Allow PIXL CLI to be installed in non-editable mode

[p-j-smith]

Description

Fixes #318 : Update PIXL CLI so that it can be installed in non-editable mode

• add optional environment variables:

  • PIXL_ROOT: path to directory containing docker-compose.yml file and projects/configs folder, either absolute or relative to the .env file
  • HOST_EXPORT_ROOT_DIR: path on host to export directory, either absolute or relative to the .env file
  • HOST_EXPORT_ROOT_DIR_MOUNT: path on host to export directory, either absolute or relative to the docker-compose.yml file
  • Note, it's necessary to have two variables for the export directory for cases where the .env file is in a different directory to the docker-compose.yml file (which it is for the system tests).

• add docs on installing and running PIXL CLI in non-editable mode

• add environment variables so the system tests can be run in non-editable mode

• run the system tests in non-editable mode in CI

Type of change

Please delete options accordingly to the description.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Suggested Checklist

• I have performed a self-review of my own code.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• I have commented my code, particularly in hard-to-understand areas.
• I have passed on my local host device. (see further details at the CONTRIBUTING document)
• Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
• I have requested review to this PR.
• I have addressed and marked as resolved all the review comments in my PR.
• Finally, I have selected squash and merge

[codecov]

Codecov Report

Attention: Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.

Project coverage is 87.59%. Comparing base (073c6dc) to head (7422fb6).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cli/src/pixl_cli/_io.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #601      +/-   ##
==========================================
- Coverage   87.61%   87.59%   -0.03%     
==========================================
  Files          76       76              
  Lines        3505     3507       +2     
==========================================
+ Hits         3071     3072       +1     
- Misses        434      435       +1     

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[p-j-smith]

we could remove these variables and require that the projects/exports folder is always in f"{PIXL_ROOT}/projects/exports"

[stefpiatek]

Fun! If I don't specify any of them in production, will they still work? I think we're fine to have a drop in coverage

[p-j-smith]

If I don't specify any of them in production, will they still work?

Yep it should do, so long as PIXL is installed in editable mode (I tested this locally by deleting these vars from test/.env and running the tests)