Dev

.github/workflows/ci.yml

@@ -0,0 +1,127 @@
+name: "CI"
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Run linter
+        run: |
+          pip install pylint==3.3.5
+          chmod +x lint.sh
+          bash lint.sh
+
+  test-rust:
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    needs: lint
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Free disk space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: false
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: test-env
+          python-version: "3.10"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+
+      - name: Install Rust toolchain
+        run: |
+          conda install -y rust=1.88.0
+
+      - name: Run Rust unit tests
+        run: |
+          cd exacto/
+          cargo test -- --nocapture
+
+  test-python:
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    needs: lint
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Free disk space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: false
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: test-env
+          python-version: "3.10"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+
+      - name: Install dependencies
+        run: |
+          conda install -y \
+            pip \
+            rust=1.88.0 \
+            pandas=2.2.3 \
+            polars=1.26.0 \
+            pyarrow=19.0.1 \
+            coveralls=4.0.1 \
+            pytest=8.3.5 \
+            pytest-cov=6.1.1
+          python -m pip install pysam==0.23.0
+          python -m pip install . --verbose
+
+      - name: Verify install
+        run: |
+          which python
+          which pip
+          python -c "import sys; print('sys.executable:', sys.executable)"
+          python -c "import pysam; print('pysam OK:', pysam.__file__)"
+          python -c "import exactolib; print('exactolib OK:', exactolib.__file__)"
+
+      - name: Run Python unit tests
+        run: |
+          chmod +x unittest.sh
+          bash unittest.sh

.gitignore

@@ -12,9 +12,12 @@ Exacto.egg-info/
 docs/.ipynb_checkpoints/
 target/
 docs/_site
-docs/.quarto
+docs/.quarto/
+docs/cli/*
+docs/pipelines/*
+!docs/cli/index.qmd
+!docs/pipelines/index.qmd
 Cargo.lock
 .nojekyll
 *.nextflow.log*
 **/.nextflow/
-

Cargo.toml

@@ -1,46 +1,47 @@
 [package]
 name = "exactolib"
-version = "0.4.5"
+version = "0.4.6"
 edition = "2021"
 
 [package.metadata.maturin]
 name = "exactolib.exactolibrs"
 
 [lib]
-name = "exactolib"
+name = "exactolibrs"
 crate-type = ["cdylib"]
 
 [dependencies]
 bstr = "1.9.0"
 chrono = "0.4"
 env_logger = "0.9"
-exacto = { path = "exacto/exacto", version = "0.4.5" }
+exacto = { path = "exacto/exacto", version = "0.4.6" }
 exitcode = "1.1.2"
 flate2 = "1.0.35"
 log = "0.4"
-noodles-bgzf = "0.34.0"
-noodles-fasta = "0.46.0"
+noodles-bgzf = "0.43.0"
+noodles-fasta = "0.56.0"
 noodles-fastq = "0.16.0"
 polars = { version = "0.45.0", features = ["csv", "ipc", "lazy", "parquet"] }
 pyo3 = { version = "0.22.0", features = ["extension-module"] }
 pyo3-polars = "0.19.0"
-serde = { version = "1.0", features = ["derive"] }
+rayon = "1.10.0"
+serde = { version = "1.0.210", features = ["derive", "rc"] }
 sysinfo = "0.32.0"
 tempfile = "3.6"
 
 [profile.dev]
 opt-level = 0
-debug = true
+debug = 1
 overflow-checks = true
 panic = 'unwind'
 incremental = true
 codegen-units = 256
 
 [profile.release]
-opt-level = 0
-debug = false
-lto = true
+opt-level = 3
+debug = 0
+lto = "thin"
 overflow-checks = false
 panic = 'unwind'
-incremental = true
-codegen-units = 1
+incremental = false
+codegen-units = 16