fix(ci): add ruff.toml, format check, coverage, merge tests.yml

.github/workflows/ci.yml

@@ -7,67 +7,58 @@ on:
     branches: [main, dev]
 
 jobs:
-  lint-and-test:
+  lint:
     runs-on: ubuntu-latest
-
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
           cache: 'pip'
 
+      - name: Install ruff
+        run: pip install ruff
+
+      - name: Check formatting
+        run: ruff format --check .
+
+      - name: Lint
+        run: ruff check . --output-format=github
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements-ci.txt
-        # Uses minimal CI requirements (no tensorflow/heavy packages)
 
-      - name: Run linter (ruff)
+      - name: Run tests
         run: |
-          ruff check . --select=E9,F63,F7,F82 --output-format=github \
-            --exclude="Dockerfile.*" \
-            --exclude="linktest/" \
-            --exclude="measurements/" \
-            --exclude="0mq/" \
-            --exclude="ratc/"
-        # E9: Runtime errors (syntax errors, etc.)
-        # F63: Invalid print syntax
-        # F7: Syntax errors in type comments
-        # F82: Undefined names in __all__
-        # Excludes: Dockerfiles (not Python), linktest (symlinks),
-        # measurements/0mq/ratc (config-dependent experimental scripts)
-
-      - name: Run tests (pytest)
-        run: |
-          set +e
           pytest --tb=short -q \
+            --cov=concore_cli --cov=concore_base \
+            --cov-report=term-missing \
             --ignore=measurements/ \
             --ignore=0mq/ \
             --ignore=ratc/ \
             --ignore=linktest/
-          status=$?
-          set -e
-          # Allow success if no tests are collected (pytest exit code 5)
-          if [ "$status" -ne 0 ] && [ "$status" -ne 5 ]; then
-            exit "$status"
-          fi
-        # Fails on real test failures, passes on no tests collected
 
   docker-build:
     runs-on: ubuntu-latest
-    # Only run when Dockerfile.py or related files change
-    if: |
-      github.event_name == 'push' ||
-      (github.event_name == 'pull_request' && 
-       contains(github.event.pull_request.changed_files, 'Dockerfile'))
-
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
       - name: Check if Dockerfile.py changed
         uses: dorny/paths-filter@v3
@@ -80,7 +71,4 @@ jobs:
 
       - name: Validate Dockerfile build
         if: steps.filter.outputs.dockerfile == 'true'
-        run: |
-          docker build -f Dockerfile.py -t concore-py-test .
-        # Validates that Dockerfile.py can be built successfully
-        # Does not push the image
+        run: docker build -f Dockerfile.py -t concore-py-test .

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.12
+    hooks:
+      - id: ruff
+        args: [--output-format=full]
+      - id: ruff-format

concore_cli/__init__.py

@@ -2,4 +2,4 @@
 
 from .cli import cli
 
-__all__ = ['cli']
+__all__ = ["cli"]

concore_cli/cli.py

@@ -13,16 +13,18 @@
 from . import __version__
 
 console = Console()
-DEFAULT_EXEC_TYPE = 'windows' if os.name == 'nt' else 'posix'
+DEFAULT_EXEC_TYPE = "windows" if os.name == "nt" else "posix"
+
 
 @click.group()
-@click.version_option(version=__version__, prog_name='concore')
+@click.version_option(version=__version__, prog_name="concore")
 def cli():
     pass
 
+
 @cli.command()
-@click.argument('name', required=True)
-@click.option('--template', default='basic', help='Template type to use')
+@click.argument("name", required=True)
+@click.option("--template", default="basic", help="Template type to use")
 def init(name, template):
     """Create a new concore project"""
     try:
@@ -31,12 +33,21 @@ def init(name, template):
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
-@click.argument('workflow_file', type=click.Path(exists=True))
-@click.option('--source', '-s', default='src', help='Source directory')
-@click.option('--output', '-o', default='out', help='Output directory')
-@click.option('--type', '-t', default=DEFAULT_EXEC_TYPE, type=click.Choice(['windows', 'posix', 'docker']), help='Execution type')
-@click.option('--auto-build', is_flag=True, help='Automatically run build after generation')
+@click.argument("workflow_file", type=click.Path(exists=True))
+@click.option("--source", "-s", default="src", help="Source directory")
+@click.option("--output", "-o", default="out", help="Output directory")
+@click.option(
+    "--type",
+    "-t",
+    default=DEFAULT_EXEC_TYPE,
+    type=click.Choice(["windows", "posix", "docker"]),
+    help="Execution type",
+)
+@click.option(
+    "--auto-build", is_flag=True, help="Automatically run build after generation"
+)
 def run(workflow_file, source, output, type, auto_build):
     """Run a concore workflow"""
     try:
@@ -45,9 +56,10 @@ def run(workflow_file, source, output, type, auto_build):
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
-@click.argument('workflow_file', type=click.Path(exists=True))
-@click.option('--source', '-s', default='src', help='Source directory')
+@click.argument("workflow_file", type=click.Path(exists=True))
+@click.option("--source", "-s", default="src", help="Source directory")
 def validate(workflow_file, source):
     """Validate a workflow file"""
     try:
@@ -58,10 +70,11 @@ def validate(workflow_file, source):
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
-@click.argument('workflow_file', type=click.Path(exists=True))
-@click.option('--source', '-s', default='src', help='Source directory')
-@click.option('--json', 'output_json', is_flag=True, help='Output in JSON format')
+@click.argument("workflow_file", type=click.Path(exists=True))
+@click.option("--source", "-s", default="src", help="Source directory")
+@click.option("--json", "output_json", is_flag=True, help="Output in JSON format")
 def inspect(workflow_file, source, output_json):
     """Inspect a workflow file and show its structure"""
     try:
@@ -70,6 +83,7 @@ def inspect(workflow_file, source, output_json):
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
 def status():
     """Show running concore processes"""
@@ -79,8 +93,9 @@ def status():
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
-@click.confirmation_option(prompt='Stop all running concore processes?')
+@click.confirmation_option(prompt="Stop all running concore processes?")
 def stop():
     """Stop all running concore processes"""
     try:
@@ -89,10 +104,11 @@ def stop():
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
+
 @cli.command()
-@click.argument('study_dir', type=click.Path(exists=True))
-@click.option('--interval', '-n', default=2.0, help='Refresh interval in seconds')
-@click.option('--once', is_flag=True, help='Print a single snapshot and exit')
+@click.argument("study_dir", type=click.Path(exists=True))
+@click.option("--interval", "-n", default=2.0, help="Refresh interval in seconds")
+@click.option("--once", is_flag=True, help="Print a single snapshot and exit")
 def watch(study_dir, interval, once):
     """Watch a running simulation study for live monitoring"""
     try:
@@ -101,5 +117,6 @@ def watch(study_dir, interval, once):
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     cli()

