Update gtfparse version requirement (#118)

* Update gtfparse version requirement In 00ece88, gtfparse version was pinned to <2 because of conflicts between gtfparse and recent versions of polars. Since 12/21/23, with gtfparse v. 2.1.0, the conflicts have been eliminated, so there is no need to keep older versions pinned. * Convert polars GTF to pandas --------- Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]>
icbi-lab · Dec 28, 2023 · 527284c · 527284c
1 parent 7badb5c
commit 527284c
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -26,7 +26,7 @@ dependencies = [
     'numpy>=1.20', # includes type annotations
     'tqdm>=4.63.0', # fixes tqdm.auto
     'pytoml',
-    'gtfparse<2',
+    'gtfparse>=2.1',
     'pycairo>=1.20; sys_platform == "win32"',
     'leidenalg',
     'pyreadr',

diff --git a/src/infercnvpy/io/_genepos.py b/src/infercnvpy/io/_genepos.py
@@ -38,7 +38,9 @@ def genomic_position_from_gtf(
     inplace
         If True, add the annotations directly to adata, otherwise return a dataframe.
     """
-    gtf = gtfparse.read_gtf(gtf_file, usecols=["seqname", "feature", "start", "end", "gene_id", "gene_name"])
+    gtf = gtfparse.read_gtf(
+        gtf_file, usecols=["seqname", "feature", "start", "end", "gene_id", "gene_name"]
+    ).to_pandas()
     gtf = (
         gtf.loc[
             gtf["feature"] == "gene",