build: migrate to uv, add ruff/ty, format all files by FIrgolitsch · Pull Request #95 · linum-uqam/linumpy

FIrgolitsch · 2026-04-01T02:04:41Z

PR #95 — Build Tooling & Formatting

Migrates the build system to modern Python tooling and applies consistent formatting across the codebase. Prerequisite for all other stacked PRs (#87, #96–#104).

Build system: setup.py → uv + pyproject.toml

Full pyproject.toml: project metadata, core deps, optional extras (gpu, gpu-cuda12, gpu-cuda13, docs, dev), entries in [project.scripts]
uv.lock for reproducible resolution
Remove setup.py, requirements.txt, requirements-pytest.txt
Dockerfile updated to use uv

Lint & format: ruff + ty

[tool.ruff] — target py312, line-length 127, rules E/F/W/I/UP/B/RUF/SIM/C4/PIE/PTH
[tool.ruff.lint.isort] — _thread_config in its own section (must import before numpy/jax to set thread caps)
[tool.ty] — linumpy-only, py312, cupy/cupyx/numba → Any, relaxed overrides for tests and GPU modules
.pre-commit-config.yaml — ruff-format, ruff lint (--fix), ty (advisory / non-blocking)
ruff format applied to all Python files; ruff check --fix applied (import ordering, f-strings, type upgrades, PTH replacements where safe)

CI & Docker

.github/workflows/python-app.yml — astral-sh/setup-uv@v5, uv sync, uv run ruff, uv run ty, uv run pytest
Dockerfile switched from pip to uv

Other

linumpy/py.typed marker
.gitignore additions for uv / ty caches and local benchmark outputs

Commits

build: migrate to uv, add ruff/ty, format all files
build: expand ruff rules, refresh uv.lock, add ty pre-commit — enables PTH/SIM/C4/PIE, refreshes uv.lock, wires ty into pre-commit as advisory

Notes

Some pre-existing lint warnings remain (a few PTH/SIM/E501) — will be mopped up in the dependent PRs as they touch those files
[project.scripts] here only contains scripts present at the branch point; each stacked PR adds its own entries

CHrlS98

I know it as mostly formatting but I still went through all the files. It has been a good opportunity to get back into the code. I have a few comments of course. Hopefully there are not too many other 125 files PR 🥲

Relocates thread-pool configuration into a dedicated config sub-package.

- Remove dead modules data_io.py and npz.py (unused). - Move Allen brain atlas helpers from io/allen.py into a new linumpy.reference sub-package. - Drop star imports from io/__init__.py. - Modernize remaining io/ modules (Path, type hints, docstrings).

- Move utils/io.py argparse helpers to a new linumpy.cli.args module. - Move utils/metrics.py into a top-level linumpy.metrics package. - Remove now-empty linumpy.utils package.

…in.py Promotes the single-file linumpy.segmentation module into a package with a dedicated brain.py module for clarity and future extension.

- imaging/transform.py: image transformation helpers. - imaging/overlay.py: overlay/composite helpers.

…osaic.quick_stitch - mosaic/discovery.py: tile-discovery helpers. - mosaic/quick_stitch.py: quick low-resolution stitching helpers.

- mosaic/grid.py: grid construction (from stitching/mosaic_grid.py). - mosaic/overlap.py: tile overlap helpers (extracted from stitching). - registration/manual.py: interactive registration GUI (from stitching/manual_registration.py). - registration/sitk.py: SimpleITK-based registration (from stitching/registration.py). - registration/phase_correlation.py: phase-correlation registration. - registration/refinement.py: multi-stage refinement helpers. - registration/transforms.py: affine/rigid transform utilities. - Drop dead modules stitching/FileUtils.py, stitching/topology.py, stitching/stitch_utils.py.

…ckage Splits the 1786-line linumpy/preproc/icorr.py module into focused modules: - intensity/normalize.py: intensity normalization helpers. - intensity/attenuation.py: attenuation correction. - intensity/psf_model.py: PSF-model-based illumination correction. - intensity/vignette.py: vignetting correction. - intensity/artifact.py: artifact removal helpers. - intensity/convert.py: intensity conversion helpers.

…ckage Splits xyzcorr.py into focused modules: - geometry/crop.py: volume cropping helpers. - geometry/resample.py: resampling utilities. - geometry/interface.py: tissue-interface detection and fitting. - geometry/galvo.py: galvo / scanner geometry helpers. Repoints linumpy.microscope.oct to use the new geometry.galvo module.

…it utils.py - stack_alignment/io.py: I/O helpers (CSV/JSON read/write). - stack_alignment/units.py: unit conversion helpers. - stack_alignment/filter.py: outlier filtering helpers. Renames the corresponding test module from test_utils_shifts.py to test_stack_alignment.py.

- psf/synthetic.py: synthesize_3d_psf helper (renamed from get_3d_psf for clarity). - psf/extract.py: extract experimental PSFs from data.

