ENH: Define all dependencies in pyproject.toml

[philippesamuel]

• Add dependency groups defined in requirements/*.in to pyproject.toml
• Add uv.lock for better reproducibility

[Lucas-C]

We should not duplicate dependency information in both this file and the requirements/ directory.

I'm OK to make the switch from requirements/ to [dependency-groups], but then:

• the requirements/ directory should be removed
• .github/workflows/github-ci.yaml should be updated to use [dependency-groups] and not requirements/
• .readthedocs.yaml should be updated to use [dependency-groups] and not requirements/
• Makefile should be updated to use [dependency-groups] and not requirements/
• docs/dev/intro.md & docs/dev/testing.md should be updated to use [dependency-groups] and not requirements/

Either we perform all those changes at once in this PR, or else the changes related to [dependency-groups] & uv.lock should be dropped

[philippesamuel]

Hi @Lucas-C, thank you for your review. In my opinion, it would be a good idea to switch from requirements/ to [dependency-groups], since pip 25.1 started supporting [dependency-groups] in pyproject.toml. This would provide a seamless experience for developers using both pip and uv.

[philippesamuel]

Hi @Lucas-C. I'm tracking down references to requirements/ and I found some in the Makefile. I'm not entirely sure how to deal with them:

pdfly/Makefile

Lines 1 to 5 in 05b4fee

	maint:
	pre-commit autoupdate
	pip-compile -U requirements/ci.in
	pip-compile -U requirements/dev.in
	pip-compile -U requirements/docs.in

Some options:

1. simply remove the pip-compile commands:

maint:
	pre-commit autoupdate

2. add references to pyproject.toml:

maint:
	pre-commit autoupdate
	pip-compile --extra=ci pyproject.toml
	pip-compile --extra=dev pyproject.toml  
	pip-compile --extra=docs pyproject.toml

3. use uv:

maint:
	pre-commit autoupdate
	uv lock

Which one aligns the best with the project?

[philippesamuel]

I think I'm getting ahead of myself. Here I'm dealing with possibly using uv for this project, instead of solving the issue with the python version. I'll update the PR and open another one to solve only #130.

[philippesamuel]

I created another, more concise PR here: #133

[Lucas-C]

Sorry for the delay in answering.

I merged your other PR, thank you.

Regarding those pip-compile commands, I think could get rid of them in favour of [dependency-groups] in pyproject.toml