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Feature/lazy loading #114

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ca169e7
implement lazy loading functionalities
HolEv Apr 8, 2026
fc3aa1e
speed up lazy loading subsetting
HolEv Apr 8, 2026
c8559f9
add scatter plot function
HolEv Apr 8, 2026
e7a0972
allow lazy loading for G&C and h5ad and allow caching of var/obs even…
HolEv Apr 28, 2026
58a602e
updated formatting
HolEv Apr 28, 2026
aa4992a
add check for CSRDataset, CSCDataset for has lazy check
HolEv May 5, 2026
dd1a26b
address PR comments
HolEv May 5, 2026
66ed4cc
remove functions not relevant for this PR
HolEv May 5, 2026
eceaf0a
bump anndata version to match loading readwrite expectations (and app…
HolEv May 5, 2026
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35 changes: 17 additions & 18 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ classifiers = [
]
dependencies = [
"adjusttext",
"anndata",
"anndata>=0.12",
"bed-reader",
"dask",
"limix-core",
Expand All @@ -41,21 +41,16 @@ dependencies = [
"requests",
"rich",
"scanpy",
"xarray",
"zarr>=3",
# for debug logging (referenced from the issue template)
"session-info",
"xarray",
"zarr>=3",
]

optional-dependencies.datasets = [
"liftover",
"sgkit[plink]", # TODO cbgen is a pain to install on mac. I think cmake issues.
"bio2zarr[all]",
]

optional-dependencies.pgen = [
"pgenlib",
"zarr>3",
"liftover",
"sgkit[plink]", # TODO cbgen is a pain to install on mac. I think cmake issues.
]

optional-dependencies.dev = [
Expand All @@ -64,9 +59,9 @@ optional-dependencies.dev = [
]
optional-dependencies.doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"linkify-it-py",
"ipykernel",
"ipython",
"linkify-it-py",
"myst-nb>=1.1",
# Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"setuptools",
Expand All @@ -93,12 +88,21 @@ optional-dependencies.mixmil = [
optional-dependencies.ml = [
"pytorch-lightning",
]
optional-dependencies.pgen = [
"pgenlib",
"zarr>3",
]

optional-dependencies.rvat = [
# installation wit pip doesn't work, install via conda install -c conda-forge chiscore
# "chiscore",
"limix-core",
"pybiomart",
]
optional-dependencies.scdrs = [
"numpy<2",
"scdrs",
]
optional-dependencies.snpeff = [
# not available via pip, has to be installed via conda install bioconda::snpeff
# "snpeff",
Expand All @@ -107,10 +111,6 @@ optional-dependencies.tensorqtl = [
"tensorqtl",
#"plink2"
]
optional-dependencies.scdrs = [
"scdrs",
"numpy<2.0.0",
]
optional-dependencies.test = [
"coverage",
"pytest",
Expand All @@ -120,6 +120,8 @@ urls.Documentation = "https://cellink-docs.readthedocs.io/"
urls.Homepage = "https://github.com/theislab/cellink"
urls.Source = "https://github.com/theislab/cellink"

scripts.cellink-pgen = "cellink.cli.pgen:main"

[tool.hatch.build.targets.wheel]
packages = [ "src/cellink" ]

Expand Down Expand Up @@ -203,6 +205,3 @@ skip = [
"docs/references.md",
"docs/notebooks/example.ipynb",
]

[project.scripts]
cellink-pgen = "cellink.cli.pgen:main"
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