feat: Add Pixi workspace to pyproject.toml by matthewfeickert · Pull Request #2638 · scikit-hep/pyhf

matthewfeickert · 2025-11-20T01:11:04Z

Description

Add Pixi workspace to pyproject.toml under [tool.pixi] table.
- Add environments for all extras and dependency-groups.
- Add Pixi tasks for all sessions in Nox.
- Create conda specific environments so the only Python package is pyhf.
Add Pixi lock file to .gitignore.
Add .pixi/config to allow for insecure run-post-link-scripts.
Add sphinx-autobuild as 'dev' dependency group requirement.
- 'dev' is chosen over 'docs' as 'docs' should include only the required
  dependencies to build and deploy the docs to the website.

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Summarize commit messages into a comprehensive review of the PR

* Add Pixi workspace to pyproject.toml under [tool.pixi] table.
   - Add environments for all extras and dependency-groups.
   - Add Pixi tasks for all sessions in Nox.
   - Create conda specific environments so the only Python package is pyhf.
* Add Pixi lock file to .gitignore.
* Add .pixi/config to allow for insecure run-post-link-scripts.
* Add sphinx-autobuild as 'dev' dependency group requirement.
   - 'dev' is chosen over 'docs' as 'docs' should include only the required
      dependencies to build and deploy the docs to the website.

codecov · 2025-11-20T01:18:13Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.24%. Comparing base (be966d4) to head (86791fd).
⚠️ Report is 24 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2638   +/-   ##
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  Coverage   98.24%   98.24%           
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  Files          65       65           
  Lines        4220     4220           
  Branches      464      464           
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  Hits         4146     4146           
  Misses         45       45           
  Partials       29       29

Flag	Coverage Δ
contrib	`98.12% <ø> (ø)`
doctest	`98.24% <ø> (ø)`
unittests-3.10	`96.44% <ø> (ø)`
unittests-3.11	`96.44% <ø> (ø)`
unittests-3.12	`96.44% <ø> (ø)`
unittests-3.13	`96.44% <ø> (ø)`
unittests-3.9	`96.49% <ø> (ø)`

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matthewfeickert · 2025-11-20T08:13:24Z

I've been making heavy use of https://pixi.sh/latest/python/pyproject_toml/#optional-dependencies for this PR and for testing.

I'm also realizing from this PR (/ remembering Issue #2622) that click-completion is in maintenance mode

pyhf/pyproject.toml

Line 67 in 6b690c5

shellcomplete = ["click_completion"]

and that there is a native Click v8 completion. c.f. https://click.palletsprojects.com/en/stable/shell-completion/#shell-completion

matthewfeickert

This adds a fully conda-package-based Pixi workspace for pyhf, such that the only Python package is pyhf itself:

$ pixi list -e dev | grep pypi
Environment: dev
pyhf                              0.7.1.dev336                                     pypi

It adds a suite of Pixi tasks as well

$ pixi task list
Tasks that can run on this machine:
-----------------------------------
benchmarks, build-docs, build-package, doctest, lint, notebooks, serve, test, test-contrib
Task           Description
benchmarks     Run the benchmarks
build-docs     Build the pyhf documentation website
build-package  Build a sdist and wheel
doctest        Run the doctest tests
lint           Run pre-commit
notebooks      Run the test suite for the notebooks
serve          Serve the docs website
test           Run the test suite on the core library
test-contrib   Run the test suite for the contrib module

and the ability to get a CUDA accelerated jaxlib environment

$ pixi list -e jax-gpu jax
Environment: jax-gpu
Name    Version  Build                            Size  Kind   Source
jax     0.7.2    pyhd8ed1ab_0                 1.78 MiB  conda  https://conda.anaconda.org/conda-forge
jaxlib  0.7.2    cuda129_py313h33cbcf4_202  166.01 MiB  conda  https://conda.anaconda.org/conda-forge
$ pixi run -e jax-gpu python
Python 3.13.11 | packaged by conda-forge | (main, Dec  6 2025, 11:24:03) [GCC 14.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import jax
>>> import pyhf
>>> jax.devices()
[CudaDevice(id=0)]

When Pixi is solving it will raise the following warnings

WARN The package `pytest-benchmark==5.2.3` does not have an extra named `histogram`
WARN The package `coverage==7.13.0` does not have an extra named `toml`
WARN The package `pytest-benchmark==5.2.3` does not have an extra named `histogram`
WARN The package `coverage==7.13.0` does not have an extra named `toml`

which can't be avoided as far as I know, given that it is trying to resolve the extras that exist in the test dependency-group

pyhf/pyproject.toml

Line 85 in 86c214d

"coverage[toml]>=6.0.0",

pyhf/pyproject.toml

Line 88 in 86c214d

"pytest-benchmark[histogram]",

and can't.

matthewfeickert · 2025-12-18T23:38:28Z

+pixi exec python-build --installer uv . && \
+pixi exec twine check --strict ./dist/*


Doing pixi exec here are these are transitory processes that don't need to have their dependencies constrain the rest of the dev environment.

Why not use package functionalities here with the pixi-build preview?

Is that faster or more convenient? That seems like more configuration for no clear benefit.

I've found it to be a little faster in pyhs3.

