Code commits
Pipeline
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Rui Xue 2f87b8c4e4838b7a0fd72e87100d24710cf43fa3
Pull request #1931: PIPE-3196: migrate the changes of PIPE-3150/PIPE-3162/PIPE-3191 to MAIN
Merge in PIPE/pipeline from PIPE-3196-clone-PIPE-3150-3162-to-main to main
* commit 'b8400037f84cab6544bf92d482bcbe93d5c48fa7': (21 commits)
PIPE-3196/PIPE-3191: Refactor `tmp_dir` to use relative paths
PIPE-3196/PIPE-3162: Optimize memory footprint by removing advanced indexing copies in Stokes I extraction
PIPE-3196/PIPE-3162: Refactor findroi parallel-hand correlation extraction by reading `POLARIZATION` table directly and support RR/LL
PIPE-3196/PIPE-3162: Use the correct data type selection
PIPE-3196/PIPE-3150: Clip absorption evidence display
PIPE-3196/PIPE-3150: Plot absorption evidence with original sign
PIPE-3196/PIPE-3150: Rename ROI ranges column
PIPE-3196/PIPE-3150: Update FindROI thresholds and evidence
PIPE-3196/PIPE-3150: Refine FindROI supporting plots
PIPE-3196/PIPE-3150: Format displayed ROI ranges
PIPE-3196/PIPE-3150: Update FindROI QA scoring
PIPE-3196/PIPE-3150: Show positive ROI ranges
PIPE-3196/PIPE-3150: Fix findroi plot font sizing
PIPE-3196/PIPE-3150: Tune findroi evidence layout
PIPE-3196/PIPE-3150: Refine findroi evidence plots
PIPE-3196/PIPE-3150: Split findroi plots by SPW
PIPE-3196/PIPE-3150: Restructure findroi summary
PIPE-3196/PIPE-3150: Improve hif_findroi weblog view
PIPE-3196/PIPE-3162: Form Stokes I in hif_findroi
PIPE-3196/PIPE-3162: Relax findroi min channel sanity check
... -
Rui Xue 9a66e1658f3057702f7a73d6b46c5d6eae3f90d7
Pull request #1928: PIPE-3197: clone PIPE-3159 to main
Merge in PIPE/pipeline from PIPE-3197-clone-pipe-3159-to-main to main
* commit 'fcffd076b446543d4590c39321000e16eda94c57':
PIPE-3197: Codestyle updates
PIPE-3197/PIPE-3159: expose additional findcont imaging parameters
PIPE-3197/PIPE-3159: clarify findcont imaging banner
PIPE-3197/PIPE-3159: refine findcont weblog layout
PIPE-3197/PIPE-3159: expose hif_findcont imaging in weblog -
Federico Montesino Pouzols a4cd62e66e125035a0cd4c98dedc2bc6303e37b5
Pull request #1888: PIPE-3023 flagdeteralma load partialpols alma loop loads flag column using tbtool.getcol
Merge in PIPE/pipeline from PIPE-3023-flagdeteralma-load_partialpols_alma-loop-loads-flag-column-using-tbtool.getcol to main
* commit '6bd22f4018437b6a63de1838abf7e9a28c4d3a03':
PIPE-3023: move taql query out of try, add unit test, fixes from review
PIPE-3023: adapt flagdeteralma unit tests for updated implementation
PIPE-3023: use TaQL query to implement the partialpol logic
PIPE-3023: fix info message about lowtrans -
Rui Xue a563feecea60971977ed1de45265e4a0e7483541
Pull request #1933: PIPE-3177: clone add spw filitering to max cube size step
Merge in PIPE/pipeline from PIPE-3177-clone-add-spw-filitering-to-max-cube-size-step to main
* commit 'f671e7e457b16131ecd95f33bf51fe8ebfdc154a':
PIPE-3127: style cleanup — lazy logging, PEP 8
cleaned message formatting slightly. moved the creation of overlimit_spws and oversize_spws out of the conditional blocks, so that they can always be printed to the log - I found this quite useful to debug and understand what was going on.
