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

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cailmdaley wants to merge 101 commits into

feat/wire-external-masks

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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de243a8
docs(orchestration): exp_persist in the rule list, and why the report omits it

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4cf639f
feat(orchestration): exp_persist packs one tar per exposure, not loose copies

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1fa6455
fix(orchestration): persist_exp never leaves a .tmp behind on failure

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a14a2f3
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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3b8c7d5
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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a434c9a
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

cailmdaley
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1a343e6

Commits on Sep 11, 2026

workflow: image simulations as an input mode of the real-data workflow

martinkilbinger
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5b88f17
workflow: image-sims merge column list, and the merge reads the workflow layout

martinkilbinger
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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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78cc0ca
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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4e0bedc
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
martinkilbinger
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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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e901cc9
Merge remote-tracking branch 'origin/develop' into feat/persist-exp-products-v2
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8e40991
merge: feat/workflow-image-sims (#894 @5ded2ca8) + develop into feat/persist-exp-products

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d84822f
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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d7ce47f
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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1685d65
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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5368d9d
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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4958d66
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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d214966
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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df20cf4
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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codex
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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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codex
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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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94e2dc1
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

Commits on Oct 1, 2026

Name the mask columns MASK_<flag value>_<name>

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a2e8068