feat: Boilerplate and overlap implementation (#1)

* Initial benchmark

* Build with datafusion-python ans sequila-native

* Overlaps boilerplate

* Basic overlap

* Dataframe input

* Overlap refactor

* Adding Dataframe tests

* Polars tests

* BioSessionContext draft

* Parameters changes

* Adding native tests

* Bioframe tests

* Adding pre-commit

* Adding pre-commit

* Adding isort

* Adding black

.github/workflows/publish_to_pypi.yml

@@ -1,157 +1,159 @@
-name: CI
-
-on:
-  push:
-    branches:
-      - main
-      - master
-    tags:
-      - '*'
-  pull_request:
-  workflow_dispatch:
-
-concurrency:
-
-  group: ${{ github.workflow }}-${{ github.ref }}
-
-  cancel-in-progress: true
-
-permissions:
-  contents: read
-
-# Make sure CI fails on all warnings, including Clippy lints
-env:
-  RUSTFLAGS: "-Dwarnings"
-
-jobs:
-  linux_tests:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        target: [x86_64]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-
-          python-version: ${{ matrix.python-version }}
-
-
-      - name: Set up Rust
-        run: rustup show
-      - uses: mozilla-actions/[email protected]
-      - run: make venv
-      - run: make pre-commit
-      - run: make install
-      - run: make test
-
-  linux:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        target: [x86_64, x86]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-
-          target: ${{ matrix.target }}
-
-          args: --release --out dist --find-interpreter
-          sccache: 'true'
-          manylinux: auto
-      - name: Upload wheels
-        uses: actions/upload-artifact@v3
-        with:
-          name: wheels
-          path: dist
-
-  windows:
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        target: [x64]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-
-          architecture: ${{ matrix.target }}
-
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-
-          target: ${{ matrix.target }}
-
-          args: --release --out dist --find-interpreter
-          sccache: 'true'
-      - name: Upload wheels
-        uses: actions/upload-artifact@v3
-        with:
-          name: wheels
-          path: dist
-
-  macos:
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        target: [x86_64, aarch64]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-
-          target: ${{ matrix.target }}
-
-          args: --release --out dist --find-interpreter
-          sccache: 'true'
-      - name: Upload wheels
-        uses: actions/upload-artifact@v3
-        with:
-          name: wheels
-          path: dist
-
-  sdist:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Build sdist
-        uses: PyO3/maturin-action@v1
-        with:
-          command: sdist
-          args: --out dist
-      - name: Upload sdist
-        uses: actions/upload-artifact@v3
-        with:
-          name: wheels
-          path: dist
-
-  release:
-    name: Release
-    if: "startsWith(github.ref, 'refs/tags/')"
-    needs: [linux, windows, macos, sdist]
-    runs-on: ubuntu-latest
-    environment: pypi
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-    steps:
-      - uses: actions/download-artifact@v3
-        with:
-          name: wheels
-      - name: Publish to PyPI
-        uses: PyO3/maturin-action@v1
-        with:
-          command: upload
-          args: --non-interactive --skip-existing *
-
+#name: CI
+#
+#on:
+#  push:
+#    branches:
+#      - main
+#      - master
+#    tags:
+#      - '*'
+#  pull_request:
+#  workflow_dispatch:
+#
+#concurrency:
+#
+#  group: ${{ github.workflow }}-${{ github.ref }}
+#
+#  cancel-in-progress: true
+#
+#permissions:
+#  contents: read
+#
+## Make sure CI fails on all warnings, including Clippy lints
+#env:
+#  RUSTFLAGS: "-Dwarnings"
+#
+#jobs:
+#  linux_tests:
+#    runs-on: ubuntu-latest
+#    strategy:
+#      matrix:
+#        target: [x86_64]
+#        python-version: ["3.8", "3.9", "3.10", "3.11"]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - uses: actions/setup-python@v4
+#        with:
+#
+#          python-version: ${{ matrix.python-version }}
+#
+#
+#      - name: Set up Rust
+#        run: rustup show
+#      - uses: mozilla-actions/[email protected]
+#      - run: make venv
+#      - run: make pre-commit
+#      - run: make install
+#      - run: make test
+#
+#  linux:
+#    runs-on: ubuntu-latest
+#    strategy:
+#      matrix:
+#        target: [x86_64, x86]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - uses: actions/setup-python@v4
+#        with:
+#          python-version: '3.10'
+#      - name: Build wheels
+#        uses: PyO3/maturin-action@v1
+#        with:
+#          target: ${{ matrix.target }}
+#
+#          args: --release --out dist --find-interpreter
+#          sccache: 'true'
+#          manylinux: auto
+#
+#      - name: Upload wheels
+#        uses: actions/upload-artifact@v3
+#        with:
+#          name: wheels
+#          path: dist
+#  windows:
+#    runs-on: windows-latest
+#    strategy:
+#      matrix:
+#        target: [x64]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - uses: actions/setup-python@v4
+#        with:
+#          python-version: '3.10'
+#
+#          architecture: ${{ matrix.target }}
+#
+#      - name: Build wheels
+#        uses: PyO3/maturin-action@v1
+#        with:
+#
+#          target: ${{ matrix.target }}
+#
+#          args: --release --out dist --find-interpreter
+#          sccache: 'true'
+#
+#      - name: Upload wheels
+#        uses: actions/upload-artifact@v3
+#        with:
+#          name: wheels
+#          path: dist
+#
+#  macos:
+#    runs-on: macos-latest
+#    strategy:
+#      matrix:
+#        target: [x86_64, aarch64]
+#    steps:
+#      - uses: actions/checkout@v3
+#      - uses: actions/setup-python@v4
+#        with:
+#          python-version: '3.10'
+#      - name: Build wheels
+#        uses: PyO3/maturin-action@v1
+#        with:
+#
+#          target: ${{ matrix.target }}
+#
+#          args: --release --out dist --find-interpreter
+#          sccache: 'true'
+#      - name: Upload wheels
+#        uses: actions/upload-artifact@v3
+#        with:
+#          name: wheels
+#          path: dist
+#    env:
+#      RUSTFLAGS: "-Clink-arg=-undefined -Clink-arg=dynamic_lookup"
+#
+#  sdist:
+#    runs-on: ubuntu-latest
+#    steps:
+#      - uses: actions/checkout@v3
+#      - name: Build sdist
+#        uses: PyO3/maturin-action@v1
+#        with:
+#          command: sdist
+#          args: --out dist
+#      - name: Upload sdist
+#        uses: actions/upload-artifact@v3
+#        with:
+#          name: wheels
+#          path: dist
+#
+#  release:
+#    name: Release
+#    if: "startsWith(github.ref, 'refs/tags/')"
+#    needs: [linux, windows, macos, sdist]
+#    runs-on: ubuntu-latest
+#    environment: pypi
+#    permissions:
+#      id-token: write  # IMPORTANT: mandatory for trusted publishing
+#    steps:
+#      - uses: actions/download-artifact@v3
+#        with:
+#          name: wheels
+#      - name: Publish to PyPI
+#        uses: PyO3/maturin-action@v1
+#        with:
+#          command: upload
+#          args: --non-interactive --skip-existing *
+#

.gitignore

@@ -7,4 +7,6 @@ venv
 *.dll
 *.pyd
 
-.idea
+.idea
+sandbox/
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+      - id: check-case-conflict
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.3
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --show-fixes, --exit-non-zero-on-fix]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: [--profile, black]
+  - repo: https://github.com/ambv/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        language_version: python3.12