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py-cellprofiler: add 4.2.6 new package (#44824)

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* py-cellprofiler: add 4.2.6 new package

* py-mysqlclient: Limit pkg-config patch to @1.4:

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

---------

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
This commit is contained in:
Pariksheet Nanda 2024-09-02 15:21:39 -04:00 committed by GitHub
parent 17d3d17d46
commit e66e572656
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var/spack/repos/builtin/packages/py-cellprofiler-core/package.py Normal file
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# 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 PyCellprofilerCore(PythonPackage):
"""Core classes and components used by CellProfiler."""
homepage = "https://github.com/CellProfiler/core"
pypi = "cellprofiler-core/cellprofiler-core-4.2.6.tar.gz"
maintainers("omsai")
license("BSD-3-Clause", checked_by="omsai")
version("4.2.6", sha256="91993485783bbab87d89a728260f10e57fda3f7335e6057393702cea774db2d7")
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-boto3@1.12.28:", type=("build", "run"))
depends_on("py-centrosome@1.2.2:", type=("build", "run"))
depends_on("py-docutils@0.15.2:", type=("build", "run"))
depends_on("py-h5py@3.6:3.7~mpi", type=("build", "run"))
depends_on("py-matplotlib@3.1.3:", type=("build", "run"))
depends_on("py-numpy@1.18.2:", type=("build", "run"))
depends_on("py-prokaryote@2.4.4:", type=("build", "run"))
depends_on("py-psutil@5.7:", type=("build", "run"))
depends_on("py-python-bioformats@4.0.7:", type=("build", "run"))
depends_on("py-python-javabridge@4.0.3:", type=("build", "run"))
depends_on("py-pyzmq@22.3:22", type=("build", "run"))
depends_on("py-scikit-image@0.18.3:0", type=("build", "run"))
depends_on("py-scipy@1.4.1:", type=("build", "run"))

