Installation

Setting up Python Environment

On the UMD cluster, first load the anaconda module and create a clone environment by typing the following commands on the terminal:
module load python/3.8/anaconda
conda create -n UMD --clone=/apps/python/3.8/anaconda

On a non-UMD cluster or local machine, download and install the latest anaconda package wget -c https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-x86_64.sh
bash Anaconda3-2022.05-Linux-x86_64.sh
Next copy-paste the following commands into the terminal:
conda init bash
conda activate UMD
conda update anaconda
conda install gdal
conda install rasterio
conda install numpy
conda install pandas
conda install geopandas
conda install scikit-learn
conda install jupyterlab
conda install matplotlib
conda install seaborn
conda install xarray
conda install rasterstats
conda install tqdm
conda install pytest
conda install sqlalchemy
conda install scikit-image
conda install scipy
conda install pysal
conda install beautifulsoup4
conda install boto3
conda install cython
conda install statsmodels
conda install future
conda install graphviz
conda install pylint
conda install mlxtend
conda install line_profiler
conda install nodejs
conda install sphinx
conda install nbsphinx
conda install catboost
conda install arrow
conda install contextily
conda install openpyxl
conda install -c conda-forge eemont
conda install -c conda-forge logzero
conda install -c conda-forge tinydb
conda install -c anaconda netcdf4
conda install -c conda-forge cachetools
conda install -c conda-forge pygeoprocessing
conda install -c conda-forge pygmt
conda install -c conda-forge dataset
conda install -c conda-forge pyresample
conda install -c conda-forge cartopy
conda install -c conda-forge eli5
conda install -c conda-forge lime
conda install -c conda-forge skrebate
conda install -c conda-forge neptune-client
conda install -c conda-forge xgboost
conda install -c conda-forge pandas-profiling
conda install -c conda-forge bottleneck
conda install -c conda-forge chardet
conda install -c conda-forge sentinelhub
conda install -c conda-forge pygam
conda install -c conda-forge watchdog
conda install -c conda-forge retrying
conda install -c conda-forge fiona
conda install -c conda-forge tpot
conda install -c conda-forge cdsapi
conda install -c conda-forge scikit-garden
conda install -c conda-forge neptune-client
conda install -c conda-forge urllib3
conda install -c ncar pynio
conda install -c conda-forge mpi4py
conda install -c conda-forge scikit-optimize
conda install -c conda-forge requests
pip install --upgrade git+https://github.com/ritviksahajpal/pygeoutil.git
pip install merf tsfresh pyshp palettable geopy geocoder palettable forestci pangres sklearn-contrib-lightning wget pangres pycountry matplotlib-scalebar
pip install git+https://github.com/GeoscienceAustralia/uncover-ml.git

MODIS NDVI

Create an account on the NASA LAADS DAAC website
Follow the instructions here to request a token for your account.
- Login by going to Profile -> Earthdata Login
- Enter your login credentials or register
- Select Profile -> Generate Token from the top menu
- Copy the token from this window and store it somewhere safe and secure
On your local machine/cluster, iIf not already installed, install octvi: https://pypi.org/project/octvi/
On the command prompt type octviconfig and at the place it asks for a token, paste the token you copied earlier.

AgERA5

Create an account on the CDS website
Follow the instructions here to install the CDS API key on your local machine/cluster
Follow these instructions to install the CDS API Key on your local machine/cluster

1. For Windows users:

(i)Login to CDS

(ii)Copy a 2 line code, which shows a url and your own uid:API key details as followed:

A.For CDS users, Go to this page and copy the 2 line code displayed in the black box in the "Install the CDS API key" section as shown below:

B.For ADS users, Go to thispage and copy the 2 line code displayed in the black box in the "Install the CDS API key" section as shown below:

(iii)Paste the 2 line code into a %USERPROFILE%.cdsapirc file, where in your windows environment, %USERPROFILE% is usually located at C:\Users\Username folder). The CDS API expects to find the .cdsapirc file in your home directory.

(iv)Install the CDS API client by running the following command in a Command Prompt window: a. pip install cdsapi # for Python 2.7
b. pip3 install cdsapi # for Python 3

(v)Once the CDS API client is installed, it can be used to request data from the datasets listed in the CDS and ADS catalogues. It is necessary to agree to the Terms of Use of every datasets that you intend to download. Attached to each dataset download form, the "Show API request" button displays the python code to be used.

2. For Mac users:

(i)Login to CDS

(ii)Copy a 2 line code, which shows a url and your own uid:API key details as followed:

A.For CDS users, Go to this page and copy the 2 line code displayed in the black box in the "Install the CDS API key" section as shown below:

B.For ADS users, Go to thispage and copy the 2 line code displayed in the black box in the "Install the CDS API key" section as shown below:

(iii)Create your key file in your home directory in your Terminal window as follows: touch ~/.cdsapirc

(iv)Edit your key file and paste the two lines you copied in Step 2 above to your .cdsapirc key file.

(v)Install the CDS API client using pip, by running the following command in your Terminal window: pip install cdsapi

(vi)Once the CDS API client is installed, it can be used to request data from the datasets listed in the CDS and ADS catalogues. It is necessary to agree to the Terms of Use of every datasets that you intend to download. Attached to each dataset download form, the "Show API request" button displays the python code to be used.

3. For Linux users:

Install the API Key

(i)If you don't have an account, please self register at the CDS registration page

(ii)If you are not logged, please login and go to the step below.

(iii)Copy the code displayed into HOME/.cdsapirc file (in your Unix/Linux environment).

Install the API Client

(i)The CDS API client is a python based library. It provides support for both Python 2.7.x and Python 3.You can Install the CDS API client via the package management system pip, by running on Unix/Linux the command shown in the box beside

Use the CDS API client for data access

(i)Once the CDS API client is installed, it can be used to request data from the datasets listed in the CDS catalogue. It is necessary to agree to the Terms of Use of every datasets that you intend to download.

(ii)Attached to each dataset download form, the following button[show API Request]displays the python code to be used. The request can be formatted using the interactive form. The api call must follow the syntax:
If not already installed, install the cdsapi python library by typing pip install cdsapi in the command prompt.