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new package: py-kb-python + dependencies (#34737)

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* new package: py-kb-python + dependencies

- py-loompy
- py-ngs-tools
- py-numpy-groupies

* Update var/spack/repos/builtin/packages/py-kb-python/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Glenn Johnson 2023-01-03 16:35:43 -06:00 committed by GitHub
parent 25cff6be14
commit ddab6c4ac3
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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyKbPython(PythonPackage):
"""Python wrapper around kallisto | bustools for scRNA-seq analysis."""
homepage = "https://github.com/pachterlab/kb_python"
pypi = "kb_python/kb_python-0.27.3.tar.gz"
version("0.27.3", sha256="dc98f6ceb4402d666b7e0d19be17c63d33e8b710a35cdc33de7c0f457122f43f")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-anndata@0.6.22.post1:", type=("build", "run"))
depends_on("py-h5py@2.10.0:", type=("build", "run"))
depends_on("py-jinja2@2.10.2:", type=("build", "run"))
depends_on("py-loompy@3.0.6:", type=("build", "run"))
depends_on("py-nbconvert@5.6.0:", type=("build", "run"))
depends_on("py-nbformat@4.4.0:", type=("build", "run"))
depends_on("py-ngs-tools@1.7.3:", type=("build", "run"))
depends_on("py-numpy@1.17.2:", type=("build", "run"))
depends_on("py-pandas@1.0.0:", type=("build", "run"))
depends_on("py-plotly@4.5.0:", type=("build", "run"))
depends_on("py-requests@2.22.0:", type=("build", "run"))
depends_on("py-scanpy@1.4.4.post1:", type=("build", "run"))
depends_on("py-scikit-learn@0.21.3:", type=("build", "run"))
depends_on("py-typing-extensions@3.7.4:", type=("build", "run"))

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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyLoompy(PythonPackage):
"""Work with Loom files for single-cell RNA-seq data."""
homepage = "https://github.com/linnarsson-lab/loompy"
pypi = "loompy/loompy-3.0.7.tar.gz"
version("3.0.7", sha256="b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-h5py", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-numba", type=("build", "run"))
depends_on("py-click", type=("build", "run"))
depends_on("py-numpy-groupies", type=("build", "run"))

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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyNgsTools(PythonPackage):
"""Reusable tools for working with next-generation sequencing (NGS)
data."""
homepage = "https://github.com/Lioscro/ngs-tools"
pypi = "ngs-tools/ngs-tools-1.8.1.tar.gz"
version("1.8.1", sha256="59d606d6c3ff3024e5e1ccad947c4d7608098fca105762e344742e16aa2f0de3")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-joblib@1.0.1:", type=("build", "run"))
depends_on("py-numba@0.53.1:", type=("build", "run"))
depends_on("py-numpy@1.19.0:", type=("build", "run"))
depends_on("py-pysam@0.16.0.1:", type=("build", "run"))
depends_on("py-shortuuid@1.0.1:", type=("build", "run"))
depends_on("py-tqdm@4.50.0:", type=("build", "run"))
depends_on("py-typing-extensions@3.7.4:", type=("build", "run"))

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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class PyNumpyGroupies(PythonPackage):
"""This package consists of a couple of optimised tools for doing things
that can roughly be considered "group-indexing operations". The most
prominent tool is `aggregate`. `aggregate` takes an array of values, and
an array giving the group number for each of those values. It then returns
the sum (or mean, or std, or any, ...etc.) of the values in each group.
You have probably come across this idea before, using `matlab` accumarray,
`pandas` groupby, or generally MapReduce algorithms and histograms. There
are different implementations of `aggregate` provided, based on plain
`numpy`, `numba` and `weave`. Performance is a main concern, and so far we
comfortably beat similar implementations in other packages (check the
benchmarks)."""
homepage = "https://github.com/ml31415/numpy-groupies"
pypi = "numpy_groupies/numpy_groupies-0.9.20.tar.gz"
version("0.9.20", sha256="923a382d6bc6876384b58a9c0503b05b9d36a660f329695c2d33e4f93fcbbe3d")
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))