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# 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 PyCellprofiler(PythonPackage):
"""CellProfiler cell image analysis software.
CellProfiler is a free open-source software designed to enable biologists
without training in computer vision or programming to quantitatively
measure phenotypes from thousands of images automatically.
"""
homepage = "https://cellprofiler.org"
pypi = "cellprofiler/CellProfiler-4.2.6.tar.gz"
git = "https://github.com/CellProfiler/CellProfiler.git"
maintainers("omsai")
license("BSD-3-Clause", checked_by="omsai")
version("4.2.6", sha256="37e2a35dccff456afda96a4442dff2d23809c8ee271607a347e386aeb4af2628")
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools@64:", type="build")
depends_on("py-setuptools-scm@8:", type="build")
depends_on("py-boto3@1.12.28:", type=("build", "run"))
depends_on("py-cellprofiler-core@4.2.6", type=("build", "run"))
depends_on("py-centrosome@1.2.2:", type=("build", "run"))
depends_on("py-docutils@0.15.2:", type=("build", "run"))
# More recent versions of h5py cause:
# AttributeError: module 'h5py' has no attribute 'Dataset
depends_on("py-h5py@3.6:3.7~mpi", type=("build", "run"))
depends_on("py-imageio@2.5:", type=("build", "run"))
depends_on("py-inflect@2.1:6", type=("build", "run"))
depends_on("py-jinja2@2.11.2:", type=("build", "run"))
depends_on("py-joblib@0.13:", type=("build", "run"))
depends_on("py-mahotas@1.4:", type=("build", "run"))
# matplotlib.cm.get_cmap does not exist in 3.9.0 onwards.
depends_on("py-matplotlib@3.1.3:3.8", type=("build", "run"))
depends_on("py-mysqlclient@1.4.6", type=("build", "run"))
depends_on("py-numpy@1.20.1:", type=("build", "run"))
depends_on("py-pillow@7.1:", type=("build", "run"))
depends_on("py-prokaryote@2.4.4:", type=("build", "run"))
depends_on("py-python-bioformats@4.0.7:", type=("build", "run"))
depends_on("py-python-javabridge@4.0.3:", type=("build", "run"))
depends_on("py-pyzmq@22.3:22", type=("build", "run"))
depends_on("py-sentry-sdk@0.18:", type=("build", "run"))
depends_on("py-requests@2.22:", type=("build", "run"))
depends_on("py-scikit-image@0.18.3:", type=("build", "run"))
depends_on("py-scikit-learn@0.20:0", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-six", type=("build", "run"))
depends_on("py-tifffile@:2022.4.21", type=("build", "run"))
depends_on("py-wxpython@4.1.0:4", type=("build", "run"))
depends_on("py-pytest", type=("run", "test"), when="@4.2.6 +tests")
# Run the post-install tests with `spack test run py-cellprofiler`. We
# need the variant to add the pytest executable to the PATH.
variant("tests", default=False, description="Post-install tests.")
# The pypi tests directory is incomplete.
resource(
name="tests-upstream",
destination="",
placement={
"tests/conftest.py": "tests/conftest.py",
"tests/gui": "tests/gui",
"tests/__init__.py": "tests/__init__.py",
"tests/modules": "tests/modules",
"tests/resources": "tests/resources",
"tests/test_cellprofiler.py": "tests/test_cellprofiler.py",
"tests/test_haralick.py": "tests/test_haralick.py",
"tests/test_knime_bridge.py": "tests/test_knime_bridge.py",
"tests/test_main.py": "tests/test_main.py",
"tests/test_nowx.py": "tests/test_nowx.py",
"tests/utilities": "tests/utilities",
},
git=git,
tag="v4.2.6",
sha256="5fb562774044d1dc8cffcddf6072d706f71e6649d566980efaab5b30f52ddfa2",
when="@4.2.6 +tests",
)
dir_tests = "tests"
# Leave 'gui' out of 'import_modules' to avoid the curently broken wxpython
# dependency.
import_modules = [
"cellprofiler",
"cellprofiler.icons",
"cellprofiler.library",
"cellprofiler.library.functions",
"cellprofiler.library.modules",
# "cellprofiler.gui",
# "cellprofiler.gui.html",
# "cellprofiler.gui.help",
# "cellprofiler.gui.module_view",
# "cellprofiler.gui.constants",
# "cellprofiler.gui.figure",
# "cellprofiler.gui.workspace_view",
# "cellprofiler.gui.preferences_view",
# "cellprofiler.gui.utilities",
# "cellprofiler.gui.preferences_dialog",
"cellprofiler.modules",
"cellprofiler.modules.plugins",
"cellprofiler.utilities",
]
@when("+tests")
def patch(self):
"""Install tests from git."""
# Install the tests module. Using a module name like "tests" may
# create a namespace collision with other spack packages in the DAG,
# but the alternative would moving tests into cellprofiler and
# extensively patching the tests to be a submodule of cellprofiler
# instead of a standalone module.
filter_file(r"find_packages\([^)]+\)", "find_packages()", "setup.py")
# Include required test data files.
with open("MANIFEST.in", "a") as h:
h.writelines("graft tests")
# For interactive unittest debugging, run:
#
# spack env create cp
# spack env activate cp
# spack add cellprofiler+tests ^hdf5~mpi
# spack install
# git clone --branch v4.2.6 --depth 1 \
# https://github.com/cellprofiler/cellprofiler
# cd cellprofiler/
# pytest --pdb -k "not TestExportToDatabase" tests/
#
# [...]
# 1412 passed, 16 skipped, 75 deselected
def test_cellprofiler_no_gui(self):
"""Test installed package."""
pytest = which("pytest")
prefix = join_path(python_purelib, self.dir_tests)
pytest(
"-v",
# Don't test against the live MySQL database.
"-k",
"not TestExportToDatabase",
prefix,
)

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# 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 PyCentrosome(PythonPackage):
"""An open source image processing library."""
homepage = "https://github.com/CellProfiler/centrosome"
pypi = "centrosome/centrosome-1.2.2.tar.gz"
maintainers("omsai")
license("BSD-3-Clause", checked_by="omsai")
version("1.2.2", sha256="4b38181d6648cb8b0e896aa2e54b5a6da2e9ebc19a8110582307f5c6da9d9964")
depends_on("python@2.7:,3.5:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-deprecation", type=("build", "run"))
depends_on("py-matplotlib@3.1.3:", type=("build", "run"))
depends_on("py-numpy@1.18.2:", type=("build", "run"))
depends_on("py-pillow@7.1:", type=("build", "run"))
depends_on("py-scikit-image@0.17.2:", type=("build", "run"))
depends_on("py-scipy@1.4.1:1.10", type=("build", "run"))

