Fix incompatibility with latest vdjdb release (#578)

* Fix incompatibility with latest vdjdb release * Update changelog
scverse · Dec 5, 2024 · 51df89e · 51df89e
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diff --git a/.gitignore b/.gitignore
@@ -138,3 +138,5 @@ dmypy.json
 .pyre/
 
 .DS_Store
+
+uv.lock
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [Unreleased]
+## v0.20.0
 
 ### Backwards-incompatible changes
 
@@ -19,8 +19,12 @@ and this project adheres to [Semantic Versioning][].
 
 ### Additions
 
--   The function `pl.logoplot_cdr3_motif` has been added that allows to plot sequence logos of
-    CDR3 sequences using [logomaker](https://logomaker.readthedocs.io/en/latest/) ([#534](https://github.com/scverse/scirpy/pull/534))
+-   Add `pl.logoplot_cdr3_motif` that allows to plot sequence logos of
+    CDR3 sequences using [logomaker](https://logomaker.readthedocs.io/en/latest/) ([#534](https://github.com/scverse/scirpy/pull/534)).
+
+### Fixes
+
+-   Make `datasets.vdjdb` compatible with the latest release of VDJDB ([#578](https://github.com/scverse/scirpy/pull/578)).
 
 ### Documentation
 

diff --git a/docs/tutorials/tutorial_3k_tcr.ipynb b/docs/tutorials/tutorial_3k_tcr.ipynb
diff --git a/src/scirpy/datasets/__init__.py b/src/scirpy/datasets/__init__.py
@@ -186,7 +186,7 @@ def vdjdb(cached: bool = True, *, cache_path="data/vdjdb.h5ad") -> AnnData:
         urllib.request.urlretrieve(url, d / "vdjdb.tar.gz")
         with zipfile.ZipFile(d / "vdjdb.tar.gz") as zf:
             zf.extractall(d)
-        df = pd.read_csv(d / "vdjdb_full.txt", sep="\t", low_memory=False)
+        df = pd.read_csv(next(iter(d.glob("**/vdjdb_full.txt"))), sep="\t", low_memory=False)
 
     tcr_cells = []
     for idx, row in tqdm(df.iterrows(), total=df.shape[0], desc="Processing VDJDB entries"):
@@ -245,7 +245,6 @@ def vdjdb(cached: bool = True, *, cache_path="data/vdjdb.h5ad") -> AnnData:
             "meta.donor.MHC",
             "meta.donor.MHC.method",
             "meta.structure.id",
-            "vdjdb.score",
         ]
         for f in INCLUDE_CELL_METADATA_FIELDS:
             cell[f] = row[f]
Original file line number	Diff line number	Diff line change
Expand Up		@@ -138,3 +138,5 @@ dmypy.json
		.pyre/

		.DS_Store

		uv.lock