UserGuide.md

+# NES User Guide
+
+- [Console Line Interface](#console-line-interface)
+
+
+## Console Line Interface
+
+The NES CLI allows you to run core operations such as reordering longitudes and checking data directly from the command line. 
+Once NES is installed, the `nes` command becomes available in your terminal.
+
+
+- [Reorder Longitudes](#reorder-longitudes
+- [Checker](#checker)
+
+To list all available subcommands:
+
+```bash
+nes -h
+```
+
+or
+
+```bash
+nes --help
+```
+
+To see help for a specific subcommand:
+
+```bash
+nes <subcommand> -h
+```
+
+For example:
+
+```bash
+nes check -h
+nes reorder -h
+```
+
+
+### Reorder Longitudes
+
+Reorders the longitude dimension in a NetCDF file, converting values from [0, 360] to [-180, 180] and shifting data accordingly.
+
+#### Syntax
+
+```bash
+nes reorder -f <input_file.nc> -o <output_file.nc>
+```
+
+#### Arguments
+
+- `-f`, `--file`: Path to the input NetCDF file. **(required)**
+- `-o`, `--output`: Path to the output NetCDF file. If omitted, the input file is not modified in-place.
+
+#### Example
+
+```bash
+nes reorder -f emissions_360.nc -o emissions_180.nc
+```
+
+### Checker
+
+Checks all variables in a NetCDF file for NaN and/or Inf values.
+
+#### Syntax
+
+```bash
+nes check -f <input_file.nc> [--nan] [--no-nan] [--inf] [--no-inf]
+```
+
+#### Arguments
+
+- `-f`, `--file`: Path to the NetCDF file to validate. **(required)**
+- `--nan`: Enable NaN checking (default: enabled).
+- `--no-nan`: Disable NaN checking.
+- `--inf`: Enable Inf checking (default: enabled).
+- `--no-inf`: Disable Inf checking.
+
+#### Example
+
+```bash
+nes check -f output.nc
+```
+
+Disables Inf checking:
+
+```bash
+nes check -f output.nc --no-inf
+```
\ No newline at end of file