SPIMprep/pixi.toml at main · khanlab/SPIMprep · GitHub

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[workspace]
authors = ["Ali Khan <alik@robarts.ca>"]
channels = ["conda-forge", "bioconda", "ome"]
name = "SPIMprep"
platforms = ["linux-64"]
version = "0.1.0"

[tasks]

# A single “umbrella” task that chains three of the above:
test_localout = """
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_local.tsv root=bids && \
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_gcs.tsv    root=bids && \
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_local.tsv root=bids use_zipstore=True
"""

test_gcsout = """
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_local.tsv root='gcs://khanlab-lightsheet/data/test_bids' && \
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_gcs.tsv    root='gcs://khanlab-lightsheet/data/test_bids' && \
  snakemake --dry-run --config samples=testing/dryrun_tests/samples_local.tsv root='gcs://khanlab-lightsheet/data/test_bids' use_zipstore=True
"""

quality_check = "isort --profile black workflow plugins/*.py -c && black workflow --check && snakefmt workflow --check"
quality_fix = "isort --profile black workflow plugins/*.py && black workflow  && snakefmt workflow"

[feature.runtime.dependencies]
snakemake = ">=9.5.1,<10"
snakebids = ">=0.14.0,<0.15"
snakemake-storage-plugin-s3 = ">=0.3.3,<0.4"
snakemake-storage-plugin-gcs = ">=1.1.4,<2"
gcsfs = ">=2025.5.1,<2026"
s3fs = ">=2025.5.1,<2026"
universal-pathlib = ">=0.2.6,<0.3"
zarr = ">=3.0.8,<4"
dask = ">=2025.5.1,<2026"
tifffile = ">=2025.6.1,<2026"
conda = ">=25.5.0,<26"
xmltodict = ">=0.14.2,<0.15"
bioformats2raw = ">=0.9.4,<0.10"
snakemake-executor-plugin-slurm = ">=1.4.0,<2"
snakemake-storage-plugin-fs = ">=1.1.2,<2"
markdown-it-py = "<4"
docutils = "<0.22"

[feature.dev.dependencies]
black   = "*"
isort   = "*"
snakefmt = "*"
pytest  = "*"

[environments.default]
features = ["runtime"]

[environments.dev]
features = ["runtime", "dev"]

[environments.dev-only]
features = ["dev"]

[pypi-dependencies]
ngff-zarr = { version = ">=0.18.1,<0.19", extras = ["all"] }
zarrnii = ">=0.8.0a1,<0.9.0"