Merge pull request #92 from Materials-Data-Science-and-Informatics/fix/validations

update/fix validations

Author: mustafasoylu

CHANGELOG.md

@@ -4,43 +4,50 @@ 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.
 
+## [v0.4.3](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.4.3) <small>(2024-07-??)</small> { id="0.4.3" }
+
+-   update python dependencies
+-   update pre-commit hook versions
+-   fix package.json person validation
+-   update poetry, julia, and package.json person validation: entries without an email wont't raise an error, they will be ignored.
+
 ## [v0.4.2](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.4.2) <small>(2024-04-30)</small> { id="0.4.2" }
 
-* fix rich logging bug for error messages and tracebacks
+-   fix rich logging bug for error messages and tracebacks
 
 ## [v0.4.1](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.4.1) <small>(2024-04-08)</small> { id="0.4.1" }
 
-* fix package.json and mkdocs.yml validation bug about optional fields
+-   fix package.json and mkdocs.yml validation bug about optional fields
 
 ## [v0.4.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.4.0) <small>(2024-03-08)</small> { id="0.4.0" }
 
-* added separate `documentation` URL to Project metadata model
-* added support for Julia `Project.toml` file
-* added support for Fortran `fpm.toml` file
-* added support for Java `pom.xml` file
-* added support for MkDocs `mkdocs.yml` file
-* added support for Rust `Cargo.toml` file
+-   added separate `documentation` URL to Project metadata model
+-   added support for Julia `Project.toml` file
+-   added support for Fortran `fpm.toml` file
+-   added support for Java `pom.xml` file
+-   added support for MkDocs `mkdocs.yml` file
+-   added support for Rust `Cargo.toml` file
 
 ## [v0.3.1](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.3.1) <small>(2024-01-23)</small> { id="0.3.1" }
 
-* fix setuptools license writing bug
+-   fix setuptools license writing bug
 
 ## [v0.3.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.3.0) <small>(2024-01-12)</small> { id="0.3.0" }
 
-* replace codemetapy with an in-house writer, which enables windows support
+-   replace codemetapy with an in-house writer, which enables windows support
 
 ## [v0.2.1](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.2.1) <small>(2023-11-29)</small> { id="0.2.1" }
 
-* **internal:** updated linters and dependencies
-* **internal:** pin codemetapy version to 2.5.2 to avoid breaking changes
-* fix bug caused by missing `config` section
+-   **internal:** updated linters and dependencies
+-   **internal:** pin codemetapy version to 2.5.2 to avoid breaking changes
+-   fix bug caused by missing `config` section
 
 ## [v0.2.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.2.0) <small>(2023-11-29)</small> { id="0.2.0" }
 
-* **internal:** Test refactoring
-* **internal:** Pydantic 2 implementation
-* Added `publication_author` field to Person model
+-   **internal:** Test refactoring
+-   **internal:** Pydantic 2 implementation
+-   Added `publication_author` field to Person model
 
 ## [v0.1.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.1.0) <small>(2023-08-10)</small> { id="0.1.0" }
 
-* First release
+-   First release

src/somesy/core/writer.py

@@ -331,7 +331,15 @@ def description(self, description: str) -> None:
     @property
     def authors(self):
         """Return the authors of the project."""
-        return self._get_property(self._get_key("authors"))
+        authors = self._get_property(self._get_key("authors"))
+        if authors is None:
+            return []
+
+        # only return authors that can be converted to Person
+        authors_validated = [
+            author for author in authors if self._to_person(author) is not None
+        ]
+        return authors_validated
 
     @authors.setter
     def authors(self, authors: List[Person]) -> None:
@@ -342,7 +350,17 @@ def authors(self, authors: List[Person]) -> None:
     @property
     def maintainers(self):
         """Return the maintainers of the project."""
-        return self._get_property(self._get_key("maintainers"))
+        maintainers = self._get_property(self._get_key("maintainers"))
+        if maintainers is None:
+            return []
+
+        # only return maintainers that can be converted to Person
+        maintainers_validated = [
+            maintainer
+            for maintainer in maintainers
+            if self._to_person(maintainer) is not None
+        ]
+        return maintainers_validated
 
     @maintainers.setter
     def maintainers(self, maintainers: List[Person]) -> None:

src/somesy/fortran/writer.py

@@ -90,11 +90,11 @@ def _from_person(person: Person):
         return person.to_name_email_string()
 
