Use hatch as build system instead of setuptools

[willingc]

This PR modernizes some packaging items and follows guidelines found in Scientific Python's guide. It resolves a number of issues found by repo-review: https://learn.scientific-python.org/development/guides/repo-review/

This PR:

• use hatch for package build
• remove bumpversion and use dynamic version with hatch
• removes setuptools and setup.py completely
• removes requirements files and uses standard pyproject.toml approach
• moves pytest config into pyproject.toml and updates items flagged by repo-review

Addresses #833 #844

To Do:

• Update binder config in tox

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.13%. Comparing base (cb2eb37) to head (73aaa13).
⚠️ Report is 24 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #848      +/-   ##
==========================================
- Coverage   91.54%   91.13%   -0.42%     
==========================================
  Files          17       17              
  Lines        1621     1635      +14     
==========================================
+ Hits         1484     1490       +6     
- Misses        137      145       +8     

see 5 files with indirect coverage changes

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[Copilot]

Pull Request Overview

This PR modernizes the packaging infrastructure by migrating from setuptools to hatch as the build system, following Scientific Python development guidelines. The changes consolidate dependency management into pyproject.toml and adopt modern Python packaging standards.

Key changes:

• Migration from setuptools to hatchling with hatch-vcs for dynamic versioning
• Consolidation of all dependencies from separate requirements files into pyproject.toml optional dependencies
• Enhanced pytest configuration with stricter settings and moved into pyproject.toml

Reviewed Changes

Copilot reviewed 14 out of 16 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
pyproject.toml	Complete restructure: new build system (hatchling), consolidated dependencies, enhanced pytest config, updated tox environments
requirements/*.txt	Removed all requirement files (s3, hdfs, github, gcs, docs, dev, azure, base) - now managed in pyproject.toml
papermill/version.py	Removed static version file - now dynamically generated by hatch-vcs
MANIFEST.in	Removed - hatch manages package inclusion via pyproject.toml configuration
.pre-commit-config.yaml	Updated repository URLs for black and mdformat hooks
.gitignore	Added papermill/version.py to ignore dynamically generated version file
.gitattributes	Added .git_archival.txt for export-subst
.git_archival.txt	New file to support git archive with version information
.github/workflows/ci.yml	Removed setuptools from pip install, removed manifest tox environment, simplified condition syntax

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[willingc]

@ofek If you have time to take a quick look at the hatch sections, I would appreciate it. Thanks 😄

[ofek]

Hey there, I left some comments!

[ofek]

1. If you specify inclusion then exclusion only acts upon what is included so here the exclusion is I think unnecessary because that's a sibling directory.
2. If you only care about shipping the package/certain directories then there is a fast-path option called only-include that prevents scanning the tree and just selects what you define.
3. It's completely up to you what you now want to ship but just a heads up that the source distribution from the latest release on PyPI includes more like the pytest and tox config:

[ofek]

nit unrelated to Hatch: based on the value of addopts I think you want the standard configuration (perhaps it's working properly because they have a fallback mechanism, not sure)

Suggested change

	[tool.pytest.ini_options]
	[tool.pytest]

[ofek]

I'm not sure what CI is doing but I think this would also be unnecessary now:

Suggested change

	python -m pip install --upgrade pip wheel coverage[toml] virtualenv tox tox-gh-actions
	python -m pip install --upgrade pip coverage[toml] virtualenv tox tox-gh-actions

[ofek]

Oh one more thing, is this accurate?

[rgbkrk]

Plenty of feedback in here from @Borda and @ofek. Thank you both for the review. Merge it when ready @willingc! Thank you!

[willingc]

Thanks @rgbkrk. I will loop back to this late in the week.