From 21d8033dc560794b8eb8b58a693e30f4d154554e Mon Sep 17 00:00:00 2001 From: falexwolf Date: Sun, 16 Dec 2018 04:24:57 +0000 Subject: [PATCH] changed default: compression=None in write --- anndata/base.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/anndata/base.py b/anndata/base.py index db4cce061..ccc0c1ef0 100644 --- a/anndata/base.py +++ b/anndata/base.py @@ -1917,7 +1917,7 @@ def _check_dimensions(self, key=None): def write_h5ad( self, filename: Optional[PathLike] = None, - compression: Optional[str] = 'gzip', + compression: Optional[str] = None, compression_opts: Union[int, Any] = None, force_dense: Optional[bool] = None ): @@ -1925,7 +1925,8 @@ def write_h5ad( .. note:: - Setting compression to `None` can dramatically speed up writing. + Setting compression to `'gzip'` can save disk space but will slow + down writing and subsequent reading. Parameters ---------- @@ -1945,12 +1946,12 @@ def write_h5ad( raise ValueError('Provide a filename!') if filename is None: filename = self.filename - if force_dense is None: force_dense = True if self.isbacked else False - _write_h5ad(filename, self, compression=compression, compression_opts=compression_opts, - force_dense=force_dense) + _write_h5ad(filename, self, compression=compression, + compression_opts=compression_opts, force_dense=force_dense) + if self.isbacked: self.file.close()