rename some modules

.github/workflows/cd.yml

@@ -20,7 +20,7 @@ jobs:
         uses: astral-sh/setup-uv@v2
         with:
           enable-cache: true
-          version: "0.6.0"
+          version: "0.8.13"
 
       - name: Install dependencies
         run: |

.github/workflows/ci.yml

@@ -13,11 +13,11 @@ jobs:
     name: CI for ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     env:
-      USING_COVERAGE: "3.9,3.13"
+      USING_COVERAGE: "3.11,3.13"
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4
@@ -30,7 +30,7 @@ jobs:
         uses: astral-sh/setup-uv@v2
         with:
           enable-cache: true
-          version: "0.6.0"
+          version: "0.8.13"
 
       - name: Run tests for ${{ matrix.python-version }}
         run: |

pyproject.toml

@@ -12,10 +12,10 @@ dependencies = [
     "bibtexparser~=1.4.0",
     "networkx~=3.0",
     "pydantic~=2.11.7",
-    "requests~=2.32.3",
-    "typer~=0.16.0",
+    "requests~=2.32.5",
+    "typer~=0.17.3",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
@@ -39,8 +39,8 @@ dev = [
     "pre-commit~=4.3.0",
     "ruff~=0.12.11",
     "mypy~=1.17.1",
-    "types-requests>=2.32.0.20241016",
-    "ipython>=8.18.1",
+    "types-requests~=2.32.4.20250809",
+    "ipython~=9.5.0",
 ]
 
 [project.scripts]
@@ -116,7 +116,7 @@ path = "src/bibx/__init__.py"
 
 [tool.tox]
 requires = ["tox>=4.24.2"]
-env_list = ["3.9", "3.10", "3.11", "3.12", "3.13"]
+env_list = ["3.11", "3.12", "3.13"]
 
 [tool.tox.env_run_base]
 deps = [

src/bibx/__init__.py

@@ -4,14 +4,14 @@
 from typing import TextIO
 
 from bibx.algorithms.sap import Sap
-from bibx.article import Article
-from bibx.builders.openalex import EnrichReferences, OpenAlexCollectionBuilder
-from bibx.builders.scopus_bib import ScopusBibCollectionBuilder
-from bibx.builders.scopus_csv import ScopusCsvCollectionBuilder
-from bibx.builders.scopus_ris import ScopusRisCollectionBuilder
-from bibx.builders.wos import WosCollectionBuilder
-from bibx.collection import Collection
 from bibx.exceptions import BibXError
+from bibx.models.article import Article
+from bibx.models.collection import Collection
+from bibx.sources.openalex import EnrichReferences, OpenAlexSource
+from bibx.sources.scopus_bib import ScopusBibSource
+from bibx.sources.scopus_csv import ScopusCsvSource
+from bibx.sources.scopus_ris import ScopusRisSource
+from bibx.sources.wos import WosSource
 
 logger = logging.getLogger(__name__)
 
@@ -28,7 +28,7 @@
     "read_wos",
 ]
 
-__version__ = "0.7.2"
+__version__ = "0.8.0"
 
 
 def query_openalex(
@@ -37,7 +37,7 @@ def query_openalex(
     enrich: EnrichReferences = EnrichReferences.BASIC,
 ) -> Collection:
     """Query OpenAlex and return a collection."""
-    return OpenAlexCollectionBuilder(query, limit, enrich=enrich).build()
+    return OpenAlexSource(query, limit, enrich=enrich).build()
 
 
 def read_scopus_bib(*files: TextIO) -> Collection:
@@ -46,7 +46,7 @@ def read_scopus_bib(*files: TextIO) -> Collection:
     :param files: Scopus bib files open.
     :return: the collection
     """
-    return ScopusBibCollectionBuilder(*files).build()
+    return ScopusBibSource(*files).build()
 
 
 def read_scopus_ris(*files: TextIO) -> Collection:
@@ -55,7 +55,7 @@ def read_scopus_ris(*files: TextIO) -> Collection:
     :param files: Scopus bib files open.
     :return: the collection
     """
-    return ScopusRisCollectionBuilder(*files).build()
+    return ScopusRisSource(*files).build()
 
 
 def read_scopus_csv(*files: TextIO) -> Collection:
@@ -64,7 +64,7 @@ def read_scopus_csv(*files: TextIO) -> Collection:
     :param files: Scopus csv files open.
     :return: the collection
     """
-    return ScopusCsvCollectionBuilder(*files).build()
+    return ScopusCsvSource(*files).build()
 