PIPE-3127 added spws reassign after field mitigation
PIPE-3127 moved large cube message trigger
fixing the two more impactful issues found by Ryan; the confusing message still needs to be dealt with
PIPE-3127 refactor mitigation to move step 1 error later into spw building loop and add supporting changes
PIPE-3127 edited the clause to only mitigate spws if less than the maxcubelimit at the end of step 1
PIPE-3127 step one added spw filter and supporting code changes cubesizes now returned as a dict -
Rui Xue c4b6900316e89fecb4f00f35d03c4181adce3abb
Pull request #1927: PIPE-2738: improve docs for `MAIN` (part1)
Merge in PIPE/pipeline from docs/PIPE-2738-improve-docs-for-MAIN to main
* commit 'b2f166936faa9be35cab37335b22e6943bbaac9f': (29 commits)
PIPE-2738: Reorganize pixi tasks, add warning suppression, rename `CASA_MPI_NPROCS` to `CASA_NPROCS`
PIPE-2738: Drop CASA 6.7.5, promote 6.7.6 to latest, add 6.7.7 support
PIPE-2738: Document two new procedure recipes
PIPE-2738: Changed front page to list table with table notes and added the link to Nobeyama Pipeline Users' Guide
PIPE-2738: update processing environment screenshots in weblog guide
PIPE-2738: fix parameter linking on CLI task pages
PIPE-2738: clarify QA score bounds and add colors in pipeline-weblog
PIPE-2738: Add `toc_sections` extension for CLI task page navigation
PIPE-2738: Updates following the feedbacks from Luke and Kotomi
PIPE-2738: Update documentation author to 'Pipeline Contributors'
PIPE-2738: Update documentation links to `ra-pipeline1 upstream
PIPE-2738: Fix Sphinx image scaling errors in CLI docstrings
PIPE-2738: Convert Markdown tables to `list-table` directives in User Guide
PIPE-2738: Apply drop-shadow to Markdown lightbox images
PIPE-2738: Style figure captions to distinguish them from body text
PIPE-2738: Remove redundant `Returns1 sections and add missing type hints in CLI tasks
PIPE-2738: Improve image visibility with drop shadows and click-to-zoom lightboxes
PIPE-2738: Improve organization and completeness of Common Task Functionality in `hif_makeimages`
PIPE-2738: Migrate additional ALMA Pipeline User Guide content of `hif_checkproductsize`, `hif_makeimages`, and `hif_makeimlist`, to CLI task docstrings
PIPE-2738: Update `hifa_diffgaincal` docstring with additional content and figures from User's Guide
... -
Rui Xue b2f166936faa9be35cab37335b22e6943bbaac9f
PIPE-2738: Reorganize pixi tasks, add warning suppression, rename `CASA_MPI_NPROCS` to `CASA_NPROCS`
- Restructure [tool.pixi.tasks] with clear section headers (Simple/Complex/Testing)
- Add `PYTHONWARNINGS=ignore::SyntaxWarning` to `casa` and `casampi` tasks
- Rename `CASA_MPI_NPROCS` to `CASA_NPROCS` (more generic, HPC standard)
- Remove deprecated `fetch-casarundata` task (CASA auto-initializes)
- Update documentation to match task reorganization and variable rename -
Rui Xue 86549d250149fee6243df27e44acd50a817b2ff4
PIPE-2738: Document two new procedure recipes
Add `procedure_hifa_polimage.xml` and `procedure_hifv_nofluxcal.xml`
to `recipes.md` with corresponding JIRA tickets. -
Rui Xue e1110f6205e855f7326017d346c309a93e7f8cde
PIPE-2738: Drop CASA 6.7.5, promote 6.7.6 to latest, add 6.7.7 support
- Update pixi features: casa675→casa676, add casa677-py312/py313
- Promote 6.7.6 to "latest release branch", 6.7.7 to "master branch"
- Update test CI matrix to cover 6.7.4, 6.7.6, 6.7.7 (all Python variants)
- Update documentation environment table and examples
- Remove deprecated casa671-py312 references- .github/workflows/test-unit-pixi.yml (version e1110f6205e855f7326017d346c309a93e7f8cde) (diffs)
- docs/source/devel/setup/pixi_tasks.md (version e1110f6205e855f7326017d346c309a93e7f8cde) (diffs)
- pixi.lock (version e1110f6205e855f7326017d346c309a93e7f8cde) (diffs)
- pyproject.toml (version e1110f6205e855f7326017d346c309a93e7f8cde) (diffs)
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Remy Indebetouw <remy@virginia.edu> 43ac5e9f012cf218e6f29393eb48e2864d8fd308
PIPE-2738: Changed front page to list table with table notes and added the link to Nobeyama Pipeline Users' Guide
