Merge pull request #111 from Materials-Data-Science-and-Informatics/feature/optional_validation

Feature/optional validation

Author: mustafasoylu

CHANGELOG.md

@@ -4,7 +4,12 @@ Here we provide notes that summarize the most important changes in each released
 
 Please consult the changelog to inform yourself about breaking changes and security issues.
 
-## [v0.6.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.6.0) <small>(2025-xx-xx)</small> { id="0.6.0" }
+## [v0.7.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.7.0) <small>(2025-xx-xx)</small> { id="0.7.0" }
+
+- make validation of output files, such as pyproject.toml, optional
+- make somesy project metadata input `version` optional
+
+## [v0.6.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.6.0) <small>(2025-02-14)</small> { id="0.6.0" }
 
 - implement CFF Entity (Organization) model for author/maintainer/contributor
 - add a new config option to use existing codemeta.json when syncing

docs/manual.md

@@ -146,7 +146,7 @@ some of the currently supported formats. Bold field names are mandatory, the oth
     | **name**          | name          | name               | name                            | name         | name           | name         | site_name        | name            | title           | name              |
     | **description**   | description   | description        | description                     | -            | description    | description  | site_description | description     | abstract        | description       |
     | **license**       | license       | license            | licenses.license                | -            | license        | license      | -                | license         | license         | license           |
-    | **version**       | version       | version            | version                         | version      | version        | version      | -                | version         | version         | version           |
+    | version       | version       | version            | version                         | version      | version        | version      | -                | version         | version         | version           |
     |                   |               |                    |                                 |              |                |              |                  |                 |                 |                   |
     | ***author=true*** | authors       | authors            | developers                      | authors      | author         | author       | site_author      | authors         | authors         | author            |
     | *maintainer=true* | maintainers   | maintainers        | -                               | -            | maintainer     | maintainers  | -                | -               | contact         | maintainer        |

src/somesy/cff/writer.py

@@ -18,6 +18,7 @@ def __init__(
         self,
         path: Path,
         create_if_not_exists: bool = True,
+        pass_validation: bool = False,
     ):
         """Citation File Format (CFF) parser.
 
@@ -35,7 +36,10 @@ def __init__(
             "maintainers": ["contact"],
         }
         super().__init__(
-            path, create_if_not_exists=create_if_not_exists, direct_mappings=mappings
+            path,
+            create_if_not_exists=create_if_not_exists,
+            direct_mappings=mappings,
+            pass_validation=pass_validation,
         )
 
     def _init_new_file(self):
@@ -53,8 +57,10 @@ def _load(self):
         with open(self.path) as f:
             self._data = self._yaml.load(f)
 
-    def _validate(self):
+    def _validate(self) -> None:
         """Validate the CFF file."""
+        if self.pass_validation:
+            return
         try:
             citation = create_citation(self.path, None)
             citation.validate()

src/somesy/cli/sync.py

@@ -152,6 +152,12 @@ def sync(
         "--merge/--overwrite",
         help="Merge codemeta.json with with an existing codemeta.json file (default: False)",
     ),
+    pass_validation: bool = typer.Option(
+        False,
+        "--pass-validation",
+        "-P",
+        help="Pass validation of metadata files (default: False)",
+    ),
 ):
     """Sync project metadata input with metadata files."""
     somesy_input = resolved_somesy_input(
@@ -175,6 +181,7 @@ def sync(
         no_sync_rust=no_sync_rust,
         rust_file=rust_file,
         merge_codemeta=merge_codemeta,
+        pass_validation=pass_validation,
     )
     run_sync(somesy_input)
 
@@ -218,6 +225,8 @@ def run_sync(somesy_input: SomesyInput):
             f"  - [italic]codemeta.json[/italic]:\t[grey]{conf.codemeta_file}[/grey]\n"
         )
     # ----
+    if conf.pass_validation:
+        logger.info("[bold yellow]Passing validation of metadata files.[/bold yellow]")
     sync_command(somesy_input)
     # ----
     logger.info("[bold green]Metadata synchronization completed.[/bold green]")

src/somesy/codemeta/writer.py

@@ -20,6 +20,7 @@ def __init__(
         self,
         path: Path,
         merge: Optional[bool] = False,
+        pass_validation: Optional[bool] = False,
     ):
         """Codemeta.json parser.
 
