Installation of CellProfiler 4 from source on M1 Macs - CellProfiler/CellProfiler GitHub Wiki

Below are two sets of installation instructions for installation of CellProfiler from source on Macs using the new Apple M1 processor.

Install homebrew Python
Install CellProfiler inside a conda environment
- For less conflict problems, it is recommended to follow the conda installation

Brew Python installation

Install brew

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Update brew
```
brew update
```

Install python 3.8

brew install [email protected]
echo export PATH="/opt/homebrew/opt/[email protected]/bin:$PATH" >> ~/.zshrc

Install Java
```
brew install java
```

For the system Java wrappers to find this JDK, symlink it with

sudo ln -sfn /opt/homebrew/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk

Set version in zshrc

echo export JAVA_HOME=$(/usr/libexec/java_home -v 1.8) >> ~/.zshrc
source ~/.zshrc

Brew install the packages req
```
brew install freetype mysql
```

Direct to brew openssl

export LDFLAGS="-L$(brew --prefix)/opt/openssl/lib"

Install hdf5
```
brew install [email protected]
```
Make sure to get the version directory correct for the version installed. Find with ls /opt/homebrew/Cellar/hdf5/
```
export HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.12.1_1/
```
Install wxPython dev build (4.1.2)
1. Download dev build of wxPython here: https://wxpython.org/Phoenix/snapshot-builds/
2. Download the latest build with the filename format: wxPython-4.1.2a1.devXXXX+XXXXXXXX.tar.gz
- Ignore the .whl files
1. Then, extract wxPython and navigate into the wxPython folder. Install with:
  - wxPython install can take a while
  - attrdict and sip are required to build wxPython
```
pip3 install attrdict sip==5.5.0
pip3 install .
```

Install CellProfiler and CellProfiler-core from source

git clone https://github.com/CellProfiler/core
cd core
pip3 install .

git clone https://github.com/CellProfiler/CellProfiler
cd CellProfiler

Edit CellProfiler setup.py and comment out the wxPython requirement since we're using a different build
```
install_requires=[
# "cellprofiler-core==4.2.1"
...
"scipy>=1.4.1",
"six",
# "wxPython==4.1.0",
...
```
From inside the CellProfiler directory, install with
```
pip3 install -e .
```
In the CellProfiler directory, start CellProfiler with:
```
python3 -m cellprofiler
```

Conda installation

Install java and set up

brew install java

# For the system Java wrappers to find this JDK, symlink it with
sudo ln -sfn /opt/homebrew/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk

# Set version in zshrc
echo export JAVA_HOME=$(/usr/libexec/java_home -v 1.8) >> ~/.zshrc
source ~/.zshrc

Create a Python3.8 environment with conda

conda create --name cellprofiler python=3.8

Activate the conda environment
```
conda activate cellprofiler
```
Install wxPython dev build (4.1.2)
1. Download dev build of wxPython here: https://wxpython.org/Phoenix/snapshot-builds/
  1. wxPython 4.1.2 is not currently available through pip
2. Download the latest build with the filename format: wxPython-4.1.2a1.devXXXX+XXXXXXXX.tar.gz
- Ignore the .whl files
1. Then, extract wxPython and navigate into the wxPython folder. Install with:
- wxPython install can take a while
- attrdict and sip are required to build wxPython
```
pip3 install attrdict sip==5.5.0
pip3 install .
```

Clone and install CellProfiler-core

git clone https://github.com/CellProfiler/core
pip install -e ./core

Clone CellProfiler

git clone https://github.com/CellProfiler/CellProfiler

Modify the setup.py in the cloned CellProfiler repo.
- Comment out cellprofiler-core and wxpython from the install_requires section, since we are installing our own versions from source:
```
...
"boto3>=1.12.28",
# "cellprofiler-core==4.2.1",
"centrosome==1.2.0",
...
"six",
# "wxPython==4.1.0",
```
Install CellProfiler
```
pip install -e ./CellProfiler
```

Install additional dependencies

# python.app for pythonw
conda install java h5py mysqlclient python.app

Open CellProfiler
- Execute this command from within the cloned CellProfiler repo (get there with cd CellProfiler)
```
pythonw -m cellprofiler
```