# Please enter the commit message for your changes. Lines starting
# with '#' will be kept; you may remove them yourself if you want to.
# An empty message aborts the commit.
#
# Author: Remy Indebetouw <remy@virginia.edu>
# Date: Wed Aug 12 13:15:43 2026 -0400
#
# interactive rebase in progress; onto eb4a7dd24
# Last commands done (30 commands done):
# pick 09f4778d8 PIPE-2738: update processing environment screenshots in weblog guide
# reword 83b481d98 # changed front page to list table with table notes added Nobeyama
# Next commands to do (3 remaining commands):
# pick 22c242bad PIPE-2738: Document two new procedure recipes
# pick f2bae51a3 PIPE-2738: Drop CASA 6.7.5, promote 6.7.6 to latest, add 6.7.7 support
# You are currently editing a commit while rebasing branch 'docs/PIPE-2738-improve-docs-for-MAIN' on 'eb4a7dd24'.
#
# Changes to be committed:
# modified: docs/README.rst
# modified: docs/source/index.rst
# modified: docs/source/users_guide/hifa_polcalimage-recipe.md
# modified: docs/source/users_guide/index.md
#- docs/README.rst (version 43ac5e9f012cf218e6f29393eb48e2864d8fd308) (diffs)
- docs/source/index.rst (version 43ac5e9f012cf218e6f29393eb48e2864d8fd308) (diffs)
- docs/source/users_guide/hifa_polcalimage-recipe.md (version 43ac5e9f012cf218e6f29393eb48e2864d8fd308) (diffs)
- docs/source/users_guide/index.md (version 43ac5e9f012cf218e6f29393eb48e2864d8fd308) (diffs)
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Rui Xue ce8fbe47c34a737699567ac2b056da85a383da80
PIPE-2738: clarify QA score bounds and add colors in pipeline-weblog
- Replace ambiguous ">0.90-1.00" score range notation with explicit mathematical inequalities (e.g., $0.90 < S \leq 1.00$) for clarity.
- Apply inline CSS styling to colorize the color names (Green, Blue, Yellow, Red) in the QA score table and the prose text below it.
Refs: PIPE-2738 -
Rui Xue 2731cabb4642a4174cfe00a01046e960df454df2
PIPE-2738: fix parameter linking on CLI task pages
Update `parameter_linking.py` to find parameter documentation even after it
has been promoted to a separate `<section id="parameters">` by the
toc_sections extension. This restores the automatic insertion of anchor links
and bold colons for parameter lists on CLI task pages. -
Rui Xue 84450a215555312ebf7e4cb7b45e5c3cf4b7e12d
PIPE-2738: update processing environment screenshots in weblog guide
Replace the single, lower-resolution `processing_env_2024.png` with two new,
higher-resolution screenshots (`weblog_runtime_env1.png` and `weblog_runtime_env2.png`)
for the Processing Environment popup window.
The layout is updated to display the two images side-by-side using an HTML
flexbox container and Sphinx `image` directives to ensure they are properly
sized, centered, and readable.
Refs: PIPE-2738- docs/source/users_guide/pipeline-weblog.md (version 84450a215555312ebf7e4cb7b45e5c3cf4b7e12d) (diffs)
- docs/source/users_guide/processing_env_2024.png (version 84450a215555312ebf7e4cb7b45e5c3cf4b7e12d) (diffs)
- docs/source/users_guide/weblog_runtime_env1.png (version 84450a215555312ebf7e4cb7b45e5c3cf4b7e12d) (diffs)
- docs/source/users_guide/weblog_runtime_env2.png (version 84450a215555312ebf7e4cb7b45e5c3cf4b7e12d) (diffs)
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Rui Xue 84be22aba94949b7ad396854e12ca2ae768664cb
PIPE-2738: Add `toc_sections` extension for CLI task page navigation
Add `toc_sections.py` to promote docstring Parameters/Notes/Examples into
real docutils sections with anchor IDs, injecting them into the Furo
right-hand TOC for easier navigation on long CLI task pages. Only injects
entries for sections that actually exist in each task's docstring.
Also adds CSS to style the promoted headings as subtle labels. -
Rui Xue 693063e5a48da06ae80221ead33ea077c0de5c6b
PIPE-2738: Convert Markdown tables to `list-table` directives in User Guide
Converted the standard Markdown tables in `pipeline-versions-and-documentation.md`, `pipeline-weblog.md`, and `weights.md` to Sphinx `{list-table}` directives. This ensures consistent table rendering and alignment across the Sphinx documentation, and enables the application of custom CSS classes (like `small-font-table`) to maintain a clean, compact visual style.- docs/source/users_guide/pipeline-versions-and-documentation.md (version 693063e5a48da06ae80221ead33ea077c0de5c6b) (diffs)
- docs/source/users_guide/pipeline-weblog.md (version 693063e5a48da06ae80221ead33ea077c0de5c6b) (diffs)
- docs/source/users_guide/weights.md (version 693063e5a48da06ae80221ead33ea077c0de5c6b) (diffs)
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Rui Xue cdb9ddeeccd165ffdcbacd7fc5a42dfc93840bf2
PIPE-2738: Improve organization and completeness of Common Task Functionality in `hif_makeimages`
- Expanded descriptions for Image Coordinates, Full Polarization IQUV Imaging, and Automatic Clean Boxes (Automasking) to include full details from Section 9.41 of the LaTeX Guide.