@@ -46,7 +47,12 @@ def __init__(
         if path.is_file() and not self.merge:
             logger.verbose("Deleting existing codemeta.json file.")
             path.unlink()
-        super().__init__(path, create_if_not_exists=True, direct_mappings=mappings)
+        super().__init__(
+            path,
+            create_if_not_exists=True,
+            direct_mappings=mappings,
+            pass_validation=pass_validation,
+        )
 
         # if merge is True, add necessary keys to the codemeta.json file
         if self.merge:
@@ -95,6 +101,8 @@ def _load(self) -> None:
 
     def _validate(self) -> None:
         """Validate codemeta.json content using pydantic class."""
+        if self.pass_validation:
+            return
         invalid_fields = validate_codemeta(self._data)
         if invalid_fields and self.merge:
             raise ValueError(

src/somesy/commands/sync.py

@@ -26,13 +26,14 @@ def _sync_file(
     file: Path,
     writer_cls: Type[ProjectMetadataWriter],
     merge_codemeta: Optional[bool] = False,
+    pass_validation: Optional[bool] = False,
 ):
     """Sync metadata to a file using the provided writer."""
     logger.verbose(f"Loading '{file.name}' ...")
     if writer_cls == CodeMeta:
-        writer = writer_cls(file, merge=merge_codemeta)
+        writer = writer_cls(file, merge=merge_codemeta, pass_validation=pass_validation)
     else:
-        writer = writer_cls(file)
+        writer = writer_cls(file, pass_validation=pass_validation)
     logger.verbose(f"Syncing '{file.name}' ...")
     writer.sync(metadata)
     writer.save(file)
@@ -49,34 +50,75 @@ def sync(somesy_input: SomesyInput):
     # update these only if they exist:
 
     if conf.pyproject_file.is_file() and not conf.no_sync_pyproject:
-        _sync_file(metadata, conf.pyproject_file, Pyproject)
+        _sync_file(
+            metadata,
+            conf.pyproject_file,
+            Pyproject,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.package_json_file.is_file() and not conf.no_sync_package_json:
-        _sync_file(metadata, conf.package_json_file, PackageJSON)
+        _sync_file(
+            metadata,
+            conf.package_json_file,
+            PackageJSON,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.julia_file.is_file() and not conf.no_sync_julia:
-        _sync_file(metadata, conf.julia_file, Julia)
+        _sync_file(
+            metadata,
+            conf.julia_file,
+            Julia,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.fortran_file.is_file() and not conf.no_sync_fortran:
-        _sync_file(metadata, conf.fortran_file, Fortran)
+        _sync_file(
+            metadata,
+            conf.fortran_file,
+            Fortran,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.pom_xml_file.is_file() and not conf.no_sync_pom_xml:
-        _sync_file(metadata, conf.pom_xml_file, POM)
+        _sync_file(
+            metadata,
+            conf.pom_xml_file,
+            POM,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.mkdocs_file.is_file() and not conf.no_sync_mkdocs:
-        _sync_file(metadata, conf.mkdocs_file, MkDocs)
+        _sync_file(
+            metadata,
+            conf.mkdocs_file,
+            MkDocs,
+            pass_validation=conf.pass_validation,
+        )
 
     if conf.rust_file.is_file() and not conf.no_sync_rust:
-        _sync_file(metadata, conf.rust_file, Rust)
+        _sync_file(
+            metadata,
+            conf.rust_file,
+            Rust,
+            pass_validation=conf.pass_validation,
+        )
 
     # create these by default if they are missing:
     if not conf.no_sync_cff:
-        _sync_file(metadata, conf.cff_file, CFF)
+        _sync_file(
+            metadata,
+            conf.cff_file,
+            CFF,
+            pass_validation=conf.pass_validation,
+        )
 
     if not conf.no_sync_codemeta:
         _sync_file(
             metadata,
             conf.codemeta_file,
             CodeMeta,
             merge_codemeta=conf.merge_codemeta,
+            pass_validation=conf.pass_validation,
         )

src/somesy/core/models.py

@@ -243,6 +243,12 @@ def at_least_one_target(cls, values):
         ),
     ] = False
 
