sylvainschmitt / downclim

Snakemake and Singularity workflow to Downscale Climate Projections

👋 Hi there!

I'm Sylvain, an ecologist at CIRAD (https://www.cirad.fr), a French research center working with developing countries on environmental and development issues. I am currently conducting research into modeling the joint effect of climate change and anthropogenic disturbance on the dynamics of Amazonian tropical forests.

More info at https://sylvainschmitt.netlify.app/.

downclim's Issues

Advice for credentials storage

Hello @thomasarsouze ,

I'm using pyesgf.logon to connect to esgf nodes and retrieve projections, which is working very well. However to use it, I need to pass user credentials to the function. In this case the openid and the password:

from pyesgf.logon import LogonManager
lm = LogonManager()
lm.logon_with_openid(openid='https://esgf-node.ipsl.upmc.fr/esgf-idp/openid/sschmitt', password="pwd", interactive=False)

Do you have any advice on the best practice to stock this credentials? I was planning on adding a new key pointing to esgf credentials in the configuration file. And then the user have to simply write the file with yaml keys openid and password to be read by the python script. I will obviously make git ignore this credential file. This is the simplest way I imagine it, but maybe this is not secure enough?

Thanks in advance,

Sylvain

Issue with snakemake in mamba environment

Hi @thomasarsouze,

I'm having an issue when running the rule "get_area" of the pipeline with snakemake in a mamba environment as recommended.

I have two installation of snakemake, a system one with sudo apt-get install snakemake and another in mamba with mamba create -c conda-forge -c bioconda -n snakemake snakemake. The system install is working well. But as soon as I use snakemake in the conda environment as follow:

conda activate snakemake
snakemake -j 1 results/countries/New-Caledonia.shp --use-conda 2> log.txt

I have an issue with RUST that I traced back adding the following line in the top of the Snakemake file: os.environ["RUST_BACKTRACE"] = "full".

I have put the error log below (pretty long). Thanks in advance for your help and let me know if you need more information.

log.txt