- Prevented Sphinx layout issues by rephrasing the "Common Task Functionality" header without a trailing colon, ensuring the `docstring_inheritance` parser correctly identifies section boundaries and injects the Parameters list at the correct location. -
Remy Indebetouw <remy@virginia.edu> 2753937d6db1c0ee93e5e989284956c90747ead4
PIPE-2738: Updates following the feedbacks from Luke and Kotomi
# Please enter the commit message for your changes. Lines starting
# with '#' will be kept; you may remove them yourself if you want to.
# An empty message aborts the commit.
#
# Author: Remy Indebetouw <remy@virginia.edu>
# Date: Wed Aug 12 09:13:29 2026 -0400
#
# interactive rebase in progress; onto eb4a7dd24
# Last commands done (25 commands done):
# pick 374814ec7 PIPE-2738: Update documentation author to 'Pipeline Contributors'
# reword 156497df7 # changes from luke and kotomi
# Next commands to do (8 remaining commands):
# pick 9a2f85107 PIPE-2738: Add `toc_sections` extension for CLI task page navigation
# pick f607042e2 PIPE-2738: clarify QA score bounds and add colors in pipeline-weblog
# You are currently editing a commit while rebasing branch 'docs/PIPE-2738-improve-docs-for-MAIN' on 'eb4a7dd24'.
#
# Changes to be committed:
# modified: pipeline/hifa/cli/hifa_diffgaincal.py
# modified: pipeline/hsd/cli/hsd_imaging.py
# -
Rui Xue 9e9d46b44ddc226bd893d7dbbadf9c744f9bb75b
PIPE-2738: Update documentation author to 'Pipeline Contributors'
Replace outdated 'Pipeline Dev. Team' with inclusive wording. -
Rui Xue 5ada67893520013259eb383f9aa267ed6f34815d
PIPE-2738: Apply drop-shadow to Markdown lightbox images
Extended the custom CSS drop-shadow styling in `custom_theme.css` to target `a[data-lightbox] img`. This ensures that screenshots embedded in MyST Markdown files (which use the Sphinx lightbox extension) receive the same consistent border and shadow effect as images embedded via standard Sphinx `.. figure::` directives. -
Rui Xue fd3c1eb9ee0ecd9e64f46112f5724f7de52dd124
PIPE-2738: Improve image visibility with drop shadows and click-to-zoom lightboxes
- Added a subtle drop shadow and border in `custom_theme.css` to help embedded screenshots and figures stand out clearly against the page background.
- Enabled the `sphinxcontrib-lightbox2` Sphinx extension (via `conf.py` and `requirements_docs.txt`) to allow users to click and expand images into full-screen overlays.
- Updated `pixi.lock` to lock the new Sphinx extension and refresh environment dependencies.- docs/source/_static/custom_theme.css (version fd3c1eb9ee0ecd9e64f46112f5724f7de52dd124) (diffs)
- docs/source/conf.py (version fd3c1eb9ee0ecd9e64f46112f5724f7de52dd124) (diffs)
- pixi.lock (version fd3c1eb9ee0ecd9e64f46112f5724f7de52dd124) (diffs)
- requirements_docs.txt (version fd3c1eb9ee0ecd9e64f46112f5724f7de52dd124) (diffs)
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Rui Xue 4949ded1bbc3fb3dc295d8af0c231449e43af71f
PIPE-2738: Migrate additional ALMA Pipeline User Guide content of `hif_checkproductsize`, `hif_makeimages`, and `hif_makeimlist`, to CLI task docstrings
- hif_checkproductsize: Migrated Section 9.34, detailing size calculations, the step-by-step mitigation cascade, QA scoring, and embedded example screenshot (guide-img028.png).
- hif_makeimages: Migrated Sections 9.28, 9.30, 9.32, 9.41, 9.42, 9.44, 9.46, and 9.48. Added scenario-based structure, dynamic range correction tables, QA notes, and embedded multiple figures.
- hif_makeimlist: Migrated Sections 9.27, 9.29, 9.31, 9.38, 9.43, 9.45, and 9.47, with a scenario-based structure and embedded weblog screenshot.- docs/source/figures/guide-img010.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/guide-img026.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/guide-img028.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/guide-img030.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/guide-img031.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/guide-img033_2022.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/polcal_imaging.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- docs/source/figures/psfphasecenter.png (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- pipeline/hif/cli/hif_checkproductsize.py (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- pipeline/hif/cli/hif_makeimages.py (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
- pipeline/hif/cli/hif_makeimlist.py (version 4949ded1bbc3fb3dc295d8af0c231449e43af71f) (diffs)
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Rui Xue 03c7108c1c8fc847ba73b202a463d9f4672bd9e9
PIPE-2738: Update `hifa_diffgaincal` docstring with additional content and figures from User's Guide
- Migrated extended explanations and context from Section 9.21 of the ALMA Pipeline User's Guide to the `hifa_diffgaincal` CLI docstring.
