khmer: new package @2.1.1 (#42450)

* khmer: new package @2.1.1

* rationalising patch

* adding dep, modifying patch

* Update var/spack/repos/builtin/packages/khmer/package.py

Indeed!

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

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

1 files changed, 32 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/khmer/package.py b/var/spack/repos/builtin/packages/khmer/package.py
new file mode 100644
index 0000000000..c93b4fbacd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/khmer/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2024 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 Khmer(PythonPackage):
+    """khmer is a software library and toolkit for k-mer based analysis and transformation
+    of nucleotide sequence data"""
+
+    homepage = "https://khmer.readthedocs.io/en/latest/"
+    pypi = "khmer/khmer-2.1.1.tar.gz"
+
+    license("BSD-3-Clause", checked_by="A-N-Other")
+
+    version("2.1.1", sha256="a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24")
+
+    # https://github.com/dib-lab/khmer/pull/1922 ...
+    conflicts("^python@3.12:")
+
+    depends_on("py-setuptools@3.4.1:", type="build")
+    depends_on("py-pytest-runner@2", type="build")
+    depends_on("py-screed@1:", type=("build", "run"))
+    # abandoned `bz2file` dependency dropped in favour of the patch below
+
+    depends_on("openmpi")
+
+    def patch(self):
+        filter_file("bz2file", "bz2", join_path("khmer", "kfile.py"))
+        filter_file("'bz2file', ", "", "setup.py")