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5 files changed, 152 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/cellpose/package.py b/var/spack/repos/builtin/packages/cellpose/package.py new file mode 100644 index 0000000000..046bd70370 --- /dev/null +++ b/var/spack/repos/builtin/packages/cellpose/package.py @@ -0,0 +1,46 @@ +# 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 Cellpose(PythonPackage): + """A generalist algorithm for cell and nucleus segmentation that can be optimized for + your own data""" + + homepage = "https://cellpose.readthedocs.io/" + pypi = "cellpose/cellpose-2.2.3.tar.gz" + + license("BSD-3-Clause", checked_by="A-N-Other") + + version("2.2.3", sha256="7ff63cb60a154ce3c0a17ff05ed27d2aaaa1a24a4c7a8160c0a4c15443366618") + + variant("gui", default=False, description="Build the GUI") + + depends_on("py-setuptools", type="build") + depends_on("py-setuptools-scm", type="build") + depends_on("py-pytest-runner", type="build") + + depends_on("py-numpy@1.20.0:", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-natsort", type=("build", "run")) + depends_on("py-tifffile", type=("build", "run")) + depends_on("py-tqdm", type=("build", "run")) + depends_on("py-numba@0.53.0:", type=("build", "run")) + depends_on("py-llvmlite", type=("build", "run")) + depends_on("py-torch@1.6:", type=("build", "run")) + # `copencv` provides `cv2` in place of opencv-python-headless specified in setup.py + # +ximgproc is required from the contrib modules + depends_on("opencv +python3+ximgproc", type=("build", "run")) + depends_on("py-fastremap", type=("build", "run")) + depends_on("py-imagecodecs", type=("build", "run")) + depends_on("py-roifile", type=("build", "run")) + + depends_on("py-pyqtgraph@0.11.0:", type=("build", "run"), when="+gui") + depends_on("py-pyqt6", type=("build", "run"), when="+gui") + depends_on("py-pyqt6-sip", type=("build", "run"), when="+gui") + depends_on("py-qtpy", type=("build", "run"), when="+gui") + depends_on("py-superqt", type=("build", "run"), when="+gui") + depends_on("py-google-cloud-storage", type=("build", "run"), when="+gui") diff --git a/var/spack/repos/builtin/packages/py-fastremap/package.py b/var/spack/repos/builtin/packages/py-fastremap/package.py new file mode 100644 index 0000000000..71103a1375 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-fastremap/package.py @@ -0,0 +1,26 @@ +# 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 PyFastremap(PythonPackage): + """Renumber and relabel Numpy arrays at C++ speed and physically convert rectangular + Numpy arrays between C and Fortran order using an in-place transposition""" + + homepage = "https://github.com/seung-lab/fastremap/" + pypi = "fastremap/fastremap-1.14.1.tar.gz" + + license("LGPL-3.0", checked_by="A-N-Other") + + version("1.14.1", sha256="067d42d6cb3b1b0789889efd1d7fae58006c82ada4a8446d40e9e838b358ee7c") + + depends_on("python@3.7:3", type=("build", "run")) + + depends_on("py-setuptools", type="build") + depends_on("py-pbr", type="build") + depends_on("py-cython", type="build") + + depends_on("py-numpy", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-pyqtgraph/package.py b/var/spack/repos/builtin/packages/py-pyqtgraph/package.py new file mode 100644 index 0000000000..8b82f99a5f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyqtgraph/package.py @@ -0,0 +1,25 @@ +# 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 PyPyqtgraph(PythonPackage): + """PyQtGraph is a pure-python graphics and GUI library intended for use in mathematics, + scientific, and engineering applications""" + + homepage = "http://www.pyqtgraph.org/" + pypi = "pyqtgraph/pyqtgraph-0.13.3.tar.gz" + + license("MIT", checked_by="A-N-Other") + + version("0.13.3", sha256="58108d8411c7054e0841d8b791ee85e101fc296b9b359c0e01dde38a98ff2ace") + + depends_on("python@3.8:", type=("build", "run")) + depends_on("py-setuptools", type="build") + + depends_on("py-numpy@1.20:", type=("build", "run")) + # This dependency listed in README.md ... + depends_on("py-pyqt6", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-roifile/package.py b/var/spack/repos/builtin/packages/py-roifile/package.py new file mode 100644 index 0000000000..47f4600748 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-roifile/package.py @@ -0,0 +1,27 @@ +# 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 PyRoifile(PythonPackage): + """Roifile is a Python library to read, write, create, and plot ImageJ ROIs""" + + homepage = "https://www.cgohlke.com/" + pypi = "roifile/roifile-2024.1.10.tar.gz" + + license("BSD-3-Clause", checked_by="A-N-Other") + + version("2024.1.10", sha256="8bbc05a96c0a291429214cb6829426378e89931d1a7d3ad945aa2fea5765e434") + + variant("all", default=True, description="Enable TIFF support") + + depends_on("python@3.9:", type=("build", "run")) + depends_on("py-setuptools", type="build") + + depends_on("py-numpy", type=("build", "run")) + + depends_on("py-matplotlib", type=("build", "run"), when="+all") + depends_on("py-tifffile", type=("build", "run"), when="+all") diff --git a/var/spack/repos/builtin/packages/py-superqt/package.py b/var/spack/repos/builtin/packages/py-superqt/package.py new file mode 100644 index 0000000000..36813fcdf3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-superqt/package.py @@ -0,0 +1,28 @@ +# 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 PySuperqt(PythonPackage): + """Missing widgets and components for PyQt/PySide""" + + homepage = "https://pyapp-kit.github.io/superqt/" + pypi = "superqt/superqt-0.6.1.tar.gz" + + license("BSD-3-Clause", checked_by="A-N-Other") + + version("0.6.1", sha256="f1a9e0499c4bbcef34b6f895eb57cd41301b3799242cd030029238124184dade") + + depends_on("python@3.8:", type=("build", "run")) + depends_on("py-hatchling", type="build") + depends_on("py-hatch-vcs", type="build") + + depends_on("py-packaging", type=("build", "run")) + depends_on("py-pygments@2.4:", type=("build", "run")) + depends_on("py-qtpy@1.1:", type=("build", "run")) + depends_on("py-typing-extensions@3.7.4.3:", type=("build", "run")) + + conflicts("^py-typing-extensions@3.10.0.0") |