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Remove old configuration and constants systems#1129

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davidorme merged 8 commits intodevelopfrom
1091-remove-old-configuration-and-constants-systems
Nov 4, 2025
Merged

Remove old configuration and constants systems#1129
davidorme merged 8 commits intodevelopfrom
1091-remove-old-configuration-and-constants-systems

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@davidorme davidorme commented Nov 4, 2025

Description

This PR:

  • corrects a wildly unjust omission from the project authors list.

Then there's some stuff with getting rid of the old configuration system:

  • removes all of the modules associated with the old configuration system,
  • removes the associated autodoc files,
  • removes references to those modules from the documentation system. In some cases this is directly by replacing with the new link but some files need widespread revision and so I've cut out broken links to get the docs to pass and then will review the contents in Document new configuration system #1104.

The variables.py file also used JSON Schema in loading and validating the variables.toml file. I've replaced that with pydantic validators and remove the jsonschema package from the project. There is a lot of overlap between the new pydantic loader classes for variables and the existing Variable dataclass, but for the moment I've kept them separate. The issue will be how to handle the post_init attributes if we move to a single pydantic class.

Fixes #1091

Type of change

  • New feature (non-breaking change which adds functionality)
  • Optimization (back-end change that speeds up the code)
  • Bug fix (non-breaking change which fixes an issue)

Key checklist

  • Make sure you've run the pre-commit checks: $ pre-commit run -a
  • All tests pass: $ poetry run pytest

Further checks

  • Code is commented, particularly in hard-to-understand areas
  • Tests added that prove fix is effective or that feature works
  • Relevant documentation reviewed and updated

@davidorme davidorme linked an issue Nov 4, 2025 that may be closed by this pull request
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codecov-commenter commented Nov 4, 2025

Codecov Report

❌ Patch coverage is 95.12195% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.39%. Comparing base (41e7951) to head (d984425).
⚠️ Report is 828 commits behind head on develop.

Files with missing lines Patch % Lines
virtual_ecosystem/core/variables.py 93.33% 2 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1129      +/-   ##
===========================================
+ Coverage    87.74%   94.39%   +6.65%     
===========================================
  Files           90       78      -12     
  Lines         7803     7035     -768     
===========================================
- Hits          6847     6641     -206     
+ Misses         956      394     -562     

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@davidorme davidorme requested a review from sallymatson November 4, 2025 06:31
{name = "Jacob Cook", email = "j.cook17@imperial.ac.uk"},
{name = "Vivienne Groner", email = "v.groner@imperial.ac.uk"},
{name = "Taran Rallings", email = "t.rallings@imperial.ac.uk"},
{name = "Sally Matson", email = "sally.matson21@imperial.ac.uk"},
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😝

Data compilation
~~~~~~~~~~~~~~~~

The :meth:`_compile_data` method is then run to compile the different individual
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:meth: ahah

@davidorme davidorme merged commit 4e4a691 into develop Nov 4, 2025
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@davidorme davidorme deleted the 1091-remove-old-configuration-and-constants-systems branch November 4, 2025 10:15
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Remove old configuration and constants systems

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