From 51ac4686b477e1afdb78dbaf22ba09b802f444b5 Mon Sep 17 00:00:00 2001
From: Alex Leute <36964815+alex391@users.noreply.github.com>
Date: Tue, 6 Aug 2024 11:52:18 -0400
Subject: [PATCH] py-anvio and py-rich-argparse: new packages (#45367)

---
 .../builtin/packages/py-anvio/package.py      | 55 +++++++++++++++++++
 .../packages/py-rich-argparse/package.py      | 23 ++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-anvio/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-rich-argparse/package.py

diff --git a/var/spack/repos/builtin/packages/py-anvio/package.py b/var/spack/repos/builtin/packages/py-anvio/package.py
new file mode 100644
index 00000000000..2a6de3f4047
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-anvio/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2023 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 PyAnvio(PythonPackage):
+    """Anvi’o is a comprehensive platform that brings together many aspects of
+    today’s cutting-edge computational strategies of data-enabled microbiology,
+    including genomics, metagenomics, metatranscriptomics, pangenomics,
+    metapangenomics, phylogenomics, and microbial population genetics in an
+    integrated and easy-to-use fashion through extensive interactive
+    visualization capabilities."""
+
+    homepage = "https://anvio.org/"
+
+    # Not available on pypi
+    url = "https://github.com/merenlab/anvio/releases/download/v8/anvio-8.tar.gz"
+
+    maintainers("alex391", "meren")
+
+    version("8", sha256="4ced91773648d9ca27a20b725ab64bc213d80b33726940f5f818240033912c04")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy@:1.24", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-bottle", type=("build", "run"))
+    depends_on("py-pysam", type=("build", "run"))
+    depends_on("py-ete3", type=("build", "run"))
+    depends_on("py-scikit-learn@1.2.2", type=("build", "run"))
+    depends_on("py-django", type=("build", "run"))
+    depends_on("py-requests", type=("build", "run"))
+    depends_on("py-mistune", type=("build", "run"))
+    depends_on("py-six", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-statsmodels", type=("build", "run"))
+    # Needs a version of py-colored newer than 1.4.2 (not listed in
+    # requirements.txt)
+    depends_on("py-colored@2:", type=("build", "run"))
+    depends_on("py-illumina-utils", type=("build", "run"))
+    depends_on("py-tabulate", type=("build", "run"))
+    depends_on("py-rich-argparse", type=("build", "run"))
+    depends_on("py-numba", type=("build", "run"))
+    depends_on("py-paste", type=("build", "run"))
+    depends_on("py-pyani", type=("build", "run"))
+    depends_on("py-psutil", type=("build", "run"))
+    depends_on("py-pandas@1.4.4", type=("build", "run"))
+    depends_on("snakemake", type=("build", "run"))
+    depends_on("py-multiprocess", type=("build", "run"))
+    depends_on("py-plotext", type=("build", "run"))
+    depends_on("py-networkx", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-rich-argparse/package.py b/var/spack/repos/builtin/packages/py-rich-argparse/package.py
new file mode 100644
index 00000000000..efc24f7b6a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-rich-argparse/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2023 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 PyRichArgparse(PythonPackage):
+    """rich-argparse improves the look and readability of argparse's help while
+    requiring minimal changes to the code."""
+
+    homepage = "https://github.com/hamdanal/rich-argparse"
+    pypi = "rich_argparse/rich_argparse-1.4.0.tar.gz"
+
+    version("1.4.0", sha256="c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19")
+
+    depends_on("python@3.7:", type=("build", "run"))
+
+    depends_on("py-hatchling@1.11.0:", type="build")
+
+    depends_on("py-rich@11.0.0:", type=("build", "run"))