- Added phase offset and residual weblog plots side-by-side (matching the PDF layout) and retained their original LaTeX filenames for traceability.
- Clarified the residual offset evaluation criteria and elaborated on the low-SNR heuristics logic.
- Fixed a Sphinx layout issue by adding a title to the `list-table` directive, preventing the `docstring_inheritance` parser from mistakenly treating the table as a new section header and mangling the `Args:` injection.- docs/source/figures/uid___A002_X116120b_X2d3a.ms.hifa_diffgaincal.s17_3.spw45_47_49_51_53_55_57_59.solintinf.gpcal.tbl-spw47-TARGET_CHECK-phase_vs_time.png (version 03c7108c1c8fc847ba73b202a463d9f4672bd9e9) (diffs)
- docs/source/figures/uid___A002_X116120b_X2d3a.ms.hifa_diffgaincal.s17_5.spw45_47_49_51_53_55_57_59.solintinf.gpcal.tbl-spw55-phase_vs_time.png (version 03c7108c1c8fc847ba73b202a463d9f4672bd9e9) (diffs)
- pipeline/hifa/cli/hifa_diffgaincal.py (version 03c7108c1c8fc847ba73b202a463d9f4672bd9e9) (diffs)
-
Rui Xue 21b93cf8102fcca508e327468e9391ee45b2dbc5
PIPE-2738: Style figure captions to distinguish them from body text
-
Rui Xue 646b9f46f67698487801b859e7ac20deeae52363
PIPE-2738: Remove redundant `Returns1 sections and add missing type hints in CLI tasks
- Stripped duplicate `Returns:` sections from 42 wrapped CLI task docstrings across the `h`, `hif`, `hifa`, and `hsdn` modules. This ensures Sphinx's `autodoc_typehints='description'` generates exactly one "Return type:" entry per task without duplication.
- Added missing Python return type hints (`-> launcher.Context` and `-> None`) to the signatures of unwrapped standard functions (`h_resume`, `h_weblog`, and `h_show_calstate`) so their return types are correctly scraped and populated in the HTML documentation.- pipeline/h/cli/h_export_calstate.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_exportdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_import_calstate.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_mssplit.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_restoredata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_resume.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_save.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_show_calstate.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/h_weblog.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/h/cli/utils.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hif/cli/hif_editimlist.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hif/cli/hif_gaincal.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hif/cli/hif_lowgainflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hif/cli/hif_makecutoutimages.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hif/cli/hif_mstransform.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_antpos.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_bandpass.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_bpsolint.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_diffgaincal.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_exportdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_flagdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_flagtargets.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_fluxcalflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_gaincalsnr.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_gfluxscale.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_gfluxscaleflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_imageprecheck.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_importdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_lock_refant.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_polcal.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_polcalflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_renorm.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_restoredata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_session_refant.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_spwphaseup.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_targetflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_timegaincal.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_tsysflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_tsysflagcontamination.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_unlock_refant.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_wvrgcal.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hifa/cli/hifa_wvrgcalflag.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hsdn/cli/hsdn_exportdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hsdn/cli/hsdn_importdata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
- pipeline/hsdn/cli/hsdn_restoredata.py (version 646b9f46f67698487801b859e7ac20deeae52363) (diffs)
-
Rui Xue 12b07190f86b2a3cce5319817efeadb952d39bba
PIPE-2738: Fix Sphinx image scaling errors in CLI docstrings
Replaced `:scale:` with `:width:` in `.. figure::` directives across 19 CLI task docstrings. This circumvents a known Sphinx/Pillow limitation where attempting to read original image files from disk for dynamic scaling fails with a `FileNotFoundError` when triggered from generated `autosummary` stubs. This resolves the image build warnings while retaining identical visual output in the HTML docs.- pipeline/hif/cli/hif_findcont.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hif/cli/hif_selfcal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_bandpass.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_bandpassflag.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_diffgaincal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_gfluxscale.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_polcal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_renorm.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_spwphaseup.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_targetflag.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_timegaincal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_tsysflagcontamination.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hifa/cli/hifa_wvrgcalflag.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_applycal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_baseline.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_imaging.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_importdata.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_k2jycal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
- pipeline/hsd/cli/hsd_skycal.py (version 12b07190f86b2a3cce5319817efeadb952d39bba) (diffs)
