Code commits
Pipeline
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Rui Xue 941723b0a49b9bfcc02a08bd92fcb0c00c334bcf
Pull request #1935: Migrate the PIPE-2738 documentation improvement to main
Merge in PIPE/pipeline from docs/PIPE-2738-improve-docs-for-main-part3 to main
* commit 'fbdf591a705f2546e47b28a96d92681e75a174b9':
PIPE-2738: fix typos in hifa_spwphaseup task docstring
PIPE-2738: Documentation build configuration and tooling updates
PIPE-2738: Update CLI and task docstrings for PL2026
PIPE-2738: Add PL2026 documentation guides, release notes, and assets
PIPE-2738: preserve original docstrings for Sphinx; fix doc rendering issues
PIPE-2738: make pdf link version-contained and use short version on pdf cover
PIPE-2738: Added SD changes from Kotomi
PIPE-2738: Added branding to the ALMA User's guide front page
PIPE-2738: dynamically strip Sphinx markup from task docstrings for terminal users
PIPE-2738: Did a readthrough of all hifa_; added back in some description that I thought was important. Also tried to check Kotomi's changes ~Aug 3 in the PLUG, that they got transferred correctly, but those should be double-checked.
PIPE-2738: Update docs badge to reference pixi-based build workflow -
Rui Xue fbdf591a705f2546e47b28a96d92681e75a174b9 m
PIPE-2738: fix typos in hifa_spwphaseup task docstring
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Rui Xue ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3 m
PIPE-2738: Documentation build configuration and tooling updates
- .readthedocs.yaml (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- pipeline/infrastructure/doctools.py (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- pyproject.toml (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- requirements_docs.txt (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
- scripts/update_references.py (version ae75f12444fcaed963e71a9bfd5e2f07bb25bcf3) (diffs)
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Rui Xue 0c87523cdcb789fe2fcb78a6843268bc7034016e m
PIPE-2738: Update CLI and task docstrings for PL2026
- pipeline/domain/datatype.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_applycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_checkproductsize.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_correctedampflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_findcont.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_findroi.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_lowgainflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_makeimages.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_makeimlist.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_mstransform.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_selfcal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/cli/hif_setmodels.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/findcont/findcont.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/findroi/findroi.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hif/tasks/makeimlist/makeimlist.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_antpos.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_bandpass.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_diffgaincal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_exportdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_flagdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_fluxcalflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_gaincalsnr.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_gfluxscale.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_imageprecheck.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_importdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_lock_refant.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_restoredata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_spwphaseup.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_targetflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_timegaincal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_tsysflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_unlock_refant.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/cli/hifa_wvrgcalflag.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hifa/tasks/imageprecheck/imageprecheck.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_baseline.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_imaging.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_importdata.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_k2jycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
- pipeline/hsd/cli/hsd_skycal.py (version 0c87523cdcb789fe2fcb78a6843268bc7034016e) (diffs)
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Rui Xue b675284a8337834d8b2b5911cc5f206929a879b8 m
PIPE-2738: Add PL2026 documentation guides, release notes, and assets
- docs/README.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_extension/jira_links.py (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/custom_theme.css (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/robots.txt (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewer_init.js (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/README.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/viewer.min.css (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/_static/viewerjs/viewer.min.js (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/acknowledgement.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/conf.py (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/misc/python3_conversion_notes.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/reference/ALMA-Imaging-Workflow.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/reference/spectral_windows.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/monolithic_casa.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/pixi_tasks.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/setup/readthedocs.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/devel/testing/unit_tests.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/examples/test2.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_hifa_diffgaincal_incHeuristic_lowSNR.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_hifa_gfluxscale_workflowtitle.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/PL2026_size_mitigation_flowchart_final.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/figures/contamination.png (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/index.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/overview.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/pipeline_tasks/individual_task.mako (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/references/readme.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/releases.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/task_reference.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/tasks.rst (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/alma-science-pipeline.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/hifa_polcalimage-recipe.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
- docs/source/users_guide/hsd_calimage-recipe.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/modifying-a-pipeline-run.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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- docs/source/users_guide/pipeline-versions-and-documentation.md (version b675284a8337834d8b2b5911cc5f206929a879b8) (diffs)
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Rui Xue 4e6b4b4dbbfd685dc27b27c71448c2d27e568319 m
Merge tag '2026.2.1.40' into docs/PIPE-2738-improve-docs-for-main-part3
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Rui Xue 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". -
Rui Xue 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 -
Remy Indebetouw <remy@virginia.edu> 69c8b34645e35010f5968f84c7e555001480fc86 m
PIPE-2738: Added SD changes from Kotomi
# Please enter the commit message for your changes. Lines starting
# with '#' will be kept; you may remove them yourself if you want to.
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# Author: Remy Indebetouw <remy@virginia.edu>
# Date: Thu Aug 13 22:12:09 2026 -0400
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# interactive rebase in progress; onto 976da6259c
# Last commands done (4 commands done):
# squash d6ba8f8fcb # forgot an acknowledgement
# reword 5a8029cb26 # changes from Kotomi
# Next commands to do (2 remaining commands):
# pick c28aeed740 PIPE-2738: make pdf link version-contained and use short version on pdf cover
# pick 6804eebfd1 PIPE-2738: preserve original docstrings for Sphinx; fix doc rendering issues
# You are currently editing a commit while rebasing branch 'docs/PIPE-2738-improve-docs-for-main-part3' on '976da6259c'.
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# Changes to be committed:
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Remy Indebetouw <remy@virginia.edu> 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
# 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: Thu Aug 13 18:36:36 2026 -0400
#
# interactive rebase in progress; onto 976da6259c
# Last commands done (3 commands done):
# squash 1a8fad2582 # grr. it didnt add these to the previous
# squash d6ba8f8fcb # forgot an acknowledgement
# Next commands to do (3 remaining commands):
# reword 5a8029cb26 # changes from Kotomi
# pick c28aeed740 PIPE-2738: make pdf link version-contained and use short version on pdf cover
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# new file: docs/source/users_guide/almalogo.png
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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)
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Rui Xue 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 -
Remy Indebetouw <remy@virginia.edu> 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.
# Please enter the commit message for your changes. Lines starting
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# An empty message aborts the commit.
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# Author: Remy Indebetouw <remy@virginia.edu>
# Date: Thu Aug 13 16:13:47 2026 -0400
#
# 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
# reword 547e325bc6 # 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.
# Next command to do (1 remaining command):
# pick a5702e6c0d PIPE-2738: dynamically strip Sphinx markup from task docstrings for terminal users
# You are currently editing a commit while rebasing branch 'docs/PIPE-2738-improve-docs-for-main-part3' on '64967c159b'.
#
# Changes to be committed:
# modified: pipeline/hifa/cli/hifa_bandpass.py
# modified: pipeline/hifa/cli/hifa_gfluxscale.py
# modified: pipeline/hifa/cli/hifa_renorm.py
# modified: pipeline/hifa/cli/hifa_tsysflagcontamination.py
# modified: pipeline/hifa/cli/hifa_wvrgcal.py
# modified: pipeline/hifa/cli/hifa_wvrgcalflag.py
# modified: pipeline/hsd/cli/hsd_applycal.py
# modified: pipeline/hsd/cli/hsd_baseline.py
# modified: pipeline/hsd/cli/hsd_importdata.py
# modified: pipeline/hsd/cli/hsd_skycal.py
#
# Untracked files:
# unit-results.xml
#- 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 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.
