Merge branch 'main' into add-logical-support

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
   - id: check-yaml
   - id: check-added-large-files
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.7
+  rev: v0.6.7
   hooks:
   - id: ruff
     args: [--fix]

README.md

@@ -102,7 +102,7 @@ Works()["W2741809807"]["open_access"]
 The previous works also for Authors, Sources, Institutions, Concepts and Topics
 
 ```python
-Authors()["A2887243803"]
+Authors()["A5027479191"]
 Authors()["https://orcid.org/0000-0002-4297-0502"]  # same
 ```
 
@@ -115,7 +115,6 @@ Works().random()
 Authors().random()
 Sources().random()
 Institutions().random()
-Concepts().random()
 Topics().random()
 Publishers().random()
 Funders().random()
@@ -354,11 +353,27 @@ Works()["W2023271753"].ngrams()
 ```
 
 
+### Serialize
+
+All results from PyAlex can be serialized. For example, save the results to a JSON file:
+
+```python
+import json
+from pathlib import Path
+from pyalex import Work
+
+with open(Path("works.json"), "w") as f:
+    json.dump(Works().get(), f)
+
+with open(Path("works.json")) as f:
+    works = [Work(w) for w in json.load(f)]
+```
+
 ## Code snippets
 
 A list of awesome use cases of the OpenAlex dataset.
 
-### Cited publications (referenced works)
+### Cited publications (works referenced by this paper, outgoing citations)
 
 ```python
 from pyalex import Works
@@ -369,6 +384,13 @@ w = Works()["W2741809807"]
 Works()[w["referenced_works"]]
 ```
 
+### Citing publications (other works that reference this paper, incoming citations)
+
+```
+from pyalex import Works
+Works().filter(cites="W2741809807").get()
+```
+
 ### Get works of a single author
 
 ```python
@@ -427,6 +449,7 @@ R users can use the excellent [OpenAlexR](https://github.com/ropensci/openalexR)
 
 > This library is a community contribution. The authors of this Python library aren't affiliated with OpenAlex.
 
+This library is maintained by [J535D165](https://github.com/J535D165) and [PeterLombaers](https://github.com/PeterLombaers).
 Feel free to reach out with questions, remarks, and suggestions. The
-[issue tracker](/issues) is a good starting point. You can also email me at
+[issue tracker](/issues) is a good starting point. You can also reach out via
 [[email protected]](mailto:[email protected]).

pyalex/api.py

@@ -23,7 +23,7 @@ def __setattr__(self, key, value):
 config = AlexConfig(
     email=None,
     api_key=None,
-    user_agent="pyalex/{__version__}",
+    user_agent=f"pyalex/{__version__}",
     openalex_url="https://api.openalex.org",
     max_retries=0,
     retry_backoff_factor=0.1,

tests/test_pyalex.py

@@ -216,7 +216,8 @@ def test_referenced_works():
     )
 
     assert set([w["id"] for w in w_new]).difference(set(w["referenced_works"])) == set()
-    # assert set(w["referenced_works"]).difference(set([w["id"] for w in w_new])) == set()
+    # assert set(w["referenced_works"]).difference(set([w["id"] for w in w_new]))
+    #  == set()
 
     assert m["count"] < len(w["referenced_works"])
 
@@ -252,12 +253,25 @@ def test_serializable(tmpdir):
         assert "W4238809453" in json.load(f)["id"]
 
 
+def test_serializable_list(tmpdir):
+    with open(Path(tmpdir, "test.json"), "w") as f:
+        json.dump(Works().get(), f)
+
+    with open(Path(tmpdir, "test.json")) as f:
+        works = [Work(w) for w in json.load(f)]
+
+    assert len(works) == 25
+    assert all(isinstance(w, Work) for w in works)
+
+
+@pytest.mark.skip("This test is not working due to unavailable API.")
 def test_ngrams_without_metadata():
     r = Works()["W2023271753"].ngrams(return_meta=False)
 
     assert len(r) == 1068
 
 
+@pytest.mark.skip("This test is not working due to unavailable API.")
 def test_ngrams_with_metadata():
     r, meta = Works()["W2023271753"].ngrams(return_meta=True)