0.5.0

Compare with 0.4.2

This release consolidates roughly two years of work — the bulk of the HCPh data
collection, the full functional- and structural-connectivity analysis, and a
security-hardened, reproducible documentation build. Changes are grouped by theme; only
milestone pull requests (and a few individual commits) are linked.

Connectivity analysis & reliability

• Functional-connectivity (FC) estimation and variability analyses, covering sparse
  inverse-covariance estimation and intra-/inter-scanner reliability quantified with the
  intraclass correlation coefficient (ICC) (#549, #551, #553).
• Bayesian modeling of structural-connectivity (SC) reliability, with a standalone worked
  example (#528, #537).
• FC-matrix loading and confound retrieval refactored into reusable load_save/confounds
  modules, and mood/state-questionnaire parsing to derive analysis confounds (sleep,
  caffeine, room environment) from the study's issue templates (#523, #527, #557).

Generalizability (multi-scanner) protocol

• SOPs for the multi-scanner "generalizability" acquisitions (Prisma / Vida / VidaFit),
  including scanner-specific handling of the alarm screen, audio system, and console
  unlocking, plus standardized protocols and scan durations (#493, #495, #497).
• Wave-2 recruitment and scheduling adjustments (#499).

Eye-tracking

• End-to-end eye-tracking → BIDS conversion and screening/QC guidance, including a revised
  conversion pipeline and drift handling (#459).

Physiological recordings

• BIOPAC/AcqKnowledge handling and physiological → BIDS conversion, including splitting
  multi-run AcqKnowledge files (#506); clarified ECG calibration instructions (#539).

Data management with DataLad

• DataLad-based data management on the Curnagl HPC cluster, derivatives organized as
  subdatasets, and a BIDS indexer driving data intake (#507, #522, #542).

Preprocessing on HPC

• fMRIPrep on Curnagl (SLURM): anatomical-only runs, micromamba environments, and
  TemplateFlow pre-download for offline compute nodes (#508, #516, #519).

Quality control

• QC/QA criteria for unprocessed and preprocessed data and for functional connectivity, and
  an analysis of the manual image-rating experience (#469).

Manuscript, figures & references

• Registered-report figures and machinery to save figure captions for automatic generation
  of the paper's supplementary material (#544); clarified methods (e.g. atlas
  dimensionality vs. number of regions) and a README listing the datasets required to
  reproduce the analyses (#555, #559); a documented data-release checklist (#538).

Site infrastructure, CI & build

• Security: removed the compromised polyfill.io CDN — sold in 2024 and serving malware
  — from the MathJax configuration (#562).
• Modernized and pinned the MkDocs/Material stack for reproducible builds, dropped the
  unmaintained mkpdfs PDF fork, and pinned the MathJax CDN with Subresource Integrity
  (#562); repaired the deploy/codespell CI workflows and fixed broken links and spelling
  (#550, #564).