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var/spack/repos/builtin/packages/py-mysqlclient/package.py
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@ -17,6 +17,7 @@ class PyMysqlclient(PythonPackage):
license("GPL-2.0-or-later")
version("2.2.4", sha256="33bc9fb3464e7d7c10b1eaf7336c5ff8f2a3d3b88bab432116ad2490beb3bf41")
version("1.4.6", sha256="f3fdaa9a38752a3b214a6fe79d7cae3653731a53e577821f9187e67cbecb2e16")
version("1.4.5", sha256="e80109b0ae8d952b900b31b623181532e5e89376d707dcbeb63f99e69cefe559")
version("1.4.4", sha256="9c737cc55a5dc8dd3583a942d5a9b21be58d16f00f5fefca4e575e7d9682e98c")
@ -26,3 +27,9 @@ class PyMysqlclient(PythonPackage):
depends_on("py-setuptools", type="build")
depends_on("mysql")
# Fix "library not found for -lzlib" as described in
# https://github.com/PyMySQL/mysqlclient/issues/584 by backporting the
# patch from @2.2.0rc1 that uses pkg-config instead of mysql_config
# https://github.com/PyMySQL/mysqlclient/pull/586/files
patch("use-pkg-config.patch", when="@1.4:2.1")

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@ -0,0 +1,172 @@
--- a/setup_posix.py 2019-11-06 02:21:07.000000000 -0500
+++ b/setup_posix.py 2024-05-13 18:22:02.200012959 -0400
@@ -1,56 +1,31 @@
-import os, sys
+import os, subprocess, sys
try:
from ConfigParser import SafeConfigParser
except ImportError:
from configparser import ConfigParser as SafeConfigParser
-# This dequote() business is required for some older versions
-# of mysql_config
-def dequote(s):
- if not s:
- raise Exception("Wrong MySQL configuration: maybe https://bugs.mysql.com/bug.php?id=86971 ?")
- if s[0] in "\"'" and s[0] == s[-1]:
- s = s[1:-1]
- return s
-
-_mysql_config_path = "mysql_config"
-
-def mysql_config(what):
- from os import popen
-
- f = popen("%s --%s" % (_mysql_config_path, what))
- data = f.read().strip().split()
- ret = f.close()
- if ret:
- if ret/256:
- data = []
- if ret/256 > 1:
- raise EnvironmentError("%s not found" % (_mysql_config_path,))
- return data
+def find_package_name():
+ """Get available pkg-config package name"""
+ packages = ["mysqlclient", "mariadb"]
+ for pkg in packages:
+ try:
+ cmd = f"pkg-config --exists {pkg}"
+ print(f"Trying {cmd}")
+ subprocess.check_call(cmd, shell=True)
+ except subprocess.CalledProcessError as err:
+ print(err)
+ else:
+ return pkg
+ raise Exception("Cannot find valid pkg-config")
+
def get_config():
from setup_common import get_metadata_and_options, enabled, create_release_file
- global _mysql_config_path
metadata, options = get_metadata_and_options()
- if 'mysql_config' in options:
- _mysql_config_path = options['mysql_config']
- else:
- try:
- mysql_config('version')
- except EnvironmentError:
- # try mariadb_config
- _mysql_config_path = "mariadb_config"
- try:
- mysql_config('version')
- except EnvironmentError:
- _mysql_config_path = "mysql_config"
-
- extra_objects = []
static = enabled(options, 'static')
-
# allow a command-line option to override the base config file to permit
# a static build to be created via requirements.txt
#
@@ -58,65 +33,51 @@
static = True
sys.argv.remove('--static')
- libs = mysql_config("libs")
- library_dirs = [dequote(i[2:]) for i in libs if i.startswith('-L')]
- libraries = [dequote(i[2:]) for i in libs if i.startswith('-l')]
- extra_link_args = [x for x in libs if not x.startswith(('-l', '-L'))]
-
- removable_compile_args = ('-I', '-L', '-l')
- extra_compile_args = [i.replace("%", "%%") for i in mysql_config("cflags")
- if i[:2] not in removable_compile_args]
-
- # Copy the arch flags for linking as well
- for i in range(len(extra_compile_args)):
- if extra_compile_args[i] == '-arch':
- extra_link_args += ['-arch', extra_compile_args[i + 1]]
+ ldflags = os.environ.get("MYSQLCLIENT_LDFLAGS")
+ cflags = os.environ.get("MYSQLCLIENT_CFLAGS")
- include_dirs = [dequote(i[2:])
- for i in mysql_config('include') if i.startswith('-I')]
-
- if static:
- # properly handle mysql client libraries that are not called libmysqlclient
- client = None
- CLIENT_LIST = ['mysqlclient', 'mysqlclient_r', 'mysqld', 'mariadb',
- 'mariadbclient', 'perconaserverclient', 'perconaserverclient_r']
- for c in CLIENT_LIST:
- if c in libraries:
- client = c
- break
-
- if client == 'mariadb':
- client = 'mariadbclient'
- if client is None:
- raise ValueError("Couldn't identify mysql client library")
-
- extra_objects.append(os.path.join(library_dirs[0], 'lib%s.a' % client))
- if client in libraries:
- libraries.remove(client)
+ pkg_name = None
+ static_opt = " --static" if static else ""
+ if not (cflags and ldflags):
+ pkg_name = find_package_name()
+ if not cflags:
+ cflags = subprocess.check_output(
+ f"pkg-config{static_opt} --cflags {pkg_name}", encoding="utf-8", shell=True
+ )
+ if not ldflags:
+ ldflags = subprocess.check_output(
+ f"pkg-config{static_opt} --libs {pkg_name}", encoding="utf-8", shell=True
+ )
+
+ cflags = cflags.split()
+ for f in cflags:
+ if f.startswith("-std="):
+ break
+ else:
+ cflags += ["-std=c99"]
- name = "mysqlclient"
- metadata['name'] = name
+ ldflags = ldflags.split()
define_macros = [
('version_info', metadata['version_info']),
('__version__', metadata['version']),
]
- create_release_file(metadata)
- del metadata['version_info']
ext_options = dict(
- library_dirs = library_dirs,
- libraries = libraries,
- extra_compile_args = extra_compile_args,
- extra_link_args = extra_link_args,
- include_dirs = include_dirs,
- extra_objects = extra_objects,
- define_macros = define_macros,
+ extra_compile_args=cflags,
+ extra_link_args=ldflags,
+ define_macros=define_macros,
)
-
# newer versions of gcc require libstdc++ if doing a static build
if static:
ext_options['language'] = 'c++'
+ print("Options for building extention module:")
+ for k, v in ext_options.items():
+ print(f" {k}: {v}")
+
+ create_release_file(metadata)
+ del metadata['version_info']
+
return metadata, ext_options
if __name__ == "__main__":

