Poetry setup

.github/workflows/publish_to_pypi.yml

@@ -21,23 +21,24 @@ permissions:
 
 # Make sure CI fails on all warnings, including Clippy lints
 env:
-  RUSTFLAGS: "-Dwarnings"
+  RUSTFLAGS: "-Dwarnings -Ctarget-cpu=native"
+  POETRY_VERSION: 1.8.4
 
 jobs:
   linux_tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         target: [x86_64]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-
           python-version: ${{ matrix.python-version }}
-
-
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
       - name: Set up Rust
         run: rustup show
       - uses: mozilla-actions/sccache-action@v0.0.3
@@ -50,12 +51,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        target: [x86_64, x86]
+        target: [x86_64]
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -80,9 +84,10 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-
           architecture: ${{ matrix.target }}
-
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -108,12 +113,13 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-
           target: ${{ matrix.target }}
-
           args: --release --out dist --find-interpreter
           sccache: 'true'
       - name: Upload wheels
@@ -128,6 +134,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:

.pre-commit-config.yaml

@@ -13,6 +13,7 @@ repos:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --show-fixes, --exit-non-zero-on-fix]
+      - id: ruff-format
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "polars_bio"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 
 [lib]
@@ -11,7 +11,7 @@ crate-type= ["cdylib"]
 datafusion-python = { git = "https://github.com/apache/datafusion-python.git", rev = "5c834934dec89bd96ff70df3b278e9d6fe78f7ec"}
 pyo3 = { version = "0.22.4", features = ["extension-module", "abi3-py38", "experimental-async"] }
 pyo3-log = "0.11.0"
-sequila-core = { git = "https://github.com/biodatageeks/sequila-native.git", rev = "4a0b7383eed84cadaa1b524f401dd419b1c0ce8d" }
+sequila-core = { git = "https://github.com/biodatageeks/sequila-native.git", rev = "1a2eeb42d26753cd68ce5d981f6471655037abab" }
 datafusion = { version = "43.0.0"}
 arrow = "53.3.0"
 tokio = "1.42.0"

Makefile

@@ -3,7 +3,8 @@ SHELL=/bin/bash
 
 venv:  ## Set up virtual environment
 	python3 -m venv .venv
-	.venv/bin/pip install -r requirements.txt
+	poetry lock --no-update
+	poetry install
 
 install: venv
 	unset CONDA_PREFIX && \
@@ -17,7 +18,6 @@ pre-commit: venv
 	cargo fmt --all && cargo clippy --all-features
 	.venv/bin/python -m ruff check polars_bio tests --fix --exit-non-zero-on-fix
 	.venv/bin/python -m ruff format polars_bio tests
-	.venv/bin/python -m mypy polars_bio tests
 
 test: venv
 	.venv/bin/python -m pytest tests