Pipeline

• 

  Rui Xue 3 days ago beed751da9a3c6555c661227f0e90d131b9ad0a7

  Merge remote-tracking branch 'origin/main' into PIPE-684-vla-mosaic-imaging
• 

  Rui Xue 5 days ago 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 5 days ago 8c6a6a273861cfa5da6e3f57ed6248f35169d7bb m

  PIPE-3252: add link to CASA Docs citation guide in acknowledgements

  • docs/source/acknowledgement.md (version 8c6a6a273861cfa5da6e3f57ed6248f35169d7bb) (diffs)
• 

  Remy Indebetouw 5 days ago 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> 5 days ago a0038a8a2d5338d32976b6ba80057eff54bc66f7 m

  fixed "present" and double Andy

  • Contributors.rst (version a0038a8a2d5338d32976b6ba80057eff54bc66f7) (diffs)
• 

  Remy Indebetouw <remy@virginia.edu> 5 days ago 0669c460be9ade6b26ce65288d1024f5d0d667bf m

  reordered chronologically, added people who contributed significantly albeit not directly in the code repo

  • Contributors.rst (version 0669c460be9ade6b26ce65288d1024f5d0d667bf) (diffs)
• 

  Rui Xue 6 days ago 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 6 days ago 8ac857aa5055fe97677559d13504a077fa590f08 m

  PIPE-3252: update release notes with ALMA task references and improve formatting

  • docs/source/releases.md (version 8ac857aa5055fe97677559d13504a077fa590f08) (diffs)
• 

  Rui Xue 6 days ago 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 6 days ago 79b00e3aef7de55ad5b9c185aa71ccd39f6d86bd m

  PIPE-3252: Add AL to Contributors list

  • Contributors.rst (version 79b00e3aef7de55ad5b9c185aa71ccd39f6d86bd) (diffs)
• 

  Rui Xue 6 days ago 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 6 days ago 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 6 days ago 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 6 days ago 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)
• 

  Rui Xue 6 days ago 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)
• 

  Rui Xue 1 week ago 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 1 week ago 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.

  • pixi.lock (version 8d3c214a77b5638e53eed418fafc0f126617e138) (diffs)
  • pyproject.toml (version 8d3c214a77b5638e53eed418fafc0f126617e138) (diffs)
  • scripts/stubs/casalith.py (version 8d3c214a77b5638e53eed418fafc0f126617e138) (diffs)
• 

  Rui Xue 1 week ago 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.

  • pipeline/infrastructure/daskhelpers.py (version 8f568c69ee1cef7d1b872cb1261b5ee41ca6a9bb) (diffs)
• 

  Rui Xue 1 week ago 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.

  • pipeline/hifv/tasks/setmodel/qa.py (version 34228abc590663d2714f3d8cc7e37e8d124b2293) (diffs)
  • pipeline/hifv/tasks/setmodel/qa_test.py (version 34228abc590663d2714f3d8cc7e37e8d124b2293) (diffs)
• 

  Takeshi Nakazato 16 Sep 2026 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 16 Sep 2026 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 16 Sep 2026 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.

  • pipeline/hifv/tasks/semiFinalBPdcals/semiFinalBPdcals.py (version 8dabe1b5b997da832ea10696bb0a42d11d6c2337) (diffs)
  • pipeline/hifv/tasks/testBPdcals/testBPdcals.py (version 8dabe1b5b997da832ea10696bb0a42d11d6c2337) (diffs)
• 

  Rui Xue 15 Sep 2026 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.