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@ -0,0 +1,23 @@
# 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 PyProkaryote(PythonPackage):
"""CellProfiler's Java dependencies."""
homepage = "https://github.com/CellProfiler/prokaryote"
pypi = "prokaryote/prokaryote-2.4.4.tar.gz"
maintainers("omsai")
license("GPL-3.0-or-later", checked_by="omsai")
version("2.4.4", sha256="0a147b8b9a0a7279aa773e6a8fe459eb49f6de479f7afe7203dc4ac10dc8b587")
depends_on("python@2.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")

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var/spack/repos/builtin/packages/py-python-bioformats/package.py
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@ -17,6 +17,7 @@ class PyPythonBioformats(PythonPackage):
license("GPL-2.0-only")
version("4.0.7", sha256="9cdadd06e2453566bfcc512eb9f774654e9fd35ee02a7fb5e8fb097812c5733b")
version("4.0.5", sha256="f9fa3a2b3c0f1eac6070dff6c513444e9fde9a1f794ec4c21fca85833dbb5192")
version("4.0.0", sha256="9a952de4d326d961af0a497753a4b71b2f7844605023d170c931d3624e036506")

1
var/spack/repos/builtin/packages/py-tifffile/package.py
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@ -18,6 +18,7 @@ class PyTifffile(PythonPackage):
version(
"2022.10.10", sha256="50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e"
)
version("2022.4.8", sha256="d4a4057e5cb7afe6e24cf7bde42a163970b593afe44c17249894ede755cf3faa")
version("2021.11.2", sha256="153e31fa1d892f482fabb2ae9f2561fa429ee42d01a6f67e58cee13637d9285b")
version("2020.10.1", sha256="799feeccc91965b69e1288c51a1d1118faec7f40b2eb89ad2979591b85324830")
version("0.12.1", sha256="802367effe86b0d1e64cb5c2ed886771f677fa63260b945e51a27acccdc08fa1")