chore: Update dependency to AFMReader

[ns-rse]

Closes #851

With renaming topofileformats > AFMReader and removing the former from PyPI we had to update the dependency.

As detailed in #851 the sum of the arrays changes on switching from topofileformats > AFMReader. The issue notes some details of investigation.

Also took the opportunity to update the installation instructions to make it clearer and include information on installing from GitHub using pip.

[MaxGamill-Sheffield]

Looks good and clean - Thanks for the update to the docs too Neil

Seems to work for the asd file we've been given, and the classic minicircles spm. A few comments though:

1. I think it'd be useful if the available channels were returned upon failure, these are printed in the logger under debug and so I think it shouldn't be too bad to implement (I can do this if necessary)
2. The logger exceptions for unclosed log files are throwing messy lines:

(asdtest) Max:TopoStats Maxgamill$ topostats process -c test/default_config.yaml 
Exception ignored in: <_io.FileIO name='/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/TopoStats-2024-06-06-10-28-12.log' mode='ab' closefd=True>
Traceback (most recent call last):
  File "/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/topostats/statistics.py", line 8, in <module>
    LOGGER = setup_logger(LOGGER_NAME)
ResourceWarning: unclosed file <_io.TextIOWrapper name='/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/TopoStats-2024-06-06-10-28-12.log' mode='a' encoding='UTF-8'>
Exception ignored in: <_io.FileIO name='/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/TopoStats-2024-06-06-10-28-12.log' mode='ab' closefd=True>
Traceback (most recent call last):
  File "/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/topostats/processing.py", line 31, in <module>
    LOGGER = setup_logger(LOGGER_NAME)
ResourceWarning: unclosed file <_io.TextIOWrapper name='/Users/Maxgamill/Desktop/Uni/PhD/topo_asd/TopoStats/TopoStats-2024-06-06-10-28-12.log' mode='a' encoding='UTF-8'>
[Thu, 06 Jun 2024 10:28:12] [INFO    ] [topostats] The YAML configuration file is valid.
[Thu, 06 Jun 2024 10:28:12] [INFO    ] [topostats] The YAML plotting configuration file is valid.

[ns-rse]

Thanks for having a look @MaxGamill-Sheffield

I'm going to avoid scope creep and keep this PR focused on switching topofileformats > AFMReader (despite cramming in changes to the docs/installation.md). Please create issues to keep track of these suggestions and they can be picked up and addressed as and when (I basically don't have time to address them right now).

[MaxGamill-Sheffield]

Looks good