for more information, see https://pre-commit.ci

for more information, see https://pre-commit.ci

for more information, see https://pre-commit.ci

This PR:

- fixes many ruff linter errors, removing unused imports and variables
- disables ruff formatting and linting for ipynb files

I verified that all tests pass on a cloud VM.

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.2 →
v0.5.4](astral-sh/ruff-pre-commit@v0.5.2...v0.5.4)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sam Ritchie <[email protected]>

This PR moves all code into a `src` directory, instead of the current
flat package structure. This is a prerequisite for the reproducible
build that @eightysteele is working on, and is a good change anyway for
a project destined to become a library.

This PR ports setup.py to pyproject.toml; this is the modern,
recommended way to configure python projects, and gives us a way to add
proper settings to things like linting, type-checking etc that match the
other projects at probcomp.

I've checked that the tests all run to the same failure as on main, the
scripts are all installed correctly, the versioning works well etc.

This PR:

- Upgrades b3d to https://github.com/probcomp/genjax/releases/tag/v0.5.0
- escapes math backslashes in python strings - these were causing
"unsupported literal" exceptions on import

GenJAX 0.5.0 doesn't break anything that b3d uses, and includes some
nice-to-have type upgrades that will make development a bit more
pleasant.

This PR:

- turns on the ruff configuration that we're using for genjax
- adds it to the pre-commit hooks
- auto-fixes most errors (unsorted imports, unused local variables etc)
- manually fixes the last few

@sritchie @nishadgothoskar after this change, run_tests.sh passes on my
machine.

This PR turns on the linter; we can't merge until we address the final
linter bugs.

- `ruff` is enabled as a GitHub Action, so that we see errors in the PRs
in github format
- `ruff` locally is added (with the same version) to
`.pre-commit-config.yml`

This PR:

- moves the body of the script into a function I can call from elsewhere
- lets the user supply an output path

@nishadgothoskar , my guess about what is going on is that you have an
empty `b3d` folder. Can you give this a try and let me know?

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.4 →
v0.5.5](astral-sh/ruff-pre-commit@v0.5.4...v0.5.5)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sam Ritchie <[email protected]>

… likelihood_experiments

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