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Wire the UNIONS external healsparse masks into the workflow (MASK_<flag value>_<name> columns) - #886

Merged

cailmdaley merged 104 commits into

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feat/wire-external-masks

Oct 6, 2026

Commits on Sep 9, 2026
- feat(orchestration): the keep list, and the script that acts on it
  
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  681f156
- feat(orchestration): exp_persist, between exp_psf and clean_exposure
  
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- docs(orchestration): exp_persist in the rule list, and why the report omits it
  
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- feat(orchestration): exp_persist packs one tar per exposure, not loose copies
  
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- fix(orchestration): persist_exp never leaves a .tmp behind on failure
  
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- docs(orchestration): drop references to the removed star-catalogue rules
  
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  d91da36
- feat(orchestration): the two campaign-level merges
  
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  626aaba
- fix(orchestration): seven defects in the campaign-level merges
  
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  fc9aa3e
- fix(create_final_cat): make the merged-catalogue writer reproducible
  
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  d774cc3
- perf(orchestration): size the two merges from the data, not from a guess
  
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  98532ce
- feat(orchestration): persist_exp keeps NAMED products, not globs
  
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  d0ecfdd
- perf(merge_starcat): accumulate arrays, not python lists of floats
  
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- feat(orchestration): the star catalogue's inputs are not a user choice
  
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  0ad6403
- fix(cfis): two stale columns in final_cat.param, and no mask column at all
  
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  90dfb00
- perf(merge_starcat): two passes, so nothing is held twice
  
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- feat(orchestration): final_cat_merge reconciles instead of rebuilding
  
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  3c29825
Commits on Sep 10, 2026
- fix(orchestration): eight defects found reviewing the merge work
  
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  78d2ce9
- feat(orchestration): the star catalogue becomes hdf5, reconciled like the tile one
  
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  0fb514b
- fix(orchestration): nine findings from the third review
  
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  4ed9fb0
- test(unit): property-based state machines for reconcile and persist_exp
  
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  e86d8c8
- fix(persist-exp): the PSF run dir is run_sp_exp_SxSePsf
  
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  1a343e6
Commits on Sep 11, 2026
- workflow: image simulations as an input mode of the real-data workflow
  
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  5b88f17
- workflow: image-sims merge column list, and the merge reads the workflow layout
  
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  4e17fee
- workflow: campaign-unique node-local tile store for image sims; candide excludes
  
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  716b160
- workflow: port the MCCD exposure chain to the workflow grammar
  
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  fdc9db4
Commits on Sep 17, 2026
- workflow: exp_psf reserves 2 cores, not 8, for the MCCD chain
  
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  836f91d
- mccd_interp: test for N_EPOCH among the column names
  
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  ad80f23
- workflow: MCCD validated through the full chain; drop the warn-only flags
  
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  2082dcf
- workflow: tile_store_root run-config key moves the tile store's bind, per campaign
  
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  9085cd0
- completeness.py: atomic write for stage log/manifest JSON
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  7637b39
- workflow/config.yaml: universal template, no cluster-specific paths
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  7aababf
- workflow: retrieve mode (symlink|vos) is a run-config key, not fixed in the ini
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  d64f88e
- config.yaml: restore real nibi defaults, keep the placeholder check as a guard
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  c7bcfdd
- Snakefile: check machine: against SP_PROFILE at parse time
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  5be4c43
- config.yaml: machines: table drives per-machine (and per-input_type) defaults
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  29442d3
- workflow: one run-config resolver for Snakefile, bin/sp and container.py
  
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  7293e3b
- run_config: `run:` name, expanded as $run in run-config paths
  
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  084e305
- added user run config template
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- bin/sp: -c/--config-file for the run config, instead of SP_RUN_CONFIG
  
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  d3b088a
- bin/sp: document -c, the two-file merge and the environment in the header
  
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  746ca9c
- improved commeents
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- final_cat_merge, star_cat_merge: record code provenance in the HDF5 attributes
  
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  3e269c4
Commits on Sep 23, 2026
- workflow smoothed; running until hdf5 file
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  fbfdf3b
Commits on Sep 25, 2026
- bin/sp: don't swallow -c/--config meant for the delegated command
  
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  0b5fae7
- workflow/README: add products_dir to the image-sims run-config example
  
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  d22c4a0
- run_template.yaml: make it resolve
  
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  5ded2ca
Commits on Sep 26, 2026
- docs(astra): record the pipeline's scientific decisions in astra.yaml
  
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  dae9e1b
- test(astra): validate decision anchors and universe pins
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- Merge remote-tracking branch 'origin/develop' into feat/persist-exp-products-v2
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- merge: feat/workflow-image-sims (#894 @5ded2ca8) + develop into feat/persist-exp-products
  
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- workflow: final_cat_merge is the one merger, for data and image sims
  
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  4b1e868
- workflow: the campaign name is `run:`, and `run:` is required
  
