Merge branch 'release/0.16.4'

Author: siebrenf

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.16.4] - 2026-06-09
+
+### Changed
+- automatically remove old cache directories
+
+### Fixed
+- adapted to a change in NCBI metadata (`ftp_path` now has a trailing slash)
+
 ## [0.16.3] - 2025-09-30
 
 ### Changed
@@ -502,6 +510,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `-r` and `--match/--no-match` option to select sequences by regex.
 
 [Unreleased]: https://github.com/vanheeringen-lab/genomepy/compare/master...develop
+[0.16.4]: https://github.com/vanheeringen-lab/genomepy/compare/0.16.3...0.16.4
 [0.16.3]: https://github.com/vanheeringen-lab/genomepy/compare/0.16.2...0.16.3
 [0.16.2]: https://github.com/vanheeringen-lab/genomepy/compare/0.16.1...0.16.2
 [0.16.1]: https://github.com/vanheeringen-lab/genomepy/compare/0.16.0...0.16.1

docs/release_checklist.md

@@ -31,6 +31,7 @@
     ```shell
     pip install uv
     uv pip install hatch 
+    rm -rf dist
     hatch build -t wheel
     uv pip install --system dist/*.whl --force-reinstall
 

genomepy/__about__.py

@@ -1,6 +1,6 @@
 """Metadata"""
 
-__version__ = "0.16.3"
+__version__ = "0.16.4"
 __author__ = (
     "Siebren Frölich, Maarten van der Sande, Tilman Schäfers and Simon van Heeringen"
 )

genomepy/caching.py

@@ -25,6 +25,15 @@ def _cast(var):
 cache_exp_other = _cast(config.get("cache_exp_other", 3.6e3))
 cache_exp_genomes = _cast(config.get("cache_exp_genomes", 6.048e5))
 
+# remove old cache directories
+if os.path.exists(user_cache_dir("genomepy")):
+    for version in os.listdir(user_cache_dir("genomepy")):
+        genomepy_cache_dir = os.path.join(user_cache_dir("genomepy"), version)
+        cache_age = time() - os.stat(genomepy_cache_dir).st_mtime
+        if cache_age > cache_exp_genomes:
+            rm_rf(genomepy_cache_dir)
+
+# create a cache directory
 genomepy_cache_dir = os.path.join(user_cache_dir("genomepy"), __version__)
 os.makedirs(genomepy_cache_dir, exist_ok=True)
 

genomepy/providers/ncbi.py

@@ -192,11 +192,13 @@ def _ftp_or_html_link(self, name, file_suffix, skip_check=False):
         NCBI's files are accessible over FTP and HTTPS
         Try HTTPS first and return the first functioning link
         """
-        genome = self.genomes[safe(name)]
-        ftp_link = genome["ftp_path"]
+        ftp_link = self.genomes[safe(name)]["ftp_path"]
+        # add a trailing slash, if missing
+        if ftp_link[-1] != "/":
+            ftp_link += "/"
         html_link = ftp_link.replace("ftp://", "https://")
         for link in [html_link, ftp_link]:
-            link += "/" + link.split("/")[-1] + file_suffix
+            link += link.split("/")[-2] + file_suffix
 
             if skip_check or check_url(link, max_tries=2, timeout=10):
                 return link

tests/test_13_annotation.py

@@ -111,7 +111,7 @@ def test_named_gtf():
     df = a.named_gtf
     assert df.index.name == "gene_name"
     assert str(a.gtf.index.dtype) == "int64"
-    assert str(df.index.dtype) == "object"
+    assert str(df.index.dtype) in ["object", "str"]  # pandas v2 == object, v3 == str
     assert set(df.at["YDL248W", "seqname"]) == {"chrIV"}