CellProfiler/pixi.toml at main · OpenMegaLab/CellProfiler · GitHub

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[project]
name = "CellProfiler"
description = """
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."""
channels = ["conda-forge"]
platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]

[tasks]
cp = { cmd = ["python", "-m", "cellprofiler"] }

[target.osx.tasks]
# run using python.app (i.e. pythonw)
cp = { cmd = ["pythonw", "-m", "cellprofiler", "-L", "10"] }
cpd = { cmd = ["pythonw", "-Wd", "-m", "cellprofiler", "-L", "10"] }

[target.osx.activation]
# needed until https://github.com/prefix-dev/pixi/issues/1573 is resolved
# python.app has a post-link script that coppies the contents of the pythonapp directory to a new python.app directory
# that is not being run, hence the need for this hack
scripts = ["scripts/link-pythonapp.sh"]

[feature.mysql.activation]
# https://github.com/PyMySQL/mysqlclient/issues/496#issuecomment-1614688099
env = { MYSQLCLIENT_CFLAGS = "-I$PIXI_PROJECT_ROOT/.pixi/envs/dev/include/mysql", MYSQLCLIENT_LDFLAGS = "-L$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib -lmysqlclient -rpath $PIXI_PROJECT_ROOT/.pixi/envs/dev/lib", PKG_CONFIG_PATH = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib/pkgconfig" }

[feature.mysql.target.linux-64.activation]
env = { MYSQLCLIENT_CFLAGS = "-I$PIXI_PROJECT_ROOT/.pixi/envs/dev/include/mysql", MYSQLCLIENT_LDFLAGS = "-L$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib" }

[feature.java.activation]
env = { JAVA_HOME = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib/jvm" }

[dependencies]
python = "3.9.*"
h5py = "<3.11"

[target.osx.dependencies]
"python.app" = ">=1.4,<2"

# enable this to avoid building wxPython wheel on Linux
# disable to build wheel from scratch
# url must be changed to match linux distro: https://extras.wxpython.org/wxPython4/extras/linux/gtk3/
[target.linux-64.pypi-dependencies]
wxPython = { url = "https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04/wxPython-4.2.1-cp39-cp39-linux_x86_64.whl" }

[target.osx-arm64.pypi-dependencies]
wxpython = "==4.2.1"

[feature.mysql.dependencies]
pkg-config = "<1.0.0"
mysql = "=8.0"

[feature.java.dependencies]
openjdk = "11.*"
maven = ">=3.9.9,<4"

[feature.mod.pypi-dependencies]
cellprofiler-library = { path = "./src/subpackages/library", extras = ["test"], editable = true }
cellprofiler-core = { path = "./src/subpackages/core", extras = ["test"], editable = true }
cellprofiler = { path = "./src/frontend", extras = ["test"], editable = true }

[feature.profile.pypi-dependencies]
py-spy = "*"
memray = "*"

[environments]
dev = ["mod", "java", "mysql"]
profile = ["mod", "java", "mysql", "profile"]