install_instructions.txt

# ---------- With installer ----------
After installing miniconda, do the following:

Step 1:
	WINDOWS: Open an Anaconda PowerShell ("powershell" for short) by clicking on: Start --> Anaconda3 (XX-bit) --> Anaconda PowerShell Prompt (Miniconda3). Right click on it and execute as an administrator
	LINUX/MAC: Open a new terminal where the this file is.

Step 2 (WINDOWS only): Copy (CTRL+C) the path to the installation files (where this file is). This can be done by clicking on the top horizontal bar of the file explorer, which will highlight the path we need to go to. For instance, after copying, my path is C:\Users\dcasasor\OneDrive - purdue.edu\postdoc\PharmaPy_dcasasor

Step 3 (WINDOWS only): Introduce the following command in the powershell: cd '<path_in_step_2>' and hit Enter. Do not include the <> characters, but do include the quotes. Replace text in between the <> characters with the path you copied in Step 2. Use CTRL+V to avoid transcription errors

Step 4: After this step, both PharmaPy dependencies and PharmaPy itself should be installed
	WINDOWS: 	Do .\InstallOnWindows.bat and hit Enter. Follow the instructions on screen
	LINUX/MAC: 	To give permissions to the installation file, do chmod +x InstallOnMac.sh. 
				Then, execute it with source InstallOnMac.sh. Follow the instructions on screen

Step 5: Activate the new environment by doing: conda activate <name_of_environment> (exclude <>)

Step 6: Test PharmaPy by moving to the tests/ directory (cd tests) and then running: python reactor_tests.py

# ---------- Manual installation ----------
Step 1: Create a conda environment named <env_name> (optional)

conda create --name <env_name> python=3.9

Step 1.1: If making a virtual environment

conda activate <env_name>

This activates the environment. You may deactivate the environment using
the command:

conda deactivate

All the packages installed will be frozen on this environment, and will be
separate from those installed on your base environment. Using this virtual
environment structure allows us to have only the packages we need to do
the analysis we need to do! If you want to use base, you may continue to step
2 without doing steps 1 and 1.1.

When user does not have a write permission to a required path, please direct the path of the directory

step 1.1.1: Disclose the available environment directories.

conda config -- show envs_dirs

step 1.1.2: Create a path
conda create --prefix <Directory address + /<env_name>>

Step 2: Install the package requirements in requirements.txt

conda install -c conda-forge --file requirements.txt

Step 3: Install PharmaPy; navigate to the source directory

python setup.py develop

Step 4: Check to see if the package is working by running a test in tests/