diff --git a/CHANGELOG.md b/CHANGELOG.md index ac7858f..235eee7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,30 @@ Notable changes to `adata-cli`. Versions are `MAJOR.MINOR.PATCH`; tags carry no `v` prefix. +## 0.11.1 + +Reads the looms other tools write, as found converting 29 real looms from +Baysor, R's LoomExperiment and anndata/loompy: all now convert, and match +`anndata.read_loom` where it can read them. + +### Fixed + +- **A `.loom` holding the matrix alone is read** + ([#59](https://github.com/cellgeni/adata-cli/pull/59)). Baysor writes some + looms as `/matrix` with no attribute groups, which were not recognised. + In a file named `.loom` that is now a loom, its cells and genes numbered; + a 7,979,604 x 8,729 one converted in 10.5 minutes at a 211 MB peak. + +- **Baysor's gene names are used** ([#59](https://github.com/cellgeni/adata-cli/pull/59)). + Baysor names genes in a `Name` attribute; its looms came out with + numbered genes. + +- **R's LoomExperiment looms read cleanly** ([#59](https://github.com/cellgeni/adata-cli/pull/59)). + The spec version, stored as a one-element array, showed as `['2.0.1']`, + and graph vertices stored as floats were truncated without a check; they + must now be whole numbers. loompy, and so `anndata.read_loom`, refuses + these files. + ## 0.11.0 Adds loom to `adata convert`, both ways. A velocyto, loompy or diff --git a/pyproject.toml b/pyproject.toml index 9fbeb90..8450fd9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ # so the distribution is published as `pyadata-cli`. The import package # and the command are both still `adata`. name = "pyadata-cli" -version = "0.11.0" +version = "0.11.1" description = "Streaming CLI for exploring and editing large AnnData .h5ad and .zarr stores" readme = "README.md" requires-python = ">=3.12" diff --git a/uv.lock b/uv.lock index c8c5b22..22fd276 100644 --- a/uv.lock +++ b/uv.lock @@ -486,7 +486,7 @@ wheels = [ [[package]] name = "pyadata-cli" -version = "0.11.0" +version = "0.11.1" source = { editable = "." } dependencies = [ { name = "h5py" },