feat: update docs

[WojtAcht]

No description provided.

[Copilot]

Pull request overview

Updates the documentation to reflect recent sampling/LON API changes in lonpy, including new configuration parameter names and newly documented metrics/config options.

Changes:

• Replace n_iterations, hash_digits, and opt_digits usage in docs with max_perturbations_without_improvement, coordinate_precision, and fitness_precision.
• Document additional metrics returned by compute_metrics() (success, deviation) and add a new section describing LONConfig for LON construction.
• Remove duplicated “Dependencies” sections from various docs pages and update examples accordingly.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
docs/user-guide/sampling.md	Updates sampler config docs + adds LONConfig section and precision parameter guidance.
docs/user-guide/examples.md	Updates example configs to new parameter names and fixes known_best scaling.
docs/user-guide/analysis.md	Documents performance metrics (success, deviation) and how to compute them separately.
docs/getting-started/quickstart.md	Updates quickstart code and metrics table for new config/metrics.
docs/getting-started/installation.md	Removes dependencies list section.
docs/getting-started/concepts.md	Updates node identification/metrics terminology to new precision + adds new metric entries.
docs/contributing.md	Removes commit message guidance section.
docs/api/index.md	Adds LONConfig to API index and removes dependencies list section.
README.md	Updates README examples to new sampler config parameters.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[pFornagiel]

If we are updating docs, we can add the new LONConfig class documentation to the docs/api/lon.md file as part of this PR:

# LON Module

::: lonpy.lon.LON
    options:
      show_root_heading: true
      show_source: true
      members:
        - from_trace_data
        - n_vertices
        - n_edges
        - vertex_names
        - vertex_fitness
        - vertex_count
        - get_sinks
        - get_global_optima_indices
        - compute_metrics
        - to_cmlon

::: lonpy.lon.CMLON
    options:
      show_root_heading: true
      show_source: true
      members:
        - from_lon
        - n_vertices
        - n_edges
        - vertex_fitness
        - vertex_count
        - get_sinks
        - get_global_sinks
        - get_local_sinks
        - compute_metrics

::: lonpy.lon.LONConfig
    options:
      show_root_heading: true
      show_source: true
      members:
        - fitness_aggregation
        - warn_on_duplicates
        - max_fitness_deviation
        - eq_atol

[pFornagiel]

I would also suggest adding a separate_signature option of mkdocstrings plugin in mkdocs.yml file:

// ... 
plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          options:
            docstring_style: google
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            heading_level: 2
            members_order: source
            show_signature_annotations: true
            separate_signature: true // <- SET TO TRUE
// ...

This changes the way function / method signatures are rendered, which really helps while reading through the page, comparison below (Left - separate_signature: false | Right - with separate_signature: true)

[Copilot]

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 13 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.