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Merged
merged 8 commits into from
Oct 13, 2020
Merged

sgkit-bgen merger #314

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53ca999
Move sgkit-bgen into main repo #256
eric-czech Oct 8, 2020
ccb2fb7
Improve docs+dtype handling and remove cachetools
eric-czech Oct 9, 2020
14210b2
Switch to pypi rechunker dependency
eric-czech Oct 9, 2020
8899b57
Suggested changes
eric-czech Oct 9, 2020
06c6b99
More docstring bgen capitalization
eric-czech Oct 9, 2020
ed9c070
Suggested changes
eric-czech Oct 10, 2020
7796448
Update relative imports
eric-czech Oct 13, 2020
f694b34
Merge branch 'master' into bgen_merger
mergify[bot] Oct 13, 2020
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2 changes: 2 additions & 0 deletions requirements-dev.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -13,5 +13,7 @@ scikit-learn
partd
fsspec
bed-reader
git+https://github.com/pangeo-data/rechunker.git
cbgen
cyvcf2; platform_system != "Windows"
yarl
9 changes: 7 additions & 2 deletions setup.cfg
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Expand Up @@ -57,6 +57,9 @@ vcf =
cyvcf2
fsspec
yarl
bgen =
rechunker
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why is this different than the dev-requirements? it can't be git based?

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I originally had it that way but it doesn't work when you pip install sgkit from github which then tries to pip install rechunker from github. I'm not sure why but I'm instead treating it as an "abstract" dependency for now (e.g. pyscaffold/pyscaffold#261 (comment)). https://github.com/pystatgen/sgkit/issues/321 for when the required changes are released.

cbgen

[coverage:report]
fail_under = 100
Expand Down Expand Up @@ -115,10 +118,12 @@ ignore_missing_imports = True
ignore_missing_imports = True
[mypy-setuptools]
ignore_missing_imports = True
[mypy-sgkit_plink.*]
ignore_missing_imports = True
[mypy-sklearn.*]
ignore_missing_imports = True
[mypy-cbgen.*]
ignore_missing_imports = True
[mypy-rechunker.*]
ignore_missing_imports = True
[mypy-bed_reader.*]
ignore_missing_imports = True
[mypy-sphinx.*]
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11 changes: 11 additions & 0 deletions sgkit/io/bgen/__init__.py
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@@ -0,0 +1,11 @@
try:
from .bgen_reader import bgen_to_zarr, read_bgen, rechunk_bgen # noqa: F401

__all__ = ["read_bgen", "bgen_to_zarr", "rechunk_bgen"]
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I don't know if we actually need those __all__ variables? in this case for example I think this doesn't change anything?

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I just did what you did with plink and tom with vcf. I plan on waiting until https://github.com/pystatgen/sgkit/pull/294 is done before making a decision on that.

except ImportError as e:
msg = (
"sgkit bgen requirements are not installed.\n\n"
"Please install them via pip :\n\n"
" pip install 'git+https://github.com/pystatgen/sgkit#egg=sgkit[bgen]'"
)
raise ImportError(str(e) + "\n\n" + msg) from e
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