Migrate build system from setuptools to maturin

[dmartmillan]

This pull request corresponds to the Migrate build system from setuptools to maturin, be able to run Rust in Python scripts. Relates to #62 issue.

Most of the tasks for this PR were already solved on the previous one (#104)

On this PR, we:

• Modified MANIFEST.IN to include Cargo.toml
• Verified that uv tool run maturin develop --release works fine. (we should take into account for a future release)
• Added tests/test_core_import.py and removed test_rust.py
• Added make release and make test for a future use.

Closes #62

[Copilot]

Pull request overview

This PR migrates OpenVariant’s packaging/build pipeline from a pure-Python backend to maturin + PyO3, introducing a Rust-backed extension module (openvariant._core) and aligning tests/CI/docs with the new build and plugin conventions.

Changes:

• Switch pyproject.toml build backend to maturin and add Rust crate scaffolding (Cargo.toml, src/) for openvariant._core.
• Update parsing/annotation delimiter handling (escape decoding + optional autodetection) and extend mapping builder to support absolute fileMapping paths.
• Update plugin naming to PascalCase, add/adjust tests, and refresh multiple documentation examples/notebooks.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_task/test_plugin.py	Adds a regression test for PascalCase plugin/context class names in generated plugin templates.
tests/test_core_import.py	Adds a smoke test asserting openvariant._core is importable.
tests/test_annotation/test_builder.py	Adds coverage for absolute-path fileMapping in mapping annotations.
tests/test_annotation/test_annotation.py	Updates delimiter expectations for the annotation fixture.
tests/data/annotation/invalid_delimiter.yaml	Removes an invalid-delimiter fixture (previously used for delimiter validation behavior).
tests/data/annotation/annotation.yaml	Changes the test annotation delimiter to a tab escape (\\t).
src/lib.rs	Defines the PyO3 module entrypoint for _core and a sample hello function.
src/error.rs	Introduces a Rust error enum (OVError) for the new core crate.
pyproject.toml	Switches build backend to maturin, configures module name, and adds a docs entrypoint + pytest config.
openvariant/variant/variant.py	Changes base parsing to skip comments pre-split and to use delimiter autodetection / direct delimiter splitting.
openvariant/tasks/plugin.py	Adds PascalCase conversion for generated plugin class names.
openvariant/plugins/get_AF/get_AF.py	Renames plugin/context classes to PascalCase.
openvariant/plugins/get_AF/init.py	Updates exports to match renamed classes.
openvariant/plugins/alteration_type/alteration_type.py	Renames plugin/context classes to PascalCase.
openvariant/plugins/alteration_type/init.py	Updates exports to match renamed classes.
openvariant/plugins/init.py	Updates public exports (__all__) to match renamed plugin/context classes.
openvariant/annotation/config_annotation.py	Removes the delimiter enum/constants and leaves format enums only.
openvariant/annotation/builder.py	Supports absolute fileMapping paths and improves mapping-file resolution.
openvariant/annotation/annotation.py	Changes delimiter validation/handling to allow escape decoding and None delimiter for autodetection.
openvariant/_docs.py	Adds a small helper for building Sphinx docs via make html.
openvariant/init.py	Bumps package version to 2.0.0.
MANIFEST.in	Includes Rust sources/Cargo manifest in sdist and adjusts included/excluded paths.
Makefile	Adds convenience targets for cargo build/test/lint/format using uv’s Python.
docs/examples/variant/save.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/variant/read.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/tasks/group_by.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/tasks/count.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/tasks/cat.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/plugin_system/get_length/get_length.py	Updates example plugin/context class names to PascalCase.
docs/examples/plugin_system/get_length/init.py	Updates example exports to match renamed classes.
docs/examples/plugin_system/add_date/add_date.py	Updates example plugin/context class names to PascalCase.
docs/examples/plugin_system/add_date/init.py	Updates example exports to match renamed classes.
docs/examples/plugin_examples.rst	Updates docs to match PascalCase plugin/context class names.
docs/examples/find_files/find_files_with_file_path.ipynb	Reformats notebook JSON/metadata and updates narrative cells.
docs/examples/find_files/find_files_with_directory_path.ipynb	Reformats notebook JSON/metadata and updates recorded Python version.
docs/examples/cli/main_cli.ipynb	Updates CLI examples and notebook structure/metadata.
docs/examples/cli/introduction_cli.ipynb	Updates CLI help examples and notebook structure/metadata.
CONTRIBUTING.md	Adds Rust toolchain/maturin developer setup instructions.
Cargo.toml	Adds Rust crate metadata for the PyO3 extension (cdylib) and dependencies.
Cargo.lock	Locks Rust dependencies for the new crate.
.gitignore	Ignores Cargo build artifacts (target/, etc.).
.github/workflows/openvariant_tester.yml	Installs Rust toolchain in CI and adjusts uv sync for linting.

