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PCA implementation #262

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Merged
merged 1 commit into from
Oct 14, 2020
Merged

PCA implementation #262

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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,4 +26,4 @@ repos:
hooks:
- id: mypy
args: ["--strict", "--show-error-codes"]
additional_dependencies: ["numpy", "xarray", "dask[array]", "scipy", "typing-extensions", "zarr", "numba"]
additional_dependencies: ["numpy", "xarray", "dask[array]", "scipy", "typing-extensions", "zarr", "numba", "dask-ml"]
2 changes: 2 additions & 0 deletions requirements-dev.txt
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Expand Up @@ -6,6 +6,7 @@ pytest-cov
pytest-datadir
pytest-mock
hypothesis
scikit-allel
statsmodels
zarr
msprime
Expand All @@ -18,3 +19,4 @@ git+https://github.com/pangeo-data/rechunker.git
cbgen
cyvcf2; platform_system != "Windows"
yarl
matplotlib
1 change: 1 addition & 0 deletions requirements.txt
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@@ -1,6 +1,7 @@
numpy
xarray
dask[array]
dask-ml
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This pulls in scikit-learn, Dask distributed and some other dependencies. That's probably OK, but thinking about if there's any way to minimise transitive dependencies here.

scipy
typing-extensions
numba
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10 changes: 7 additions & 3 deletions setup.cfg
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Expand Up @@ -28,6 +28,7 @@ install_requires =
numpy
xarray
dask[array]
dask-ml
scipy
zarr
numba
Expand Down Expand Up @@ -87,15 +88,14 @@ ignore =
profile = black
default_section = THIRDPARTY
known_first_party = sgkit
known_third_party = dask,fire,glow,hail,hypothesis,invoke,msprime,numba,numpy,pandas,pkg_resources,pyspark,pytest,setuptools,sgkit_plink,sklearn,sphinx,typing_extensions,xarray,yaml,zarr
known_third_party = allel,dask,fire,glow,hail,hypothesis,invoke,msprime,numba,numpy,pandas,pkg_resources,pyspark,pytest,setuptools,sgkit_plink,sklearn,sphinx,typing_extensions,xarray,yaml,zarr
multi_line_output = 3
include_trailing_comma = True
force_grid_wrap = 0
use_parentheses = True
line_length = 88

[mypy-allel.*]
ignore_missing_imports = True

[mypy-callee.*]
ignore_missing_imports = True
[mypy-cyvcf2.*]
Expand All @@ -104,6 +104,8 @@ ignore_missing_imports = True
ignore_missing_imports = True
[mypy-fsspec.*]
ignore_missing_imports = True
[mypy-dask_ml.*]
ignore_missing_imports = True
[mypy-numpy.*]
ignore_missing_imports = True
[mypy-pandas.*]
Expand Down Expand Up @@ -132,6 +134,8 @@ ignore_missing_imports = True
ignore_missing_imports = True
[mypy-yarl.*]
ignore_missing_imports = True
[mypy-allel.*]
ignore_missing_imports = True
[mypy-sgkit.*]
allow_redefinition = True
[mypy-sgkit.*.tests.*]
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2 changes: 2 additions & 0 deletions sgkit/__init__.py
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Expand Up @@ -12,6 +12,7 @@
from .stats.association import gwas_linear_regression
from .stats.hwe import hardy_weinberg_test
from .stats.pc_relate import pc_relate
from .stats.pca import pca
from .stats.popgen import Fst, Tajimas_D, divergence, diversity
from .stats.regenie import regenie
from .testing import simulate_genotype_call_dataset
Expand All @@ -38,4 +39,5 @@
"pc_relate",
"simulate_genotype_call_dataset",
"variables",
"pca",
]
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