Fix doctor command and check for SOCRATES updates

[nichollsh]

Description

• Uses the packaging package to reliably check if modules are up to date with proteus doctor
• Checks SOCRATES against latest release on FormingWorlds/SOCRATES
• Checks correct fwl-aragog package, rather than deprecated aragog one
• Add tests for proteus doctor command
• Did not add new documentation since the command is already described

Closes #646

Future PRs should also check the Obliqua repo for updates, once a release has been made for it.

Validation of changes

Works on Fedora 43 with Python 3.12:

(proteus) [16:47:41] harrison@delphinium:~/Projects/PROTEUS
$ proteus doctor
Packages
fwl-aragog: ok
fwl-calliope: ok
fwl-janus: ok
fwl-proteus: Local version 25.11.19 is newer than latest release 25.10.15
fwl-mors: ok
fwl-zephyrus: Local version 25.10.28 is newer than latest release 25.3.11
fwl-zalmoxis: ok
AGNI: ok
SOCRATES: ok

Environment variables
FWL_DATA: ok
RAD_DIR: ok
ZALMOXIS_ROOT: ok
FC_DIR: ok
LA_DIR: Variable not set.

Checklist

• I have followed the contributing guidelines
• My code follows the style guidelines of this project
• I have performed a self-review of my code
• My changes generate no new warnings or errors
• I have checked that the tests still pass on my computer
• I have updated the docs, as appropriate
• I have added tests for these changes, as appropriate
• I have checked that all dependencies have been updated, as required

Relevant people

@timlichtenberg @egpbos

[Copilot]

Pull request overview

Improves proteus doctor by using reliable version parsing/comparison, expanding checks (SOCRATES + additional env vars), and adding unit tests to prevent regressions like downgrade suggestions.

Changes:

• Switch version comparison logic to packaging.version.Version and add a “local is newer than latest release” status.
• Update checked packages (use fwl-aragog) and add a SOCRATES latest-release check via GitHub.
• Expand environment variable checks and add unit tests covering version-status logic and expected env vars.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
src/proteus/doctor.py	Implements packaging-based version comparison, adds SOCRATES + env var checks, updates aragog package name.
tests/test_doctor.py	Adds unit tests for BasePackage.get_status_message() behaviors and expected env vars list.
pyproject.toml	Adds packaging dependency to support robust version parsing.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 69.50%. Comparing base (6fb36f6) to head (6790192).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #669      +/-   ##
==========================================
+ Coverage   69.15%   69.50%   +0.35%     
==========================================
  Files          98       98              
  Lines       10214    10225      +11     
  Branches     1422     1425       +3     
==========================================
+ Hits         7063     7107      +44     
+ Misses       2811     2805       -6     
+ Partials      340      313      -27     

Flag	Coverage Δ
unit-tests	57.55% <100.00%> (+0.10%)	⬆️

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[nichollsh]

@egpbos @timlichtenberg the patch coverage is now 100% and the tests are passing, so the PR is ready for review.