Merge pull request #126 from GavinHuttley/develop

ENH: suppress verbose warnings from h5py

src/ensembl_lite/_db_base.py

@@ -1,5 +1,6 @@
 import contextlib
 import dataclasses
+import os
 import sqlite3
 
 from ensembl_lite._util import PathType, SerialisableMixin
@@ -147,16 +148,22 @@ def __setstate__(self, state):
  obj._file = None
 
  def __del__(self):
- with contextlib.suppress(ValueError, AttributeError):
- self._file.flush()
-
- with contextlib.suppress(AttributeError):
- self._file.close()
-
- self._is_open = False
+ self.close()
 
  def close(self):
- if self._is_open:
- self._file.flush()
- self._file.close()
+ """closes the hdf5 file"""
+ # hdf5 dumps content to stdout if resource already closed, so
+ # we trap that here, and capture expected exceptions raised in the process
+ with open(os.devnull, "w") as devnull:
+ with (
+ contextlib.redirect_stderr(devnull),
+ contextlib.redirect_stdout(devnull),
+ ):
+ with contextlib.suppress(ValueError, AttributeError):
+ if self._is_open:
+ self._file.flush()
+
+ with contextlib.suppress(AttributeError):
+ self._file.close()
+
  self._is_open = False

src/ensembl_lite/_genomedb.py

@@ -973,6 +973,8 @@ def get_gene_table_for_species(
  "score",
  "strand",
  "phase",
+ "symbol",
+ "description",
  )
  rows = []
  for i, record in enumerate(annot_db.get_records_matching(biotype="gene")):