Merge develop into main

.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+name: CI
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+env:
+  CARGO_TERM_COLOR: always
+  RUST_BACKTRACE: 1
+
+jobs:
+  check:
+    name: Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo check --all-targets
+
+  test:
+    name: Test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo test --all-targets
+
+  fmt:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rustfmt
+      - run: cargo fmt --all -- --check
+
+  clippy:
+    name: Clippy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+        with:
+          components: clippy
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo clippy --all-targets -- -D warnings
+
+  docs:
+    name: Docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo doc --no-deps --all-features
+        env:
+          RUSTDOCFLAGS: -D warnings

.github/workflows/docs.yml

@@ -0,0 +1,29 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main, develop]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: pip install mkdocs-material mkdocstrings[python]
+
+      - name: Deploy to gh-pages
+        run: mkdocs gh-deploy --force

.github/workflows/release.yml

@@ -0,0 +1,75 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    name: Build ${{ matrix.target }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            target: x86_64-unknown-linux-gnu
+            artifact: charmer-linux-x86_64
+          - os: ubuntu-latest
+            target: x86_64-unknown-linux-musl
+            artifact: charmer-linux-x86_64-musl
+          - os: macos-latest
+            target: x86_64-apple-darwin
+            artifact: charmer-macos-x86_64
+          - os: macos-latest
+            target: aarch64-apple-darwin
+            artifact: charmer-macos-aarch64
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: dtolnay/rust-toolchain@stable
+        with:
+          targets: ${{ matrix.target }}
+
+      - name: Install musl tools
+        if: matrix.target == 'x86_64-unknown-linux-musl'
+        run: sudo apt-get install -y musl-tools
+
+      - uses: Swatinem/rust-cache@v2
+
+      - name: Build
+        run: cargo build --release --target ${{ matrix.target }}
+
+      - name: Package
+        run: |
+          cd target/${{ matrix.target }}/release
+          tar czf ../../../${{ matrix.artifact }}.tar.gz charmer
+          cd ../../..
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.artifact }}
+          path: ${{ matrix.artifact }}.tar.gz
+
+  release:
+    name: Create Release
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+
+      - name: Create release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: artifacts/**/*.tar.gz
+          generate_release_notes: true

.gitignore

@@ -3,3 +3,31 @@ Cargo.lock
 .DS_Store
 *.swp
 *.swo
+
+# Test pipeline outputs
+tests/pipelines/*/results/
+tests/pipelines/*/.snakemake/
+tests/pipelines/*/dag.png
+
+# Pixi
+.pixi/
+pixi.lock
+
+# Documentation
+site/
+
+# VHS output
+docs/assets/*.gif
+docs/assets/*.webm
+docs/assets/*.mp4
+
+# IDE
+.idea/
+.vscode/
+*.code-workspace
+
+# Coverage
+*.profraw
+*.profdata
+coverage/
+lcov.info

Cargo.toml

@@ -4,20 +4,21 @@ members = ["crates/*"]
 
 [workspace.package]
 version = "0.1.0"
-edition = "2024"
+edition = "2021"
+rust-version = "1.85"
 license = "MIT"
 authors = ["Jay Hesselberth"]
 
 [workspace.dependencies]
 # TUI
-ratatui = "0.29"
-crossterm = "0.28"
+ratatui = "0.30.0-beta.0"
+crossterm = "0.29"
 
 # Async
-tokio = { version = "1.35", features = ["full"] }
+tokio = { version = "1.43", features = ["full"] }
 
 # File watching
-notify = "6.1"
+notify = "8.2"
 
 # Serialization
 serde = { version = "1.0", features = ["derive"] }
@@ -27,24 +28,29 @@ serde_json = "1.0"
 chrono = { version = "0.4", features = ["serde"] }
 
 # CLI
-clap = { version = "4.4", features = ["derive"] }
+clap = { version = "4.5", features = ["derive"] }
 
 # Paths
 camino = { version = "1.1", features = ["serde1"] }
 
 # Regex for parsing
-regex = "1.10"
+regex = "1.11"
 
 # Base64 for snakemake filenames
 base64 = "0.22"
 
 # Error handling
-thiserror = "1.0"
-miette = { version = "7.0", features = ["fancy"] }
+thiserror = "2.0"
+miette = { version = "7.4", features = ["fancy"] }
+
+# Clipboard
+arboard = "3"
 
 # Internal crates
 charmer-core = { path = "crates/charmer-core" }
+charmer-parsers = { path = "crates/charmer-parsers" }
 charmer-slurm = { path = "crates/charmer-slurm" }
+charmer-lsf = { path = "crates/charmer-lsf" }
 charmer-state = { path = "crates/charmer-state" }
 charmer-monitor = { path = "crates/charmer-monitor" }
 charmer-cli = { path = "crates/charmer-cli" }