Code commits
Pipeline
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Rui Xue 6ecc99029229649dd32a98e3427f3a85754aaff8
Merge remote-tracking branch 'origin/PIPE-3221-flagging-command-order-from-hifa_tsysflag-might-not-be-deterministic' into PIPE-3222-redundant-edgechan-flag-command-in-h_tsysflag
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Rui Xue 3a559c545d136093429d82edb2f2105d8d759c4b
Merge remote-tracking branch 'origin/main' into PIPE-3222-redundant-edgechan-flag-command-in-h_tsysflag
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Rui Xue 2ede876d89735978035e997d9c03da97a9fcf8bd m
Pull request #2014: PIPE-2949: to MAIN
Merge in PIPE/pipeline from PIPE-2949-hif_editimlist-resolves-spw_name-to-real-id-instead-of-virtual-id to main
* commit 'b31be0595fc9d529d7711c429207a54a5125bd8f':
PIPE-2949: resolve spw name to virtual ID and populate target vis in `editimlist`
PIPE-2949: use first ms for field/spw lookups -
Patrick Bos b49a22799e68a5cc7fdef6b9936e5552f6a5c7f4 m
Pull request #2027: Shorten AGENTS.md and split specific tasks into skills
Merge in PIPE/pipeline from egp-shorten-agents-md to main
* commit 'e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f':
shorten AGENTS.md and split specific tasks out into skills
add test-unit pixi command output file to gitignore -
Ajay Vibhute 95592fb80df30dc6d2288c8f735dae540cfd237e m
Pull request #2030: PIPE-3013: adding editmode replace to template_hifa_cubeimage.xml
Merge in PIPE/pipeline from PIPE-3013-main-hifa_cubeimage-recipe-should-have-editmode-replace-parameter-set-for-hif_editimlist to main
* commit '3f3715c90f74ee8b00e2c93e5c861bb4804a3d82':
PIPE-3013: adding editmode replace to template_hifa_cubeimage.xml -
Rui Xue b376514f96fefbbcb64959d23ed12835ba0d1f8c m
Pull request #2025: PIPE-3275: fix scalar conversion crash in subband QA
Merge in PIPE/pipeline from PIPE-3275-numpy-2.5-crash-qa-of-hifa_bandpass to main
* commit 'aa06d07a366fd6393970c3a46ac21a6adddbdb15':
PIPE-3275: fix scalar conversion crash in subband QA -
Ajay Vibhute 3f3715c90f74ee8b00e2c93e5c861bb4804a3d82 m
PIPE-3013: adding editmode replace to template_hifa_cubeimage.xml
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E. G. Patrick Bos <egpbos@gmail.com> e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f m
shorten AGENTS.md and split specific tasks out into skills
This reduces default context token use by about half. With all skills loaded, context reduction is still about 25%- .skills/commit-style/SKILL.md (version e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f) (diffs)
- .skills/docs-build/SKILL.md (version e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f) (diffs)
- .skills/python-code-standards/SKILL.md (version e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f) (diffs)
- AGENTS.md (version e857c0f99b3a53356d9a9a1d550777aaf5ec1c1f) (diffs)
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E. G. Patrick Bos <egpbos@gmail.com> 9a75c9748fd80459e367713fa2d6a584293fed4e m
add test-unit pixi command output file to gitignore
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Rui Xue aa06d07a366fd6393970c3a46ac21a6adddbdb15 m
PIPE-3275: fix scalar conversion crash in subband QA
Extract a 0-dimensional scalar from subb_spk using .flat indexing in evalPerAntBP_Platform. In NumPy 2.0+, indexing a 2D slice with a flat argmax index returns a 1D array rather than a scalar, causing downstream string formatting to fail with TypeError. -
Rui Xue 4b0551017851ee500cf1f4f6d65c67328b48fb72 m
Pull request #2023: PIPE-3211: start casa/casampi tasks in INIT_CWD (similar to what has been done in `stack-man`)
Merge in PIPE/pipeline from PIPE-3211-start-casa-casampi-pixi-tasks-with-init-cwd to main
* commit '3c43082d7a61f56b515ae64ff6d5ed73ab1a123d':
PIPE-3211: update pixi tasks guide and environment specs
PIPE-3211: start casa/casampi tasks in INIT_CWD (similar to what has been done in `stack-man`) -
Rui Xue 3c43082d7a61f56b515ae64ff6d5ed73ab1a123d m
PIPE-3211: update pixi tasks guide and environment specs
Update pixi developer documentation to align with recent task and environment configurations:
- Document INIT_CWD working directory semantics and thread pool clamping for casa and casampi tasks.
- Add missing bundle-assets and update-references task descriptions.
- Remove duplicate environment table entry and update dated references.
- Sync conda migration examples with openmpi-mpicxx and casatasks pins.
- Clean up the common tasks quick reference table. -
Rui Xue fc436ff14b9fb879ef409889fe22c930b712091c m
PIPE-3211: start casa/casampi tasks in INIT_CWD (similar to what has been done in `stack-man`)
Start pixi tasks `casa` and `casampi` in the directory where pixi was invoked (`INIT_CWD`) instead of the workspace root. Default threading in `tasks.casa` to the lesser of available CPUs and 4 across Linux and macOS, while preserving explicit user overrides. -
Hajime Ezawa 1a4f5aa660536310ee611105ee310d066642389e m
Pull request #1967: PIPE-3105 hsd imaging possible improvement on the weblog layout for no detection of off line range
Merge in PIPE/pipeline from PIPE-3105-hsd_imaging-possible-improvement-on-the-weblog-layout-for-no-detection-of-off-line-range to main
* commit '225d8766fe66577455e9438ff6cdac281e41ae11':
PIPE-3105: bug fix
PIPE-3105: bug fix and corrections
PIPE-3105: optimized the default for min_gap_width of _pick_excess_ranges()
PIPE-3105: improve np.array masking
PIPE-3105: explicitly specify constant_values for np.pad
PIPE-3105: bug fix
PIPE-3105: add/correct type annotations
PIPE-3105: optimize/correct whitespaces
PIPE-3105: replace .format() to f-string, typo correction
PIPE-3105: output excess ranges to LOG
PIPE-3105: always show two plots regardless the detection status -
Rui Xue fea5b728022fea7766f6e3fa3d683f33cb4872e0 m
PIPE-2949: use first ms for field/spw lookups
Switch from inp.vis[-1] to inp.vis[0] for reference MS, which follows convention in other related tasks. -
Rui Xue b31be0595fc9d529d7711c429207a54a5125bd8f m
PIPE-2949: resolve spw name to virtual ID and populate target vis in `editimlist`
- Resolve SPW names and center frequencies to virtual SPW IDs via `real2virtual_spw_id` in `hif_editimlist`.
