cellpose: new package @2.2.3 (spack#42403)

* py-fastremap: new package @1.14.1

* py-pyqtgraph: new package @0.13.3

* py-roifile: new package @2024.1.10

* py-superqt: new package @0.6.1

* cellpose: new package @2.2.3

* Appeasing black ...

* Dropping the cuda variant

* Update var/spack/repos/builtin/packages/py-fastremap/package.py

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

* Adding python version dependency

* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py

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

* Update var/spack/repos/builtin/packages/py-pyqtgraph/package.py

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

* Update var/spack/repos/builtin/packages/py-roifile/package.py

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

* Update var/spack/repos/builtin/packages/py-superqt/package.py

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

* Adding missing dep & conflict

* Appeasing black

* Adding missing py- prefix for dep

* Switching over to py-pyqt6

* Switching over to py-pyqt6

---------

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

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")

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"))

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"))

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")

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")