  • pipeline/hifv/tasks/semiFinalBPdcals/semiFinalBPdcals.py (version 15dcc142b4d05281e356875261f733e0c026ef78) (diffs)
• 

  Rui Xue 15 Sep 2026 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 14 Sep 2026 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 14 Sep 2026 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 14 Sep 2026 bfd57924b3a31bacb83ed99ab683e92b53822bfc m

  PIPE-3211: clean up pyproject.toml by removing unnecessary line breaks and comments

  • .dockerignore (version bfd57924b3a31bacb83ed99ab683e92b53822bfc) (diffs)
  • pyproject.toml (version bfd57924b3a31bacb83ed99ab683e92b53822bfc) (diffs)
• 

  Rui Xue 14 Sep 2026 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 13 Sep 2026 4f052fb9e0c1e9af3f020512d7b8fb4a0ac52c03 m

  Merge branch 'main' into PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic
• 

  Rui Xue 11 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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.

  • pyproject.toml (version 79d49872125a4170b64ea819c286bb465459a632) (diffs)
• 

  Rui Xue 10 Sep 2026 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.

  • docs/source/dependencies.md (version 7242f0943dc9ff5d969f976c8c4050cdcf2e8ab3) (diffs)
  • pixi.lock (version 7242f0943dc9ff5d969f976c8c4050cdcf2e8ab3) (diffs)
  • pyproject.toml (version 7242f0943dc9ff5d969f976c8c4050cdcf2e8ab3) (diffs)
• 

  Rui Xue 10 Sep 2026 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.

  • docs/source/dependencies.md (version c5814b3059e280ff7102a2e49dfea61ca1740b97) (diffs)
  • pixi.lock (version c5814b3059e280ff7102a2e49dfea61ca1740b97) (diffs)
  • pyproject.toml (version c5814b3059e280ff7102a2e49dfea61ca1740b97) (diffs)
• 

  Rui Xue 10 Sep 2026 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 10 Sep 2026 05f7e92c5c32b44b1c005b054229de35d298e55b m

  PIPE-3211: update `astropy` dependency to version 8.0

  • pyproject.toml (version 05f7e92c5c32b44b1c005b054229de35d298e55b) (diffs)
• 

  Rui Xue 10 Sep 2026 c51df6219e629aa1991514534969533117f189b2 m

  PIPE-3211: remove stale test procedures for `hifa_cal_tier0` and `hifa_calimage_tier0`; should use `scripts/procedure_add_parallel.py` instead.

  • pipeline/recipes/tests/test_procedure_hifa_cal_tier0.xml (version c51df6219e629aa1991514534969533117f189b2) (diffs)
  • pipeline/recipes/tests/test_procedure_hifa_calimage_tier0.xml (version c51df6219e629aa1991514534969533117f189b2) (diffs)
• 

  Rui Xue 10 Sep 2026 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.

  • pixi.lock (version 08dc2a857608a09d87d0209a3a8065e1c22e25a5) (diffs)
  • pyproject.toml (version 08dc2a857608a09d87d0209a3a8065e1c22e25a5) (diffs)
• 

  Rui Xue 10 Sep 2026 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`

  • pipeline/infrastructure/renderer/templates/resources/README.md (version 6919fb4f257da7fffc1aaa1ccb8390336b5e583f) (diffs)
  • scripts/README.md (version 6919fb4f257da7fffc1aaa1ccb8390336b5e583f) (diffs)
  • scripts/update_references.py (version 6919fb4f257da7fffc1aaa1ccb8390336b5e583f) (diffs)
• 

  Rui Xue 10 Sep 2026 9d3fc84477d803a0c67f325e7375d13af31a6caa m

  PIPE-3211/PIPE-2930: Remove duplicated test tasks from `pyproject.toml` and update Numpy version constraint in `requirements.txt`

  • pyproject.toml (version 9d3fc84477d803a0c67f325e7375d13af31a6caa) (diffs)
  • requirements.txt (version 9d3fc84477d803a0c67f325e7375d13af31a6caa) (diffs)
• 

  Rui Xue 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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 10 Sep 2026 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.