- Populate imlist_entry['vis'] for all imaging modes so downstream `hif_makeimages`/`tclean` receives the expected MS list.
- Normalize vislist and guard reference MS resolution in editimlist.
- Add fallback in CleanTaskFactory to use image_heuristics.vislist if target['vis'] is unset. -
Rui Xue 036f9701c1309560d2aeabbe58336600d231515f m
Pull request #2020: PIPE-3252 docs branching and rtd versioning
Merge in PIPE/pipeline from PIPE-3252-docs-branching-and-rtd-versioning to main
* commit '1de46b530b0126c4fa373a3cb8dd5160a0e0a14b':
docs: update Jira ticket and figure directives.
Add link to CAS-14874 on Jira
Update CASA 2026 known issues to include the CAS-14874 bug. -
Rui Xue 1de46b530b0126c4fa373a3cb8dd5160a0e0a14b m
docs: update Jira ticket and figure directives.
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Patrick Sheehan 4c652b4d83dda3657222a9f7652b50a00fbaf4ec m
Update CASA 2026 known issues to include the CAS-14874 bug.
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Patrick Sheehan ee57b4397297f156c41fc692b96abe0481c87656 m
Add link to CAS-14874 on Jira
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Rui Xue e7b6405653ac1ea6c3d71cfc6da408d58e6f3a5b m
Pull request #2017: PIPE-3252: Document RTD branching strategy and version mapping
Merge in PIPE/pipeline from PIPE-3252-docs-branching-and-rtd-versioning to main
* commit 'd0d258de128b74e3e2d4cdde776a00598eddb77b':
PIPE-3252: Restructure RTD docs sections and add descriptions for the branch/tag-RTD-version mapping
PIPE-3252: Expand the docs build path in `.gitignore`
PIPE-3252: Document RTD branching strategy and version mapping -
Rui Xue d0d258de128b74e3e2d4cdde776a00598eddb77b m
PIPE-3252: Restructure RTD docs sections and add descriptions for the branch/tag-RTD-version mapping
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Rui Xue 388f15af0cb4cb87ef3cf753ba74ba3ab5cd5226 m
PIPE-3252: Expand the docs build path in `.gitignore`
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Rui Xue b69d2a417af62c280f002ac73fdffbfa772de35c m
PIPE-3252: Document RTD branching strategy and version mapping
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Rui Xue 85a334903820b9841ba363dd5dec79fe92d113cd m
Pull request #2016: PIPE-3272: Add flux service query script and clairfy the new 4-digit "DataConditions" from 2026AUG
Merge in PIPE/pipeline from PIPE-3272-add-flux-service-query-script to main
* commit '4c62d794f7473aa7df7449b637c1f5ecfdd072e0':
PIPE-3272: reference ICT tickets for 4th DataConditions digit
PIPE-3272: update DataConditions parsing in dbfluxes for 4-digit codes
PIPE-3272: add `dbfluxes_query.py` script for catalogue lookups -
Rui Xue a7f8802d696f85d31b747a8dc52651366f1cf9c2 m
Pull request #1960: PIPE-3237: optimize unflagged data checks in `hif_findroi` and `ImageParamsHeuristics`
Merge in PIPE/pipeline from PIPE-3237-hif_findroi-very-inefficient-for-cases-with-many-fields-x-eb-x-spw to main
* commit '82fe783a77d453ed5300b9485da639fd9933cecc':
PIPE-3237: warn once when `hif_findroi` skips a virtual spw
PIPE-3237: simplify target field name list construction in `findroi.py`
PIPE-3237: optimize unflagged data checks in `hif_findroi` and `ImageParamsHeuristics` -
Rui Xue 4c62d794f7473aa7df7449b637c1f5ecfdd072e0 m
PIPE-3272: reference ICT tickets for 4th DataConditions digit
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Rui Xue a3a8f9ac972247979d0280b51154721cd9104f16 m
PIPE-3272: update DataConditions parsing in dbfluxes for 4-digit codes
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Rui Xue 293163dd05b17927cc2382fa157dbef71af89217 m
PIPE-3272: add `dbfluxes_query.py` script for catalogue lookups
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Rui Xue df553e34d6e0e53244ac27c105e7fb0bf296f60f m
Pull request #1955: PIPE-684/PIPE-3218/PIPE-3255: VLA mosaic imaging
Merge in PIPE/pipeline from PIPE-684-vla-mosaic-imaging to main
* commit 'beed751da9a3c6555c661227f0e90d131b9ad0a7': (52 commits)
PIPE-684: handle per-MS field lists and streamline center_field_ids
PIPE-684: set VLA pblimit_image to 0.1 for mosaic non-cube imaging
PIPE-3247/PIPE-3248: Improve field name rendering with text wrapping
PIPE-684: consolidate flagged SPW warnings and skip fully flagged targets in makeimlist
PIPE-3218: display spectral window lists as ranges in `exportdata` tables
PIPE-684: Enable per-field mitigation parameter lookups in `makeimlist`
PIPE-684: Add optional field parameter to `hm_cell/hm_imsize` lookups
PIPE-684: improve `wrap_long_str` - track line length instead of using old modulo arithmetic
PIPE-684: fix multi-target product size mitigation with per-(field,spw) keying
PIPE-3218: fix HTML line breaks for long field names
PIPE-684: Fix product size calculation and add field filtering
PIPE-684: disable self-calibration heuristics for VLA mosaic targets
PIPE-3218: wrap long source names in exportdata.mako weblog tables
PIPE-3218: wrap long source names in `hifv_exportdata` weblog tables
PIPE-684: export `wrap_long_str` in pipeline.infrastructure.utils
