Update documentation

README.md

@@ -36,18 +36,20 @@ for the risk of Septoria, Easy to map and calculate based on weather data alone.
 The model has been implemented by [Tor-Einar Skog](https://nibio.no/en/employees/tor-einar-skog), [NIBIO](https://nibio.no/en). It is designed to fit into the gridded pest prediction models of [VIPS](https://nibio.no/en/services/vips).
 
 ### Software requirements
-The model can only be run on Linux, as some of the tools mentioned below are only available on Linux. The development and testing of the model has been done using [Ubuntu Linux 22.04LTS](https://ubuntu.com/).
+The model can only be run on Linux, as some of the tools mentioned below are only available on Linux. The development and testing of the model has been done using [Ubuntu Linux](https://ubuntu.com/), versions 22/24.
+
 #### CDO and GDAL
-The heavy lifting in this model is done by the tools [CDO](https://code.mpimet.mpg.de/projects/cdo) and [GDAL](https://gdal.org/). These tools need to be installed and available. CDO is only available on Linux.
+The heavy lifting in this model is done by the tools [CDO](https://code.mpimet.mpg.de/projects/cdo) and [GDAL](https://gdal.org/). These tools need to be installed and available. GDAL can be installed by your package manager. CDO is only available on Linux. CDO (and Python, see below) is managed by [MiniConda](https://docs.anaconda.com/free/miniconda/index.html). All requirements must be specified in the `conda_environment.yml` file.
 
 #### Python requirements
-The Python requirements are specified in `requirements.txt` file, and are included in the virtualenv created by the `run_SEPTREFHUM.sh` (see below).
+The Python requirements are specified in `conda_environment.yml` file, and are included in the conda environment created by the `run_SEPTREFHUM.sh` (see below).
 
 ### Input data requirements
 The model (as per 2023-10-25) assumes that weather data files named `met_1_0km_nordic-[YYYY-MM-DD].nc` are available in the `in/` folder. The files must contain hourly timesteps with the following weather parameters:
 
 * RR (Rainfall in mm)
 * UM (Relative humidity in %)
+* TM (Temperature in °C)
 
 ### Running the model
 It is required that you have set the following environment variables:
@@ -93,9 +95,10 @@ MAPSERVER_EXTENT="-1.5831861262936526 52.4465003983706595 39.2608060398730458 71
 ```bash
 $ ./run_SEPTREFHUM.sh
 ```
-This creates a Python virtualenv, installs all the Python dependencies, runs the model and stores output in a log file. 
+This creates a Conda environment, installs all the CDO/Python dependencies, runs the model and stores output in a log file. 
 
 Alternatively, primarily for development purposes, you can run the Python script SEPTREFHUM directly:
+
 ```bash
 $ ./SEPTREFHUM.py
 ```
@@ -117,13 +120,13 @@ A [Jinja2](https://pypi.org/project/Jinja2/) template mapfile (for [Mapserver](h
 
 Examples of the two layers are shown below
 
-![WARNING_STATUS example. Showing Norway and surrounding area](./WARNING_STATUS_layer_example.png)
+![WARNING_STATUS example. Showing Europe and surrounding areas](./WARNING_STATUS_layer_example.png)
 
-*WARNING_STATUS example. Showing Norway*
+*WARNING_STATUS example. Showing Europe and surrounding areas*
 
-![WHS (Wet Hour Sum) example. Showing Norway and surrounding area](./WHS_layer_example.png)
+![WHS (Wet Hour Sum) example. Showing Europe and surrounding areas](./WHS_layer_example.png)
 
-*WHS (Wet Hour Sum) example. Showing Norway*
+*WHS (Wet Hour Sum) example. Showing Europe and surrounding areas*
 
 ## Notes to self
 

requirements.txt

+# Not in use anymore. Please specify your Python requirements in /conda_environment.yml
 Jinja2
 netCDF4
 pytz