 
 def read_wos(*files: TextIO) -> Collection:
@@ -73,7 +73,7 @@ def read_wos(*files: TextIO) -> Collection:
     :param files: WoS files open.
     :return: the collection
     """
-    return WosCollectionBuilder(*files).build()
+    return WosSource(*files).build()
 
 
 def read_any(file: TextIO) -> Collection:

src/bibx/algorithms/sap.py

@@ -4,8 +4,8 @@
 import networkx as nx
 from networkx.algorithms.community.louvain import louvain_communities
 
-from bibx.article import Article
-from bibx.collection import Collection
+from bibx.models.article import Article
+from bibx.models.collection import Collection
 
 YEAR = "year"
 LEAF = "leaf"

src/bibx/cli.py

@@ -15,7 +15,7 @@
     read_wos,
 )
 from bibx.algorithms.sap import Sap
-from bibx.builders.openalex import EnrichReferences
+from bibx.sources.openalex import EnrichReferences
 
 app = typer.Typer()
 

src/bibx/clients/openalex.py

@@ -1,7 +1,6 @@
 import logging
 from concurrent.futures import ThreadPoolExecutor, as_completed, wait
 from enum import Enum
-from typing import Optional, Union
 
 import requests
 from pydantic import BaseModel, ValidationError
@@ -29,7 +28,7 @@ class Author(BaseModel):
 
     id: str
     display_name: str
-    orcid: Optional[str] = None
+    orcid: str | None = None
 
 
 class WorkAuthorship(BaseModel):
@@ -51,10 +50,10 @@ class WorkKeyword(BaseModel):
 class WorkBiblio(BaseModel):
     """Work bibliographic information from the openalex API."""
 
-    volume: Optional[str] = None
-    issue: Optional[str] = None
-    first_page: Optional[str] = None
-    last_page: Optional[str] = None
+    volume: str | None = None
+    issue: str | None = None
+    first_page: str | None = None
+    last_page: str | None = None
 
 
 class WorkLocationSource(BaseModel):
@@ -69,25 +68,25 @@ class WorkLoacation(BaseModel):
     """Location of the work from the openalex API."""
 
     is_oa: bool
-    landing_page_url: Optional[str] = None
-    pdf_url: Optional[str] = None
-    source: Optional[WorkLocationSource]
+    landing_page_url: str | None = None
+    pdf_url: str | None = None
+    source: WorkLocationSource | None
 
 
 class Work(BaseModel):
     """A work from the openalex API."""
 
     id: str
     ids: dict[str, str]
-    doi: Optional[str] = None
-    title: Optional[str] = None
+    doi: str | None = None
+    title: str | None = None
     publication_year: int
     authorships: list[WorkAuthorship]
     cited_by_count: int
     keywords: list[WorkKeyword]
     referenced_works: list[str]
     biblio: WorkBiblio
-    primary_location: Optional[WorkLoacation] = None
+    primary_location: WorkLoacation | None = None
 
 
 class ResponseMeta(BaseModel):
@@ -110,8 +109,8 @@ class OpenAlexClient:
 
     def __init__(
         self,
-        base_url: Optional[str] = None,
-        email: Optional[str] = None,
+        base_url: str | None = None,
+        email: str | None = None,
     ) -> None:
         self.base_url = base_url or "https://api.openalex.org"
         self.session = requests.Session()
@@ -124,7 +123,7 @@ def __init__(
             }
         )
 
-    def _fetch_works(self, params: dict[str, Union[str, int]]) -> WorkResponse:
+    def _fetch_works(self, params: dict[str, str | int]) -> WorkResponse:
         response = self.session.get(
             f"{self.base_url}/works",
             params=params,

src/bibx/models/__init__.py

@@ -0,0 +1 @@
+"""Models for the bibx package."""

src/bibx/article.py → src/bibx/models/article.py

@@ -1,6 +1,6 @@
 from collections.abc import Mapping
 from dataclasses import dataclass, field
-from typing import Optional, TypeVar, Union
+from typing import TypeVar
 
 T = TypeVar("T")
 
