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pixi.toml
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[project]
name = "CellProfiler42x"
version = "4.2.8"
description = "Dev environment for CP42x"
authors = ["Nodar Gogoberidze <gnodar01@gmail.com>"]
channels = ["conda-forge"]
#platforms = ["osx-64"]
# on windows, in git bash: bash --rcfile <(pixi shell-hook -e dev | sed 's/^export Path=/export PATH=/' | tr ';' ':')
#platforms = ["win-64", "osx-64"]
platforms = ["win-64", "osx-64", "linux-64"]
# platforms = ["osx-64", "osx-arm64"]
# platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
[feature.mod.tasks]
cpwd = { cmd = ["python", "-Wd", "-m", "cellprofiler"] }
cp = { cmd = ["python", "-m", "cellprofiler"] }
[feature.mod.target.osx.tasks]
cpwd = { cmd = ["$PIXI_PROJECT_ROOT/.pixi/envs/dev/pythonapp/Contents/MacOS/python", "-Wd", "-m", "cellprofiler"], env = { PYTHONEXECUTABLE = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/bin/python" } }
cp = { cmd = ["$PIXI_PROJECT_ROOT/.pixi/envs/dev/pythonapp/Contents/MacOS/python", "-m", "cellprofiler"], env = { PYTHONEXECUTABLE = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/bin/python" } }
[feature.mysql.target.unix.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 $PIXI_PROJECT_ROOT/.pixi/envs/dev/lib" }
[feature.mysql.target.linux-64.activation]
# env = { MYSQLCLIENT_CFLAGS = "-I$PIXI_PROJECT_ROOT/.pixi/envs/dev/include/mysql", MYSQLCLIENT_LDFLAGS = "-L$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib" }
# usage of `%` or `$` and `\\` or `/` will depend on if using e.g. cmd.exe or git bash or ...
[feature.java.target.win-64.activation]
env = { JAVA_HOME = "%PIXI_PROJECT_ROOT%\\.pixi\\envs\\dev\\Library\\lib\\jvm", JDK_HOME = "%PIXI_PROJECT_ROOT%\\.pixi\\envs\\dev\\Library\\lib\\jvm" }
#env = { JAVA_HOME = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/Library/lib/jvm", JDK_HOME = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/Library/lib/jvm" }
#env = { JAVA_HOME = "$PIXI_PROJECT_ROOT\\.pixi\\envs\\dev\\Library\\lib\\jvm", JDK_HOME = "$PIXI_PROJECT_ROOT\\.pixi\\envs\\dev\\Library\\lib\\jvm" }
[feature.java.activation]
env = { JAVA_HOME = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib/jvm", JDK_HOME = "$PIXI_PROJECT_ROOT/.pixi/envs/dev/lib/jvm" }
[dependencies]
setuptools = "64.*"
scipy = "==1.9.0"
numpy = ">=1.20.1,<1.25.0"
contourpy = "==1.1.1"
[target.win-64.dependencies]
python = "3.8.*"
[target.unix.dependencies]
python = "3.9.*"
[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-22.04/wxPython-4.2.2-cp39-cp39-linux_x86_64.whl" }
[feature.mysql.dependencies]
wheel = ">=0.45.0, <0.46"
mysql = "=8.0"
[feature.mysql.pypi-options]
no-build-isolation = ["mysqlclient"]
[feature.java.dependencies]
openjdk = "11.*"
maven = ">=3.9.9,<4"
[feature.mod.pypi-dependencies]
# python-javabridge = { path = "./python-javabridge", editable = true }
# python-bioformats = { path = "./python-bioformats", editable = true }
# centrosome = { path = "./centrosome", editable = true }
cellprofiler-release = { path = "./release", editable = true }
cellprofiler-core = { path = "./core", extras = ["test", "dev"], editable = true }
cellprofiler = { path = "./cp", extras = ["test", "build", "docs"], editable = true }
build = ">=1.2.2, <2"
[environments]
dev = ["mysql", "java", "mod"]