  • docs/source/acknowledgement.md (version 44db00801842e89d4d13c3f5ab24ae640fcfddcc) (diffs)
• 

  Rui Xue 10 Sep 2026 c7fb9fc782c4403fad4e2dea6c8ec0b94f4bf205 m

  PIPE-3240: Fix mp.min typo and handle empty peak prominences in model_break

  • pipeline/extern/tsys_contamination.py (version c7fb9fc782c4403fad4e2dea6c8ec0b94f4bf205) (diffs)
• 

  Rui Xue 09 Sep 2026 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)
• 

  Rui Xue 08 Sep 2026 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 08 Sep 2026 8e292b95f92e36ed0cbf0c8f02a3d2acab947b6e m

  PIPE-2738: update task reference manual title formatting

  • docs/source/conf.py (version 8e292b95f92e36ed0cbf0c8f02a3d2acab947b6e) (diffs)
• 

  Rui Xue 08 Sep 2026 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 08 Sep 2026 fbdf591a705f2546e47b28a96d92681e75a174b9 m

  PIPE-2738: fix typos in hifa_spwphaseup task docstring

  • pipeline/hifa/cli/hifa_spwphaseup.py (version fbdf591a705f2546e47b28a96d92681e75a174b9) (diffs)
• 

  Rui Xue 08 Sep 2026 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)
• 

  Rui Xue 08 Sep 2026 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)
• 

  Rui Xue 08 Sep 2026 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)
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• 

  Rui Xue 08 Sep 2026 4e6b4b4dbbfd685dc27b27c71448c2d27e568319 m

  Merge tag '2026.2.1.40' into docs/PIPE-2738-improve-docs-for-main-part3
• 

  Andres Guzman <andres.guzman@Andress-MacBook-Pro.local> 08 Sep 2026 35988508df47ccb506245375b4aeba684087ef4a m

  PIPE-3240. Apply the three changes in the ticket description.

  • pipeline/extern/tsys_contamination.py (version 35988508df47ccb506245375b4aeba684087ef4a) (diffs)
• 

  Takeshi Nakazato 06 Sep 2026 b9106cae3b557a37333cf2492ade928904ba0732 m

  Merge branch 'main' into PIPE-3228-clone-hsd_imaging-fail-of-atm-line-identification-in-contamination-plots
• 

  Takeshi Nakazato 06 Sep 2026 338283376f4a25d66ff5ef5cbe9bdbaafc563398 m

  Pull request #1958: PIPE-3154 overwrite exisitng k2jy caltable
  Merge in PIPE/pipeline from PIPE-3154-hsd_k2jycal-jy-k-factors-get-multiplied-when-k2jycal-is-repeated-for-runs-with-h_resume to main
  
  * commit '3d4ebb69ecbf9c1a0adbe5196d8d8c5e3b94fae4':
    Overwriting caltable is notified by a warning message.
    PIPE-3154 overwrite exisitng k2jy caltable
• 

  Rui Xue 04 Sep 2026 00d8798865bd24ee3a10fcb0c097a8983e8621cf m

  Pull request #1963: PIPE-3202: Use source IDs and source names for wvrgcal `tie` heuristic
  Merge in PIPE/pipeline from PIPE-3202-field-name-sent-to-wvrgcal-tie-without-quotation-mark to main
  
  * commit '1636dc36e47e756d51d9bf8727eebbe1c7620ac0':
    PIPE-3202: Use source IDs and source names for wvrgcal `tie` heuristic
• 

  Rui Xue 04 Sep 2026 9f7eb8f132034bae2b6c9acd13ab5493ee4138f2 m

  Pull request #1962: PIPE-3239: Add bpsolint_mode parameter to VLA bandpass tasks
  Merge in PIPE/pipeline from PIPE-3239-add-task-parameter-to-testbpdcals-semifinalbpdcals-and-finalcals-to-turn-off-bandpass to main
  
  * commit '501eb1e7b1af4d891059640bbeb27cc4a44c0344':
    PIPE-3239: Clean up bandpass heuristics logging and simplify helper functions
    PIPE-3239: Use Mock with Context spec in bandpass_test
    PIPE-3239: Add bpsolint_mode parameter to VLA bandpass tasks
• 

  Rui Xue 04 Sep 2026 1636dc36e47e756d51d9bf8727eebbe1c7620ac0 m

  PIPE-3202: Use source IDs and source names for wvrgcal `tie` heuristic
  Update `_calculate_tie` in `WvrgcalHeuristics` to use `field.source_id`
  and `field.source.name` rather than field IDs and names. Because `wvrgcal`
  solves per source (`segsource=True`), the `tie` parameter expects source
  specifications. This also ensures multiple pointings in mosaic targets
  collapse into their shared source ID and name.

