.2.2}/s7/pydantic_models/_utils.py

@@ -150,7 +150,7 @@ def try_load_from_url(
             "assert_dict_exception_msg should be a string when assert_dict is True."
         )
 
-    with httpx.Client(follow_redirects=True) as client:
+    with httpx.Client(follow_redirects=True, timeout=10) as client:
         try:
             response = client.get(
                 str(source),

{soft7-0.2.0 → soft7-0.2.2}/s7/pydantic_models/soft7_entity.py

@@ -30,7 +30,6 @@ from pydantic.functional_validators import (
     model_validator,
 )
 from pydantic.networks import UrlConstraints
-from pydantic_core import Url
 
 from s7.exceptions import EntityNotFound
 from s7.pydantic_models._utils import (
@@ -50,7 +49,8 @@ if TYPE_CHECKING:  # pragma: no cover
 
 
 SOFT7IdentityURIType = Annotated[
-    Url, UrlConstraints(allowed_schemes=["http", "https", "file"], host_required=True)
+    AnyUrl,
+    UrlConstraints(allowed_schemes=["http", "https", "file"], host_required=True),
 ]
 
 
@@ -78,7 +78,7 @@ def SOFT7IdentityURI(url: str) -> SOFT7IdentityURIType:
         url = url.split("#", maxsplit=1)[0].split("?", maxsplit=1)[0]
         return SOFT7IdentityURIType(url)
 
-    raise TypeError(f"Expected str or Url, got {type(url)}")
+    raise TypeError(f"Expected str or AnyUrl, got {type(url)}")
 
 
 SOFT7EntityPropertyType = Union[

{soft7-0.2.0 → soft7-0.2.2}/s7/pydantic_models/soft7_instance.py

@@ -60,26 +60,32 @@ class SOFT7EntityInstance(BaseModel):
             if entity_property_value.shape
         }
 
-        dimensions = self.dimensions.model_copy() if self.dimensions else {}
-        properties = self.properties.model_copy()
-
         for property_name, shape in shaped_properties.items():
-            property_value = getattr(properties, property_name)
+            property_value = getattr(self.properties, property_name)
 
             # Let us ignore None valued properties
             if property_value is None:
                 continue
 
             # Retrieve the dimension values for dimensions in the shape
-            try:
-                literal_dimensions = [
-                    getattr(dimensions, dimension_name) for dimension_name in shape
-                ]
-            except AttributeError as exc:
-                raise ValueError(
-                    f"Property {property_name!r} is shaped, but not all the dimensions "
-                    "are defined"
-                ) from exc
+            if self.dimensions is None:
+                if shape:
+                    raise ValueError(
+                        f"Property {property_name!r} is shaped, but no dimensions are "
+                        "defined for the instance."
+                    )
+                literal_dimensions = []
+            else:
+                try:
+                    literal_dimensions = [
+                        getattr(self.dimensions, dimension_name)
+                        for dimension_name in shape
+                    ]
+                except AttributeError as exc:
+                    raise ValueError(
+                        f"Property {property_name!r} is shaped, but not all the "
+                        "dimensions are defined"
+                    ) from exc
 
             if not all(isinstance(_, int) for _ in literal_dimensions):
                 raise TypeError(
@@ -91,7 +97,7 @@ class SOFT7EntityInstance(BaseModel):
                 literal_dimensions = cast(list[int], literal_dimensions)
 
             # Get the inner most (non-list) Python type/class
-            property_type = properties.model_fields[property_name].annotation
+            property_type = self.properties.model_fields[property_name].annotation
 
             while True:
                 _temp = property_type

{soft7-0.2.0 → soft7-0.2.2}/tests/factories/test_datasource_factory.py

@@ -20,6 +20,9 @@ if TYPE_CHECKING:
     from requests_mock import Mocker
 
 
+pytestmark = pytest.mark.httpx_mock(can_send_already_matched_responses=True)
+
+
 def test_create_datasource(
     soft_entity_init: dict[str, str | dict],
     soft_datasource_init: dict[str, Any],
@@ -553,7 +556,7 @@ Attributes:
                 "x-soft7-unit": "Å",
             },
             "soft7___dimensions": {
-                "allOf": [{"$ref": "#/$defs/MolecularSpeciesDataSourceDimensions"}],
+                "$ref": "#/$defs/MolecularSpeciesDataSourceDimensions",
                 "default": {"N": 5},
             },
             "soft7___identity": {

{soft7-0.2.0 → soft7-0.2.2}/tests/oteapi_plugin/test_soft7_function.py

@@ -16,6 +16,8 @@ if TYPE_CHECKING:
     from s7.pydantic_models.soft7_entity import SOFT7Entity
     from s7.pydantic_models.soft7_instance import SOFT7EntityInstance
 
+pytestmark = pytest.mark.httpx_mock(can_send_already_matched_responses=True)
+
 
 def test__flatten_mapping(httpx_mock: HTTPXMock, static_folder: Path) -> None:
     """Test the `_flatten_mapping()` method."""