Add py-nanoplot and py-nanostat (#41190)

* Add py-nanoplot and py-nanostat

* Add myself as spack package maintainer

* Remove python version requirement

* Remove python dependency

* Apply suggestions from code review

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

* Update package.py: remove python dependency

* Set dependency types

* Update py-nanomath package.py

* Update py-nanoplot package.py

* Update py-nanostat package.py

* Add missing py-python-deprecated dependency

* Make kaleido a source package

* Fix py-nanoget deps

* Kaleido lint

* Nanoget lint

* Nanomath lint

* Nanoplot lint

* Nanostat lint

* Another kaleido lint I missed

* py-nanoplot missed lint

* py-nanostat missed lint

* py-kaleido even more missed lint

* The linter really can't make up its mind

* The linter REALLY can't make up its mind

* Add py-python-deprecated package

---------

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

6 files changed, 136 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-kaleido/package.py b/var/spack/repos/builtin/packages/py-kaleido/package.py
new file mode 100644
index 0000000000..b9d65bc800
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-kaleido/package.py
@@ -0,0 +1,21 @@
+# 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 PyKaleido(PythonPackage):
+    """Static image export for web-based visualization libraries with zero dependencies"""
+
+    homepage = "https://github.com/wdecoster/nanostat"
+    url = "https://github.com/plotly/Kaleido/archive/refs/tags/v0.2.1.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("0.2.1", sha256="fdb673a9759835d4f455990fc1ff8919bd100a0d34f2d3de7bd5eeb2162b57ec")
+
+    depends_on("py-setuptools", type="build")
+
+    build_directory = join_path("repos", "kaleido", "py")
diff --git a/var/spack/repos/builtin/packages/py-nanoget/package.py b/var/spack/repos/builtin/packages/py-nanoget/package.py
new file mode 100644
index 0000000000..dfb86cfbdd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nanoget/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 PyNanoget(PythonPackage):
+    """Functions to extract information from Oxford Nanopore sequencing data and alignments"""
+
+    homepage = "https://github.com/wdecoster/nanoget"
+    pypi = "nanoget/nanoget-1.19.3.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("1.19.3", sha256="da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b")
+
+    depends_on("py-setuptools", type=("build",))
+    depends_on("py-pandas@2.0.0:", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-biopython", type=("build", "run"))
+    depends_on("py-pysam@0.10.0.1:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-nanomath/package.py b/var/spack/repos/builtin/packages/py-nanomath/package.py
new file mode 100644
index 0000000000..f9db95f64a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nanomath/package.py
@@ -0,0 +1,22 @@
+# 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 PyNanomath(PythonPackage):
+    """A few simple math function for other Oxford Nanopore processing scripts"""
+
+    homepage = "https://github.com/wdecoster/nanomath"
+    pypi = "nanomath/nanomath-1.3.0.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("1.3.0", sha256="c35a024b10b34dd8f539cefed1fd69e0a46d18037ca48bed63c7941c67ae028e")
+
+    depends_on("py-setuptools", type=("build",))
+    depends_on("py-python-deprecated", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-numpy@1.9:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-nanoplot/package.py b/var/spack/repos/builtin/packages/py-nanoplot/package.py
new file mode 100644
index 0000000000..080ae62bf0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nanoplot/package.py
@@ -0,0 +1,30 @@
+# 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 PyNanoplot(PythonPackage):
+    """Plotting scripts for long read sequencing data"""
+
+    homepage = "https://github.com/wdecoster/NanoPlot"
+    pypi = "NanoPlot/NanoPlot-1.42.0.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("1.42.0", sha256="0f8fd2cffd33a346b3306716058c6cb4091c931e8ab502f10b17a28749e8b6d9")
+
+    depends_on("py-setuptools", type=("build",))
+    depends_on("py-biopython", type=("build", "run"))
+    depends_on("py-pysam@0.10.0.1:", type=("build", "run"))
+    depends_on("py-pandas@1.1.0:", type=("build", "run"))
+    depends_on("py-numpy@1.16.5:", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-python-dateutil", type=("build", "run"))
+    depends_on("py-nanoget@1.19.1:", type=("build", "run"))
+    depends_on("py-nanomath@1.0.0:", type=("build", "run"))
+    depends_on("py-plotly@5.4.0:", type=("build", "run"))
+    depends_on("py-pyarrow", type=("build", "run"))
+    depends_on("py-kaleido", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-nanostat/package.py b/var/spack/repos/builtin/packages/py-nanostat/package.py
new file mode 100644
index 0000000000..d15151d530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nanostat/package.py
@@ -0,0 +1,21 @@
+# 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 PyNanostat(PythonPackage):
+    """Calculate statistics for Oxford Nanopore sequencing data and alignments"""
+
+    homepage = "https://github.com/wdecoster/nanostat"
+    pypi = "NanoStat/NanoStat-1.6.0.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("1.6.0", sha256="e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079")
+
+    depends_on("py-setuptools", type=("build",))
+    depends_on("py-nanoget@1.13.2:", type=("build", "run"))
+    depends_on("py-nanomath@1.0.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-python-deprecated/package.py b/var/spack/repos/builtin/packages/py-python-deprecated/package.py
new file mode 100644
index 0000000000..3af97f84c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-deprecated/package.py
@@ -0,0 +1,19 @@
+# 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 PyPythonDeprecated(PythonPackage):
+    """Python @deprecated decorator to deprecate old python classes, functions or methods."""
+
+    homepage = "https://github.com/vrcmarcos/python-deprecated"
+    pypi = "Python-Deprecated/Python-Deprecated-1.1.0.tar.gz"
+
+    maintainers("Pandapip1")
+
+    version("1.1.0", sha256="a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f")
+
+    depends_on("py-setuptools", type=("build",))