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- workflow: no PSF persistence under psf_model: fake
  
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  3386347
- test(grammar): check the image-sims final_cat.param too
  
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  89f00b5
- Merge remote-tracking branch 'origin/docs/astra-decision-record' into HEAD
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- docs(astra): record the pipeline's scientific decisions in astra.yaml
  
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  09edd5e
- test(astra): validate decision anchors and universe pins
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  206b48d
- test(astra): resolve Snakemake rule anchors; JSON report mode
  
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  9f9ec5e
- docs(astra): rewrite the decision record against develop
  
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- docs(claude): point the scientific-decisions section at the anchor test
  
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  a6eff5e
- feat(make_cat): fixed per-epoch slot count via N_EPOCH_SLOTS
  
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  62a2699
- feat(workflow): save fixed-slot per-epoch PSF data in tile make_cat
  
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  512e7bf
- fix(workflow): five review findings on the #894 merge
  
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  b2a4d19
- workflow: scientific contracts for the campaign products
  
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- test(workflow): the campaign name has one source, and products one root
  
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  5fcc99e
- test(final_cat_merge): columns, per-epoch slots, never-fit rows, missing names
  
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  e768908
- docs(astra): correct seven rationale claims against the code
  
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  e3f6f4a
- Merge remote-tracking branch 'origin/docs/astra-decision-record' into feat/persist-exp-products-v2
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  27b59f7
- Merge remote-tracking branch 'origin/feat/make-cat-fixed-epoch-slots' into feat/persist-exp-products-v2
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  eb05d3a
- Merge remote-tracking branch 'origin/docs/astra-decision-record' into feat/persist-exp-products-v2
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- config(cfis): final_cat.param carries the 12 per-epoch slots (EXP_ID, CCD, HSM_*_PSF)
  
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  3358105
- docs(astra): two lints this stack resolves — IMAFLAGS_ISO is not merged, the MCCD chain runs
  
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  bac6eea
- config(cfis): final_cat.param keeps NUMBER
  
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- fix(workflow): the sims overlay resolves gauss_3.0_7x7.conv; `sp -- …` drops its separator
  
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  05e7381
- fix(workflow): refuse psf_model=mccd at parse time
  
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  45a9f1b
- fix(workflow): refuse reclamation when products_dir is run_dir
  
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  16df7ae
- fix(workflow): run_config expands to a fixed point and reports any leftover $
  
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  96abec8
- fix(persist_exp): the manifest records each member's sha256
  
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  072b705
- fix(hdf5_reconcile): one type per column across a campaign
  
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  d179f2b
- test(hdf5_reconcile): isolate schema invalidation from source stamps
  
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  187968e
- fix(build_index): readiness is the tiles row, not the retained edges
  
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  70d7a20
- fix(hdf5_reconcile): delete an abandoned tmp before the free-space check
  
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  5a61aaf
- fix(hdf5_reconcile): each provenance record replaces the last
  
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  47b2ec5
- fix(workflow): a reclaimed exposure's clean waits on its tar, not the manifest
  
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  b15d442
- test(conftest): the candide hostname test matches the whole bare name
  
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  5b56a68
- test(workflow): add an isolated Snakemake DAG driver
  
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  33391a4
- test(workflow): enforce campaign DAG scope and product custody
  
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- test(workflow): pin prologues and shells at campaign boundaries
  
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  0e279d1
- test(workflow): the DAG harness follows the parse-time guards
  
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  a846e08
- feat(cfis): wire the UNIONS external masks into the workflow
  
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  2c12bf5
- fix(file_io): recognize numpy bool arrays when picking the FITS column type
  
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  3453e8f
- docs(astra): the shear catalogue's default MASK_n* cut is the six r-mask bits
  
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  54c569a
- test(masks): final_cat.param's MASK_n* names match MASK_EXT_PATHS; the six-bit OR reproduces mask_r
  
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- test(workflow): update the params pin — SP_INPUT_MASKS joins every data prologue
  
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  dc11dab
Commits on Sep 28, 2026
- Merge origin/develop (#879 squash, #875, #854, #905, #911, #894) into feat/wire-external-masks
  
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  a1cb926
Commits on Sep 29, 2026
- Clarify HSC and Pan-STARRS mask bit labels
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  0a65f63
Commits on Sep 30, 2026
- Merge develop into external-mask branch
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  6fe0842
- State current star halo bit labels from mask producer schema
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  d43c70d
- Describe halo bit identities and guard per-map catalogue columns
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  af641f8
- Clarify flag values and current mask-column comments
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  f3f87db
Commits on Oct 1, 2026
- Name the mask columns MASK_<flag value>_<name>
  
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  a2e8068
Commits on Oct 5, 2026
- Merge develop into feat/wire-external-masks
  
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  c2b5a7d
- Drop star halos from the default external-mask cut
  
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  c28938b
- Drop the mask_default_cut decision: ShapePipe makes no mask choice
  
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  baa6430

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