  • pipeline/hifa/heuristics/wvrgcal.py (version 1636dc36e47e756d51d9bf8727eebbe1c7620ac0) (diffs)
• 

  Rui Xue 04 Sep 2026 501eb1e7b1af4d891059640bbeb27cc4a44c0344 m

  PIPE-3239: Clean up bandpass heuristics logging and simplify helper functions
  - Switch to lazy logging in do_bandpass for bpsolint_mode heuristics
  - Simplify _compute_median_snr, ensuring immediate subtable cleanup and typed docstrings
  - Normalize band casing in is_high_frequency_band and deduplicate HIGH_BANDS
  - Log warning and debug traceback if exception occurs during SPW frequency lookup
  - Add unit test for exception logging in bandpass_test.py

  • pipeline/hifv/heuristics/bandpass.py (version 501eb1e7b1af4d891059640bbeb27cc4a44c0344) (diffs)
  • pipeline/hifv/heuristics/bandpass_test.py (version 501eb1e7b1af4d891059640bbeb27cc4a44c0344) (diffs)
• 

  Rui Xue 03 Sep 2026 2e06c9acbcdffb0ecd6458f2dbc418add8499bdd m

  Pull request #1940: PIPE-3202: Use field IDs for wvrgcal `tie` parameter
  Merge in PIPE/pipeline from PIPE-3202-field-name-sent-to-wvrgcal-tie-without-quotation-mark to main
  
  * commit 'f5ba3be8c9a4ee3e821ee27eaa2ac57ef685afe1':
    PIPE-3202: Use field IDs for wvrgcal `tie` parameter
• 

  Dirk Muders 03 Sep 2026 182fa7011757f867f355ceaa94a251d9cdaa6f39 m

  Pull request #1959: PIPE-3052/PIPE-3231: Unset default vis parameter to avoid misleading weblog inputs rendering.
  Merge in PIPE/pipeline from PIPE-3052_PIPE-3231_Fix_vis_parameter_weblog_rendering to main
  
  * commit '08605545421f702c55ae4ff63dc9b69009a9c436':
    PIPE-3052/PIPE-3231: Fetch vis name from the results object rather than the (now empty) inputs.vis variable when writing VLASS specific metadata.
    PIPE-3052/PIPE-3231: Unset default vis parameter to avoid misleading weblog inputs rendering.
• 

  Takeshi Nakazato 02 Sep 2026 3d4ebb69ecbf9c1a0adbe5196d8d8c5e3b94fae4 m

  Merge branch 'main' into PIPE-3154-hsd_k2jycal-jy-k-factors-get-multiplied-when-k2jycal-is-repeated-for-runs-with-h_resume
• 

  Takeshi Nakazato 02 Sep 2026 02e68fb570ef5d0d1e7b23b1dac27702ba6d17a9 m

  Overwriting caltable is notified by a warning message.

  • pipeline/hsd/tasks/k2jycal/k2jycal.py (version 02e68fb570ef5d0d1e7b23b1dac27702ba6d17a9) (diffs)
• 

  Rui Xue 01 Sep 2026 41253463e189477bf5caaa9b151cf9fdba27acb6 m

  PIPE-3239: Use Mock with Context spec in bandpass_test
  Fix context type error in bandpass unit tests by specifying `spec=Context`
  when creating mock pipeline contexts for task inputs classes.