concore_cli/commands/__init__.py

@@ -5,4 +5,11 @@
 from .stop import stop_all
 from .watch import watch_study
 
-__all__ = ['init_project', 'run_workflow', 'validate_workflow', 'show_status', 'stop_all', 'watch_study']
+__all__ = [
+    "init_project",
+    "run_workflow",
+    "validate_workflow",
+    "show_status",
+    "stop_all",
+    "watch_study",
+]

concore_cli/commands/init.py

@@ -1,9 +1,7 @@
-import os
-import shutil
 from pathlib import Path
 from rich.panel import Panel
 
-SAMPLE_GRAPHML = '''<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+SAMPLE_GRAPHML = """<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://www.yworks.com/xml/schema/graphml/1.1/ygraphml.xsd" xmlns:y="http://www.yworks.com/xml/graphml">
   <key for="node" id="d6" yfiles.type="nodegraphics"/>
   <key for="edge" id="d10" yfiles.type="edgegraphics"/>
@@ -21,9 +19,9 @@
     </node>
   </graph>
 </graphml>
-'''
+"""
 
-SAMPLE_PYTHON = '''import concore
+SAMPLE_PYTHON = """import concore
 
 concore.default_maxtime(100)
 concore.delay = 0.02
@@ -36,9 +34,9 @@
         val = concore.read(1,"data",init_simtime_val)
     result = [v * 2 for v in val]
     concore.write(1,"result",result,delta=0)
-'''
+"""
 
-README_TEMPLATE = '''# {project_name}
+README_TEMPLATE = """# {project_name}
 
 A concore workflow project.
 
@@ -63,38 +61,41 @@
 - Add Python/C++/MATLAB scripts to `src/`
 - Use `concore validate workflow.graphml` to check your workflow
 - Use `concore status` to monitor running processes
-'''
+"""
+
 
 def init_project(name, template, console):
     project_path = Path(name)
-    
+
     if project_path.exists():
         raise FileExistsError(f"Directory '{name}' already exists")
-    
+
     console.print(f"[cyan]Creating project:[/cyan] {name}")
-    
+
     project_path.mkdir()
-    (project_path / 'src').mkdir()
-    
-    workflow_file = project_path / 'workflow.graphml'
-    with open(workflow_file, 'w') as f:
+    (project_path / "src").mkdir()
+
+    workflow_file = project_path / "workflow.graphml"
+    with open(workflow_file, "w") as f:
         f.write(SAMPLE_GRAPHML)
-    
-    sample_script = project_path / 'src' / 'script.py'
-    with open(sample_script, 'w') as f:
+
+    sample_script = project_path / "src" / "script.py"
+    with open(sample_script, "w") as f:
         f.write(SAMPLE_PYTHON)
-    
-    readme_file = project_path / 'README.md'
-    with open(readme_file, 'w') as f:
+
+    readme_file = project_path / "README.md"
+    with open(readme_file, "w") as f:
         f.write(README_TEMPLATE.format(project_name=name))
-    
+
     console.print()
-    console.print(Panel.fit(
-        f"[green]✓[/green] Project created successfully!\n\n"
-        f"Next steps:\n"
-        f"  cd {name}\n"
-        f"  concore validate workflow.graphml\n"
-        f"  concore run workflow.graphml",
-        title="Success",
-        border_style="green"
-    ))
+    console.print(
+        Panel.fit(
+            f"[green]✓[/green] Project created successfully!\n\n"
+            f"Next steps:\n"
+            f"  cd {name}\n"
+            f"  concore validate workflow.graphml\n"
+            f"  concore run workflow.graphml",
+            title="Success",
+            border_style="green",
+        )
+    )