PIPE-684: condense long composite field names in QA and log messages
PIPE-684: merge weblog table columns in findcont and VLA exportdata
PIPE-684: use `self.spwids` for field lookup and frequency calculation in VLA heuristics
PIPE-684: optimize logging and improve VLA field intent docs
PIPE-684: Refactor mosaic detection with modern Python standards and comprehensive tests
... -
Rui Xue 82fe783a77d453ed5300b9485da639fd9933cecc m
PIPE-3237: warn once when `hif_findroi` skips a virtual spw
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Rui Xue 148f12af9c82315bbf9cd6b156b49b44be725d98 m
PIPE-3237: simplify target field name list construction in `findroi.py`
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Hajime Ezawa 225d8766fe66577455e9438ff6cdac281e41ae11 m
PIPE-3105: bug fix
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Hajime Ezawa 6a39bf2a14dd5632b7824bd2c58832a84801daa3 m
Merge branch 'main' of https://open-bitbucket.nrao.edu/scm/pipe/pipeline into PIPE-3105-hsd_imaging-possible-improvement-on-the-weblog-layout-for-no-detection-of-off-line-range
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Hajime Ezawa 56745139edf63b1a6dd4dc351ecde473f08e2156 m
Pull request #1968: PIPE-3246: add overwrite=True to image_args
Merge in PIPE/pipeline from PIPE-3246-hsd_imaging-sometimes-hsd_imaging-crashes-with-runtimeerror-output-file-exists to main
* commit '1113f6eeab147278cd16547f836b6d5012ed49df':
PIPE-3246: add overwrite=True to image_args -
Rui Xue e334846327e00b2cda5bb860498fa94a3f63db6f m
Pull request #2006: PIPE-3252/PIPE-3264
Merge in PIPE/pipeline from PIPE-3252-docs-update-to-main to main
* commit '721235e8ba3766673fef78026556b927f802fdcb':
PIPE-3252: add AGENTS.md and align ruff pre-commit
PIPE-3252: add JM to the contributor list -
Rui Xue 721235e8ba3766673fef78026556b927f802fdcb m
PIPE-3252: add AGENTS.md and align ruff pre-commit
- Add AGENTS.md defining operational directives, architectural invariants, modern Python standards, and developer guidelines.
- Point .github/copilot-instructions.md to AGENTS.md as the canonical authority for AI assistant instructions.
- Switch .pre-commit-config.yaml to local hooks invoking pixi-managed ruff to guarantee parity across IDE, pre-commit, and agent workflows. -
Rui Xue 86ba85641552eef9b6f903264182026fbe19f74e m
PIPE-3252: add JM to the contributor list
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Rui Xue beed751da9a3c6555c661227f0e90d131b9ad0a7 m
Merge remote-tracking branch 'origin/main' into PIPE-684-vla-mosaic-imaging
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Rui Xue 09e7ce9075867e9c005c6a45926f0500ec33c5d9 m
Pull request #2003: PIPE-3252: add link to CASA Docs citation guide in acknowledgements
Merge in PIPE/pipeline from PIPE-3252-add-casa-citation-page to main
* commit '8c6a6a273861cfa5da6e3f57ed6248f35169d7bb':
PIPE-3252: add link to CASA Docs citation guide in acknowledgements -
Rui Xue 8c6a6a273861cfa5da6e3f57ed6248f35169d7bb m
PIPE-3252: add link to CASA Docs citation guide in acknowledgements
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Remy Indebetouw a0586fcdb966530af2d64068f1c84376fdbd5144 m
Pull request #2000: reordered chronologically, added people who contributed significantly albeit not directly in the code repo
Merge in PIPE/pipeline from PIPE-3263-doc-updates to main
* commit 'a0038a8a2d5338d32976b6ba80057eff54bc66f7':
fixed "present" and double Andy
reordered chronologically, added people who contributed significantly albeit not directly in the code repo -
Remy Indebetouw <remy@virginia.edu> a0038a8a2d5338d32976b6ba80057eff54bc66f7 m
fixed "present" and double Andy
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Remy Indebetouw <remy@virginia.edu> 0669c460be9ade6b26ce65288d1024f5d0d667bf m
reordered chronologically, added people who contributed significantly albeit not directly in the code repo
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Rui Xue 6ebe41c7f7a634c6c0bd19ec6bc9a3dede8771da m
Pull request #1998: PIPE-3252: update release notes with ALMA task references and improve formatting
Merge in PIPE/pipeline from PIPE-3252-append-alma-task-ref-to-plug-main to main
* commit '8ac857aa5055fe97677559d13504a077fa590f08':
PIPE-3252: update release notes with ALMA task references and improve formatting -
Rui Xue 8ac857aa5055fe97677559d13504a077fa590f08 m
PIPE-3252: update release notes with ALMA task references and improve formatting
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Rui Xue 17dd28330aea2d87240b0db9ff1e5883da443528 m
Pull request #1996: PIPE-3252: Add AL to Contributors list
Merge in PIPE/pipeline from PIPE-3252-append-alma-task-ref-to-plug-main to main
* commit '79b00e3aef7de55ad5b9c185aa71ccd39f6d86bd':
PIPE-3252: Add AL to Contributors list -
Rui Xue 79b00e3aef7de55ad5b9c185aa71ccd39f6d86bd m
PIPE-3252: Add AL to Contributors list
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Rui Xue d4c1cf365fb7cf6405ee6f69b5aa57c67cc1c050 m
Pull request #1988: PIPE-3260: Fix false QA failures in `VLASetjy`
