Wrap into pip-installable package by thomaswilliamsastro · Pull Request #292 · PhangsTeam/phangs_imaging_scripts

thomaswilliamsastro · 2026-02-19T15:53:33Z

Pretty sizeable refactor, but this enables pip-installing the pipeline, which means we can finally keep a handle on python/CASA versions.

I've transferred the author list from the paper, and maintainers from the contributors list. If there's anyone missing, please let me know!

Fix step occasionally being 0 in noise cube generation
Add dependabot, and build actions to ensure package installs correctly on Python matrix
Add CODEOWNERS, so PRs get assigned automatically
Update CITATION.md to CITATION.cff, and format correctly
Rename LICENSE.rst to just LICENSE
Rewrite pyproject.toml to allow pip-installation
- Expand list of authors/maintainers/citation.cff
Rename README.rst to README.md
- Significant reformatting and updating to reflect packaging
- Include details on chunked imaging
Remove setup.cfg/setup.py
Remove unused _astropy_init.py
Remove unused conftest.py
Remove unused data/ directory in phangsPipeline
Remove unused and very outdated PHANGSPipelineReadme.md in phangsPipeline
Moved casaBlankCleanRecipe to scripts, and renamed
Refactored versioning throughout, now pulls automatically from the package
Fully align CASA version throughout
General import tidy-up
Move various example scripts into scripts/ directory
Consolidate run script into run_pipeline_phangs-alma.py
Update README.md to include link to v3.2
Move links from akleroy->PhangsTeam throughout
Add CHANGES.rst, and workflow to make sure CHANGES.rst has been edited on a PR

e-koch

Added a few comments but have concerns over required/optional dependencies (that we've arleady started discussing offline).

.github/workflows/build.yml

phangsPipeline/tests/__init__.py

phangsPipeline/__init__.py

scripts/calctimeonsource.py

phangsPipeline/casaSingleDishALMAWrapper.py

phangsPipeline/casaVisRoutines.py

phangsPipeline/ftplane_convolution.py

scripts/print_uv_ranges.py

pyproject.toml

tox.ini

pyproject.toml

thomaswilliamsastro · 2026-02-24T14:27:06Z

Note to self after ADR today: Once comments have been implemented, run some test imaging end-to-end on monolithic/pip-installed CASA versions on Mac/Linux machine

e-koch

Thanks @thomaswilliamsastro ! I'm happy with moving forward with merging and pushing development in v4.X.

thomaswilliamsastro · 2026-02-25T13:10:47Z

End-to-end testing:

pure Python, MacBook. Runs successfully
monolithic CASA, MacBook. Runs successfully
pure Python, Linux. Runs successfully
monolithic CASA, Linux. Runs successfully

So I think we're basically ready to merge here. Note that I've had to pin one dependency, protobuf to 3.2.0. This is a known CASA issue (https://casadocs.readthedocs.io/en/stable/notebooks/introduction.html#Known-Issues), and hopefully isn't forever

thomaswilliamsastro · 2026-03-24T11:40:13Z

@e-koch I've just done the mammoth rebase and conflict resolution. I'm running through end-to-end on one test case to make sure nothing weird has been introduced, but it would be good to get eyes over this again quickly

e-koch · 2026-04-07T23:48:07Z

@thomaswilliamsastro -- we should update the README here, too. And a clear link to the v3.2 release for prior CASA version.

thomaswilliamsastro · 2026-04-08T08:45:37Z

@thomaswilliamsastro -- we should update the README here, too. And a clear link to the v3.2 release for prior CASA version.

@e-koch Done. Also edited the links to point at the new repo wherever they appeared

e-koch

@thomaswilliamsastro this is looking great! I added a couple minor comments.

The only part I have a lingering concern about is triggering a spectral-cube import at the package level for the derived handler. I'd rather we keep an if/else check there for whether spectral-cube is installed as it'll become the main friction point for most people still using the pipeline in a monolithic environment.

e-koch · 2026-04-11T12:56:17Z

phangsPipeline/handlerDerived.py

 import numpy as np

+from . import handlerTemplate
+from . import utilsFilenames
+from .scConvolution import smooth_cube


These still need a check for whether spectral-cube is installed so we should migrate this back into the init or have a file-wide if/else. Otherwise the package level imports will fail in a monolithic CASA environment.

Sorted, I think -- I've added a function to check spectral_cube is importable, and only then will the derivedHandler import

pyproject.toml

e-koch · 2026-04-11T13:28:04Z

README.md

+pip install -e .
+```
+
+If you are using a monolithic CASA installation, you can run this within


We should give a few more details here. Probably linking to https://casadocs.readthedocs.io/en/stable/notebooks/frequently-asked-questions.html#Astropy-in-monolithic-CASA

and noting that the old "append to path" in the config.py file is still an option (since that's how most people will likely continue to use for a bit to not break existing workflows)

Added a link here

run_pipeline_phangs-alma.py

@e-koch

- Fix step occasionally being 0 in noise cube generation - Add dependabot, and build actions to ensure package installs correctly on Python matrix - Add CODEOWNERS, so PRs get assigned automatically - Update CITATION.md to CITATION.cff, and format correctly - Rename LICENSE.rst to just LICENSE - Rewrite pyproject.toml to allow pip-installation - Expand list of authors/maintainers/citation.cff - Rename README.rst to README.md - Significant reformatting and updating to reflect packaging - Include details on chunked imaging - Remove setup.cfg/setup.py - Remove unused _astropy_init.py - Remove unused conftest.py - Remove unused data/ directory in phangsPipeline - Remove unused and very outdated PHANGSPipelineReadme.md in phangsPipeline - Moved casaBlankCleanRecipe to scripts, and renamed - Refactored versioning throughout, now pulls automatically from the package - Fully align CASA version throughout - General import tidy-up - Move various example scripts into scripts/ directory - Consolidate run script into run_pipeline_phangs-alma.py - Update README.md to include link to v3.2 - Move links from akleroy->PhangsTeam throughout - Add CHANGES.rst, and workflow to make sure CHANGES.rst has been edited on a PR - Address comments from @e-koch

thomaswilliamsastro · 2026-04-11T19:10:46Z

@e-koch Comments addressed, I haven't resolved the two potentially more sticky points but they should be fine now (I hope)

thomaswilliamsastro requested a review from e-koch February 19, 2026 15:53

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e-koch linked an issue Apr 7, 2026 that may be closed by this pull request

Notice: You are using astropy TestRunner that will be deprecated #253

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e-koch merged commit 054e091 into master Apr 11, 2026
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thomaswilliamsastro deleted the package-up branch April 11, 2026 19:57

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