Address review comments

docs/install.md

@@ -92,3 +92,8 @@ _**Note**: if you have already installed spack locally and you want to upgrade t
 a newer version, you might first have to clear the cache to avoid conflicts:
 `spack clean -m`_
 
+It is recommended to always have the python virtual environment active when working with `excalibur-tests`.
+However, it should be noted that since `Spack` is not installed via `pip`, it will be installed outside of the
+python virtual environment. Also, keep in mind that the Spack environments that are discussed in the next section 
+are different and independent of the python virtual environment.
+

docs/setup.md

@@ -81,7 +81,8 @@ configuration.  The numbers you need to watch out for are:
 
 When using Spack as build system, ReFrame needs a [Spack
 environment](https://spack.readthedocs.io/en/latest/environments.html) to run
-its tests. Follow these steps to create a Spack environment for a new system:
+its tests. The Spack environment is separate and independent of the python
+virtual environment. Follow these steps to create a Spack environment for a new system:
 
 #### Create the environment
 ```sh

docs/tutorial/getting-started.md

@@ -1,18 +1,20 @@
 # Getting Started on HPC systems
 
-These tutorials have been ran in in-person workshops on various HPC systems in the UK. It should be possible to run on any of the [supported systems](../systems.md), or to [set up the tools](../setup.md) on a local machine. If you have access to one of the systems we've previously used, this tutorial helps you get set up. Otherwise, please consult the [documentation](../install.md)
+These tutorials have been run in in-person workshops on various HPC systems in the UK. 
+It should be possible to run on any of the [supported systems](../systems.md), or to [set up the tools](../setup.md) on a local machine. 
+If you have access to one of the systems we've previously used, this tutorial helps you get set up. Otherwise, please consult the [documentation](../install.md)
 
 ## Connecting
 
 === "Cosma"
 
-	To run these tutorials on Cosma, you need to [connect to Cosma via ssh](https://cosma.readthedocs.io/en/latest/ssh.html). You will need
+	To run these tutorials on Cosma, you will need to [connect to Cosma via ssh](https://cosma.readthedocs.io/en/latest/ssh.html). You will need
 
 	1. A Cosma account. You can [request a new account](https://cosma.readthedocs.io/en/latest/account.html) if you haven't got one you can use. You can use an existing Cosma account to complete the tutorials.
 	2. A command line terminal with an ssh client. Most Linux and Mac systems come with these preinstalled. Please see [Connecting to ARCHER2](https://docs.archer2.ac.uk/user-guide/connecting/#command-line-terminal) for more information and Windows instructions.
 
 === "ARCHER2"
-	To run these tutorials on ARCHER2, you need to [connect to ARCHER2 via ssh](https://docs.archer2.ac.uk/user-guide/connecting/). You will need
+	To run these tutorials on ARCHER2, you will need to [connect to ARCHER2 via ssh](https://docs.archer2.ac.uk/user-guide/connecting/). You will need
 
 	1. An ARCHER2 account. You can [request a new account](https://docs.archer2.ac.uk/quick-start/quickstart-users/#request-an-account-on-archer2) if you haven't got one you can use. You can use an existing ARCHER2 account to complete the tutorials.
 	2. A command line terminal with an ssh client. Most Linux and Mac systems come with these preinstalled. Please see [Connecting to ARCHER2](https://docs.archer2.ac.uk/user-guide/connecting/#command-line-terminal) for more information and Windows instructions.

docs/tutorial/postprocessing_tutorial.md

@@ -8,7 +8,8 @@ Now let's browse the benchmark performance results, and create plots to visualis
 
 ### Postprocessing features 
 
-The postprocessing can be performed either on a GUI or a CLI. It takes as input either a single perflog or a path that contains perflogs, and it is driven by a configuration YAML file (more on this later). Its outputs can be csv files of the whole or filtered perflog contents, as well as plots.
+The postprocessing can be performed either on a GUI or a CLI. It takes as input either a single perflog or a path that contains perflogs, and it is driven by a configuration YAML file (more on this later). 
+Its outputs can be csv files of the whole or filtered perflog contents, as well as plots.
 
 ![Screenshot from 2024-04-25 17-01-41](https://hackmd.io/_uploads/HkWxlWOZ0.png)
 

docs/tutorial/setup-python.md

@@ -1,7 +1,8 @@
 === "Cosma"
 
     This tutorial is run on the [Cosma](https://cosma.readthedocs.io/en/latest/) supercomputer.
-    It should be straightforward to run on a different platform, the requirements are  `gcc`, `git` and `python3`. (for the later parts you also need `make`, `autotools`, `cmake` and `spack`).
+    It should be straightforward to run on a different platform, the requirements are  `gcc 4.5`, `git 2.39` and `python 3.7`. 
+	(for the later parts you also need `make`, `autotools`, `cmake` and `spack` but these can be installed locally).
     Before proceeding to install ReFrame, we recommend creating a python virtual environment to avoid clashes with other installed python packages.
     First load a newer python module.
     ```bash

docs/use.md

@@ -75,6 +75,13 @@ reframe -c benchmarks/apps/sombrero -r --performance-report -S env_vars=OMP_PLAC
 runs the `benchmarks/apps/sombrero` benchmark setting the environment variable `OMP_PLACES`
 to `threads`.
 
+### Output directories
+
+By default `reframe` creates three output directories (`stage`, `output` and `perflogs`) in the directory 
+where it is run. Output can be written to a different base directory using the [`--prefix` command-line option](https://reframe-hpc.readthedocs.io/en/stable/manpage.html#cmdoption-prefix).
+
+The individual output directories can also be changed using the `--stage`, `--outputdir` and `--perflogdir` options.
+
 ## Usage on unsupported systems
 
 The configuration provided in [`reframe_config.py`](https://github.com/ukri-excalibur/excalibur-tests/blob/main/benchmarks/reframe_config.py) lets you run the