     @staticmethod
-    def _to_person(person_obj: Any) -> Person:
+    def _to_person(person_obj: Any) -> Optional[Person]:
         """Cannot convert from free string to person object."""
         try:
             return Person.from_name_email_string(person_obj)
-        except ValueError:
+        except (ValueError, AttributeError):
             logger.warning(f"Cannot convert {person_obj} to Person object.")
             return None
 

src/somesy/julia/models.py

@@ -1,6 +1,7 @@
 """Julia model."""
 
 import uuid
+from logging import getLogger
 from typing import Optional, Set
 
 from packaging.version import parse as parse_version
@@ -9,11 +10,13 @@
     EmailStr,
     Field,
     TypeAdapter,
+    ValidationError,
     field_validator,
 )
 from typing_extensions import Annotated
 
 EMailAddress = TypeAdapter(EmailStr)
+logger = getLogger("somesy")
 
 
 class JuliaConfig(BaseModel):
@@ -48,15 +51,25 @@ def validate_version(cls, v):
     @field_validator("authors")
     @classmethod
     def validate_email_format(cls, v):
-        """Validate email format."""
+        """Validate person format, omit person that is not in correct format, don't raise an error."""
+        if v is None:
+            return []
+        validated = []
         for author in v:
-            if (
-                not isinstance(author, str)
-                or " " not in author
-                or not EMailAddress.validate_python(author.split(" ")[-1][1:-1])
-            ):
-                raise ValueError("Invalid email format")
-        return v
+            try:
+                if not (
+                    not isinstance(author, str)
+                    or " " not in author
+                    or not EMailAddress.validate_python(author.split(" ")[-1][1:-1])
+                ):
+                    validated.append(author)
+                else:
+                    logger.warning(
+                        f"Invalid email format for author {author}, omitting."
+                    )
+            except ValidationError:
+                logger.warning(f"Invalid format for author {author}, omitting.")
+        return validated
 
     @field_validator("uuid")
     @classmethod

src/somesy/julia/writer.py

@@ -54,9 +54,13 @@ def _from_person(person: Person):
         return person.to_name_email_string()
 
     @staticmethod
-    def _to_person(person_obj: str) -> Person:
+    def _to_person(person_obj) -> Optional[Person]:
         """Parse name+email string to a Person."""
-        return Person.from_name_email_string(person_obj)
+        try:
+            return Person.from_name_email_string(person_obj)
+        except (ValueError, AttributeError):
+            logger.warning(f"Cannot convert {person_obj} to Person object.")
+            return None
 
     def sync(self, metadata: ProjectMetadata) -> None:
         """Sync output file with other metadata files."""

src/somesy/mkdocs/writer.py

@@ -62,13 +62,11 @@ def save(self, path: Optional[Path] = None) -> None:
     @property
     def authors(self):
         """Return the only author from the source file as list."""
-        authors = []
-        try:
-            self._to_person(self._get_property(self._get_key("authors")))
-            authors = [self._get_property(self._get_key("authors"))]
-        except AttributeError:
-            logger.warning("Cannot convert authors to Person object.")
-        return authors
+        authors = self._get_property(self._get_key("authors"))
+        if authors is None or self._to_person(authors) is None:
+            return []
+        else:
+            return [authors]
 
     @authors.setter
     def authors(self, authors: List[Person]) -> None:
@@ -82,9 +80,13 @@ def _from_person(person: Person):
         return person.to_name_email_string()
 
     @staticmethod
-    def _to_person(person: str):
+    def _to_person(person: str) -> Optional[Person]:
         """MkDocs Person is a string with full name."""
-        return Person.from_name_email_string(person)
+        try:
+            return Person.from_name_email_string(person)
+        except (ValueError, AttributeError):
+            logger.warning(f"Cannot convert {person} to Person object.")
+            return None
 
     def sync(self, metadata: ProjectMetadata) -> None:
         """Sync the MkDocs object with the ProjectMetadata object."""

src/somesy/package_json/models.py

@@ -1,13 +1,16 @@
 """package.json validation models."""
 
