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Build branch allow-compressed-output-bundles with version allow-compressed-output-bundles (f951825)

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Build pipeline: openpipelines-bio.openpipeline-spatial.allow-compressed-oumm2z7

Source commit: f951825e3f

Source message: cleanup
This commit is contained in:
CI
2025-08-27 16:53:27 +00:00
parent 008f51517b
commit cfb110c6bb
59 changed files with 452 additions and 115 deletions
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2
target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
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@@ -320,7 +320,7 @@ build_info:
output: "target/executable/convert/from_xenium_to_spatialdata"
executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
viash_version: "0.9.4"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

12
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
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@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1392,11 +1392,13 @@ from unzip_archived_folder import unzip_archived_folder
logger = setup_logger()
logger.info("Reading in Xenium data...")
if zipfile.is_zipfile(par["input"]):
par["input"] = unzip_archived_folder(par["input"])
if zipfile.is_zipfile(par["input"]):
xenium_output_bundle = unzip_archived_folder(par["input"])
else:
xenium_output_bundle = par["input"]
sdata = xenium(
par["input"],
xenium_output_bundle,
cells_boundaries=par["cells_boundaries"],
nucleus_boundaries=par["nucleus_boundaries"],
cells_as_circles=par["cells_as_circles"],