Installation

Follow the Base Package installation below. Using the package manager miniconda is highly recommened.

Base package

For a basic install there are 3 main options:

Download and unzip the package repository and run the following command from the project's root folder:
```
pip install .
```

(Requires git) Create a new venv or conda enviroment and run:

pip install git+https://github.com/ggolde/pyFiberPhotometry.git

(Requires conda) Download and unzip the package repository. In the terminal navigate to the project's root folder and run:
```
conda env create --name photometry --file=envs/basic_env.yml
```

Then activate your enviroment and install pyFiberPhotometry through pip:

conda activate photometry
pip install .

FLMM support (requires conda)

The following tutorial is for adding support for the advanced analysis method Functional Linear Mixed Modeling after installing the basic enviroment. The setup can be a pain but the FMM analysis framework can be very insightful. For more information about FMM for photometry data see the original paper by Dr. Loewinger.

Install all R packages avaliable from conda:

conda activate photometry
conda install -c conda-forge r-base=4.4.3 r-essentials
conda install -c conda-forge r-lme4=1.1_35.5 r-mass=7.3_64 r-mvtnorm=1.2_6 r-gridextra=2.3 r-rfast=2.1.0 r-matrix=1.7_2 r-arrangements r-here r-devtools r-rcurl

Then run the install_FLMM.R script with your conda enviroment active.
```
Rscript envs/install_FLMM.R
```

If you get an error like Error: C17 standard requested but CC17 is not defined for any of your packages try creating the file ~/.R/Makevars and add the following to it depending on your platform:
```
CC17 = clang                # for MacOS
CC17 = gcc                  # for Linux and Windows
C17FLAGS = -O2 -std=gnu17   # for all
```

Install the fastFMM Python wrapper with:
```
pip install fast-fmm-rpy2
```
With your conda enviroment active verify rpy2 is working properly with:
```
python -m rpy2.situation
```

If you get a and error similar to Error importing in API mode: ImportError("dlopen(..._rinterface_cffi_api.abi3.so, 0x0002): Library not loaded: .../lib/libRblas.dylib, you will have to set the enviroment variable R_HOME within your conda enviroment then unintall and reinstall rpy2.
```
conda activate photometry
conda env config vars set R_HOME="$(R RHOME)"
conda deactivate
conda activate photometry
```
```
pip uninstall rpy2 -y
pip uninstall rpy2-rinterface -y
pip uninstall rpy2-robjects -y
conda install -c conda-forge rpy2
```