Installation

Clone the repo

To download the DAP software and associated data, clone the GitHub repo by executing:

git clone https://github.com/sdss/mangadap.git

This will create a mangadap directory in the current directory. Although we try to keep the master branch of the repository stable, we recommend using the most recent tag. You can do so by executing:

cd mangadap
./checkout_current_tag

Note

There is a distribution of the DAP that can be installed via pip, but we’re still working out the bugs.

Install Python 3

The DAP is supported for Python 3 only. To install Python, you can do so along with a full package manager, like Anaconda, or you can install python 3 directly from python.org.

Install the DAP code

To install the DAP and ensure its dependencies are met, ensure your at in the top-level mangadap directory and run (preferred):

pip3 install -e .

This approach is preferred because it eases uninstalling the code:

pip3 uninstall sdss-mangadap

Alternatively, if you anticipate making changes to the DAP code, run:

python3 setup.py develop

To install only the DAP dependencies, run:

pip3 install -r requirements.txt

Test your installation

To test the installation, you can do one of the following:

  • Run the tests via the setup script:

    python3 setup.py test

  • Run the tests using pytest directly:

    cd mangadap/tests
python3 -m pytest .

Some tests requires a set of “remote” data that are not located in the repo for space considerations. Downloading the data used by these tests currently requires SDSS Collaboration Access. The link in the last sentence points to a description of how this access is granted for Marvin using a ~\.netrc file. The DAP uses the same ~\.netrc file to authenticate access to the data.sdss.org host for downloading the test data. Once you have your ~\.netrc file, you can download the necessary test data and rerun the tests to include usage of that data like this:

python3 download_test_data.py
cd mangadap/tests
python3 -m pytest .

Local Environment Setup

The DAP uses environmental variables to define the paths to specific data and other repositories. If these are not defined, warnings will be issued every time the DAP is installed or imported. The relevant environmental variables, their default, and their usage are provided below.

Variable

Default

Comments

MANGADRP_VER

v3_0_1 (i.e., MPL-10)

Version of the DRP, used for path construction

MANGA_SPECTRO_REDUX

$HOME/MaNGA/redux

Root path for the reduced data

MANGADAP_VER

mangadap.__version__

Version of the DAP, used for path construction

MANGA_SPECTRO_ANALYSIS

$HOME/MaNGA/analysis

Root path for the analysis data

These environmental variables can be added to, e.g., your .bash_profile file in your home directory or be included in a script that is sourced when you want to run the DAP. The lines added to your .bash_profile file could look something like this:

export MANGA_SPECTRO_REDUX=/Volumes/MaNGA/redux
export MANGA_SPECTRO_ANALYSIS=/Volumes/MaNGA/analysis

export MANGADRP_VER=v3_0_1

export MANGADAP_VER=3.0.0

Note

  • The DAP checks that these variables are defined every time it is imported. If they are not, warnings are raised and the defaults are used.

  • Some of these same variables are defined by Marvin. It is possible to have both Marvin and the DAP point to the same directory, but beware that this may mean that some of the files get overwritten!

  • Two additional variables ($MANGACORE_VER and $MANGACORE_DIR) are used in a specific mode of survey-level execution of the DAP. However, this is a niche usage mode and is effectively never used. See Batch execution using automatically generated scripts.

  • The DAP expects to find the DRP LOGCUBE and LOGRSS files in the directory $MANGA_SPECTRO_REDUX/$MANGADRP_VER/[PLATE]/stack, where [PLATE] is the desired plate number. The LOGRSS files are required if you want to properly account for Spatial Covariance. This path can be altered when executing the DAP.

  • The DAP expects to find/write data to $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER. This path can be altered when executing the DAP, but the directory structure below this used by the DAP to organize its outputs cannot be changed.

  • $MANGADAP_VER is only used to set the path names, not to select the specific version of the DAP that should be used. The version of the DAP used is always the one installed by your python environment.

Problems?

We have limited support to offer installation help. However, if you have problems, particularly those that you think may be a more general problem, please submit an issue.