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Merge pull request #44 from elmbeech/main
update physicell install instruction and rename custom.cpp set_microenv to add_substrate.
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‎man/HOWTO_physicell.md‎

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To install PhysiCell, please follow the instruction written for your operating system:
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+ [Linux](https://github.com/Dante-Berth/PhysiGym/blob/main/man/physicell_setup_poweruser_linux_v20250227a.pdf) 🐧
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+ [MacOSX](https://github.com/Dante-Berth/PhysiGym/blob/main/man/physicell_setup_poweruser_apple_v20250227a.pdf) 🍐
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+ [Linux](https://github.com/Dante-Berth/PhysiGym/blob/main/man/physicell_install_linux.md) 🐧
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+ [MacOSX](https://github.com/Dante-Berth/PhysiGym/blob/main/man/physicell_install_apple.md) 🍐
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+ [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install) 🪟
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‎man/TUTORIAL_physigym_model.md‎

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1.5 Edit the *custom_modules/custom.cpp* file.
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We will need a function that will update the microenvironment with the drug we add.
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At the bottom of the file, add this function to update the microenvironment.
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We will need a function that can add substrate (drug) to the microenvironment.
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At the bottom of the file, add this function.
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```C++
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int set_microenv(std::string s_substrate, double r_dose) {
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int add_substrate(std::string s_substrate, double r_dose) {
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// update substrate concentration
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int k = microenvironment.find_density_index(s_substrate);
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for (unsigned int n=0; n < microenvironment.number_of_voxels(); n++) {
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```C++
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// add substrate
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int set_microenv(std::string s_substrate, double r_dose);
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int add_substrate(std::string s_substrate, double r_dose);
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```
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```C++
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// add drug
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set_microenv("drug", parameters.doubles("drug_dose"));
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add_substrate("drug", parameters.doubles("drug_dose"));
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```
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2.2 Edit the custom_modules/extending/physicellmodule.cpp file for observation.