Updates all 43 linum_*.py scripts plus 2 script tests to use the new sub-packages introduced in this refactor: linumpy.preproc.icorr -> linumpy.intensity.{normalize,attenuation, psf_model,vignette, artifact,convert} linumpy.preproc.xyzcorr -> linumpy.geometry.{crop,resample, interface,galvo} linumpy.shifts.utils -> linumpy.stack_alignment.{io,units,filter} linumpy.psf.psf_estimator -> linumpy.psf.{synthetic,extract} linumpy.stitching -> linumpy.mosaic.{grid,overlap,discovery, quick_stitch} and linumpy.registration.{manual,sitk, phase_correlation, refinement,transforms} linumpy.utils_images -> linumpy.imaging.{transform,overlay} linumpy.utils.io -> linumpy.cli.args linumpy.utils.metrics -> linumpy.metrics linumpy.io.allen -> linumpy.reference.allen linumpy.segmentation -> linumpy.segmentation.brain linumpy.reconstruction -> linumpy.mosaic.{discovery,quick_stitch} linumpy._thread_config -> linumpy.config.threads

- Update setuptools `packages.find` and ruff `per-file-ignores` to reflect the renamed/split modules (intensity/, geometry/, mosaic/, registration/, stack_alignment/, etc.). - Update isort `thread-config` section to reference linumpy.config.threads. - Refresh uv.lock to pick up incidental dependency updates. - Pre-existing tooling tweaks (expanded ruff rule set, ty config, GPU dependency cleanup) carried in the working tree.

Refreshes all transitive package versions to current resolutions (idna, magicgui, ome-zarr, pre-commit, pydantic, pytest, ruff, ty, typer, virtualenv, etc.).

Removed pins on numpy, scipy, hyperactive, pynrrd, and numcodecs. basicpy 2.0.0 (latest available) transitively pins scipy<1.13, which forces numpy<2; override that ceiling via [tool.uv].override-dependencies so we resolve modern numpy 2.x and scipy 1.17 across the stack.

This was referenced Apr 17, 2026

feat: add slice-config module and generator CLI #103

Merged

feat: add manual-alignment export, refinement, and global-transform tools #104

Merged

FIrgolitsch force-pushed the pr-a-build-tooling branch from 8c93c45 to 687b26f Compare April 17, 2026 22:15

FIrgolitsch mentioned this pull request Apr 17, 2026

feat: slice interpolation for missing sections (z-morph) #87

Open

CHrlS98 requested changes Apr 22, 2026

View reviewed changes

FIrgolitsch requested a review from CHrlS98 April 23, 2026 19:49

FIrgolitsch force-pushed the pr-a-build-tooling branch 2 times, most recently from a48129d to 82b44be Compare April 23, 2026 21:09

This was referenced Apr 23, 2026

docs: update documentation and add RECONST_2_5D_WORKFLOW #105

Closed

feat: add slice-config module and generator CLI #106

Open

feat: add manual-alignment export, refinement, and global-transform tools #107

Open

FIrgolitsch force-pushed the pr-a-build-tooling branch from 82b44be to ce8e35d Compare April 23, 2026 21:23

FIrgolitsch added 11 commits April 23, 2026 17:27

build: migrate to uv, add ruff/ty, format all files

7dab059

build: expand ruff rules, refresh uv.lock, add ty pre-commit

fab13ea

refactor(config): move _thread_config to linumpy.config.threads

dc0dd14

Relocates thread-pool configuration into a dedicated config sub-package.

refactor(utils): split utils/ into linumpy.cli and linumpy.metrics

8352b98

- Move utils/io.py argparse helpers to a new linumpy.cli.args module. - Move utils/metrics.py into a top-level linumpy.metrics package. - Remove now-empty linumpy.utils package.

refactor(segmentation): convert segmentation.py into segmentation/bra…

7119293

…in.py Promotes the single-file linumpy.segmentation module into a package with a dedicated brain.py module for clarity and future extension.

refactor(imaging): split utils_images.py into linumpy.imaging package

e30f8dc

- imaging/transform.py: image transformation helpers. - imaging/overlay.py: overlay/composite helpers.

refactor(mosaic): split reconstruction.py into mosaic.discovery and m…

67dc9c8

…osaic.quick_stitch - mosaic/discovery.py: tile-discovery helpers. - mosaic/quick_stitch.py: quick low-resolution stitching helpers.

FIrgolitsch added 10 commits April 23, 2026 17:27

refactor(psf): split psf_estimator.py into psf.synthetic and psf.extract

5ae5e44

- psf/synthetic.py: synthesize_3d_psf helper (renamed from get_3d_psf for clarity). - psf/extract.py: extract experimental PSFs from data.

chore(deps): uv lock --upgrade across the board

319d746

Refreshes all transitive package versions to current resolutions (idna, magicgui, ome-zarr, pre-commit, pydantic, pytest, ruff, ty, typer, virtualenv, etc.).

docs: add comprehensive project documentation

98c5b43

docs: update pipeline, GPU, workflow, and script references

5af19a8

chore: add AGENTS.md to .gitignore; sync XYZ_to_ZYX.py help text

e140014

chore: apply code quality cleanup to arch modules

cc75fc8

FIrgolitsch force-pushed the pr-a-build-tooling branch from ce8e35d to cc75fc8 Compare April 23, 2026 21:28

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build: migrate to uv, add ruff/ty, format all files#95

build: migrate to uv, add ruff/ty, format all files#95
FIrgolitsch wants to merge 21 commits intomainfrom
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FIrgolitsch commented Apr 1, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR #95 — Build Tooling & Formatting

Build system: setup.py → uv + pyproject.toml

Lint & format: ruff + ty

CI & Docker

Other

Commits

Notes

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