projects.yaml

# projects.yaml — the science body map.
#
# One row per science project. This file is CODE, not ledger: `sync_cli` and
# `local_path` are paths the batch conductor will execute under, so a change
# here is always a human's turn (scripts/ledger_merge.py leaves it for review,
# exactly like PyAutoMind/repos.yaml).
#
# THE BOUNDARY. Science repos are NOT added to PyAutoMind/repos.yaml — that map
# is the workspace; this one is the science. A project reaches the organism
# through its row here and nowhere else.
#
# Schema — a restricted YAML subset that scripts/cortex.py parses with the
# stdlib (REFERENCE.md "The restricted YAML subset"). It is also real YAML:
# `yaml.safe_load` reads it identically, and a test keeps the two in step.
#
#   <key>:                        # column 0, ^[a-z][a-z0-9_]*$ — the project key
#     remote: <owner/repo | none> # the remote — PyAutoLabs for active projects; a
#                                 # personal remote is recorded as a fact with a `note:`
#     local_path: <abs path>      # the laptop checkout
#     ral_root: <abs path>        # the project root on RAL (/mnt/ral/jnightin/<category>/<project>)
#     mirror: <abs path | none>   # the laptop pull root the sync CLI fills (holds data, not science)
#     sync_cli: <path>            # the project's sync CLI, relative to local_path
#     sync_verbs: [a, b, c]       # the verbs that CLI has — a flow list of bare words, the only list
#     ledger: <path>              # the project's own commentary ledger, relative to local_path
#     assistant: <name | none>    # the domain assistant this project's work enters through — a
#                                 # workspace-relative repo name such as `autolens_assistant`, or
#                                 # `none`; the Cortex names it, never reads it
#     witness_file: <glob>        # where a run's witness lands, relative to the mirror
#     partition: gpu | ral | both # which SLURM partition(s) the project runs on
#     status: active | dormant | planned | retired   # `cortex.py retire` writes the last
#     note: <text>                # OPTIONAL, and the only optional field — free text
#                                 # about the row; an empty `note:` is drift
#
# Scalars are bare unless they contain `#`, `:` or edge spaces (then "..."
# with no escapes); comments on their own line or after ` #`; no block lists,
# no deeper nesting, no anchors, no `---`. Every field but `note` is required;
# an unknown field is an error.
#
# THE WORKSPACE-PATHS EXCEPTION. `local_path` and `mirror` are absolute laptop
# paths OUTSIDE the PyAutoLabs workspace — the Science folder under /mnt/c/…
# where the datasets, output trees and pulled results live. This file is the
# one place in the organism that carries such a path; a task file or a ruling
# reaches a project through its row here, never with a bare path of its own.

# --------------------------------------------------------------------------- #
# active
# --------------------------------------------------------------------------- #
inference_programme:
  remote: PyAutoLabs/autolens_profiling
  local_path: /home/jammy/Code/PyAutoLabs/lens/autolens_profiling
  ral_root: /mnt/ral/jnightin/profiling/autolens_profiling
  mirror: /mnt/c/Users/Jammy/Science/archive/inference_programme
  sync_cli: hpc/sync
  sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
  ledger: results/notes/inference/PROGRAMME.md
  assistant: none
  witness_file: results/searches/**/*.json
  partition: both
  status: retired
  note: "retired 2026-09-07: restarting from scratch: the project setup was unsatisfactory and it informed how the Cortex manages projects; RAL outputs stashed at /mnt/ral/jnightin/inference_programme_retired_2026-09-07"

subhalo_validation:
  remote: PyAutoLabs/subhalo_validation
  local_path: /mnt/c/Users/Jammy/Science/active/subhalo_validation
  ral_root: /mnt/ral/jnightin/active/subhalo_validation
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "pulls land in the checkout (PULL_DIRS output results); run_chain.sh chains A→B afterok; witness evidence_increase < 5, subhalo_stage, test_mode"

subhalo:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/active/subhalo
  ral_root: /mnt/ral/jnightin/active/subhalo
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, sync, status]
  ledger: README.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: both
  status: active
  note: "registered 2026-10-15 by human decision (PyAutoCortex#67), overriding schema decision 52(a) for this tree: not a git repo, so remote none; ledger is the generic PyAutoLens project-template README; SLACS sample under dataset/, output/ empty, no results/ yet; hpc/sync.conf targets HPC_BASE=/mnt/ral/jnightin/active; batch_cpu submits still say --partition=cpu (no such partition on RAL); ral_root not yet created on RAL; witness undefined until a science task pre-registers one"