‎man/physicell_install_apple.md‎

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# Setup PhysiCell on macOS
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We will install everything PhysiCell related under the src folder that we will place in your home directory.
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If you prefer another folder name, please adjust the commands accordingly.
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## &#x1F34E; Operating system dependencies.
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### &#x2728; Install Brew:
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Follow the instruction to download and install brew.
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Basically, copy the installation command, paste it into the Terminal (found at Applications / Utilities), and press the enter key.
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+ https://brew.sh/
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Don't forget to put brew under your $PATH.
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```bash
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if ! grep -Fq '/opt/homebrew/bin' ~/.zshrc
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then
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echo 'export PATH=/opt/homebrew/bin:$PATH' >> ~/.zshrc
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fi
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if ! grep -Fq '/opt/homebrew/bin' ~/.bash_profile
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then
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echo 'export PATH=/opt/homebrew/bin:$PATH' >> ~/.bash_profile
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fi
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if ps -p $$ | grep zsh
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then
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source ~/.zshrc
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else
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source ~/.bash_profile
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fi
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```
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### &#x2728; Install GCC, ImageMagick, and FFmpeg (required by PhysiCell):
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```bash
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brew install gcc imagemagick ffmpeg
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```
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## &#x1F34E; Basic PhyiCell installation
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### &#x2728; Install PhysiCell:
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Copy the installation command, paste it into the Terminal (found at Applications / Utilities), and press the enter key.
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```bash
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if [ -d ~/src/PhysiCell ]
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then
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echo "ERROR : /Users/$USER/src/PhysiCell already exists! please delete the folder if you want to do a reinstallation. installation terminated."
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else
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mkdir -p ~/src
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cd ~/src
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if ! grep -Fq 'export PHYSICELL_CPP=' ~/.zshrc
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then
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echo export PHYSICELL_CPP=$(bash -c "compgen -c" | grep -m 1 -e '^g++-[0-9]\+') >> ~/.zshrc
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fi
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if ! grep -Fq 'export PHYSICELL_CPP=' ~/.bash_profile
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then
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echo export PHYSICELL_CPP=$(bash -c "compgen -c" | grep -m 1 -e '^g++-[0-9]\+') >> ~/.bash_profile
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fi
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if ps -p $$ | grep zsh
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then
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source ~/.zshrc
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else
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source ~/.bash_profile
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fi
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curl -L https://github.com/MathCancer/PhysiCell/archive/refs/tags/$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt).zip > download.zip
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unzip download.zip
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rm download.zip
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rm -fr PhysiCell
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mv PhysiCell-$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) PhysiCell
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fi
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```
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### &#x2728; Test the PhyiCell installation with the template sample project:
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```bash
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cd ~/src/PhysiCell
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```
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```bash
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make template
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```
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```bash
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make -j8
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```
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```bash
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./project
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```
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```bash
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make jpeg
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```
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```bash
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make gif
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```
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```bash
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make movie
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```
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## &#x1F34E; Essential installation
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We will generate a python3 environment with the default python installation, where we will install all PhysiCell modelling related python libraries.
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We will name this python3 environment pcvenv (PhysiCell virtual environment).
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### &#x2728; Install PhysiCell-Studio:
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Copy the installation command, paste it into the Terminal (found at Applications / Utilities), and press the enter key.
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```bash
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if [ -d ~/src/PhysiCell-Studio ]
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then
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echo "ERROR : /Users/$USER/src/PhysiCell-Studio already exists! please delete the folder if you want to do a reinstallation. installation terminated."
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else
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cd ~/src
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python3 -m venv pcvenv
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if ! grep -Fq 'alias pcvenv=' ~/.zshrc
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then
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echo "alias pcvenv=\"source /Users/$USER/src/pcvenv/bin/activate\"" >> ~/.zshrc
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fi
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if ! grep -Fq 'alias pcvenv=' ~/.bash_profile
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then
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echo "alias pcvenv=\"source /Users/$USER/src/pcvenv/bin/activate\"" >> ~/.bash_profile
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fi
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source /Users/$USER/src/pcvenv/bin/activate
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curl -L https://github.com/PhysiCell-Tools/PhysiCell-Studio/archive/refs/tags/v$(curl https://raw.githubusercontent.com/PhysiCell-Tools/PhysiCell-Studio/refs/heads/main/VERSION.txt).zip > download.zip
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unzip download.zip
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rm download.zip
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rm -fr PhysiCell-Studio
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mv PhysiCell-Studio-$(curl https://raw.githubusercontent.com/PhysiCell-Tools/PhysiCell-Studio/refs/heads/main/VERSION.txt) PhysiCell-Studio
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pip3 install -r PhysiCell-Studio/requirements.txt
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cd ~/src/pcvenv/bin/
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echo "python3 /Users/$USER/src/PhysiCell-Studio/bin/studio.py \$*" > pcstudio
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chmod 775 pcstudio
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cd ~/src
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fi
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```
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### &#x2728; Test the PhysiCell-Studio installation:
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```bash
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cd ~/src/PhysiCell
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pcvenv
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pcstudio
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```
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### &#x2728; Official PhysiCell Studio manual:
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+ https://github.com/PhysiCell-Tools/Studio-Guide/tree/main
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## &#x1F34E; Advanced installation
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### &#x2728; Install PhysiCell Data Loader (pcdl) and iPython:
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```bash
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pcvenv
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pip3 install pcdl ipython
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```
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### &#x2728; Test the pcdl installation:
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```bash
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ipython
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```
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```python
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import pcdl
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```
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```python
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exit()
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```
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### &#x2728; Official pcdl manual:
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+ https://github.com/PhysiCell-Tools/python-loader
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## &#x1F34F; IDE VSCode integration (optional)
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1. Install vs code, either from your operating system’s app store or from https://code.visualstudio.com/ .
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2. Generate a vs code profile for physicell:
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```
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File | New Window with Profile
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Name: physicell
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Icon: choose something cool.
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Create
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Add Folder: Users/<username>/src
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click the profile icon (default is a gearwheel) on the left side bottom corner.
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Profile > physicell
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```
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3. Open the Folder:
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```
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File | Open Folder… | src | Open
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Yes, I trust the authors
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```
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4. Install the official python and C++ extensions into the profile:
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```
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click the profile icon (default is a gearwheel) on the left side bottom corner.
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Profile > physicell
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Extension: Python Install
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Extension: C/C++ Install
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```
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5. Link pcvenv (the python environment we generated above):
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```
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View | Command Palette… | Python: Select Interpreter |
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Enter interpreter path… | Find… | src/pcvenv
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```

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