 import re
+from logging import getLogger
 from typing import List, Optional, Union
 
 from pydantic import BaseModel, EmailStr, Field, field_validator
 from typing_extensions import Annotated
 
 from somesy.core.types import HttpUrlStr
 
+logger = getLogger("somesy")
+
 
 class PackageAuthor(BaseModel):
     """Package author model."""
@@ -74,7 +77,7 @@ class PackageJsonConfig(BaseModel):
 
     # convert package author to dict if it is a string
     @classmethod
-    def convert_author(cls, author: str) -> PackageAuthor:
+    def convert_author(cls, author: str) -> Optional[PackageAuthor]:
         """Convert author string to PackageAuthor model."""
         # parse author string to "name <email> (url)" format with regex
         author_match = re.match(NPM_PKG_AUTHOR, author)
@@ -84,6 +87,8 @@ def convert_author(cls, author: str) -> PackageAuthor:
         author_email = author_match[2]
         author_url = author_match[3]
 
+        if author_email is None:
+            return None
         return PackageAuthor(name=author_name, email=author_email, url=author_url)
 
     @field_validator("name")
@@ -116,7 +121,17 @@ def validate_people(cls, v):
         people = []
         for p in v:
             if isinstance(p, str):
-                people.append(cls.convert_author(p))
-            else:
+                author = cls.convert_author(p)
+                if author is not None:
+                    people.append(cls.convert_author(p))
+                else:
+                    logger.warning(
+                        f"Invalid email format for maintainer/contributor {p}, omitting."
+                    )
+            elif p.email is not None:
                 people.append(p)
+            else:
+                logger.warning(
+                    f"Invalid email format for maintainer/contributor {p}, omitting."
+                )
         return people

src/somesy/package_json/writer.py

@@ -35,6 +35,12 @@ def __init__(
     @property
     def authors(self):
         """Return the only author of the package.json file as list."""
+        # check if the author has the correct format
+        if isinstance(author := self._get_property(self._get_key("authors")), str):
+            author = PackageJsonConfig.convert_author(author)
+            if author is None:
+                return []
+
         return [self._get_property(self._get_key("authors"))]
 
     @authors.setter
@@ -43,10 +49,49 @@ def authors(self, authors: List[Person]) -> None:
         authors = self._from_person(authors[0])
         self._set_property(self._get_key("authors"), authors)
 
+    @property
+    def maintainers(self):
+        """Return the maintainers of the package.json file."""
+        # check if the maintainer has the correct format
+        maintainers = self._get_property(self._get_key("maintainers"))
+        # return empty list if maintainers is None
+        if maintainers is None:
+            return []
+
+        maintainers_valid = []
+
+        for maintainer in maintainers:
+            if isinstance(maintainer, str):
+                maintainer = PackageJsonConfig.convert_author(maintainer)
+                if maintainer is None:
+                    continue
+            maintainers_valid.append(maintainer)
+        return maintainers_valid
+
+    @maintainers.setter
+    def maintainers(self, maintainers: List[Person]) -> None:
+        """Set the maintainers of the project."""
+        maintainers = [self._from_person(m) for m in maintainers]
+        self._set_property(self._get_key("maintainers"), maintainers)
+
     @property
     def contributors(self):
         """Return the contributors of the package.json file."""
-        return self._get_property(self._get_key("contributors"))
+        # check if the contributor has the correct format
+        contributors = self._get_property(self._get_key("contributors"))
+        # return empty list if contributors is None
+        if contributors is None:
+            return []
+
+        contributors_valid = []
+
+        for contributor in contributors:
+            if isinstance(contributor, str):
+                contributor = PackageJsonConfig.convert_author(contributor)
+                if contributor is None:
+                    continue
+            contributors_valid.append(contributor)
+        return contributors_valid
 
     @contributors.setter
     def contributors(self, contributors: List[Person]) -> None:
@@ -91,9 +136,12 @@ def _to_person(person) -> Person:
         """Convert package.json dict or str for person format to project metadata person object."""
         if isinstance(person, str):
             # parse from package.json format
-            person = PackageJsonConfig.convert_author(person).model_dump(
-                exclude_none=True
-            )
+            person = PackageJsonConfig.convert_author(person)
+
+            if person is None:
+                return None
+
+            person = person.model_dump(exclude_none=True)
 
         names = list(map(lambda s: s.strip(), person["name"].split()))
         person_obj = {