-
Rui Xue 71780bf53070f8f69a4494e163085df7af6b14e8
PIPE-2738: Update documentation links to `ra-pipeline1 upstream
-
Remy Indebetouw <remy@virginia.edu> aedc68351e5e92b6751050da4b12b6d09853b7c6
PIPE-2738: Added the initial draft of the full User's guide
# Please enter the commit message for your changes. Lines starting
# with '#' will be kept; you may remove them yourself if you want to.
# An empty message aborts the commit.
#
# Author: Remy Indebetouw <remy@virginia.edu>
# Date: Tue Aug 11 10:55:42 2026 -0400
#
# interactive rebase in progress; onto eb4a7dd24
# Last commands done (13 commands done):
# squash e0e188f36 # fixed internal links, first programmatically, and then did a manual pass through the text. added sections created from recipes, listing the tasks in the recipe in order
# squash fbefb6990 # delete old files`
# Next commands to do (20 remaining commands):
# pick e67624278 PIPE-2738: Update `hifa_diffgaincal` docstring with additional content and figures from User's Guide
# pick bdad5e7cc PIPE-2738: Migrate additional ALMA Pipeline User Guide content of `hif_checkproductsize`, `hif_makeimages`, and `hif_makeimlist`, to CLI task docstrings
# You are currently rebasing branch 'docs/PIPE-2738-improve-docs-for-MAIN' on 'eb4a7dd24'.
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-
Rui Xue cb48af9b52894dfe58f5a985c4367904137f65b8
PIPE-2738: Enable `intersphinx` for automatic CASA task cross-referencing
Re-configure Sphinx intersphinx extension to automatically link CASA tasks
(e.g., mstransform, tclean) to CASAdocs documentation. Links are
automatically validated at build time. -
Remy Indebetouw bcdc480a386de2202fe5c148ca9aaba87b0daa58
PIPE-2738: Initial rearrangement of front page and `index.rst``
- Moved a couple of items to Dev section
- Added VLA refs link
- Added initial "helper" and "weights" users guide sections
# with '#' will be kept; you may remove them yourself if you want to.
# An empty message aborts the commit.
#
# Author: Remy Indebetouw <rindebet@nrao.edu>
# Date: Sun Aug 9 10:02:04 2026 -0400
#
# interactive rebase in progress; onto eb4a7dd24
# Last commands done (8 commands done):
# squash 91360e791 # initial "helper" and "weights" users guide sections
# squash 1ef877601 # minor edits; trying to figure out how to get auto-links to casa and PL tasks
# Next commands to do (25 remaining commands):
# pick 6fa687c26 PIPE-2738: Enable `intersphinx` for automatic CASA task cross-referencing
# pick b7a5297d5 Full User's guide - first attempt; needs red references updated.
# You are currently rebasing branch 'docs/PIPE-2738-improve-docs-for-MAIN' on 'eb4a7dd24'.
#
# Changes to be committed:
# modified: docs/README.rst
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#- docs/README.rst (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
- docs/source/index.rst (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
- docs/source/timeline.md (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
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- docs/source/users_guide/weights.md (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
- pipeline/hif/tasks/makeimages/makeimages.py (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
-
Rui Xue 1f9675c38bc50fdf7245f6dd459f92573fbf9a4c
PIPE-2738: Add clickable parameter anchors with auto-fading highlights
- Add clickable anchors to parameter names for easy URL copying
- Replace ' -- ' separator with bold ' : ' for visual clarity
- Flatten <p> tags to render descriptions inline while preserving section headers
- Add 3-second fade animation for highlighted parameters (GitHub-style) -
Rui Xue 5c050a5aa02ece1fc8f0b4ce0112457f7b3e7e8f
PIPE-2738: Add docstring to `FindROIInputs`
- Add Args docstring to `FindROIInputs.__init__`
- Remove redundant Returns section from hif_findroi CLI function -
Rui Xue f671e7e457b16131ecd95f33bf51fe8ebfdc154a
Merge remote-tracking branch 'origin/PIPE-3127-add-spw-filitering-to-max-cube-size-and-max-product-size-image-mitigation-steps' into PIPE-3177-clone-add-spw-filitering-to-max-cube-size-step
-
Rui Xue b8400037f84cab6544bf92d482bcbe93d5c48fa7
PIPE-3196/PIPE-3191: Refactor `tmp_dir` to use relative paths
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Rui Xue 1510eed13986b5a2fed597888d11de4b07f669d7
PIPE-3196/PIPE-3162: Optimize memory footprint by removing advanced indexing copies in Stokes I extraction
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Rui Xue f347fa1c55e3b2416fc12b46171cf8882001bcdb
PIPE-3196/PIPE-3162: Refactor findroi parallel-hand correlation extraction by reading `POLARIZATION` table directly and support RR/LL
