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a8feee9
Refresh emcee plan for post-merge surface
AndrewSazonov May 24, 2026
a5e832c
Document /draft-adr /review-adr /draft-plan /review-plan shortcuts
AndrewSazonov May 24, 2026
421bfa2
Sync copilot-instructions with current API and branch conventions
AndrewSazonov May 24, 2026
82cca79
Refine shortcut triggers and loop behavior
AndrewSazonov May 24, 2026
2c9462a
Add emcee minimizer implementation plan
AndrewSazonov May 24, 2026
1f9c449
Add /implement-plan and switch shortcuts to sentinel-based handoff
AndrewSazonov May 24, 2026
5d213cc
Clean up and formatting
AndrewSazonov May 24, 2026
4ff0098
Add emcee runtime dependency
AndrewSazonov May 24, 2026
cf08a55
Register emcee minimizer enum value
AndrewSazonov May 24, 2026
f7b5779
Remove emcee version pin
AndrewSazonov May 24, 2026
85af677
Add EmceeMinimizer category class
AndrewSazonov May 24, 2026
4f41db9
Add EmceeMinimizer engine class
AndrewSazonov May 24, 2026
c03c5e4
Wire emcee resume through fit stack
AndrewSazonov May 24, 2026
1d3908a
Append-on-save plus explicit truncate-on-new-fit prep
AndrewSazonov May 24, 2026
67a1b06
Route emcee posterior through fit_result and sidecar
AndrewSazonov May 24, 2026
26e6b3c
Add ed-25 emcee tutorial
AndrewSazonov May 24, 2026
54674e5
Mark emcee phase 1 review gate
AndrewSazonov May 24, 2026
fd29dec
Improve emcee sampler progress reporting
AndrewSazonov May 24, 2026
59bc73e
Restore emcee default parallel sampling
AndrewSazonov May 24, 2026
e48c459
Align emcee sampling progress totals
AndrewSazonov May 24, 2026
6dd7690
Trim deterministic fit-parameter CIF columns
AndrewSazonov May 24, 2026
40ca462
Omit empty fit bounds multiplier column
AndrewSazonov May 24, 2026
c4ea21c
Suppress duplicate LSQ exit reason
AndrewSazonov May 24, 2026
e9ff3dd
Persist Bayesian runtime seed and timing
AndrewSazonov May 24, 2026
b6c42a7
Add notebook stop control for fitting
AndrewSazonov May 24, 2026
b80bcf7
Use Jupyter server interrupt for stop fitting
AndrewSazonov May 24, 2026
735eb5e
Clear stop fitting button on interrupt
AndrewSazonov May 24, 2026
cb32ec5
Default emcee resume steps from minimizer settings
AndrewSazonov May 24, 2026
c068259
Fallback to fresh emcee fit when resume chain is missing
AndrewSazonov May 24, 2026
3efc2ab
Resume emcee from persisted sampler state
AndrewSazonov May 24, 2026
b3277e3
Update emcee default proposal moves and thinning
AndrewSazonov May 25, 2026
8cdb047
Introduce emcee minimizer tutorials
AndrewSazonov May 25, 2026
e2fda13
Format switch warnings as bullet lists
AndrewSazonov May 25, 2026
d4ad498
Improve fitting output and peak warnings
AndrewSazonov May 25, 2026
f5c014e
Add ADR on fit results display naming
AndrewSazonov May 25, 2026
910f900
Replace arviz with custom diagnostics
AndrewSazonov May 25, 2026
477460c
Update tutorial archives and reduce steps
AndrewSazonov May 25, 2026
3ed6478
Update notebooks
AndrewSazonov May 25, 2026
08b7ccc
Share emcee minimizer defaults
AndrewSazonov May 25, 2026
3a3f5a4
Remove unused sidecar warning wrapper
AndrewSazonov May 25, 2026
f7ff71f
Keep DREAM parallel worker syncing
AndrewSazonov May 25, 2026
063f993
Use native emcee sampler setting keys
AndrewSazonov May 25, 2026
20167eb
Document emcee tutorial split
AndrewSazonov May 25, 2026
c3c023d
Use eager emcee sidecar imports
AndrewSazonov May 25, 2026
028bfe8
Clarify emcee integration test phase
AndrewSazonov May 25, 2026
ac229a4
Remove redundant emcee initialization map
AndrewSazonov May 25, 2026
6bbb3dd
Apply non-py formatting
AndrewSazonov May 25, 2026
30fa356
Update notebooks
AndrewSazonov May 25, 2026
5b51d6d
Add emcee phase 2 verification tests
AndrewSazonov May 25, 2026
71e9ad5
Apply pixi run fix auto-fixes
AndrewSazonov May 25, 2026
6a21cea
Apply remaining pixi run fix auto-fixes
AndrewSazonov May 25, 2026
f8b745e
Complete emcee static checks
AndrewSazonov May 25, 2026
963241f
Record emcee unit test verification
AndrewSazonov May 25, 2026
60116ca
Fix emcee result synchronization
AndrewSazonov May 25, 2026
d9fd220
Add live elapsed time to benchmark runs
AndrewSazonov May 25, 2026
3a36a3e
Isolate sequential tutorial project path
AndrewSazonov May 25, 2026
36b4243
Document emcee fit options refinement
AndrewSazonov May 25, 2026
82e20a2
Record emcee Phase 2 bug-fix note
AndrewSazonov May 25, 2026
61b9ab4
Document emcee benchmark tooling note
AndrewSazonov May 25, 2026
c304885
Expand emcee minimizer category tests
AndrewSazonov May 25, 2026
59083e6
Document emcee tutorial verification note
AndrewSazonov May 25, 2026
7adca53
Improve benchmark tutorial progress table
AndrewSazonov May 25, 2026
d8d5733
Update tutorial benchmarks for emcee minimizer
AndrewSazonov May 25, 2026
52917b8
Clean up
AndrewSazonov May 25, 2026
57f63a7
Formatting
AndrewSazonov May 25, 2026
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253 changes: 0 additions & 253 deletions .github/copilot-instructions.md

