Pipeline

• 

  Rui Xue 14 Sep 2026 62d0284b0eb2bfe226c950f2020117c260320c51

  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`
• 

  Rui Xue 11 Sep 2026 050c7ff9597ba670223e7d6e55ce1419bd0f2fc6

  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 74823d13b4eddac41d072131f0e80b908a971467

  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 99c9b87a741c4f3802da8bb954e72287ba074e1a

  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

  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 c5814b3059e280ff7102a2e49dfea61ca1740b97

  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 79d49872125a4170b64ea819c286bb465459a632

  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 c51df6219e629aa1991514534969533117f189b2

  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 7242f0943dc9ff5d969f976c8c4050cdcf2e8ab3

  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 05f7e92c5c32b44b1c005b054229de35d298e55b

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

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

  Rui Xue 10 Sep 2026 9d3fc84477d803a0c67f325e7375d13af31a6caa

  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

  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

  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 6919fb4f257da7fffc1aaa1ccb8390336b5e583f

  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 08dc2a857608a09d87d0209a3a8065e1c22e25a5

  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 9912dcb94977a770df4c6263bc0ff59a38a03ee9

  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)