  • pipeline/hifv/heuristics/bandpass_test.py (version 41253463e189477bf5caaa9b151cf9fdba27acb6) (diffs)
• 

  Rui Xue 01 Sep 2026 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35 m

  PIPE-3239: Add bpsolint_mode parameter to VLA bandpass tasks
  Add task parameter `bpsolint_mode` to `hifv_testBPdcals`, `hifv_semiFinalBPdcals`,
  and `hifv_finalcals` to control bandpass spectral solint optimization heuristics.
  This prevents spectral averaging from corrupting bandpass solutions at lower
  frequencies (X-band and below) where low S/N is frequently caused by RFI rather
  than true low signal.
  
  Supported modes:
  - 'auto' (default): optimize only for Ku-band and higher frequencies (>= 12 GHz)
  - 'on': optimize for all bands
  - 'off': disable optimization for all bands

  • pipeline/hifv/cli/hifv_finalcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/cli/hifv_semiFinalBPdcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/cli/hifv_testBPdcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/heuristics/bandpass.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/heuristics/bandpass_test.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/tasks/finalcals/finalcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/tasks/semiFinalBPdcals/semiFinalBPdcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
  • pipeline/hifv/tasks/testBPdcals/testBPdcals.py (version 86f6ee03ed3ab62fa8de02efa058921ebc5d7e35) (diffs)
• 

  Takeshi Nakazato 31 Aug 2026 8e5c0d0fe950fabb183fabb692450113183c62f5 m

  Merge branch 'main' into PIPE-3206-hsd_flagdata-offset-pointing-plots-for-ephemeris-data-is-not-updated-after-deterministic
• 

  Dirk Muders 28 Aug 2026 08605545421f702c55ae4ff63dc9b69009a9c436 m

  PIPE-3052/PIPE-3231: Fetch vis name from the results object rather than the (now empty) inputs.vis variable when writing VLASS specific metadata.

  • pipeline/hif/tasks/makeimages/makeimages.py (version 08605545421f702c55ae4ff63dc9b69009a9c436) (diffs)
• 

  Dirk Muders 27 Aug 2026 a4d92349827c7ab174b2cf21292e282102232f73 m

  PIPE-3052/PIPE-3231: Unset default vis parameter to avoid misleading weblog inputs rendering.

  • pipeline/hif/tasks/makeimages/makeimages.py (version a4d92349827c7ab174b2cf21292e282102232f73) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 a3b14f085163806f35739eb216d1e1d15fcb2e83 m

  updated schematic diagram

  • pipeline/hsd/heuristics/SDcalatmcorr_test.py (version a3b14f085163806f35739eb216d1e1d15fcb2e83) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 5334b87ca06d01b4a99a854d5d44e06596390e6d m

  fix wrong index in docstring

  • pipeline/hsd/heuristics/SDcalatmcorr_test.py (version 5334b87ca06d01b4a99a854d5d44e06596390e6d) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 a8eac6156a26777bd455c5fba7942683b8eb14b9 m

  format docstring

  • pipeline/hsd/heuristics/SDcalatmcorr_test.py (version a8eac6156a26777bd455c5fba7942683b8eb14b9) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 9d3cb26e9bf4ed7dfc4f40e8f9b76e8b2db694af m

  cache interpolator object for each baseband

  • pipeline/hsd/heuristics/SDcalatmcorr.py (version 9d3cb26e9bf4ed7dfc4f40e8f9b76e8b2db694af) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 ade56df83caf7662134a90c7a435b34732da71a9 m

  avoid unbound local warning

  • pipeline/hsd/heuristics/SDcalatmcorr.py (version ade56df83caf7662134a90c7a435b34732da71a9) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 01708e6be3fd75e60ad0ad8ad92e517163f330f1 m

  ensure ascending order

  • pipeline/hsd/heuristics/SDcalatmcorr.py (version 01708e6be3fd75e60ad0ad8ad92e517163f330f1) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 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.