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[FedericaBrando]

Great David!

I've run uv build (below the output), and then install the tar.gz in a clean conda environment. I tested the

>>> import openvariant._core as _core
...
... _core.hello()
...
Hello, OpenVariant!

and worked, so, good to go!

╰╴❯ uv build
Building source distribution...
Running `maturin pep517 write-sdist --sdist-directory /home/fbrando/Desktop/bgtools/openvariant/dist`
🍹 Building a mixed python/rust project
🔗 Found pyo3 bindings
📡 Using build options features from pyproject.toml
From `cargo package --list --allow-dirty --manifest-path /home/fbrando/Desktop/bgtools/openvariant/Cargo.toml`:
warning: manifest has no description, license, license-file, documentation, homepage or repository
  |
  = note: see https://doc.rust-lang.org/cargo/reference/manifest.html#package-metadata for more info
📦 Built source distribution to /home/fbrando/Desktop/bgtools/openvariant/dist/open_variant-2.0.0.tar.gz
open_variant-2.0.0.tar.gz
Building wheel from source distribution...
Running `maturin pep517 build-wheel -i /home/fbrando/.cache/uv/builds-v0/.tmpuvOdC7/bin/python --compatibility off`
🍹 Building a mixed python/rust project
🐍 Found CPython 3.13 at /home/fbrando/.cache/uv/builds-v0/.tmpuvOdC7/bin/python
🔗 Found pyo3 bindings
📡 Using build options features from pyproject.toml
   Compiling target-lexicon v0.13.5
   Compiling proc-macro2 v1.0.106
   Compiling unicode-ident v1.0.24
   Compiling quote v1.0.45
   Compiling libc v0.2.186
   Compiling heck v0.5.0
   Compiling thiserror v2.0.18
   Compiling once_cell v1.21.4
   Compiling pyo3-build-config v0.28.3
   Compiling syn v2.0.117
   Compiling pyo3-ffi v0.28.3
   Compiling pyo3-macros-backend v0.28.3
   Compiling pyo3 v0.28.3
   Compiling thiserror-impl v2.0.18
   Compiling pyo3-macros v0.28.3
   Compiling openvariant-core v2.0.0 (/home/fbrando/.cache/uv/sdists-v9/.tmpiUVHkP/open_variant-2.0.0)
    Finished `release` profile [optimized] target(s) in 10.15s
📦 Built wheel for CPython 3.13 to /home/fbrando/.cache/uv/sdists-v9/.tmpiUVHkP/open_variant-2.0.0/target/wheels/open_variant-2.0.0-cp313-cp313-linux_x86_64.whl
/home/fbrando/.cache/uv/sdists-v9/.tmpiUVHkP/open_variant-2.0.0/target/wheels/open_variant-2.0.0-cp313-cp313-linux_x86_64.whl
Successfully built dist/open_variant-2.0.0.tar.gz
Successfully built dist/open_variant-2.0.0-cp313-cp313-linux_x86_64.whl

The build works, there is a warning from cargo about the alck of metadata in the manifest that eventually we should address.