Installation instructions

# Python Environment¶

Grizli has been developed within a miniconda Python environment. Module dependencies, including general utilities like numpy, scipy, and matplotlib and astronomy tools like astropy and specific software for dealing with space-telescope data (stsci.tools, drizzlepac, etc.) are installed using the provided requirements.txt file (see below). Most development is done in a python 3.7 environment on a MacBook Pro running Mojave 10.14.6. The basic build is tested in (Linux) python 3.6, 3.7 and 3.8 with the GitHub actions continuous integration (CI) tools, but the current test suite does not yet test much of the full functionality of the code.

## Preferred installation with conda/pip¶

The environment can be installed with pip and the requirements.txt file, which was added in 2021 to enable the github “actions” CI testing environment (migrated from travis-ci.org). The instructions below assume you have conda installed, e.g., with miniconda.

# Generate a conda environment named "grizli-dev" or anything else
# This will just provide the base python distribution (incl. pip)
conda create -n grizli-dev python=3.7

# Activate the environment.  This needs to be done each time you
# start a new terminal, or put it in ~/.bashrc
conda activate grizli-dev

# or some other location, even /tmp/
cd /usr/local/share/python

# Fetch the grizli repo
git clone https://github.com/gbrammer/grizli.git
cd grizli

# Compile and install the grizli module.  Only needs to be done
# once or after updating the repository (e.g., with git pull).
# "--editable" builds the cython extensions needed for pytest
pip install --editable . -r requirements.txt

# One last dependency that doesn't install with pip and is needed
# for the WFC3/IR pipeline calwf3
conda install hstcal

pip install pytest
pytest


If you are planning to run simultaneous fits to grism spectra plus photometry using the eazy-py connection, install eazy-py from the repository to ensure that you get its dependencies.

cd /usr/local/share/python # location from above
conda activate grizli-dev # or whatever was chosen above

# Fetch the eazy-py repo
git clone --recurse-submodules https://github.com/gbrammer/eazy-py.git
cd eazy-py

# Only needs to be done once or after updating the repository.
pip install . -r requirements.txt

# Run basic tests with pytest
# (pysynphot failure is not critical)
pytest


Once you’ve built the code, proceed to Set up directories and fetch config files.

## Installation with conda and environment.yml¶

Note

As of May 2021 the conda/pip installation above is favored since the CI tests were migrated from travis to GitHub actions, which are run on each push to the repository.

An environment.yml file is included with the grizli distribution to provide an automatic way of installing the required dependencies, getting them from conda, pip, and directly from github as necessary. To use this file, do the following

cd /usr/local/share/python # or some other location, even /tmp/

# Fetch the grizli repo
git clone https://github.com/gbrammer/grizli.git
cd grizli

# Generate a conda environment named "grizli-dev" or anything else
# (Note environment_min.yml renamed to environment.yml for >0.10.0)
conda env create -f environment.yml -n grizli-dev

# Activate the environment.  This needs to be done each time you
# start a new terminal, or put it in ~/.bashrc
conda activate grizli-dev

# Compile and install the grizli module.  Only needs to be done
# once or after updating the repository.
python setup.py install


## Manual installation of dependencies¶

There are a few additional modules that grizli may use but that aren’t explicitly listed in the requirements.txt file.

Amazon Web Services - If you’re running the full HST reduction pipeline with grizli, the code can automatically pull FITS files from the public AWS S3 bucket mirror of the archive. This requires the AWS command line tools and the boto3 module:

# Put your AWS credentials, etc. in ~/.aws
pip install awscli
pip install boto3


lacosmicx - Fast Python implementation of Pieter van Dokkum’s L.A.Cosmic (2001PASP..113.1420V) software for identifying cosmic rays in single images. The image preparation wrapper scripts in grizli.prep run lacosmicx if a supplied list of direct or grism images contains only a single file.

git clone https://github.com/cmccully/lacosmicx.git
cd lacosmicx
python setup.py install


Note

The lacosmicx dependency was removed from environment.yml file 2019.12.31 because it was breaking on OSX Mojave 10.14.6 with a compilation error like unsupported option '-fopenmp'. The workaround below with the Homebrew version of gcc may work after verifying the correct path to the gcc-8 executable:

brew install gcc
CC=/usr/local/Cellar/gcc/10.2.0/bin/gcc-10 pip install git+https://github.com/cmccully/lacosmicx.git


# Set up directories and fetch config files¶

Grizli requires a few environmental variables to be set that point to directory location of configuration files. The “export” lines below can be put into the ~/.bashrc or ~/.bash_profile setup files so that the system variables are set automatically when you start a new terminal/shell session.

# Put these lines in ~/.bashrc
export GRIZLI="${HOME}/grizli" # or anywhere else export iref="${GRIZLI}/iref/"  # for WFC3 calibration files
export jref="${GRIZLI}/jref/" # for ACS calibration files # Make the directories, assuming they don't already exist mkdir$GRIZLI
mkdir $GRIZLI/CONF # needed for grism configuration files mkdir$GRIZLI/templates # for redshift fits

mkdir $iref mkdir$jref


There are configuration and reference files not provided with the code repository that must be downloaded. Helper scripts are provided to download files that are currently hard-coded:

>>> import grizli.utils
>>> # set ACS=True below to get files necessary for G800L processing
>>> grizli.utils.fetch_default_calibs(ACS=False) # to iref/iref
>>> grizli.utils.fetch_config_files()            # to $GRIZLI/CONF  The grism redshift fits require galaxy SED templates that are provided with the repository but that need to be in a specific directory, $GRIZLI/templates. This is done so that users can modify/add templates in that directory without touching the files in the repository itself. For default processing they can by symlinked from the repository:

>>> import grizli.utils