This file was deleted.

4 changes: 4 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,10 @@ CMakeLists.txt.user*
*.log
*.zip

# Agents
AGENTS.md
CLAUDE.md

# ED
# Used to fetch tutorials data during their runtime. Need to have '/' at
# the beginning to avoid ignoring 'data' module in the src/.
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5 changes: 0 additions & 5 deletions AGENTS.md

This file was deleted.

1 change: 0 additions & 1 deletion CLAUDE.md

This file was deleted.

21 changes: 19 additions & 2 deletions docs/dev/adrs/accepted/analysis-cif-fit-state.md
Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,17 @@ pre-fit scalar snapshots:
- `param_unique_name`
- `fit_min`
- `fit_max`
- `fit_bounds_uncertainty_multiplier`
- `start_value`
- `start_uncertainty`

When any row has uncertainty-derived bounds, `_fit_parameter` also
stores the provenance field:

- `fit_bounds_uncertainty_multiplier`

For Bayesian fit projections, `_fit_parameter` also stores per-parameter
posterior summaries:

- `posterior_best_sample_value`
- `posterior_median`
- `posterior_uncertainty`
Expand Down Expand Up @@ -104,6 +112,10 @@ Deterministic fit-result classes add compact fit output counts:
- `degrees_of_freedom`
- `covariance_available`
- `correlation_available`

When the LSQ backend provides a termination reason that differs from the
common `_fit_result.message`, deterministic fit results also store:

- `exit_reason`

Do not persist a `_deterministic_parameter_result` category. Final
Expand All @@ -127,11 +139,16 @@ Bayesian fit-result classes store scalar outputs under `_fit_result.*`:
- `sampler_completed`
- `credible_interval_inner`
- `credible_interval_outer`
- `acceptance_rate_mean`
- `resolved_random_seed`
- `gelman_rubin_max`
- `effective_sample_size_min`
- `best_log_posterior`

When the backend reports an acceptance rate, Bayesian fit results also
store:

- `acceptance_rate_mean`

Bayesian per-parameter posterior summaries are stored on the
corresponding `_fit_parameter` rows. Their row order defines the saved
posterior parameter order.
Expand Down
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