euclid:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/active/euclid
  ral_root: /mnt/ral/jnightin/active/euclid
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, sync, status]
  ledger: CLAUDE.md
  assistant: none
  witness_file: catalogue/**/*.csv
  partition: both
  status: dormant
  note: "NO PyAutoLabs remote by ruling 2026-09-01: tracks DR1 tile-keyed catalogue CSV, personal remote Jammy2211/euclid-dr1-modeling, nested Overleaf paper repo, 34 GB; code half = PyAutoLabs/euclid_strong_lens_modeling_pipeline; witness undefined until a science task pre-registers one; dormant 2026-09-07: superseded by euclid_dr1_prelim, which phase 4 births; local output/ cleared 2026-09-07 (60 GB of May–June DR1 grade_ab runs, still on RAL under /mnt/ral/jnightin/euclid); superseded by euclid_dr1 (euclid_dr1_prelim defunct) per the human 2026-10-15; folder kept under Science/active and RAL active/ by human decision 2026-10-14; RAL tree moved to the category layout 2026-10-15"

euclid_dr1_prelim:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/archive/euclid_dr1_prelim
  ral_root: /mnt/ral/jnightin/archive/euclid_dr1_prelim
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, sync, status]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-09-25: retire euclid_dr1_prelim; tree moved to z_vault by the human"

euclid_dr1:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/euclid_dr1
  ral_root: /mnt/ral/jnightin/euclid_dr1
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-09-11: the actual DR1 run on the sep1 segmentation delivery (Segmentation.zip = 3 nested batch zips, 15032 tiles, every tile already in the pipeline dataset layout); born by cloning euclid_strong_lens_modeling_pipeline main with config/visualize colormap back to autoarray; first task reruns the ten euclid_dr1_prelim lenses on the new data; remote none until the human creates one"

analytic_gaussian:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/active/analytic_gaussian
  ral_root: /mnt/ral/jnightin/active/analytic_gaussian
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, status, submit, push-submit, jobs, sacct, cancel, tail, du, check]
  ledger: wiki/project/state.md
  assistant: autofit_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-09-09 as the graphical-ep campaign's phase-1 keystone at ensemble scale; benchmark model with a closed-form posterior, borrowed from autofit_workspace_test scripts/graphical (PR #92 lineage); CPU-only, no dataset (every draw is simulated in memory from its seed); remote none until the human runs gh repo create PyAutoLabs/analytic_gaussian --private"

ep_toy_gaussian:
  remote: PyAutoLabs/ep_toy_gaussian
  local_path: /mnt/c/Users/Jammy/Science/active/ep_toy_gaussian
  ral_root: /mnt/ral/jnightin/active/ep_toy_gaussian
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, status, submit, push-submit, jobs, sacct, cancel, tail, du, check]
  ledger: wiki/project/state.md
  assistant: autofit_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-09-10 as the graphical-ep campaign's confidence test on the PyAutoFit#1405 collapse toy at N=50: joint BlackJAX NUTS vs EP x3 on identical data; model and EP settings verbatim from complete/2026/07 ep_toy_diagnostic; CPU-only, data simulated in memory from its seed; remote PyAutoLabs/ep_toy_gaussian (private) created 2026-09-10"

# --------------------------------------------------------------------------- #
# dormant — git repos only. The non-git trees (euclid_group, z_*) are
# storage, not projects, and aris_PJ011646 is an assistant clone; none get a
# row (subhalo, non-git, is the one exception: registered active 2026-10-15). `ral_root` is the planned path and `sync_verbs` is unverified on every
# row below — each note says so.
# --------------------------------------------------------------------------- #
profiling:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/archive/profiling
  ral_root: /mnt/ral/jnightin/archive/profiling
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-10-14: human moved the tree to z_vault 2026-10-14"

cowls_diana:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/archive/cowls_diana
  ral_root: /mnt/ral/jnightin/archive/cowls_diana
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-10-14: human moved the tree to z_vault 2026-10-14"

subhalo_simulations:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/archive/subhalo_simulations
  ral_root: /mnt/ral/jnightin/archive/subhalo_simulations
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-10-14: superseded by subhalo_validation; tree moved to z_vault 2026-10-14"

slope_hierarchy:
  remote: Jammy2211/slope_hierarchy
  local_path: /mnt/c/Users/Jammy/Science/complete/slope_hierarchy
  ral_root: /mnt/ral/jnightin/complete/slope_hierarchy
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-09-08: wrapped up 2026-07-22 at N=5; succeeded by slope_hierarchy_scale; tree vaulted under z_projects_complete/"