@@ -20,15 +20,15 @@ class Article:
     label: str
     ids: set[str]
     authors: list[str] = field(default_factory=list)
-    year: Optional[int] = None
-    title: Optional[str] = None
-    journal: Optional[str] = None
-    volume: Optional[str] = None
-    issue: Optional[str] = None
-    page: Optional[str] = None
-    doi: Optional[str] = None
-    _permalink: Optional[str] = None
-    times_cited: Optional[int] = None
+    year: int | None = None
+    title: str | None = None
+    journal: str | None = None
+    volume: str | None = None
+    issue: str | None = None
+    page: str | None = None
+    doi: str | None = None
+    _permalink: str | None = None
+    times_cited: int | None = None
     references: list["Article"] = field(default_factory=list)
     keywords: list[str] = field(default_factory=list)
     sources: set[str] = field(default_factory=set)
@@ -61,7 +61,7 @@ def key(self) -> str:
         return next(iter(sorted(self.ids)))
 
     @property
-    def simple_label(self) -> Optional[str]:
+    def simple_label(self) -> str | None:
         """Return a simple label for the article."""
         pieces = {
             "AU": self.authors[0].replace(",", "") if self.authors else None,
@@ -76,7 +76,7 @@ def simple_label(self) -> Optional[str]:
         return ", ".join(value for value in pieces.values() if value)
 
     @property
-    def permalink(self) -> Optional[str]:
+    def permalink(self) -> str | None:
         """Return the permalink of the article."""
         if self._permalink is not None:
             return self._permalink
@@ -85,7 +85,7 @@ def permalink(self) -> Optional[str]:
         return None
 
     @property
-    def simple_id(self) -> Optional[str]:
+    def simple_id(self) -> str | None:
         """Return a simple ID for the article."""
         if not self.authors or self.year is None:
             return None
@@ -112,7 +112,7 @@ def set_simple_label(self) -> "Article":
 
     def info(
         self,
-    ) -> dict[str, Union[str, int, list[str], None]]:
+    ) -> dict[str, str | int | list[str] | None]:
         """Return a dictionary with the information of the article."""
         return {
             "permalink": self.permalink,

src/bibx/collection.py → src/bibx/models/collection.py

@@ -140,7 +140,7 @@ def published_by_year(self) -> dict[int, int]:
 
         :return: a dictionary with the number of articles published each year.
         """
-        current_year = datetime.datetime.now(datetime.timezone.utc).year
+        current_year = datetime.datetime.now(datetime.UTC).year
         years = {}
         for year in range(self._first_year, current_year + 1):
             years[year] = 0
@@ -164,7 +164,7 @@ def cited_by_year(self) -> dict[int, int]:
 
         :return: a dictionary with the number of citations each year.
         """
-        current_year = datetime.datetime.now(datetime.timezone.utc).year
+        current_year = datetime.datetime.now(datetime.UTC).year
         cited_items_per_year = {}
         for year in range(self._first_year, current_year + 1):
             cited_items_per_year[year] = 0

src/bibx/builders/base.py → src/bibx/sources/base.py

@@ -1,9 +1,9 @@
 from typing import Protocol
 
-from bibx.collection import Collection
+from bibx.models.collection import Collection
 
 
-class CollectionBuilder(Protocol):
+class Source(Protocol):
     """Protocol for classes that build collections of articles."""
 
     def build(self) -> Collection:

src/bibx/builders/openalex.py → src/bibx/sources/openalex.py

@@ -1,14 +1,13 @@
 import logging
 from collections import Counter
 from enum import Enum
-from typing import Optional
 from urllib.parse import urlparse
 
-from bibx.article import Article
 from bibx.clients.openalex import OpenAlexClient, Work
-from bibx.collection import Collection
+from bibx.models.article import Article
+from bibx.models.collection import Collection
 
-from .base import CollectionBuilder
+from .base import Source
 
 logger = logging.getLogger(__name__)
 
@@ -25,15 +24,15 @@ class EnrichReferences(Enum):
     FULL = "full"
 
 
-class OpenAlexCollectionBuilder(CollectionBuilder):
+class OpenAlexSource(Source):
     """Builder for collections of articles from the OpenAlex API."""
 
     def __init__(
         self,
         query: str,
         limit: int = 600,
         enrich: EnrichReferences = EnrichReferences.BASIC,
-        client: Optional[OpenAlexClient] = None,
+        client: OpenAlexClient | None = None,
     ) -> None:
         self.query = query
         self.limit = limit