feat: improve docs

[WojtAcht]

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[codecov]

Codecov Report

Attention: Patch coverage is 89.04110% with 8 lines in your changes missing coverage. Please review.

Project coverage is 77.36%. Comparing base (57ed1d2) to head (5e377ef).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
pyhms/demes/shade_deme.py	16.66%	5 Missing ⚠️
pyhms/demes/sobol_deme.py	25.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #90      +/-   ##
==========================================
+ Coverage   77.30%   77.36%   +0.05%     
==========================================
  Files          67       67              
  Lines        3150     3145       -5     
==========================================
- Hits         2435     2433       -2     
+ Misses        715      712       -3     

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[Copilot]

Pull Request Overview

This pull request primarily refactors deme initialization to use a unified DemeInitArgs object across multiple modules, while also updating plotting parameters and example notebook configurations.

• Refactored deme constructors in several modules (e.g., EA, DE, CMA, Local, Sobol, LHS, Shade) to accept a single DemeInitArgs parameter.
• Updated the landscape approximator and kriging plotting functions with new parameters and legend settings.
• Modified example notebook code to use updated sprout functions and adjusted evaluation limits.

Reviewed Changes

Copilot reviewed 15 out of 17 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test/test_tree_format.py	Updated test to import and use DemeInitArgs for CMADeme creation.
pyhms/tree.py	Replaced init_root with init_from_config and updated legend setup.
pyhms/demes/*.py	Unified deme constructors to use DemeInitArgs; updated variable names accordingly.
pyhms/demes/initialize.py	Changed init_from_config to use merged config-to-deme mapping with DemeInitArgs.
pyhms/cluster/landscape_approximator.py	Enhanced plateau contour plotting API.
pyhms/cluster/kriging.py	Adjusted threshold computation and legend configuration in contour plots.
examples/landscape_approximation.ipynb	Updated notebook parameters and sprout condition for better demo behavior.

Files not reviewed (2)

• docs/custom_demes.rst: Language not supported
• docs/index.rst: Language not supported

Comments suppressed due to low confidence (2)

pyhms/cluster/kriging.py:91

• The threshold calculation has been changed from using the population median to the 10th quantile of z. Please verify that this change aligns with the intended behavior for plateau detection.

threshold = np.quantile(z, 0.1)

examples/landscape_approximation.ipynb:150

• The evaluation limit was reduced from 10000 to 1000, which may affect the tree run duration. Confirm that this change is intentional and does not negatively impact experimental outcomes.

global_stop_condition = SingularProblemEvalLimitReached(1000)