Pipeline

• 

  Rui Xue 3 days ago 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.

  • docs/source/devel/usage/recipes.md (version 86549d250149fee6243df27e44acd50a817b2ff4) (diffs)
• 

  Rui Xue 3 days ago 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

  • docs/source/devel/setup/pixi_tasks.md (version b2f166936faa9be35cab37335b22e6943bbaac9f) (diffs)
  • pyproject.toml (version b2f166936faa9be35cab37335b22e6943bbaac9f) (diffs)
• 

  Rui Xue 3 days ago 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)
• 

  Remy Indebetouw <remy@virginia.edu> 3 days ago 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)
• 

  Rui Xue 3 days ago 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.

  • docs/source/_extension/toc_sections.py (version 84be22aba94949b7ad396854e12ca2ae768664cb) (diffs)
  • docs/source/_static/custom_theme.css (version 84be22aba94949b7ad396854e12ca2ae768664cb) (diffs)
  • docs/source/conf.py (version 84be22aba94949b7ad396854e12ca2ae768664cb) (diffs)
• 

  Rui Xue 3 days ago 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

  • docs/source/users_guide/pipeline-weblog.md (version ce8fbe47c34a737699567ac2b056da85a383da80) (diffs)
• 

  Rui Xue 3 days ago 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.

  • docs/source/_extension/parameter_linking.py (version 2731cabb4642a4174cfe00a01046e960df454df2) (diffs)
• 

  Rui Xue 3 days ago 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)
• 

  Rui Xue 3 days ago 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.

  • pipeline/hif/cli/hif_makeimages.py (version cdb9ddeeccd165ffdcbacd7fc5a42dfc93840bf2) (diffs)
• 

  Remy Indebetouw <remy@virginia.edu> 3 days ago 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
  #

  • pipeline/hifa/cli/hifa_diffgaincal.py (version 2753937d6db1c0ee93e5e989284956c90747ead4) (diffs)
  • pipeline/hsd/cli/hsd_imaging.py (version 2753937d6db1c0ee93e5e989284956c90747ead4) (diffs)
• 

  Rui Xue 3 days ago 71780bf53070f8f69a4494e163085df7af6b14e8

  PIPE-2738: Update documentation links to `ra-pipeline1 upstream

  • docs/README.rst (version 71780bf53070f8f69a4494e163085df7af6b14e8) (diffs)
  • docs/source/conf.py (version 71780bf53070f8f69a4494e163085df7af6b14e8) (diffs)
• 

  Rui Xue 3 days ago 9e9d46b44ddc226bd893d7dbbadf9c744f9bb75b

  PIPE-2738: Update documentation author to 'Pipeline Contributors'
  Replace outdated 'Pipeline Dev. Team' with inclusive wording.

  • docs/source/conf.py (version 9e9d46b44ddc226bd893d7dbbadf9c744f9bb75b) (diffs)
• 

  Rui Xue 3 days ago 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.

  • docs/source/_static/custom_theme.css (version 5ada67893520013259eb383f9aa267ed6f34815d) (diffs)
• 

  Rui Xue 3 days ago 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)
• 

  Rui Xue 3 days ago 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)
• 

  Rui Xue 3 days ago 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)
• 

  Rui Xue 3 days ago 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 3 days ago 21b93cf8102fcca508e327468e9391ee45b2dbc5

  PIPE-2738: Style figure captions to distinguish them from body text

  • docs/source/_static/custom_theme.css (version 21b93cf8102fcca508e327468e9391ee45b2dbc5) (diffs)
• 

  Rui Xue 3 days ago 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 3 days ago 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)
• 

  Remy Indebetouw <remy@virginia.edu> 3 days ago 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'.
  #
  # Changes to be committed:
  #        modified:   docs/source/index.rst
  #        new file:   docs/source/users_guide/PL2025_observingMode_matrix.png
  #        new file:   docs/source/users_guide/alma-science-pipeline.md
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  #        new file:   docs/source/users_guide/hsd_calimage-recipe.md
  #        new file:   docs/source/users_guide/index.md
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  #        modified:   docs/source/users_guide/weights.md
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  #

  • docs/source/index.rst (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/PL2025_observingMode_matrix.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/alma-science-pipeline.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/bytask.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/data-processing-files.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/guide-image-contamination.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/guide-img019.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/guide-img020.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/guide-img021.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/helper-text-files.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/helper_files.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/hifa_polcalimage-recipe.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/homepage_b2b_2024.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/hsd_calimage-recipe.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/index.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/modifying-a-pipeline-run.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/ms_overview_1.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/ms_overview_2.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/pipeline-versions-and-documentation.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/pipeline-weblog.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/plotcommand1.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/plotcommand2.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/processing_env_2024.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/quick-start.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/securitypage.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/timegaincal_bottomhalf.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/tsys.png (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/weights.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
  • docs/source/users_guide/whats-new.md (version aedc68351e5e92b6751050da4b12b6d09853b7c6) (diffs)
• 

  Rui Xue 3 days ago 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.

  • docs/source/conf.py (version cb48af9b52894dfe58f5a985c4367904137f65b8) (diffs)
  • docs/source/devel/reference/ALMA-Imaging-Workflow.md (version cb48af9b52894dfe58f5a985c4367904137f65b8) (diffs)
  • pipeline/hif/cli/hif_mstransform.py (version cb48af9b52894dfe58f5a985c4367904137f65b8) (diffs)
• 

  Remy Indebetouw 3 days ago 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
  #        modified:   docs/source/index.rst
  #        modified:   docs/source/timeline.md
  #        new file:   docs/source/users_guide/helper_files.md
  #        new file:   docs/source/users_guide/weights.md
  #        modified:   pipeline/hif/tasks/makeimages/makeimages.py
  #

  • docs/README.rst (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
  • docs/source/index.rst (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
  • docs/source/timeline.md (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
  • docs/source/users_guide/helper_files.md (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
  • docs/source/users_guide/weights.md (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
  • pipeline/hif/tasks/makeimages/makeimages.py (version bcdc480a386de2202fe5c148ca9aaba87b0daa58) (diffs)
• 

  Rui Xue 3 days ago 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)

  • docs/source/_extension/parameter_linking.py (version 1f9675c38bc50fdf7245f6dd459f92573fbf9a4c) (diffs)
• 

  Rui Xue 3 days ago 5c050a5aa02ece1fc8f0b4ce0112457f7b3e7e8f

  PIPE-2738: Add docstring to `FindROIInputs`
  - Add Args docstring to `FindROIInputs.__init__`
  - Remove redundant Returns section from hif_findroi CLI function

  • pipeline/hif/cli/hif_findroi.py (version 5c050a5aa02ece1fc8f0b4ce0112457f7b3e7e8f) (diffs)
  • pipeline/hif/tasks/findroi/findroi.py (version 5c050a5aa02ece1fc8f0b4ce0112457f7b3e7e8f) (diffs)