Provide examples and update command line interface

[K20shores]

• All examples are easily used from the command line
• Color can be added to the output
• Verbose logging can be enabled and more added
• CSV output is put directly into the terminal, but can also be printed
• Logging format updated to be slightly easier to readf

:: music_box -h                                        
usage: music_box [-h] [-c CONFIG] [-e {CB5,Chapman,FlowTube,Analytical}] [-o OUTPUT] [-v] [--color-output] [--plot PLOT]

MusicBox simulation runner.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Path to the configuration file. If --example is provided, this argument is ignored.
  -e {CB5,Chapman,FlowTube,Analytical}, --example {CB5,Chapman,FlowTube,Analytical}
                        Name of the example to use. Overrides --config.
                        Available examples:
                        CB5: Carbon bond 5
                        Chapman: The Chapman cycle with conditions over Boulder, Colorado
                        FlowTube: A fictitious flow tube experiment
                        Analytical: An example of an analytical solution to a simple chemical system
  -o OUTPUT, --output OUTPUT
                        Path to save the output file, including the file name. If not provided, result will be printed to the console.
  -v, --verbose         Increase logging verbosity. Use -v for info, -vv for debug.
  --color-output        Enable color output for logs.
  --plot PLOT           Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).

Can be used like this

music_box -e Chapman
music_box -e Chapman -o output.csv
music_box -e Chapman -o output/solution.csv
music_box -e Chapman -o output.csv -v
music_box -e Chapman -o output.csv -vv --color-output

Looks like this

and simple plots can be made if gnuplot is installed

music_box -e Chapman -o output.csv --plot CONC.O1D                              

                                                                                                                        
                                                                                                                        
           -18                                            Time vs Species                                               
       2x10    +----------------------------------------------------------------------------------------------------+   
           -18 |          +   **     +           +*         +        * +          +     **    +          +  *       |   
     1.8x10    |-+            **                 **                  **                 **         CONC.O1D********-|   
           -18 |             ***                 ***                * *                 **                 * *      |   
     1.6x10-18 |-+           * *                 * *                * *                ** *                * *    +-|   
     1.4x10    |-+           *  *               ** *                * *                *  *                * *    +-|   
           -18 |             *  *               *  *                * **               *  *               ** *      |   
     1.2x10    |-+           *  *               *  *                *  *               *  *               *  **   +-|   
           -18 |             *  *               *  *               *   *               *  *               *   *     |   
Value  1x10    |-+           *  *               *   *              *   *               *  *               *   *   +-|   
           -19 |            *   *               *   *              *   *               *  **              *   *     |   
       8x10    |-+          *   **              *   *              *   *              **   *              *   *   +-|   
           -19 |            *    *             **   *              *   **             *    *              *   *     |   
       6x10-19 |-+          *    *             *    *              *    *             *    *             **   *   +-|   
       4x10    |-+          *    *             *    *             **    *             *    *             *    **  +-|   
           -19 |            *    *             *    **            *     *             *    *             *     *    |   
       2x10    |-+         **    *             *     *            *     *            **    **            *     *  +-|   
               |          +*     **  +        ** +   *      +     *    +**        +  *      * +          *     *    |   
             0 +----------------------------------------------------------------------------------------------------+   
               0        50000      100000      150000     200000     250000     300000      350000     400000     450000