From 3368a98210903b77ffef7a0d1ffb707cccf9caa5 Mon Sep 17 00:00:00 2001 From: George Young Date: Sun, 4 Jun 2023 23:55:16 +0100 Subject: py-htseq: add 2.0.3, switch to PyPI (#37935) * py-htseq: add 0.12.3, switching over to new GitHub repo * py-htseq: add 0.12.3, switching over to new GitHub repo Style fixes * py-htseq: add 2.0.3, switch to PyPI * py-htseq: add 2.0.3, switch to PyPI * Update package.py * Update var/spack/repos/builtin/packages/py-htseq/package.py Co-authored-by: Adam J. Stewart * Removing SWIG --------- Co-authored-by: LMS Bioinformatics Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/py-htseq/package.py | 26 ++++++++++++++++------ 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-htseq/package.py b/var/spack/repos/builtin/packages/py-htseq/package.py index 2fec5c544a..5049ed9b13 100644 --- a/var/spack/repos/builtin/packages/py-htseq/package.py +++ b/var/spack/repos/builtin/packages/py-htseq/package.py @@ -10,15 +10,27 @@ class PyHtseq(PythonPackage): """HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.""" - homepage = "https://htseq.readthedocs.io/en/release_0.9.1/overview.html" - url = "https://github.com/simon-anders/htseq/archive/release_0.9.1.tar.gz" + homepage = "https://htseq.readthedocs.io/en/master/index.html" + pypi = "HTSeq/HTSeq-2.0.3.tar.gz" - version("0.11.2", sha256="dfc707effa699d5ba9034e1bb9f13c0fb4e9bc60d31ede2444aa49c7e2fc71aa") - version("0.9.1", sha256="28b41d68aa233fce0d57699e649b69bb11957f8f1b9b7b82dfe3415849719534") + version("2.0.3", sha256="c7e7eb29bdc44e80d2d68e3599fa8a8f1d9d6475624dcf1b9644285a8a9c0fac") + version("0.11.2", sha256="65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc") + version("0.9.1", sha256="af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485") + variant("qa", default=True, description="Quality assessment") + variant("mtx", default=True, description="BigWig manipulation", when="@2:") + variant("mtx", default=True, description="mtx output files", when="@2:") + variant("h5ad", default=True, description="h5ad output files", when="@2:") + variant("loom", default=True, description="loom output files", when="@2:") + + # build-only dependencies depends_on("py-setuptools", type="build") + depends_on("py-cython@0.29.5:", type="build") + # run dependencies depends_on("py-numpy", type=("build", "run")) depends_on("py-pysam", type=("build", "run")) - depends_on("py-matplotlib", type=("build", "run")) - depends_on("py-cython", type=("build", "run")) - depends_on("swig", type=("build", "run")) + # variant dependencies + depends_on("py-matplotlib@1.4:", type=("build", "run"), when="+qa") + depends_on("py-scipy@1.5.0:", type=("build", "run"), when="+mtx") + depends_on("py-anndata", type=("build", "run"), when="+h5ad") + depends_on("py-loompy", type=("build", "run"), when="+loom") -- cgit v1.2.3-70-g09d2