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fix: update datasets with obsm keys that fail Seurat 5 regex requirements #708

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merged 5 commits into from
Dec 13, 2023
Merged

fix: update datasets with obsm keys that fail Seurat 5 regex requirements #708

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3decc75
fix: update datasets with obsm keys that fail Seurat 5 regex requirem…
nayib-jose-gloria Dec 13, 2023
fcf47e4
Bump version: 4.0.0 → 4.0.1-rc.0
nayib-jose-gloria Dec 13, 2023
2e1a621
Bump version: 4.0.1-rc.0 → 4.0.1-rc.0
nayib-jose-gloria Dec 13, 2023
b7e44ec
Bump version: 4.0.1-rc.0 → 4.0.1
nayib-jose-gloria Dec 13, 2023
be15dce
fix version
nayib-jose-gloria Dec 13, 2023
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 4.0.0
current_version = 4.0.1
commit = True
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
serialize =
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2 changes: 1 addition & 1 deletion cellxgene_schema_cli/cellxgene_schema/__init__.py
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@@ -1 +1 @@
__version__ = "4.0.0"
__version__ = "4.0.1"
3 changes: 3 additions & 0 deletions cellxgene_schema_cli/cellxgene_schema/migrate.py
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Expand Up @@ -132,6 +132,9 @@
if collection_id == "d17249d2-0e6e-4500-abb8-e6c93fa1ac6f" and dataset_id == "a5d5c529-8a1f-40b5-bda3-35208970070d":
dataset.obs.rename(columns={"tissue_type": "sample_tissue_type"}, inplace=True)

if collection_id == "dea97145-f712-431c-a223-6b5f565f362a":
dataset.obsm["X_Three-D"] = dataset.obsm.pop("X_3D")

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dataset.obs["tissue_type"] = "tissue"
dataset.obs["tissue_type"] = np.where(
dataset.obs.tissue_ontology_term_id.str.contains("(cell culture)"), "cell culture", dataset.obs["tissue_type"]
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2 changes: 1 addition & 1 deletion cellxgene_schema_cli/setup.py
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Expand Up @@ -5,7 +5,7 @@

setup(
name="cellxgene-schema",
version="4.0.0",
version="4.0.1",
url="https://github.com/chanzuckerberg/single-cell-curation",
license="MIT",
author="Chan Zuckerberg Initiative",
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