Outputs Update #1- Gudrun Output File Organising

[rhinoella]

First stage of solving #457

Organises the files outputted by Gudrun in the following manner:

input_file_name/
 ├── SampleBackgrounds/
 |      ├── SampleBackground1/
 |              ├── NIMRODxxx/
 |                       ├── NIMRODxxx.rat
 |                       ├── NIMRODxxx.grp
 |                       ├── ....
 |
 ├── NormalisationBackground/
 |       ├── NIMRODxxx/
 |                 ├── ....
 |
 ├── Normalisation/
 |       ├── NIMRODxxx/
 |                ├── ....
 |
 ├── sample_name_1/
 |       ├── NIMRODxxx/
 |       |          ├── Outputs/
 |       |          |      ├── NIMRODxxx.rat
 |       |          |      ├── NIMRODxxx.grp
 |       |          |      ├── ....
 |       |          ├── Diagnostics/
 |       |                ├── NIMRODxxx.trans01
 |       |                ├── NIMRODxxx.gr2
 |       |                ├── ....
 |       ├── container_name/
 |       |          ├── ....
 |       ├── sample_name.sample

Every time Gudrun is run for a specified input file, it will use the same input_file_name folder, overriding the SampleBackgrounds, NormalisationBackground and Normalisation folders, but creating a new sample output folder.

If you iterate Gudrun, the sample folder will be structured like this:

 |
 ├── sample_name_2/
 |      ├── IterateByXX_1/
 |      |          ├── NIMRODxxx/
 |      |          |         ├── ....
 |      |          ├── container_name/
 |      |          |         ├── ....
 |      |          ├── sample_name.sample
 |      |                   ├── ....
 |      ├── IterateByXX_2/
 |                ├── ....

[github-actions]

Test Results

    3 files      3 suites   1h 0m 11s ⏱️
  92 tests   92 ✔️ 0 💤 0 ❌
276 runs  276 ✔️ 0 💤 0 ❌

Results for commit 3352fc4.

♻️ This comment has been updated with latest results.

[trisyoungs]

Looks good, and I like the new directory layout of the output files.

One question to maybe just have a quick chat about - where are the lists of file types that are considered "diagnostic" vs "output" stored? Might be nice to check those through before we merge ahead.

[rhinoella]

Looks good, and I like the new directory layout of the output files.

One question to maybe just have a quick chat about - where are the lists of file types that are considered "diagnostic" vs "output" stored? Might be nice to check those through before we merge ahead.

They are specified right here:

GudPy/gudpy/core/output_file_handler.py

Lines 26 to 54 in 9a027e1

	self.Outputs = {
	"sampleOutputs": [
	"dcs01",
	"dcsd01",
	"dcse01",
	"dcst01",
	"dscw01",
	"mdcs01",
	"mdcsd01",
	"mdcse01",
	"mdcsw01",
	"mint01",
	"mgor01",
	"mdor01",
	"gud",
	"sample"
	],
	"sampleDiagnostics": [
	"abs01",
	"bak",
	"gr1",
	"gr2",
	"mul01",
	"mut01",
	"pla01",
	"rawmon",
	"smomon",
	"trans01"
	],

@trisyoungs