Given that for this PR I wanted to get things working and in a single file, and scipp-atlas/pyhs3#145 has shown us that for now we would need to also use pixi.toml I'd prefer to skip this till pixi-build is fully out of preview.

matthewfeickert · 2025-12-18T23:39:07Z

+default = { solve-group = "default" }
+jax = { features = ["jax"], solve-group = "default" }
+jax-cpu = { features = ["jax-cpu"], solve-group = "default" }
+jax-gpu = { features = ["jax-gpu"], solve-group = "gpu" }


Add jax-gpu environment so can get a CUDA enabled jaxlib on demand.

matthewfeickert · 2025-12-18T23:47:40Z

cc @MoAly98 @ikrommyd given discussion on scikit-hep/coffea#1503

matthewfeickert · 2025-12-19T00:02:12Z

Note that as you can't specify default environments for tasks yet (c.f. prefix-dev/pixi#5140) when you run

pixi run test

you'll be asked to select an environment

$ pixi run test
? The task 'test' can be run in multiple environments.

Please select an environment to run the task in: ›
❯ test
  dev

Currently the only way to avoid this is to specify the environment at runtime

pixi run --environment test test

.

* Add Pixi workspace to pyproject.toml under [tool.pixi] table. * Add Pixi lock file to .gitignore.

matthewfeickert · 2025-12-27T04:29:30Z

cc @kratsg for review.

kratsg · 2025-12-27T13:40:14Z

+rsync -r ./src/pyhf/schemas ./docs/_build/html/
+"""
+
+[tool.pixi.feature.docs.tasks.serve]


I would also add a [...tasks.watch] that does sphinx-autobuild --open-browser -n -T -b html docs docs/_build/html which autoreloads when changes are made.

Done, but in dev environment.

kratsg · 2025-12-27T13:41:34Z

+pixi exec python-build --installer uv . && \
+pixi exec twine check --strict ./dist/*


Why not use package functionalities here with the pixi-build preview?

kratsg · 2025-12-27T17:01:16Z

Note that as you can't specify default environments for tasks yet (c.f. prefix-dev/pixi#5140) when you run

Technically, you can do this by simply keeping the task to a single environment. There's some clever restructuring one can do if you don't need all envs all at once.

matthewfeickert · 2026-01-05T18:38:12Z

Technically, you can do this by simply keeping the task to a single environment. There's some clever restructuring one can do if you don't need all envs all at once.

@kratsg indeed. We probably can try to do extra clever things moving forward, but I might suggest that we postpone until we can reevaluate the pixi-build backends.

matthewfeickert self-assigned this Nov 20, 2025

matthewfeickert added the feat/enhancement New feature or request label Nov 20, 2025

matthewfeickert added this to pyhf v0.8.0 Nov 20, 2025

github-project-automation Bot moved this to In progress in pyhf v0.8.0 Nov 20, 2025

matthewfeickert mentioned this pull request Nov 20, 2025

Find alternative to click-completion which is now in maintenance mode #2622

Closed

matthewfeickert force-pushed the feat/add-pixi-workspace-config branch from a560690 to 5a00bf4 Compare December 16, 2025 22:26

matthewfeickert mentioned this pull request Dec 16, 2025

feat: supporting pixi environment managing scikit-hep/coffea#1503

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matthewfeickert force-pushed the feat/add-pixi-workspace-config branch 2 times, most recently from e6fa7de to 78d2be8 Compare December 18, 2025 19:48

matthewfeickert commented Dec 18, 2025

View reviewed changes

matthewfeickert marked this pull request as ready for review December 18, 2025 23:42

matthewfeickert requested review from henryiii and kratsg December 18, 2025 23:43

matthewfeickert requested a review from lukasheinrich December 18, 2025 23:56

ikrommyd mentioned this pull request Dec 19, 2025

ci: try pixi scikit-hep/uproot5#1193

Draft

matthewfeickert added 11 commits December 26, 2025 13:16

feat: Add Pixi workspace to pyproject.toml

9954ee0

* Add Pixi workspace to pyproject.toml under [tool.pixi] table. * Add Pixi lock file to .gitignore.

stub out test environment

19276ac

Use rich instead of tqdm

4babc5e

Allow for insecure run-post-link-scripts

1711da7

Add docs environment

3f17536

Add docs building pixi tasks

ed3c3be

Add dev feature and environment

e15fa82

Add test tasks

5a5bf63

Add additional test tasks

ef687ca

use python-graphviz to get graphviz from conda-forge

d25855f

Add nox to get all conda packages except pyhf

0c397c7

matthewfeickert added 3 commits December 26, 2025 13:16

Add lint and build-package tasks

3cb5d00

Update rich lower bound

d67b7d9

Add numpy lower bound

2885793

matthewfeickert force-pushed the feat/add-pixi-workspace-config branch from a5155b3 to 2885793 Compare December 26, 2025 19:19

kratsg requested changes Dec 27, 2025

View reviewed changes

github-project-automation Bot moved this from In progress to Review in progress in pyhf v0.8.0 Dec 27, 2025

build: Add sphinx-autobuild as dev dependency

86791fd

matthewfeickert requested a review from kratsg January 5, 2026 18:08

kratsg approved these changes Jan 5, 2026

View reviewed changes

matthewfeickert merged commit b191d3d into scikit-hep:main Jan 5, 2026
22 checks passed

matthewfeickert deleted the feat/add-pixi-workspace-config branch January 5, 2026 18:39

github-project-automation Bot moved this from Review in progress to Done in pyhf v0.8.0 Jan 5, 2026

matthewfeickert mentioned this pull request Jan 14, 2026

chore: Add default environments for Pixi tasks #2661

Merged

4 tasks

		pixi exec python-build --installer uv . && \
		pixi exec twine check --strict ./dist/*

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