Merge improvements made in test-fix branch to master branch

README.md

@@ -9,10 +9,12 @@ The documentation of the base package `neurodesign` is available at [ReadTheDocs
 ## File description
 
 ```
-├── docs                    Contains the source code to generate the documentation with sphinx.
-├── examples                Contains scripts to perform a design optimalisation.
+├── docs                    Contains the source code to generate the documentation with sphinx (WIP).
+├── manuals                 Contains comprehensive markdown documentation on neurodesign-plus.
 └── neurodesign             Folder with the source code of the python package
     └── media               Folder contains the logo of neurodesign, which is used in the reports.
+├── tests                   Contains scripts to test modifications to the package.
+└── tutorials               Contains .ipynb tutorials on neurodesign-plus, the base functions and the new functions.
 ```
 
 ## Overview of Modifications
@@ -27,7 +29,7 @@ The modifications focus on the `classes.py` file, specifically enhancing the `Ex
 
 ## Installation & Setup
 
-See [link](./SETUP.md) for environment setup and installation instructions.
+See [link](./manuals/SETUP.md) for environment setup and installation instructions.
 
 ---
 
@@ -69,18 +71,21 @@ The Neurodesign Python package optimizes these experiments based on four metrics
 
 During optimization, you can assign weights to these metrics to reflect what matters most for your experiment.
 
+**See [link](./manuals/METRICS.md) for guidelines on interpreting metrics when optimising designs.**
+
 ---
 
 ## Modifications Documentation
 
-See [link](./TECHNICAL_CHANGES.md) for a detailed summary of changes relative to the upstream Neurodesign package.
+See [link](./manuals/TECHNICAL_CHANGES.md) for a detailed summary of changes relative to the upstream Neurodesign package.
 
-With these new parameters and changes in the package, it is simply a matter of defining the parameters required for the specific use case and the tool will perform the optimization. 
+With these new parameters and changes in the package, it is simply a matter of defining the parameters required for the specific use case and the tool will perform the optimization.
 
 **Note** that precedence for order follows as (if all provided):
-* Fixed ordering
-* Controlled ordering 
-* Random ordering
+
+- Fixed ordering
+- Controlled ordering
+- Random ordering
 
 The same holds for conditional_ITI and stimuli_durations.
 
@@ -89,25 +94,28 @@ The same holds for conditional_ITI and stimuli_durations.
 ## Tutorials
 
 Tutorial notebooks / scripts are under `tutorials/`.
+
 ```
 tutorials
-├── base_functions                                 Contains tutorials of the different base package functions.
-├── new_functions                                  Contains tutorials on using the modifications.
-└── tutorial_neurodesign_base_overview             Base tutorial of the neurodesign package.
+├── base_functions                                    Contains tutorials of the different base package functions.
+├── new_functions                                     Contains tutorials on using the modifications.
+├── tutorial_1_neurodesign_base_overview              Base tutorial of the neurodesign package.
+└── tutorial_2_comparing_designs_across_experiments   Tutorial on comparing designs across diverse experiment definitions.
 ```
 
 For quick access, find the tutorials in the table below:
 | # | Tutorial | Link |
 | :---: | :--- | :---: |
-| 1 | **tutorial_neurodesign_base_overview** | [View](./tutorials/tutorial_neurodesign_base_overview.ipynb) |
-| 2 | **tutorial_base_compare_and_simulate** | [View](./tutorials/base_functions/tutorial_base_compare_and_simulate.ipynb) |
-| 3 | **tutorial_base_comparing_designs** | [View](./tutorials/base_functions/tutorial_base_comparing_designs.ipynb) |
-| 4 | **tutorial_base_discovering_best_design** | [View](./tutorials/base_functions/tutorial_base_discovering_best_design.ipynb) |
-| 5 | **tutorial_base_optimizating_and_report** | [View](./tutorials/base_functions/tutorial_base_optimizating_and_report.ipynb) |
-| 6 | **tutorial_new_controlled_probabalistic_ordering** | [View](./tutorials/new_functions/tutorial_new_controlled_probabalistic_ordering.ipynb) |
-| 7 | **tutorial_new_fixed_order** | [View](./tutorials/new_functions/tutorial_new_fixed_order.ipynb) |
-| 8 | **tutorial_new_varied_ITI** | [View](./tutorials/new_functions/tutorial_new_varied_ITI.ipynb) |
-| 9 | **tutorial_new_varied_stimuli_durations** | [View](./tutorials/new_functions/tutorial_new_varied_stimuli_durations.ipynb) |
+| 1 | **tutorial_1_neurodesign_base_overview** | [View](./tutorials/tutorial_1_neurodesign_base_overview.ipynb) |
+| 2 | **tutorial_2_comparing_designs_across_experiments** | [View](./tutorials/tutorial_2_comparing_designs_across_experiments.ipynb) |
+| 3 | **tutorial_base_compare_and_simulate** | [View](./tutorials/base_functions/tutorial_base_compare_and_simulate.ipynb) |
+| 4 | **tutorial_base_comparing_designs** | [View](./tutorials/base_functions/tutorial_base_comparing_designs.ipynb) |
+| 5 | **tutorial_base_discovering_best_design** | [View](./tutorials/base_functions/tutorial_base_discovering_best_design.ipynb) |
+| 6 | **tutorial_base_optimizating_and_report** | [View](./tutorials/base_functions/tutorial_base_optimizating_and_report.ipynb) |
+| 7 | **tutorial_new_controlled_probabalistic_ordering** | [View](./tutorials/new_functions/tutorial_new_controlled_probabalistic_ordering.ipynb) |
+| 8 | **tutorial_new_fixed_order** | [View](./tutorials/new_functions/tutorial_new_fixed_order.ipynb) |
+| 9 | **tutorial_new_varied_ITI** | [View](./tutorials/new_functions/tutorial_new_varied_ITI.ipynb) |
+| 10 | **tutorial_new_varied_stimuli_durations** | [View](./tutorials/new_functions/tutorial_new_varied_stimuli_durations.ipynb) |
 
 ## Credits