Merge in PIPE/pipeline from PIPE-3260-false-qa-warning-about-lack-of-flux-calibrator-in-hifv_vlasetjy-task to main
* commit '34228abc590663d2714f3d8cc7e37e8d124b2293':
PIPE-3260: Fix false QA failures in `VLASetjy` -
Rui Xue b0920bd33c2728cf8292bc773bf49ed5cb9e5ca4 m
Pull request #1983: PIPE-3258: fix reference antenna fallback and caltable cleanup in `hifv_semiFinalBPdcals`
Merge in PIPE/pipeline from PIPE-3258-antenna-fully-flagged-during-bandpass-scan-still-used-as-refant to main
* commit '8dabe1b5b997da832ea10696bb0a42d11d6c2337':
PIPE-3258: preserve list type in refant fallback and align testBPdcals
PIPE-3258: fix reference antenna fallback and caltable cleanup in `hifv_semiFinalBPdcals` -
Rui Xue 0e65d3296eb61d1facf16f2708c2a9cd6711f316 m
Pull request #1992: PIPE-3252 append alma task ref to plug main
Merge in PIPE/pipeline from PIPE-3252-append-alma-task-ref-to-plug-main to main
* commit 'c32c5ee6f49ee372db9c51fcd18132440540ac23':
PIPE-3252: partition dev docs and add contributors page
PIPE-3252: include ALMA tasks in User's Guide PDF and clean up doc links -
Rui Xue c32c5ee6f49ee372db9c51fcd18132440540ac23 m
PIPE-3252: partition dev docs and add contributors page
- partition dev toctrees and `conf.py` exclusions between public and internal builds
- move `dependencies.md` under `devel/setup/` and update cross-references
- add Contributors to Basics navigation with courtesy note
- tweak citation and transition notices in `docs/README.rst`
- clean up "CASA pipeline tasks" terminology across documentation- Contributors.rst (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/README.rst (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/conf.py (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/contributors.rst (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/devel/reference/callibrary.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/devel/setup/dependencies.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/devel/setup/index.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/devel/testing/diffing_execution_logs.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/devel/usage/running_pipeline.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/index.rst (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/qa.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
- docs/source/users_guide/pipeline-versions-and-documentation.md (version c32c5ee6f49ee372db9c51fcd18132440540ac23) (diffs)
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Rui Xue 9b876959674a29dd5f275d64375dd01d13d472fe m
PIPE-3252: include ALMA tasks in User's Guide PDF and clean up doc links
- Add `users_guide/alma_tasks.rst` and Sphinx hooks in conf.py to resolve task hyperlinks in `users_guide.pdf` while excluding them from HTML builds.
- Drop "known_issues" from `users_guide/index.md` to eliminate duplicate toctree warnings and align navigation hierarchy with VLA.
- Fix broken cross-references, link syntax, code fences, and typos across the PLUG documentation files.- docs/source/conf.py (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/alma_tasks.rst (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/data-processing-files.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/helper-text-files.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/index.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/known_issues.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/lowSNR-workflow.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
- docs/source/users_guide/pipeline-weblog.md (version 9b876959674a29dd5f275d64375dd01d13d472fe) (diffs)
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Rui Xue c394948a650b5fbd04e48e7d39f16e711270d163 m
Pull request #1990: PIPE-3262
Merge in PIPE/pipeline from PIPE-3262 to main
* commit '8d3c214a77b5638e53eed418fafc0f126617e138':
PIPE-3262: prevent MPI import deadlock and drop `casaplotserver` in pixi
PIPE-3262: avoid unconditional mpi4py import in `daskhelpers.py` -
Rui Xue 8d3c214a77b5638e53eed418fafc0f126617e138 m
PIPE-3262: prevent MPI import deadlock and drop `casaplotserver` in pixi
- Add dynamic `scripts/stubs/casalith.py` to defer MPI initialization to casashell script scope and avoid casatasks import-lock deadlocks (CAS-14037).
- Propagate PYTHONPATH with scripts/stubs in pixi `casa` and `casampi` tasks.
- Remove unused `casaplotserver` dependency from `pyproject.toml` and lockfile. -
Rui Xue 8f568c69ee1cef7d1b872cb1261b5ee41ca6a9bb m
PIPE-3262: avoid unconditional mpi4py import in `daskhelpers.py`
Use `MPIEnvironment.mpi_processor_rank` instead of `mpi4py.MPI.COMM_WORLD.Get_rank()` to prevent unmanaged `MPI_Init` calls and potentially crashes in macOS serial sessions environments with OpenMPI build/version mismatches. -
Rui Xue 34228abc590663d2714f3d8cc7e37e8d124b2293 m
PIPE-3260: Fix false QA failures in `VLASetjy`
- `pipeline/hifv/tasks/setmodel/qa.py`: filter standard calibrators to fields with AMPLITUDE intent, safeguard statistics lookups, and disambiguate MS field names in messages.
- `pipeline/hifv/tasks/setmodel/qa_test.py`: add unit tests covering single/multiple calibrators, pointing aliases, and edge cases. -
Takeshi Nakazato 0660fcc12294974a6420446a231dcac6217fd3ab m
Pull request #1961: PIPE-3206 hsd flagdata offset pointing plots for ephemeris data is not updated after deterministic
Merge in PIPE/pipeline from PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic to main
* commit '4f052fb9e0c1e9af3f020512d7b8fb4a0ac52c03':
PIPE-3206 better condition to check if the target is ephemeris -
Takeshi Nakazato 5b6b584ff3fa9d99e0aab0be3f1cbd46b23919e5 m
Pull request #1957: PIPE-3228 clone hsd imaging fail of atm line identification in contamination plots
Merge in PIPE/pipeline from PIPE-3228-clone-hsd_imaging-fail-of-atm-line-identification-in-contamination-plots to main
* commit 'b9106cae3b557a37333cf2492ade928904ba0732':
updated schematic diagram
fix wrong index in docstring
format docstring
cache interpolator object for each baseband
avoid unbound local warning
ensure ascending order
PIPE-3226 fix a bug in interpolating tau
add unit test for SDcalatmcorr -
Rui Xue 8dabe1b5b997da832ea10696bb0a42d11d6c2337 m
PIPE-3258: preserve list type in refant fallback and align testBPdcals
Use list slicing instead of `np.delete` for refant fallback, clean up delay caltables on retry in testBPdcals, and streamline docstrings. -
Rui Xue 15dcc142b4d05281e356875261f733e0c026ef78 m
PIPE-3258: fix reference antenna fallback and caltable cleanup in `hifv_semiFinalBPdcals`
Propagate the updated reference antenna list in the delaycal retry loop, clean up preexisting delay caltables, and guard against empty antenna lists. -
Rui Xue fb50ffeb80b378fda7ec498eff8147372a29d87b m
Pull request #1982: PIPE-3211: update GitHub Actions workflows, add git-resilient helper, and fix doc badge clicks
Merge in PIPE/pipeline from PIPE-3211-update-gh-workflows to main
* commit '2271c07d0be45594b7856f9734d4ee9d92b7ae73':
PIPE-3211: modernize GitHub Actions workflows, add git-resilient helper, and fix doc badge clicks -
Rui Xue 2271c07d0be45594b7856f9734d4ee9d92b7ae73 m
PIPE-3211: modernize GitHub Actions workflows, add git-resilient helper, and fix doc badge clicks
- Add .github/scripts/git-resilient.sh with in-memory tuning, retries, and native HTTP timeouts
- Modernize workflows to Pixi, align artifact actions to @v7, and upgrade to checkout@v5 / cache@v5
- Make Bitbucket scheduled sync resilient to on-prem server downtime
- Remove legacy conda workflows (build-gh-pages.yml, env-setup-run-template.yml, test-unit.yml)
- Unify Pages deployment under official actions and remove third-party peaceiris/actions-gh-pages
- Fix Viewer.js lightbox hijacking on Sphinx doc badges and document LaTeX prerequisites- .github/scripts/git-resilient.sh (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/build-gh-pages-pixi.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/build-gh-pages.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/env-setup-run-template-pixi.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/env-setup-run-template.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/sync-from-open-bitbucket.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/test-unit-pixi.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- .github/workflows/test-unit.yml (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- docs/source/_static/custom_theme.css (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- docs/source/_static/viewer_init.js (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
- docs/source/devel/setup/readthedocs.md (version 2271c07d0be45594b7856f9734d4ee9d92b7ae73) (diffs)
-
Rui Xue 363f65f480c16c4b39c6e96e23983877248f687f m
Pull request #1981: PIPE-3211: clean up pyproject.toml by removing unnecessary line breaks and comments
Merge in PIPE/pipeline from PIPE-3211-followup to main
* commit 'bfd57924b3a31bacb83ed99ab683e92b53822bfc':
PIPE-3211: clean up pyproject.toml by removing unnecessary line breaks and comments -
Rui Xue bfd57924b3a31bacb83ed99ab683e92b53822bfc m
PIPE-3211: clean up pyproject.toml by removing unnecessary line breaks and comments
-
Rui Xue 62d0284b0eb2bfe226c950f2020117c260320c51 m
Pull request #1973: PIPE-3211
Merge in PIPE/pipeline from PIPE-3211 to main
* commit '050c7ff9597ba670223e7d6e55ce1419bd0f2fc6':
PIPE-3251/PIPE-3252: clarify parallel imaging docstrings
PIPE-3211: update `astropy` dependency to version 8.0
PIPE-3211: remove stale test procedures for `hifa_cal_tier0` and `hifa_calimage_tier0`; should use `scripts/procedure_add_parallel.py` instead.
PIPE-3211: single-source dynamic version from `pipeline._version.py`
PIPE-3211: define CASA aliases upfront and add export option for dependencies
PIPE-3211: update CI/CD workflow trigger path filters
PIPE-3211: prune redundant six dependency and obsolete egg package data
PIPE-3211: prune obsolete and unused documentation dependencies
PIPE-3211: prune redundant and obsolete development dependencies
PIPE-3211: bump runtime dependencies in `pyproject.toml` and update `pixi.lock`
PIPE-3211: fold requirements into `pyproject.toml` and add CASA dependency installer
PIPE-3211: migrate dynamic versioning to in-tree build backend and remove `setup.py`
PIPE-3211: add documentation for weblog resources and developer scripts
PIPE-3211: decouple weblog asset minification from `setup.py`
PIPE-3211/PIPE-2930: Remove duplicated test tasks from `pyproject.toml` and update Numpy version constraint in `requirements.txt` -
Takeshi Nakazato 4f052fb9e0c1e9af3f020512d7b8fb4a0ac52c03 m
Merge branch 'main' into PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic
-
Rui Xue ec0d64616bb1e25c69cdbdc3475801c422703a87 m
PIPE-684: handle per-MS field lists and streamline center_field_ids
- Support both string and per-MS sequence field selections in `center_field_ids`, fixing `AttributeError` from `.split()` when `inputs.field` is a list (e.g. in VLASS).
- Leverage `ms.get_fields(task_arg=...)` in `center_field_ids` to natively resolve field IDs, names, and selections via domain tools.
- Pass `fields` instead of flattened `field_names` in `phasecenter` to align with the per-MS heuristics contract.
- Add type hints and docstrings for `phasecenter` and `center_field_ids`. -
Rui Xue 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6 m
PIPE-3251/PIPE-3252: clarify parallel imaging docstrings
- Clarify `parallel` docstrings in makeimlist, checkproductsize, and imageprecheck: document automatic fallback to serial imager (PySynthesisImager) when parallel=True in serial sessions, and remove references to tclean(parallel=True).
- Add note in makeimages docstring citing CASAdocs regarding CASA built-in tclean parallelization behavior for spectral cubes vs. continuum.- pipeline/hif/heuristics/imageparams_vlass_single_epoch_continuum.py (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
- pipeline/hif/tasks/checkproductsize/checkproductsize.py (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
- pipeline/hif/tasks/makeimages/makeimages.py (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
- pipeline/hif/tasks/makeimlist/makeimlist.py (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
- pipeline/hifa/tasks/imageprecheck/imageprecheck.py (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
- pixi.lock (version 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6) (diffs)
-
Rui Xue 7242f0943dc9ff5d969f976c8c4050cdcf2e8ab3 m
PIPE-3211: prune obsolete and unused documentation dependencies
- Remove legacy Python 2/3 compatibility shim future and redundant transitive dependency urllib3 from docs optional-dependencies.
- Remove dead PyPI dummy package nodejs (Node.js is provided by Conda).
- Remove unused Sphinx extensions (nbsphinx, sphinx-autoapi), unused theme (sphinx_rtd_theme), and ipympl widget not active in conf.py.
- Update documentation list in `docs/source/dependencies.md`.
- Synchronize and prune `pixi.lock` across docs environments. -
Rui Xue 74823d13b4eddac41d072131f0e80b908a971467 m
PIPE-3211: update CI/CD workflow trigger path filters
- Replace deleted setup.py and environment*.yml paths with active
project components (scripts/**, pixi.lock, MANIFEST.in).
- Ensure modifications to in-tree build backend, asset bundler,
and dependency installer trigger test and docs workflows.- .github/workflows/build-gh-pages-pixi.yml (version 74823d13b4eddac41d072131f0e80b908a971467) (diffs)
- .github/workflows/build-gh-pages.yml (version 74823d13b4eddac41d072131f0e80b908a971467) (diffs)
- .github/workflows/test-unit-pixi.yml (version 74823d13b4eddac41d072131f0e80b908a971467) (diffs)
- .github/workflows/test-unit.yml (version 74823d13b4eddac41d072131f0e80b908a971467) (diffs)
-
Rui Xue 99c9b87a741c4f3802da8bb954e72287ba074e1a m
PIPE-3211: single-source dynamic version from `pipeline._version.py`
- Configure setuptools dynamic version via attr = "pipeline._version.version"
in pyproject.toml instead of file = "version".
- Update `scripts/build_backend.py` to eliminate root version file generation,
leaving `pipeline/_version.py` as the single source of truth for both build
and runtime.
- Remove redundant /version ignore from .gitignore and package-data.
- Add docstrings to `build_backend.py` PEP 517/660 hooks and format with Ruff.- .gitignore (version 99c9b87a741c4f3802da8bb954e72287ba074e1a) (diffs)
- pyproject.toml (version 99c9b87a741c4f3802da8bb954e72287ba074e1a) (diffs)
- scripts/README.md (version 99c9b87a741c4f3802da8bb954e72287ba074e1a) (diffs)
- scripts/build_backend.py (version 99c9b87a741c4f3802da8bb954e72287ba074e1a) (diffs)
-
Rui Xue 7d3b841391659d55a82dd233871517f4b0d2dd5a m
PIPE-3211: define CASA aliases upfront and add export option for dependencies
- Move CASA environment shortcuts and aliases (`casa_pip`, `casa_python`)
upfront under Prerequisites in monolithic CASA documentation.
- Add `--export [FILE]` (`-o`) option to `scripts/install_dependencies.py`
to extract dependencies in requirements.txt format.
- Add TOML parser fallback (tomllib -> tomli -> pip._vendor.tomli) in
`scripts/install_dependencies.py` for Python < 3.11 (monolithic CASA) support.
- Document standalone Python 3.11+ tomllib one-liners with standard line wrapping.
- Clarify test execution commands in `daskhelpers_test.py` docstring.
- Cross-reference monolithic CASA environment setup from pytest reference guide.- docs/source/devel/setup/monolithic_casa.md (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
- docs/source/devel/testing/pytest_reference.md (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
- docs/source/qa.md (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
- pipeline/infrastructure/daskhelpers_test.py (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
- scripts/README.md (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
- scripts/install_dependencies.py (version 7d3b841391659d55a82dd233871517f4b0d2dd5a) (diffs)
-
Rui Xue c51df6219e629aa1991514534969533117f189b2 m
PIPE-3211: remove stale test procedures for `hifa_cal_tier0` and `hifa_calimage_tier0`; should use `scripts/procedure_add_parallel.py` instead.
-
Rui Xue 79d49872125a4170b64ea819c286bb465459a632 m
PIPE-3211: prune redundant six dependency and obsolete egg package data
- Remove redundant top-level six requirement from pixi pypi-dependencies
(not imported by Pipeline; resolved transitively where needed).
- Remove obsolete '*.egg' pattern from setuptools package-data. -
Rui Xue 05f7e92c5c32b44b1c005b054229de35d298e55b m
PIPE-3211: update `astropy` dependency to version 8.0
-
Rui Xue c5814b3059e280ff7102a2e49dfea61ca1740b97 m
PIPE-3211: prune redundant and obsolete development dependencies
- Remove legacy linters and formatters (black, isort, flake8, pylint, pydocstyle, pycodestyle) superseded by ruff.
- Remove deprecated pytest-forked (covered by pytest-xdist) and unused CLI inspector johnnydep from dev dependencies.
- Update developer documentation in `docs/source/dependencies.md`.
- Synchronize and prune `pixi.lock` across all environments. -
Rui Xue 08dc2a857608a09d87d0209a3a8065e1c22e25a5 m
PIPE-3211: bump runtime dependencies in `pyproject.toml` and update `pixi.lock`
- Bump bdsf to ~=1.14 and drop macOS platform/version constraint now that native wheels support Python 3.13+ on Apple Silicon.
- Bump low-risk runtime dependencies: intervaltree to ~=3.2, mako to ~=1.4, and pypubsub to ==4.0.7.
- Synchronize pixi.lock across all environments. -
Rui Xue 9912dcb94977a770df4c6263bc0ff59a38a03ee9 m
PIPE-3211: decouple weblog asset minification from `setup.py`
- Add `scripts/bundle_assets.py` and track pre-generated minified CSS/JS bundles
- Remove minification commands and jsmin/csscompressor from `setup.py` and build-system requires
- Add bundle-assets pixi task and move minification dependencies to `requirements_dev.txt`- pipeline/infrastructure/renderer/templates/resources/css/all.min.css (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- pipeline/infrastructure/renderer/templates/resources/js/pipeline_common.min.js (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- pipeline/infrastructure/renderer/templates/resources/js/pipeline_plots.min.js (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- pyproject.toml (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- requirements_dev.txt (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- scripts/bundle_assets.py (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
- setup.py (version 9912dcb94977a770df4c6263bc0ff59a38a03ee9) (diffs)
-
Rui Xue 3e14baf569ff0feea0bb288ba1c74d6dab451268 m
PIPE-3211: fold requirements into `pyproject.toml` and add CASA dependency installer
- Declare dependencies and optional extras (dev, docs, exp) statically in `pyproject.toml` per PEP 621, removing dynamic dependency file tables.
- Remove `requirements*.txt` and legacy `Dockerfile`.
- Add `scripts/install_dependencies.py` to allow installing dependencies into monolithic CASA environments without installing Pipeline.
- Update `MANIFEST.in` to include `scripts/install_dependencies.py` in sdists.
- Update developer and setup documentation to reflect `pyproject.toml` as SSoT.- Dockerfile (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- MANIFEST.in (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- docs/source/dependencies.md (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- docs/source/devel/setup/conda_setup.rst (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- docs/source/devel/setup/monolithic_casa.md (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- docs/source/qa.md (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- pixi.lock (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- pyproject.toml (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- requirements.txt (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- requirements_dev.txt (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- requirements_docs.txt (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- requirements_exp.txt (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- scripts/README.md (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- scripts/bundle_assets.py (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
- scripts/install_dependencies.py (version 3e14baf569ff0feea0bb288ba1c74d6dab451268) (diffs)
-
Rui Xue 9d3fc84477d803a0c67f325e7375d13af31a6caa m
PIPE-3211/PIPE-2930: Remove duplicated test tasks from `pyproject.toml` and update Numpy version constraint in `requirements.txt`
-
Rui Xue 6919fb4f257da7fffc1aaa1ccb8390336b5e583f m
PIPE-3211: add documentation for weblog resources and developer scripts
- Add `templates/resources/README.md` documenting vendor assets, bundling, and licenses
- Add `scripts/README.md` documenting maintenance and utility scripts
- Fix minor docstring formatting in `scripts/update_references.py` -
Rui Xue 17c5d5815dfaf728dd7209b4e630cde9ae0a282e m
PIPE-3211: migrate dynamic versioning to in-tree build backend and remove `setup.py`
- Add in-tree PEP 517/660 build backend wrapper (`scripts/build_backend.py`)
delegating to `setuptools.build_meta` to generate NRAO Git versioning
on-demand during build and installation.
- Configure `build-backend = "build_backend"` and `version = { file = "version" }`
in `pyproject.toml`.
- Add `MANIFEST.in` to include `scripts/build_backend.py` in source distributions.
- Remove legacy `setup.py` and ignore generated `/version` in `.gitignore`.
- Document `build_backend.py` in `scripts/README.md`.- .gitignore (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
- MANIFEST.in (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
- pyproject.toml (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
- scripts/README.md (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
- scripts/build_backend.py (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
- setup.py (version 17c5d5815dfaf728dd7209b4e630cde9ae0a282e) (diffs)
-
Rui Xue 29cff76c4fd3245bc64db0053f61774cff205fe0 m
Pull request #1974: PIPE-3251: Fallback to `PySynthesisImager` in serial CASA session when `parallel=True`
Merge in PIPE/pipeline from PIPE-3251-fallback-to-pysynthesisimager-in-a-serial-casa-session-when-parallel-true-for to main
* commit 'b50c8ea978c605e96d1961f213ebad974c87615f':
PIPE-3251: Fallback to `PySynthesisImager` in serial CASA session when `parallel=True` -
Andres Guzman 1f1b1cd216b977a61b80fb30fd4ceee9fd383e70 m
Pull request #1970: PIPE-3240.
Merge in PIPE/pipeline from PIPE-3240-fixes-to-extern-code-tsys_contamination to main
* commit 'c7fb9fc782c4403fad4e2dea6c8ec0b94f4bf205':
PIPE-3240: Fix mp.min typo and handle empty peak prominences in model_break
PIPE-3240. Apply the three changes in the ticket description. -
Rui Xue 44b7d0d26085365533abe8f12f47ddf4778c9ebe m
Pull request #1978: PIPE-3252: update citation example to Pipeline 2026.2.0 and CASA 6.7.4
Merge in PIPE/pipeline from PIPE-3252-update-acknowledgement-to-main to main
* commit '44db00801842e89d4d13c3f5ab24ae640fcfddcc':
PIPE-3252: update citation example to Pipeline 2026.2.0 and CASA 6.7.4 -
Rui Xue 44db00801842e89d4d13c3f5ab24ae640fcfddcc m
PIPE-3252: update citation example to Pipeline 2026.2.0 and CASA 6.7.4
- Bump example citation versions in acknowledgement.md to Pipeline 2026.2.0.27
and CASA 6.7.4-8.
- Clarify cross-reference link to software design overview. -
Rui Xue c7fb9fc782c4403fad4e2dea6c8ec0b94f4bf205 m
PIPE-3240: Fix mp.min typo and handle empty peak prominences in model_break
-
Rui Xue b50c8ea978c605e96d1961f213ebad974c87615f m
PIPE-3251: Fallback to `PySynthesisImager` in serial CASA session when `parallel=True`
- Add fallback in imageparams heuristics to revert to serial imaging mode when parallel=True is requested but no CASA MPI session is active.
- Clarify parallel synthesis imaging docstrings in makeimlist, imageprecheck, and checkproductsize.- pipeline/hif/heuristics/imageparams_base.py (version b50c8ea978c605e96d1961f213ebad974c87615f) (diffs)
- pipeline/hif/heuristics/imageparams_vlass_single_epoch_continuum.py (version b50c8ea978c605e96d1961f213ebad974c87615f) (diffs)
- pipeline/hif/tasks/checkproductsize/checkproductsize.py (version b50c8ea978c605e96d1961f213ebad974c87615f) (diffs)
- pipeline/hif/tasks/makeimlist/makeimlist.py (version b50c8ea978c605e96d1961f213ebad974c87615f) (diffs)
- pipeline/hifa/tasks/imageprecheck/imageprecheck.py (version b50c8ea978c605e96d1961f213ebad974c87615f) (diffs)
-
Hajime Ezawa 39d3d4222f0101c06a1a7bf7fd7816795370c983 m
PIPE-3105: bug fix and corrections
-
Rui Xue 0c9ad4a7f5ad701bd618ee484bf476351051b988 m
Pull request #1971: PIPE-2738: update task reference manual title formatting
Merge in PIPE/pipeline from PIPE-2738-main-update-refman-title to main
* commit '8e292b95f92e36ed0cbf0c8f02a3d2acab947b6e':
PIPE-2738: update task reference manual title formatting -
Rui Xue 8e292b95f92e36ed0cbf0c8f02a3d2acab947b6e m
PIPE-2738: update task reference manual title formatting
-
Rui Xue 302d80afc5c8d1f2c54c5f934078817de2cd77ba m
PIPE-684: set VLA pblimit_image to 0.1 for mosaic non-cube imaging
- Add optional `gridder` parameter to `pblimits` across base, VLA, and VLASS image heuristics classes.
