From a624efff297336a9483ba7ea45368b16ea9d629e Mon Sep 17 00:00:00 2001
From: Oscar Arbelaez <oscar@arbelaez.dev>
Date: Sat, 28 Jun 2025 09:33:04 +0100
Subject: [PATCH 1/3] Fix issue with typer

---
 pyproject.toml  |  4 ++--
 src/bibx/cli.py | 13 ++++++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index bd8ca4c..543915c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "networkx~=3.0",
     "pydantic~=2.10.6",
     "requests~=2.32.3",
-    "typer[all]~=0.9.0",
+    "typer[all]~=0.16.0",
 ]
 requires-python = ">=3.9"
 classifiers = [
@@ -44,7 +44,7 @@ dev = [
 ]
 
 [project.scripts]
-bibx = "bibx.cli:app"
+bibx = "bibx.cli:main"
 
 [tool.ruff.lint]
 select = [
diff --git a/src/bibx/cli.py b/src/bibx/cli.py
index ad391e9..189b3ef 100644
--- a/src/bibx/cli.py
+++ b/src/bibx/cli.py
@@ -21,7 +21,7 @@
 
 
 @app.callback()
-def main(
+def set_verbose(
     verbose: Annotated[  # noqa: FBT002
         bool, typer.Option("--verbose", "-v", help="Enable verbose logging.")
     ] = False,
@@ -99,14 +99,8 @@ def openalex(
         help="how to handle references",
         default=EnrichReferences.BASIC,
     ),
-    verbose: bool = typer.Option(
-        help="be more verbose",
-        default=False,
-    ),
 ) -> None:
     """Run the sap algorithm on a seed file of any supported format."""
-    if verbose:
-        logging.basicConfig(level=logging.INFO)
     c = query_openalex(" ".join(query), enrich=enrich)
     s = Sap()
     graph = s.create_graph(c)
@@ -115,5 +109,10 @@ def openalex(
     rprint(graph)
 
 
+def main() -> None:
+    """Entry point for the CLI."""
+    app()
+
+
 if __name__ == "__main__":
     app()

From bf8af29ce21894875d16217cef8f1c597df36efd Mon Sep 17 00:00:00 2001
From: Oscar Arbelaez <oscar@arbelaez.dev>
Date: Sat, 28 Jun 2025 09:33:34 +0100
Subject: [PATCH 2/3] Fix issue with files without id

---
 src/bibx/builders/wos.py | 4 ++--
 src/bibx/collection.py   | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/bibx/builders/wos.py b/src/bibx/builders/wos.py
index 43273ac..c46decb 100644
--- a/src/bibx/builders/wos.py
+++ b/src/bibx/builders/wos.py
@@ -261,7 +261,7 @@ def __init__(self, *isi_files: TextIO) -> None:
     def build(self) -> Collection:
         """Build a collection of articles from Web of Science (WoS) ISI files."""
         articles = self._get_articles_from_files()
-        return Collection(list(articles))
+        return Collection(Collection.deduplicate_articles(list(articles)))
 
     def _get_articles_as_str_from_files(self) -> Iterable[str]:
         for file in self._files:
@@ -369,7 +369,7 @@ def _parse(cls, key: str, value: list[str]) -> dict:
         if key in cls.FIELDS:
             field = cls.FIELDS[key]
             parsed_value = field.parse(value)
-            return {new_key: parsed_value for new_key in [field.key, *field.aliases]}
+            return dict.fromkeys([field.key, *field.aliases], parsed_value)
 
         logger.debug("Found an unknown field with key %s and value %s", key, value)
         return {key: _ident(value)}
diff --git a/src/bibx/collection.py b/src/bibx/collection.py
index fc33677..48c91f3 100644
--- a/src/bibx/collection.py
+++ b/src/bibx/collection.py
@@ -46,6 +46,8 @@ def _uniqe_articles_by_id(cls, articles: list[Article]) -> dict[str, Article]:
         graph = nx.Graph()
         id_to_article: defaultdict[str, list[Article]] = defaultdict(list)
         for article in cls._all_articles(articles):
+            if not article.ids:
+                continue
             first, *rest = article.ids
             # Add a loop edge so that the unique articles are included
             graph.add_edge(first, first)
@@ -74,7 +76,7 @@ def _uniqe_articles_by_id(cls, articles: list[Article]) -> dict[str, Article]:
                     articles.append(article)
                     visited.add(id(article))
             merged = reduce(Article.merge, articles)
-            article_by_id.update({id_: merged for id_ in ids})
+            article_by_id.update(dict.fromkeys(ids, merged))
 
         return article_by_id
 

From 571c9054d1a673e3a2e3e3acb50ff7e282cf0ee3 Mon Sep 17 00:00:00 2001
From: Oscar Arbelaez <oscar@arbelaez.dev>
Date: Sat, 28 Jun 2025 10:40:26 +0100
Subject: [PATCH 3/3] Update version

---
 src/bibx/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bibx/__init__.py b/src/bibx/__init__.py
index 4b8d583..5cef193 100644
--- a/src/bibx/__init__.py
+++ b/src/bibx/__init__.py
@@ -28,7 +28,7 @@
     "read_wos",
 ]
 
-__version__ = "0.6.3"
+__version__ = "0.7.0"
 
 
 def query_openalex(