Refactor and update Soundscape Analysis documentation structure#141
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
pixi controls the format of environment.yml; reformatting it breaks the file. Global exclude covers prettier, trailing-whitespace, and all other hooks cleanly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
publish-pypi now waits for publish-conda so a conda failure can't leave us with a duplicate PyPI upload on retry. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Removed documentation badge from README.
- Remove EmbeddedRPackage proxy (bypassed by its own module) - Remove _state.session and _state.circe fields; add circe_sourced: bool - Flatten check_dependencies() — remove redundant nested check_r_availability() calls inside check_sn_package() and check_circe_package() - Remove _confirm_install_r_packages() and all TTY/env-var auto-install logic; ImportError with clear instructions instead - initialize_r_session() returns None (no caller used the dict return) - Remove is_session_active() thin wrapper - Fix double-check in install_r_packages() - Extract _np2rmat() in _rsn_wrapper, replacing 3x duplicated R matrix boilerplate - Batch-draw in sample_mtsn (max(n,64) per R call) instead of n=1 per candidate - Update tests to assert on _state.active / _state.circe_sourced directly Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Remove remaining scaffolding and collapse the CircE two-step API: - Drop importlib.metadata and NoReturn imports (both now dead) - Remove _state.stats — loaded but never accessed by any wrapper - Remove is_ready property — active=True is set atomically after all packages load, so the check in get_r_session() can never trigger - Inline the _raise_*_error inner closures in all three check functions; raises directly in except blocks, removing ~20 lines of define-then-call scaffolding with no diagnostic benefit - Simplify check_circe_package(): drop redundant _get_circe_embedded_paths() call and outer try/except — _source_embedded_circe_scripts() already converts every exception to ImportError internally - Merge bfgs() + extract_bfgs_fit() into bfgs_fit() returning dict[str, Any]; the ro.ListVector intermediate never left the call chain and is now gone - Update circe.py: compute_bfgs_fit() calls bfgs_fit(), from_bfgs() accepts fit_stats: dict instead of a raw R ListVector - Update tests: TestBfgsWrapper uses bfgs_fit() directly; drop the test that asserted on the internal ro.ListVector type Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Move CircE and skew-normal wrapper functions into `_r_wrapper`, remove the old split modules, and update imports and tests to use the unified internal API.
Removed separate CircE wrapper and skew-normal wrapper sections — all three are now documented from the single _r_wrapper module. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Agent-Logs-Url: https://github.com/MitchellAcoustics/Soundscapy/sessions/d8340c82-4312-4551-8333-b0328a7a0c9d Co-authored-by: MitchellAcoustics <22335636+MitchellAcoustics@users.noreply.github.com>
…tVector input Agent-Logs-Url: https://github.com/MitchellAcoustics/Soundscapy/sessions/9e7d4c44-7307-4f40-b931-578e0ab982a4 Co-authored-by: MitchellAcoustics <22335636+MitchellAcoustics@users.noreply.github.com>
…from_bfgs() Agent-Logs-Url: https://github.com/MitchellAcoustics/Soundscapy/sessions/9e7d4c44-7307-4f40-b931-578e0ab982a4 Co-authored-by: MitchellAcoustics <22335636+MitchellAcoustics@users.noreply.github.com>
…t_bfgs_stats() Agent-Logs-Url: https://github.com/MitchellAcoustics/Soundscapy/sessions/9e7d4c44-7307-4f40-b931-578e0ab982a4 Co-authored-by: MitchellAcoustics <22335636+MitchellAcoustics@users.noreply.github.com>
…plification refactor(r_wrapper): consolidate internal R wrapper into single module
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Agent-Logs-Url: https://github.com/MitchellAcoustics/Soundscapy/sessions/375278d7-1cef-4efd-b0d9-92eb3ae33348 Co-authored-by: MitchellAcoustics <22335636+MitchellAcoustics@users.noreply.github.com>
Refactor and update Soundscape Analysis documentation structure
- Version 0.8.4.dev1 → 0.8.4 - Root CHANGELOG: add 0.8.3 patch entry and full 0.8.4 release notes (docs overhaul, r_wrapper refactor, CI/CD fixes) - docs/CHANGELOG: stamp [Unreleased] → 0.8.4 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This pull request delivers a major overhaul of the documentation for the Soundscapy project, focusing on improved structure, clarity, and user onboarding. It introduces a new "About Soundscape Analysis" background page, significantly reorganizes the documentation for easier navigation, updates installation and API instructions, and refines the changelog. Additionally, minor updates are made to workflow files and project metadata.
Documentation overhaul and structure:
index.md) with clearer installation instructions, capability tiers, and a new "Where to start" section; improves the tutorials index with a guided starting table; and restructures the API reference for clarity and easier navigation. [1] [2] [3]Changelog and news:
CHANGELOG.mdwith detailed entries for the documentation overhaul and recent refactoring, and removes outdated news sections from the documentation. [1] [2]Project configuration and workflow updates:
.github/FUNDING.ymlfile to enable GitHub Sponsors and other funding platforms.frozen: truefor Pixi environments and adjusting job dependencies. [1] [2] [3].pre-commit-config.yamlto prevent formatting of generatedenvironment.ymlfiles.Minor README updates: