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Takeshi Nakazato aae06797d595843586eed600982f3e71e7b7dd53
Merge branch 'main' into PIPE-3232-fix-errors-in-log_qa-when-weblog-rendering-is-disabled
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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 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 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 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 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)
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Takeshi Nakazato 4f052fb9e0c1e9af3f020512d7b8fb4a0ac52c03 m
Merge branch 'main' into PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic
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Takeshi Nakazato b9106cae3b557a37333cf2492ade928904ba0732 m
Merge branch 'main' into PIPE-3228-clone-hsd_imaging-fail-of-atm-line-identification-in-contamination-plots
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Takeshi Nakazato 8e5c0d0fe950fabb183fabb692450113183c62f5 m
Merge branch 'main' into PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic
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Takeshi Nakazato a3b14f085163806f35739eb216d1e1d15fcb2e83 m
updated schematic diagram
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Takeshi Nakazato 5334b87ca06d01b4a99a854d5d44e06596390e6d m
fix wrong index in docstring
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Takeshi Nakazato a8eac6156a26777bd455c5fba7942683b8eb14b9 m
format docstring
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Takeshi Nakazato 9d3cb26e9bf4ed7dfc4f40e8f9b76e8b2db694af m
cache interpolator object for each baseband
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Takeshi Nakazato ade56df83caf7662134a90c7a435b34732da71a9 m
avoid unbound local warning
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Takeshi Nakazato 01708e6be3fd75e60ad0ad8ad92e517163f330f1 m
ensure ascending order
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Takeshi Nakazato f28c21e62e1f42b1eeea60f3e363a12bc9af0a35 m
PIPE-3226 fix a bug in interpolating tau
In addition to the bug fix, SDcalatmtorr.getCalAtmData has been simplified to return tau only. Based on this simplification, the function was renamed to getTau. -
Takeshi Nakazato d3ccf6ee1989e3ec06399ef339576de38fb6d120 m
add unit test for SDcalatmcorr
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Takeshi Nakazato caef04eab9c993336608eadd623e5d0e8751f43e m
PIPE-3206 better condition to check if the target is ephemeris
The new condition is consistent with the one used in htmlrenderer.py.