- Update VLA heuristics to set `pblimit_image = 0.1` for non-cube mosaic imaging (keeping 0.2 for cube and -0.1 for single-field continuum).- pipeline/hif/heuristics/imageparams_base.py (version 302d80afc5c8d1f2c54c5f934078817de2cd77ba) (diffs)
- pipeline/hif/heuristics/imageparams_vla.py (version 302d80afc5c8d1f2c54c5f934078817de2cd77ba) (diffs)
- pipeline/hif/heuristics/imageparams_vlass_single_epoch_continuum.py (version 302d80afc5c8d1f2c54c5f934078817de2cd77ba) (diffs)
- pipeline/hif/tasks/tclean/tclean.py (version 302d80afc5c8d1f2c54c5f934078817de2cd77ba) (diffs)
-
Rui Xue 963956e8bd22165cc051817a887b04312b9ee253 m
PIPE-3247/PIPE-3248: Improve field name rendering with text wrapping
- Wrap long comma-separated field names weblogs of `findcont` and `uvcontsub`
- Save and present only first field name by parsing composite field names in joint mask sky plots -
Rui Xue 941723b0a49b9bfcc02a08bd92fcb0c00c334bcf m
Pull request #1935: Migrate the PIPE-2738 documentation improvement to main
Merge in PIPE/pipeline from docs/PIPE-2738-improve-docs-for-main-part3 to main
* commit 'fbdf591a705f2546e47b28a96d92681e75a174b9':
PIPE-2738: fix typos in hifa_spwphaseup task docstring
PIPE-2738: Documentation build configuration and tooling updates
PIPE-2738: Update CLI and task docstrings for PL2026
PIPE-2738: Add PL2026 documentation guides, release notes, and assets
PIPE-2738: preserve original docstrings for Sphinx; fix doc rendering issues
PIPE-2738: make pdf link version-contained and use short version on pdf cover
PIPE-2738: Added SD changes from Kotomi
PIPE-2738: Added branding to the ALMA User's guide front page
PIPE-2738: dynamically strip Sphinx markup from task docstrings for terminal users
PIPE-2738: Did a readthrough of all hifa_; added back in some description that I thought was important. Also tried to check Kotomi's changes ~Aug 3 in the PLUG, that they got transferred correctly, but those should be double-checked.
PIPE-2738: Update docs badge to reference pixi-based build workflow -
Rui Xue fbdf591a705f2546e47b28a96d92681e75a174b9 m
PIPE-2738: fix typos in hifa_spwphaseup task docstring
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Rui Xue ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3 m
PIPE-2738: Documentation build configuration and tooling updates
- .readthedocs.yaml (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- pipeline/infrastructure/doctools.py (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- pyproject.toml (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- requirements_docs.txt (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- scripts/update_references.py (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
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Rui Xue 0c87523cdcb789fe2fcb78a6843268bc7034016e m
PIPE-2738: Update CLI and task docstrings for PL2026
- pipeline/domain/datatype.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_applycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_checkproductsize.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_correctedampflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_findcont.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_findroi.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_lowgainflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_makeimages.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_makeimlist.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_mstransform.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_selfcal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_setmodels.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/findcont/findcont.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/findroi/findroi.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/makeimlist/makeimlist.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_antpos.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_bandpass.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_diffgaincal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_exportdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_flagdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_fluxcalflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_gaincalsnr.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_gfluxscale.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_imageprecheck.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_importdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_lock_refant.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_restoredata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_spwphaseup.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_targetflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_timegaincal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_tsysflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_unlock_refant.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_wvrgcalflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/tasks/imageprecheck/imageprecheck.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_baseline.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_imaging.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_importdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_k2jycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_skycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
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Rui Xue b675284a8337834d8b2b5911cc5f206929a879b8 m
PIPE-2738: Add PL2026 documentation guides, release notes, and assets
- docs/README.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_extension/jira_links.py (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/custom_theme.css (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/robots.txt (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewer_init.js (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/README.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/viewer.min.css (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/viewer.min.js (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/acknowledgement.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/conf.py (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/misc/python3_conversion_notes.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/reference/ALMA-Imaging-Workflow.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/reference/spectral_windows.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/monolithic_casa.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/pixi_tasks.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/readthedocs.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/testing/unit_tests.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/examples/test2.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_hifa_diffgaincal_incHeuristic_lowSNR.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_hifa_gfluxscale_workflowtitle.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_size_mitigation_flowchart_final.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/contamination.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/elevation_difference.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/index.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/overview.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/pipeline_tasks/individual_task.mako (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/pipeline_tasks/pipeline_tasks.mako (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/references.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/references/pipeline.bib (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/references/readme.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/releases.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/task_reference.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/tasks.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/tickets/pipe3061.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/CAS-14703-phase_vs_time.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/PIPE-2644-popup.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/PIPEREQ-316_example1.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/PIPEREQ-316_example2.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/alma-science-pipeline.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/bytopiclow.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/data-processing-files.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/helper-text-files.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/hifa_polcalimage-recipe.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/hsd_calimage-recipe.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/index.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/known_issues.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/lowSNR-workflow.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/modifying-a-pipeline-run.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/ms_overview_2.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/pipeline-versions-and-documentation.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/pipeline-weblog.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/plotcommand1.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/quick-start.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/timegaincal_bottomhalf.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/weights.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/whats-new-2025.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/whats-new-2026.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/whatsnew/Polcal_bandpass_after_lockrefant_unregister.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/whatsnew/dev_virtual_spw_stage11.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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Rui Xue 4e6b4b4dbbfd685dc27b27c71448c2d27e568319 m
Merge tag '2026.2.1.40' into docs/PIPE-2738-improve-docs-for-main-part3