  • pipeline/hsd/heuristics/SDcalatmcorr.py (version f28c21e62e1f42b1eeea60f3e363a12bc9af0a35) (diffs)
  • pipeline/hsd/tasks/imaging/imaging.py (version f28c21e62e1f42b1eeea60f3e363a12bc9af0a35) (diffs)
  • pipeline/qa/scorecalculator.py (version f28c21e62e1f42b1eeea60f3e363a12bc9af0a35) (diffs)
• 

  Takeshi Nakazato 26 Aug 2026 d3ccf6ee1989e3ec06399ef339576de38fb6d120 m

  add unit test for SDcalatmcorr

  • pipeline/hsd/heuristics/SDcalatmcorr_test.py (version d3ccf6ee1989e3ec06399ef339576de38fb6d120) (diffs)
• 

  Takeshi Nakazato 24 Aug 2026 b3e9beaa6fa601965b2149654f1e3bcd164c5456 m

  PIPE-3154 overwrite exisitng k2jy caltable

  • pipeline/hsd/tasks/k2jycal/k2jycal.py (version b3e9beaa6fa601965b2149654f1e3bcd164c5456) (diffs)
• 

  Rui Xue 17 Aug 2026 f5ba3be8c9a4ee3e821ee27eaa2ac57ef685afe1 m

  PIPE-3202: Use field IDs for wvrgcal `tie` parameter
  Send string-formatted field IDs rather than field names to the `wvrgcal` task to bypass the `tie` parameter's non-standard CASA parsing behavior (see PIPE-3202/CAS-14850).

  • pipeline/hifa/heuristics/wvrgcal.py (version f5ba3be8c9a4ee3e821ee27eaa2ac57ef685afe1) (diffs)
• 

  Rui Xue 14 Aug 2026 4773ad5a5b6f8c692b33c176809a2a44ce762c9c m

  PIPE-2738: make pdf link version-contained and use short version on pdf cover
  - Copy `taskdocs.pdf` directly into the html/ output bundle in .readthedocs.yaml
  - Update `README.rst` to use a relative path for the PDF download link
  - Set Sphinx `release` to the short version in `conf.py` to clean up the PDF cover
  - Add comments explaining the usage of Sphinx version variables

  • .readthedocs.yaml (version 4773ad5a5b6f8c692b33c176809a2a44ce762c9c) (diffs)
  • docs/README.rst (version 4773ad5a5b6f8c692b33c176809a2a44ce762c9c) (diffs)
  • docs/source/conf.py (version 4773ad5a5b6f8c692b33c176809a2a44ce762c9c) (diffs)
• 

  Rui Xue 14 Aug 2026 5f3f8ff23b5e91a0f817189cf8517f80230319ab m

  PIPE-2738: preserve original docstrings for Sphinx; fix doc rendering issues
  Split docstring cleaning: keep original for Sphinx introspection,
  clean wrapper only for terminal display. Restores figures, cross-refs,
  tables, and code blocks in HTML/PDF documentation.
  
  Also update PDF cover: title to include observatories, author to
  "Pipeline Contributors".

  • docs/source/conf.py (version 5f3f8ff23b5e91a0f817189cf8517f80230319ab) (diffs)
  • pipeline/h/cli/utils.py (version 5f3f8ff23b5e91a0f817189cf8517f80230319ab) (diffs)
• 

  Remy Indebetouw <remy@virginia.edu> 14 Aug 2026 69c8b34645e35010f5968f84c7e555001480fc86 m

  PIPE-2738: Added SD changes from Kotomi
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  # Author:    Remy Indebetouw <remy@virginia.edu>
  # Date:      Thu Aug 13 22:12:09 2026 -0400
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  • pipeline/hsd/cli/hsd_atmcor.py (version 69c8b34645e35010f5968f84c7e555001480fc86) (diffs)
  • pipeline/hsd/cli/hsd_imaging.py (version 69c8b34645e35010f5968f84c7e555001480fc86) (diffs)
  • pipeline/hsd/cli/hsd_importdata.py (version 69c8b34645e35010f5968f84c7e555001480fc86) (diffs)
• 