-
Rui Xue 0ee14157201db437ae3e416f49d87da4dd1bfcc0
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ryanaloomis <ryan.a.loomis@gmail.com> a9373c521f333f36248492cdf1a2ac1b4e13cf0e
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ryanaloomis <ryan.a.loomis@gmail.com> 3449f1975ef1a2f1c0e2b1e586d0ca5ad0c4da4b
PIPE-3196/PIPE-3150: Plot absorption evidence with original sign
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ryanaloomis <ryan.a.loomis@gmail.com> 2e430c471cce62c31d4ec680ce1f951fc9ce8f26
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ryanaloomis <ryan.a.loomis@gmail.com> 987e43bf88faf3b6460ccb9b60427deb9b52266b
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ryanaloomis <ryan.a.loomis@gmail.com> e81c8a96072384da02d6876dc8d4cf88953750be
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ryanaloomis <ryan.a.loomis@gmail.com> b577c1178486a57cb0bee4c31585e718dbe93d7a
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ryanaloomis <ryan.a.loomis@gmail.com> 9f59b103c4cda79e99c9e06ee524369a63a1f80c
PIPE-3196/PIPE-3150: Update FindROI QA scoring
- pipeline/hif/heuristics/findroi.py (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
- pipeline/hif/tasks/findroi/findroi.py (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
- pipeline/hif/tasks/findroi/qa.py (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
- pipeline/hif/tasks/findroi/renderer.py (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
- pipeline/hif/tasks/findroi/resultobjects.py (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
- pipeline/hif/templates/findroi.mako (version 9f59b103c4cda79e99c9e06ee524369a63a1f80c) (diffs)
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ryanaloomis <ryan.a.loomis@gmail.com> 429781578ef69fe474ead097503122d4607fe687
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ryanaloomis <ryan.a.loomis@gmail.com> ea3ee195b246fcd05b510c96245623c2a9baa286
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ryanaloomis <ryan.a.loomis@gmail.com> 463bb2944ac8235c728330657671b5cce6a9860a
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ryanaloomis <ryan.a.loomis@gmail.com> e7a43e7688bc33a94079503a52a2d6c5a0b46d56
PIPE-3196/PIPE-3150: Refine findroi evidence plots
- pipeline/hif/tasks/findroi/plots.py (version e7a43e7688bc33a94079503a52a2d6c5a0b46d56) (diffs)
- pipeline/hif/tasks/findroi/renderer.py (version e7a43e7688bc33a94079503a52a2d6c5a0b46d56) (diffs)
- pipeline/hif/templates/findroi.mako (version e7a43e7688bc33a94079503a52a2d6c5a0b46d56) (diffs)
- pipeline/infrastructure/renderer/logger.py (version e7a43e7688bc33a94079503a52a2d6c5a0b46d56) (diffs)
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ryanaloomis <ryan.a.loomis@gmail.com> d2be1386bceb2e7ced6b73550dc8954b16d61c80
PIPE-3196/PIPE-3150: Split findroi plots by SPW
- pipeline/hif/heuristics/findroi.py (version d2be1386bceb2e7ced6b73550dc8954b16d61c80) (diffs)
- pipeline/hif/tasks/findroi/plots.py (version d2be1386bceb2e7ced6b73550dc8954b16d61c80) (diffs)
- pipeline/hif/tasks/findroi/renderer.py (version d2be1386bceb2e7ced6b73550dc8954b16d61c80) (diffs)
- pipeline/hif/templates/findroi.mako (version d2be1386bceb2e7ced6b73550dc8954b16d61c80) (diffs)
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ryanaloomis <ryan.a.loomis@gmail.com> 910137d9b953ac71196e3184c981e51bd6d724ac
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ryanaloomis <ryan.a.loomis@gmail.com> 18ad59d201ae77f6594c9e58c255dfca00994658
PIPE-3196/PIPE-3150: Improve hif_findroi weblog view
- pipeline/hif/heuristics/findroi.py (version 18ad59d201ae77f6594c9e58c255dfca00994658) (diffs)
- pipeline/hif/tasks/findroi/plots.py (version 18ad59d201ae77f6594c9e58c255dfca00994658) (diffs)
- pipeline/hif/tasks/findroi/renderer.py (version 18ad59d201ae77f6594c9e58c255dfca00994658) (diffs)
- pipeline/hif/templates/findroi.mako (version 18ad59d201ae77f6594c9e58c255dfca00994658) (diffs)
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ryanaloomis <ryan.a.loomis@gmail.com> 71cd09a1109ed1c6ca2ad1d2bdb0455ef6c57095
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ryanaloomis <ryan.a.loomis@gmail.com> 507055c85650804a861d04acae132c161683491d
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ryanaloomis <ryan.a.loomis@gmail.com> c1bfbe20ffadb02d25bcb3455b981eef06e66e06
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Rui Xue fcffd076b446543d4590c39321000e16eda94c57
PIPE-3197: Codestyle updates
- Convert ImagingStatus to `Enum` for type-safe status constants
- Add type hints (PEP 604/585) to all helper functions
