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

* 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>

4 files changed, 119 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-kb-python/package.py b/var/spack/repos/builtin/packages/py-kb-python/package.py
new file mode 100644
index 0000000000..098a938a16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-kb-python/package.py
@@ -0,0 +1,34 @@
+# 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"))
diff --git a/var/spack/repos/builtin/packages/py-loompy/package.py b/var/spack/repos/builtin/packages/py-loompy/package.py
new file mode 100644
index 0000000000..3bd0e231b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-loompy/package.py
@@ -0,0 +1,26 @@
+# 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"))
diff --git a/var/spack/repos/builtin/packages/py-ngs-tools/package.py b/var/spack/repos/builtin/packages/py-ngs-tools/package.py
new file mode 100644
index 0000000000..1196b16b8a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ngs-tools/package.py
@@ -0,0 +1,28 @@
+# 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"))
diff --git a/var/spack/repos/builtin/packages/py-numpy-groupies/package.py b/var/spack/repos/builtin/packages/py-numpy-groupies/package.py
new file mode 100644
index 0000000000..89f4fc4713
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-numpy-groupies/package.py
@@ -0,0 +1,31 @@
+# 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"))