+    # property to pass validation for all inputs/outputs
+    pass_validation: Annotated[
+        Optional[bool],
+        Field(description="Pass validation for all output files."),
+    ] = False
+
     def log_level(self) -> SomesyLogLevel:
         """Return log level derived from this configuration."""
         return SomesyLogLevel.from_flags(
@@ -644,7 +650,7 @@ def at_least_one_author(self) -> ProjectMetadata:
 
     name: Annotated[str, Field(description="Project name.")]
     description: Annotated[str, Field(description="Project description.")]
-    version: Annotated[str, Field(description="Project version.")]
+    version: Annotated[Optional[str], Field(description="Project version.")] = None
     license: Annotated[LicenseEnum, Field(description="SPDX License string.")]
 
     homepage: Annotated[

src/somesy/core/writer.py

@@ -37,6 +37,7 @@ def __init__(
         create_if_not_exists: Optional[bool] = False,
         direct_mappings: FieldKeyMapping = None,
         merge: Optional[bool] = False,
+        pass_validation: Optional[bool] = False,
     ) -> None:
         """Initialize the Project Metadata Output Wrapper.
 
@@ -50,16 +51,19 @@ def __init__(
             create_if_not_exists: Create an empty CFF file if not exists. Defaults to True.
             direct_mappings: Dict with direct mappings of keys between somesy and target
             merge: Merge the output file with an existing file. Defaults to False.
+            pass_validation: Pass validation for all output files. Defaults to False.
 
         """
         self._data: DictLike = {}
         self.path = path if isinstance(path, Path) else Path(path)
         self.create_if_not_exists = create_if_not_exists
         self.direct_mappings = direct_mappings or {}
         self.merge = merge
+        self.pass_validation = pass_validation
         if self.path.is_file():
             self._load()
-            self._validate()
+            if not self.pass_validation:
+                self._validate()
         else:
             if self.create_if_not_exists:
                 self._init_new_file()
@@ -86,7 +90,7 @@ def _load(self):
         """
 
     @abstractmethod
-    def _validate(self):
+    def _validate(self) -> None:
         """Validate the target file data.
 
         Implement this method so that it checks

src/somesy/fortran/writer.py

@@ -18,7 +18,11 @@
 class Fortran(ProjectMetadataWriter):
     """Fortran config file handler parsed from fpm.toml."""
 
-    def __init__(self, path: Path):
+    def __init__(
+        self,
+        path: Path,
+        pass_validation: Optional[bool] = False,
+    ):
         """Fortran config file handler parsed from fpm.toml.
 
         See [somesy.core.writer.ProjectMetadataWriter.__init__][].
@@ -28,7 +32,12 @@ def __init__(self, path: Path):
             "maintainers": ["maintainer"],
             "documentation": IgnoreKey(),
         }
-        super().__init__(path, create_if_not_exists=False, direct_mappings=mappings)
+        super().__init__(
+            path,
+            create_if_not_exists=False,
+            direct_mappings=mappings,
+            pass_validation=pass_validation,
+        )
 
     @property
     def authors(self):
@@ -71,6 +80,8 @@ def _validate(self) -> None:
         In order to preserve toml comments and structure, tomlkit library is used.
         Pydantic class only used for validation.
         """
+        if self.pass_validation:
+            return
         config = dict(self._get_property([]))
         logger.debug(
             f"Validating config using {FortranConfig.__name__}: {pretty_repr(config)}"

src/somesy/julia/writer.py

@@ -18,12 +18,20 @@
 class Julia(ProjectMetadataWriter):
     """Julia config file handler parsed from Project.toml."""
 
-    def __init__(self, path: Path):
+    def __init__(
+        self,
+        path: Path,
+        pass_validation: Optional[bool] = False,
+    ):
         """Julia config file handler parsed from Project.toml.
 
         See [somesy.core.writer.ProjectMetadataWriter.__init__][].
         """
-        super().__init__(path, create_if_not_exists=False)
+        super().__init__(
+            path,
+            create_if_not_exists=False,
+            pass_validation=pass_validation,
+        )
 
     def _load(self) -> None:
         """Load Project.toml file."""
@@ -36,6 +44,8 @@ def _validate(self) -> None:
         In order to preserve toml comments and structure, tomlkit library is used.
         Pydantic class only used for validation.
         """
+        if self.pass_validation:
+            return
         config = dict(self._get_property([]))
         logger.debug(
             f"Validating config using {JuliaConfig.__name__}: {pretty_repr(config)}"