slope_hierarchy_scale:
  remote: PyAutoLabs/slope_hierarchy_scale
  local_path: /mnt/c/Users/Jammy/Science/active/slope_hierarchy_scale
  ral_root: /mnt/ral/jnightin/active/slope_hierarchy_scale
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, sync, status, submit, push-submit, jobs, tail, check]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: both
  status: active
  note: "born 2026-09-08 as graphical-ep phase 3, code borrowed from slope_hierarchy (vaulted under z_projects_complete/); private remote created 2026-09-08"

pj011646:
  remote: Jammy2211/PJ011646
  local_path: /mnt/c/Users/Jammy/Science/archive/PJ011646
  ral_root: /mnt/ral/jnightin/archive/PJ011646
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-10-02: Human requested both PJ011646 and aris_PJ011646 archived intact to z_vault on laptop and RAL; superseded by pj011646_final"

concr:
  remote: Jammy2211/cosmology_and_cancer
  local_path: /mnt/c/Users/Jammy/Science/archive/concr
  ral_root: /mnt/ral/jnightin/archive/concr
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull]
  ledger: README.md
  assistant: none
  witness_file: results/**/*.json
  partition: both
  status: retired
  note: "retired 2026-10-14: human moved the tree to z_vault 2026-10-14"

ic50_workspace:
  remote: Jammy2211/ic50_workspace
  local_path: /mnt/c/Users/Jammy/Science/active/ic50_workspace
  ral_root: /mnt/ral/jnightin/active/ic50_workspace
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: NOTES.md
  assistant: none
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "personal remote, recorded as a fact — not a PyAutoLabs repo; activated 2026-09-09 for graphical-ep phase 4, ral_root created and first runs submitted; NOTES.md predates the graphical/HPC work and needs a refresh"

autolens_inference:
  remote: PyAutoLabs/autolens_inference
  local_path: /home/jammy/Code/PyAutoLabs/lens/autolens_inference
  ral_root: /mnt/ral/jnightin/inference/autolens_inference
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: both
  status: active
  note: "born 2026-09-10 as the from-scratch restart of inference_programme (retired PyAutoCortex#22); nothing inherited; phase 1 = birth (PyAutoMind#399), first task slam_hst_base"

autofit_inference:
  remote: PyAutoLabs/autofit_inference
  local_path: /home/jammy/Code/PyAutoLabs/fit/autofit_inference
  ral_root: /mnt/ral/jnightin/inference/autofit_inference
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [pull, logs, status, submit, jobs, sacct, cancel, tail, du, check]
  ledger: wiki/project/state.md
  assistant: autofit_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-10-07 as search-extensibility B1 (PyAutoMind#492); harness B2; B3 wave-1 pilot (autofit_inference#4) flipped this to active 2026-10-08"

euclid_sersics:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/euclid_sersics
  ral_root: /mnt/ral/jnightin/euclid_sersics
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: catalogue/**/*.csv
  partition: ral
  status: retired
  note: "retired 2026-09-25: retire euclid_sersics as well; local tree deleted 2026-10-14 (no actionable results)"

pj011646_final:
  remote: none
  local_path: /mnt/c/Users/Jammy/Science/complete/PJ011646_final
  ral_root: /mnt/ral/jnightin/complete/PJ011646_final
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, status, submit, jobs, sacct, tail, du, check]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/tables/*.json
  partition: gpu
  status: retired
  note: "retired 2026-10-14: complete; tree moved to z_projects_complete 2026-10-14"

euclid_detailed:
  remote: PyAutoLabs/euclid_detailed
  local_path: /mnt/c/Users/Jammy/Science/active/euclid_detailed
  ral_root: /mnt/ral/jnightin/active/euclid_detailed
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-10-15: advanced SLaM remodel (light[1] MGE 4x30 + point, 1250 source pixels, power-law mass[1]) of 31 euclid_dr1 grade-A threshold-100 success lenses flagged by eye — 20 source_residuals, 11 lens_light_residuals; euclid_dr1 fits pulled to output_dr1; source_lp JAX-CPU then numba-CPU like euclid_dr1; not yet submitted"

cowls:
  remote: PyAutoLabs/cowls
  local_path: /mnt/c/Users/Jammy/Science/active/cowls
  ral_root: /mnt/ral/jnightin/active/cowls
  mirror: none
  sync_cli: hpc/sync
  sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs]
  ledger: wiki/project/state.md
  assistant: autolens_assistant
  witness_file: results/**/*.json
  partition: ral
  status: active
  note: "born 2026-10-15: euclid_detailed SLaM pipeline (light[1] MGE 4x30 + point, 1250 source pixels, power-law mass) applied to COWLS JWST lenses, starting with M25 COSJ100024+015334 (F444W default, mask_extra_galaxies noise-scaled); source_lp JAX-CPU then numba-CPU; not yet submitted"