- Replace f-string logging with lazy formatting
- Implement robust regex-based "ppb" string parsing
- Add NaN/infinity handling in float formatting
- Improve docstrings (Google Style) with Args/Returns
- Wrap long lines to comply with 120-char limit -
ryanaloomis <ryan.a.loomis@gmail.com> 5da35a12c416c542f46a347aec6582765d750207
PIPE-3197/PIPE-3159: expose additional findcont imaging parameters
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ryanaloomis <ryan.a.loomis@gmail.com> a63be2f6b532bd37258b59b47826235c36fe2d1f
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ryanaloomis <ryan.a.loomis@gmail.com> 9f3cf43c586c039408a9f15e99fff696765ef5cf
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ryanaloomis <ryan.a.loomis@gmail.com> 9c7434e2f29d32998a27990c1785dc376d3c0e6b
PIPE-3197/PIPE-3159: expose hif_findcont imaging in weblog
- pipeline/hif/tasks/findcont/findcont.py (version 9c7434e2f29d32998a27990c1785dc376d3c0e6b) (diffs)
- pipeline/hif/tasks/findcont/renderer.py (version 9c7434e2f29d32998a27990c1785dc376d3c0e6b) (diffs)
- pipeline/hif/tasks/findcont/resultobjects.py (version 9c7434e2f29d32998a27990c1785dc376d3c0e6b) (diffs)
- pipeline/hif/templates/findcont.mako (version 9c7434e2f29d32998a27990c1785dc376d3c0e6b) (diffs)
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Rui Xue eb4a7dd244954c4ab2f0085b6af7c66ce147ff02
PIPE-2738: Update Pixi installation version to v0.71.0 in Read the Docs configuration
-
Rui Xue bea3db71ad368b49bc53f5c20dc0807e39fa7004
PIPE-2738: Update `pixi.lock`
-
Rui Xue da4fe50a41df892c6ad4401327a99dc9ec87abc6
PIPE-2738: Upgrade Pixi to v0.71.0 for Rich Platforms syntax support
- Update GitHub Actions workflow to use pixi v0.71.0
- Document minimum Pixi version requirement
- Restore inline platform constraint syntax in `pyproject.toml` -
Rui Xue d25c830b97692313e0caae561668df7d7ea6459a
PIPE-2738: Migrate pixi config from deprecated system-requirements to platforms
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Rui Xue 7b2f7e410e5a6e3398c92f57cd55dced97e0709d m
Merge tag '2026.1.1.102' into PIPE-3127-add-spw-filitering-to-max-cube-size-and-max-product-size-image-mitigation-steps
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Rui Xue 204d4b1283b1fc602b74245588b34b21123a76d8 m
PIPE-3127: style cleanup — lazy logging, PEP 8
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Remy Indebetouw f0466d063aab7f58de89f520cce5a72265b0d816 m
cleaned message formatting slightly. moved the creation of overlimit_spws and oversize_spws out of the conditional blocks, so that they can always be printed to the log - I found this quite useful to debug and understand what was going on.
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Luke Maud a53b4762a6dfde8dfffda8d2fb75fadf0b87855e m
PIPE-3127 added spws reassign after field mitigation
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Federico Montesino Pouzols 6bd22f4018437b6a63de1838abf7e9a28c4d3a03 m
PIPE-3023: move taql query out of try, add unit test, fixes from review
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Luke Maud 399f80efeb8f932bffa706ae9761371c0e07ef03 m
PIPE-3127 moved large cube message trigger
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Federico Montesino Pouzols 241a5220970ae39c6088f7948096c4da8acb50f8 m
PIPE-3023: adapt flagdeteralma unit tests for updated implementation
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Federico Montesino Pouzols 5fdf963d96474439e846d0e49dda0b6e08427b3d m
PIPE-3023: use TaQL query to implement the partialpol logic
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Federico Montesino Pouzols 849190fff7c45ce0aab3707c82deb633ec150e2e m
PIPE-3023: fix info message about lowtrans
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Remy Indebetouw <remy@virginia.edu> 0b1523f48c0c784a9195bbdee15f6e9bf8d00ed8 m
fixing the two more impactful issues found by Ryan; the confusing message still needs to be dealt with
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Luke Maud 6169124e2910a5966dac230c5cde6532e72a94dc m
PIPE-3127 refactor mitigation to move step 1 error later into spw building loop and add supporting changes
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Luke Maud 8b7ce9a36fd6be1710f1c276f6bc32f9180c9c32 m
PIPE-3127 edited the clause to only mitigate spws if less than the maxcubelimit at the end of step 1
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Luke Maud 63300c1984fa75d1d71a5864327bbb7f33f6a862 m
PIPE-3127 step one added spw filter and supporting code changes cubesizes now returned as a dict