  Remy Indebetouw <remy@virginia.edu> 14 Aug 2026 d9d5254f58dbaa6326b457615268ae5903a2bc5a m

  PIPE-2738: Added branding to the ALMA User's guide front page
  - Added an acknowledgement and log files
  - Added a line to the selfcal weblog page for PL2026
  
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  # Author:    Remy Indebetouw <remy@virginia.edu>
  # Date:      Thu Aug 13 18:36:36 2026 -0400
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  • docs/source/users_guide/almalogo.png (version d9d5254f58dbaa6326b457615268ae5903a2bc5a) (diffs)
  • docs/source/users_guide/executive_logos.png (version d9d5254f58dbaa6326b457615268ae5903a2bc5a) (diffs)
  • docs/source/users_guide/guide-img001.png (version d9d5254f58dbaa6326b457615268ae5903a2bc5a) (diffs)
  • docs/source/users_guide/index.md (version d9d5254f58dbaa6326b457615268ae5903a2bc5a) (diffs)
  • pipeline/hif/templates/selfcal.mako (version d9d5254f58dbaa6326b457615268ae5903a2bc5a) (diffs)
• 

  Rui Xue 13 Aug 2026 976da6259c95c0d27d42ace5ae4d532e6efe2d20 m

  PIPE-2738: dynamically strip Sphinx markup from task docstrings for terminal users
  Updated `cli_wrapper` to automatically scrub Sphinx-specific reST directives
  from task docstrings at runtime. This ensures that users running `help()` or `?`
  in interactive environments (like IPython or casashell) see clean, readable
  plain text instead of raw markup.
  
  Specifically, this strips:
  - Cross-reference roles (e.g., `:func:` -> ``` `func_name` ```)
  - `.. figure::` blocks (retaining only the caption)
  - `.. list-table::` blocks (retaining only the title and list items)
  - `.. code-block::` directives

  • pipeline/h/cli/utils.py (version 976da6259c95c0d27d42ace5ae4d532e6efe2d20) (diffs)
• 

  Remy Indebetouw <remy@virginia.edu> 13 Aug 2026 a59f81c2cf82fd17e5ff80567f715eacbbe04279 m

  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.
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  # Author:    Remy Indebetouw <remy@virginia.edu>
  # Date:      Thu Aug 13 16:13:47 2026 -0400
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  # interactive rebase in progress; onto 64967c159b
  # Last commands done (2 commands done):
  #    pick 7fa0e71b65 PIPE-2738: Update docs badge to reference pixi-based build workflow
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  #        modified:   pipeline/hifa/cli/hifa_wvrgcalflag.py
  #        modified:   pipeline/hsd/cli/hsd_applycal.py
  #        modified:   pipeline/hsd/cli/hsd_baseline.py
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  • pipeline/hifa/cli/hifa_bandpass.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hifa/cli/hifa_gfluxscale.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hifa/cli/hifa_renorm.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hifa/cli/hifa_tsysflagcontamination.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hifa/cli/hifa_wvrgcal.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hifa/cli/hifa_wvrgcalflag.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hsd/cli/hsd_applycal.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hsd/cli/hsd_baseline.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hsd/cli/hsd_importdata.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
  • pipeline/hsd/cli/hsd_skycal.py (version a59f81c2cf82fd17e5ff80567f715eacbbe04279) (diffs)
• 

  Rui Xue 13 Aug 2026 7fa0e71b6510fd83268a631466825cc0b221a988 m

  PIPE-2738: Update docs badge to reference pixi-based build workflow
  Change README badge link from build-gh-pages.yml to build-gh-pages-pixi.yml.

  • docs/README.rst (version 7fa0e71b6510fd83268a631466825cc0b221a988) (diffs)
• 

  Takeshi Nakazato 07 Aug 2026 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.

  • pipeline/hsd/tasks/flagging/flagdeteralmasd.py (version caef04eab9c993336608eadd623e5d0e8751f43e) (diffs)