install_notes.txt

## Distribution
Use anaconda distribution for setting up python environments.
https://www.anaconda.com/distribution/

## Installation

> conda env create --file cosmos3requirements.yml -n cosmostools3
> source activate cosmostools3
> python setup.py develop
> conda install -c conda-forge ipywidgets

(This installs and passes tests on Mac OSX 10.15.3 and Ubuntu 18.04.1 with conda version 4.8.3)

For windows machines, use cosmos3requirement_windows.yml.
(This has been tested on ....TODO)



Note: There is a small possibility that due to a certain quirk in loading ome.tif files in import_raw_cosmos_data.py, you may need to use python2 for that script. It is possible the library call to load the files has now been properly upgraded for python3 and this is irrelevant. If it is necessary, you can likely just call python2 within the cosmos3 environment, or start a new environment (this has not been very well tested) with

> conda env create --file install_stuff/cosmos2requirements.yml -n cosmos2 python=2.7
> source activate cosmos2
> python setup.py develop

(This installs on Mac OSX 10.15.3)

For linux-64, if the cosmos2requirements.yml approach does not work, you 
Should instead be able to use the spec_file:
> conda create --name cosmos2 --file cosmosdata2_spec_file.txt

(This installs on Ubuntu 18.04.1)