Downloading Repository¶
The first thing that needs to be done is to download the repository from Github: https://github.com/vcalderon2009/SDSS_Conformity_Analysis:
git clone https://github.com/vcalderon2009/SDSS_Conformity_Analysis.git
This will download all of the necessary scripts to run the analysis on the SDSS DR7 catalogues.
Installing Environment & Dependencies¶
To use the scripts in this repository, you must have Anaconda installed on the system that will be running the scripts. This will simplify the process of installing all the dependencies.
For reference, see: Anaconda - Managing environments
The package counts with a Makefile with useful functions. You must use this Makefile to ensure that you have all the necessary dependencies, as well as the correct conda environment.
Once Anaconda has been installed, you can use the Makefile to
- Install the Anaconda environment
conformity
. - Update the project environment
conformity
. - Install the
src
package via pip.
Makefile functions¶
- Show all available functions in the Makefile
$: make show-help
1_halo_fracs_calc 1-halo Quenched Fractions - Calculations
1_halo_mcf_calc 1-halo Marked Correlation Function - Calculations
2_halo_fracs_calc 2-halo Quenched Fractions - Calculations
2_halo_mcf_calc 2-halo Marked Correlation Function - Calculations
clean Deletes all build, test, coverage, and Python artifacts
clean-build Remove build artifacts
clean-pyc Removes Python file artifacts
clean-test Remove test and coverage artifacts
cosmo_utils_install Installing cosmo-utils
cosmo_utils_remove Removing cosmo-utils
cosmo_utils_upgrade Upgrading cosmo-utils
download_dataset Download required Dataset
environment Set up python interpreter environment - Using environment.yml
lint Lint using flake8
plot_figures Figures
remove_calc_screens Remove Calc. screen session
remove_catalogues Remove downloaded catalogues
remove_environment Delete python interpreter environment
remove_plot_screens Remove Plot screen session
src_env Import local source directory package
src_remove Remove local source directory package
src_update Updated local source directory package
test_environment Test python environment is setup correctly
update_environment Update python interpreter environment
- Create the environment from the environment.yml file:
$: make environment
- Activate the new environment conformity.
$: source activate conformity
- To update the environment.yml file (when the required packages have changed):
$: make update_environment
- Deactivate the new environment:
$: source deactivate
Auto-activate environment¶
To make it easier to activate the necessary environment, one can check out *conda-auto-env* which activates the necessary environment automatically.
Download Dataset¶
In order to be able to run the scripts in this repository, one needs to first download the required datasets. One can do that by running the following command from the main directory and using the Makefile:
$: make download_dataset
This command will download the required catalogues for the analysis to
the data/external/
directory.
Depending on the variables used for the analysis, one can download different sets of catalogues, depending on what kind of catalogues they want to use it for.
Note
In order to make use of this commands, one will need
wget. If wget is not
available, one can download the files from
http://lss.phy.vanderbilt.edu/groups/data_vc/DR7/sdss_catalogues/
and put them in /data/external/SDSS
.
Steps and Commands¶
By running the following commands, one is able to replicate the results found in Calderon et al. (2018).
git clone https://github.com/vcalderon2009/SDSS_Conformity_Analysis.git
cd SDSS_Conformity_Analysis/
make environment
source activate conformity
python test_environment.py
make download_dataset
make 1_halo_fracs_calc
make 1_halo_mcf_calc
make 2_halo_fracs_calc
make 2_halo_mcf_calc
make plot_figures
open /reports/figures/SDSS/Paper_Figures/
This is the sequence of commands used to create the results shown in Calderon et al. (2018). The scripts already have default values. If one wishes to perform the analysis using a different set of parameters, these can be changed in the Makefile, or by simply calling the functions in the Makefile as:
make SAMPLE="20" download_dataset
This command will download the datasets for the Mr20
galaxy and
group galaxy catalogues.