2. Installation¶

The Recipe System is distributed as part of DRAGONS. DRAGONS is available as a conda package. The installation instructions below will install all the necessary dependencies.

The use of the bash shell is recommended.

2.1. Install Anaconda¶

2.1.1. Download and install Anaconda¶

If you already have Anaconda installed, you can skip this step and go to the Install DRAGONS section below. If not, then your first step is to get and install Anaconda. You can download it from the Anaconda website. We recommend clicking on the “Get Additional Installers” instead of using the green Download button as it will allow you to do a finer selection. Here we show how to use the “Command Line Installer”

Download Anaconda: https://www.anaconda.com/distribution/#download-section

Warning

M1 MacOS Users!!! DRAGONS is not yet built with the M1 architecture. The x86 build will work anyway. But you have to be careful when you install Anaconda.

We recommend that you use the “64-bit Command Line Installer”, ie. the non-M1 version. This version is the x86 (aka Intel) build. When using that version, by default, x86 binaries of the various conda packages will be installed.

M1 can run x86 binaries via the Rosetta interface. It is seamless.

The current version of DRAGONS has been tested with Python 3.9 and Python 3.10. We recommend that you install the standard Python 3 version of Anaconda, the specific Python version can be adjusted later, if necessary.

If you have downloaded the graphical installer, follow the graphical installer instructions. Install in your home directory. It should be the default.

If you have downloaded the command-line installer (recommended), type the following in a terminal, replacing the .sh file name to the name of the file you have downloaded. The /bin/bash -l line is not needed if you are already using bash. The command-line installer allows for more customization of the installation.

$ /bin/bash -l
$ chmod a+x Anaconda3-2022.10-MacOSX-x86_64.sh
$ ./Anaconda3-2022.10-MacOSX-x86_64.sh

($ indicates the terminal prompt.)

Note

To prevent the Anaconda “base” environment from loading automatically, do:

$ conda config --set auto_activate_base false

2.1.2. Verify Anaconda installation¶

We recommend the use of the bash shell:

$ /bin/bash -l

Make sure that ~/anaconda3/bin/conda is in your PATH by doing:

$ which conda

The Anaconda installer should have added conda configurations to the ~/.bash_profile for you. If conda is not found, try:

$ source ~/.bash_profile

If activate is still not found, you might have to add export PATH=~/anaconda3/bin:$PATH to your ~/.bash_profile using your favorite text editor, and run the source command above again.

Note

Sometimes the Anaconda installer will install the software in ~/anaconda3 instead of simply ~/anaconda. Just check in your home directory which one of the tow possibilities was used.

The code Anaconda adds to the .bash_profile will automatically activate anaconda. To activate or deactivate Anaconda manually:

$ conda activate
$ conda deactivate

2.2. Install DRAGONS¶

With Anaconda installed and ready to go, now we can install DRAGONS and the necessary dependencies.

Add conda-forge and the Gemini channel. Those channels host the conda packages that we will need.

$ conda config --add channels conda-forge
$ conda config --add channels http://astroconda.gemini.edu/public

The next step is to create a virtual environment and install the DRAGONS software and its dependencies in it. The name of the environment can be anything you like. Here we use “dragons” as the name and we install Python 3.10.

$ conda create -n dragons python=3.10 dragons ds9

To use this environment, activate it:

$ conda activate dragons

You will need to activate the environment whenever you start a new shell. If you are planning to use it all the time, you might want to add the command to your .bash_profile, after the “conda init” block.

Note

For Linux users only.

As a side note, if you are going to use PyRAF regularly, for example to reduce Gemini data not yet supported in DRAGONS, you should install the iraf-all and pyraf-all conda packages as well.

$ conda create -n geminiconda python=3.10 iraf-all pyraf-all ds9 dragons

DRAGONS and the Recipe System do not need IRAF or PyRAF, however. See the Gemini website for information on how to configure IRAF (https://www.gemini.edu/observing/phase-iii/reducing-data/gemini-iraf-data-reduction-software)

2.3. Configure DRAGONS¶

DRAGONS requires a configuration file dragonsrc that is located in ~/.dragons/:

$ cd ~
$ mkdir .dragons
$ cd .dragons
$ touch dragonsrc

Open dragonsrc with your favorite editor and add these lines:

[interactive]
browser = safari

[calibs]
databases = ~/.dragons/dragons.db get

The browser can be set to any of “safari”, “chrome”, or “firefox”, depending on your preferences. The path and name of the calibration database can be anything, as long at the path exists. The “get” means that DRAGONS will get calibrations from that database. The “store” option can be added after the “get” to have DRAGONS automatically add new processed calibrations to the database. See any of the tutorials to see the calibration manager in action.

On a new installation, you will need to configure ds9 buffer configurations:

$ cd ~
$ cp $CONDA_PREFIX/lib/python3.10/site-packages/gempy/numdisplay/imtoolrc ~/.imtoolrc
$ vi .bash_profile   # or use your favorite editor

  Add this line to the .bash_profile:
    export IMTOOLRC=~/.imtoolrc

While not specific at all to DRAGONS, it is recommended to increase the Operating System limit on the number of opened files. We have seen an increase in reports of the error “Too many open files.”

In your .bash_profile, add the following line to overcome that OS limitation:

ulimit -n 1024

2.4. Test the installation¶

Start up the Python interpreter and import astrodata and the gemini_instruments packages:

$ python
>>> import astrodata
>>> import gemini_instruments

If the imports are successful, i.e. no errors show up, exit Python (Ctrl-D).

Now test that reduce runs. There may be some delay as package modules are compiled and loaded:

$ reduce --help

This will print the reduce help to the screen.

If you have Gemini FITS files available, you can test that the Recipe System is functioning as expected as follow (replace the file name with the name of your file):

$ reduce N20180106S0700.fits -r prepare

If all is well, you will see something like:

                    --- reduce, v3.1.0 ---
All submitted files appear valid
Found 'prepare' as a primitive.
================================================================================
RECIPE: prepare
================================================================================
PRIMITIVE: prepare
------------------
  PRIMITIVE: validateData
  -----------------------
  .
  PRIMITIVE: standardizeStructure
  -------------------------------
  .
  PRIMITIVE: standardizeHeaders
  -----------------------------
     PRIMITIVE: standardizeObservatoryHeaders
     ----------------------------------------
     Updating keywords that are common to all Gemini data
     .
     PRIMITIVE: standardizeInstrumentHeaders
     ---------------------------------------
     Updating keywords that are specific to NIRI
     .
  .
.
Wrote N20180106S0700_prepared.fits in output directory

reduce completed successfully.