nf-meta 0.2.4__tar.gz → 0.3.0.dev0__tar.gz

{nf_meta-0.2.4/src/nf_meta.egg-info → nf_meta-0.3.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nf-meta
-Version: 0.2.4
+Version: 0.3.0.dev0
 Summary: nf-meta is a cli tool for building, validating and running meta-pipelines based on the Nextflow workflow language
 Author-email: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
 License-Expression: Apache-2.0
@@ -85,7 +85,7 @@ This project features a small editor which intends to ease the creation and upda
 of these config files, by visualizing the config as a graph and 
 offering user-firendly form for entering and validating values.
 
-![editor](assets/nf-meta-screenshot.png)
+![editor](https://raw.githubusercontent.com/bmds-tue/nf-meta/main/assets/nf-meta-screenshot.png)
 
 
 ## Metapipeline Runners

{nf_meta-0.2.4 → nf_meta-0.3.0.dev0}/README.md

@@ -61,7 +61,7 @@ This project features a small editor which intends to ease the creation and upda
 of these config files, by visualizing the config as a graph and 
 offering user-firendly form for entering and validating values.
 
-![editor](assets/nf-meta-screenshot.png)
+![editor](https://raw.githubusercontent.com/bmds-tue/nf-meta/main/assets/nf-meta-screenshot.png)
 
 
 ## Metapipeline Runners

{nf_meta-0.2.4 → nf_meta-0.3.0.dev0}/pyproject.toml

@@ -13,7 +13,7 @@ namespaces = false
 
 [project]
 name = "nf-meta"
-version = "0.2.4"
+version = "0.3.0-dev"
 description = "nf-meta is a cli tool for building, validating and running meta-pipelines based on the Nextflow workflow language"
 readme = "README.md"
 authors = [
@@ -47,6 +47,7 @@ dev = [
     "twine>=6.2.0",
     "pytest>=9.0.3",
     "pytest-mock>=3.15.1",
+    "mypy>=2.1.0",
     "types-networkx>=3.6.1.20260408",
     "types-pyyaml>=6.0.12.20260408",
     "types-requests>=2.33.0.20260503",
@@ -54,3 +55,11 @@ dev = [
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.mypy]
+python_version = "3.12"
+mypy_path = "src"
+
+[[tool.mypy.overrides]]
+module = ["uvicorn", "uvicorn.*"]
+ignore_missing_imports = true

nf_meta-0.3.0.dev0/src/nf_meta/__main__.py

@@ -0,0 +1,135 @@
+import click
+from functools import wraps
+from nf_meta.core.errors import (
+    GraphValidationError,
+    ValidationError,
+    format_errors_for_cli,
+)
+from nf_meta.runner import (
+    run_metapipeline,
+    get_registered_runners,
+    RunOptions,
+    NfMetaRunnerError,
+)
+from nf_meta.core.graph import MetaworkflowGraph
+from nf_meta.core.session import start_session
+from nf_meta.editor import get_registered_editors, EditorOptions, run_editor
+
+
+@click.group()
+@click.version_option()
+def cli() -> None:
+    return
+
+
+@click.command("editor")
+@click.option("--verbose", "-v", is_flag=True, help="Enables verbose mode")
+@click.option(
+    "--editor",
+    "-e",
+    type=click.Choice(get_registered_editors()),
+    default="browser",
+    help="Editor backend to use",
+)
+@click.option("--host", help="Host to bind the editor server to")
+@click.option(
+    "--port",
+    type=int,
+    help="Port for the editor server (auto-assigned if omitted)",
+)
+@click.argument("config", required=False, type=click.Path())
+def edit_browser(config, verbose, editor, host, port):
+    try:
+        start_session(config)
+        opts = EditorOptions(editor_name=editor)
+        if host is not None:
+            opts.host = host
+        if port is not None:
+            opts.port = port
+        run_editor(opts)
+    except (GraphValidationError, ValidationError) as e:
+        click.echo(format_errors_for_cli(e))
+        raise SystemExit(1)
+    except FileNotFoundError as e:
+        click.echo(click.style(e, fg="red"))
+        raise SystemExit(1)
+
+
+@click.command("validate")
+@click.argument("config", type=click.Path())
+@click.option("--verbose", "-v", is_flag=True, help="Enables verbose mode")
+def validate_config(config, verbose):
+    try:
+        g = MetaworkflowGraph.from_file(config)
+        click.echo(click.style("✓ Config is valid", fg="green"))
+    except (GraphValidationError, ValidationError) as e:
+        click.echo(format_errors_for_cli(e))
+        raise SystemExit(1)
+    except FileNotFoundError as e:
+        click.echo(click.style(e, fg="red"))
+        raise SystemExit(1)
+
+
+@click.command("run")
+@click.argument("config", type=click.Path())
+@click.option("--verbose", "-v", is_flag=True, help="Enables verbose mode")
+@click.option(
+    "--runner",
+    "-r",
+    prompt=True,
+    type=click.Choice(get_registered_runners()),
+    default="python",
+)
+@click.option("--resume", is_flag=True, help="Resume a previous run")
+@click.option(
+    "--output-lines",
+    "-l",
+    default="25",
+    type=int,
+    help="Number of lines of workflow output to stream to output window (Only for Python Runner!)",
+)
+@click.option("--start", "-s", type=str, help="ID of workflow to start from")
+@click.option("--target", "-t", type=str, help="ID of workflow to run until")
+@click.option(
+    "--profile",
+    "-p",
+    type=str,
+    help="Nextflow profile to apply globally, taking precedent over config values.",
+)
+@click.option(
+    "--stub",
+    is_flag=True,
+    help="Run all workflows as stub runs (passes -stub to Nextflow)",
+)
+def run(config, verbose, runner, resume, output_lines, start, target, profile, stub):
+    try:
+        run_options = RunOptions(
+            runner_name=runner,
+            verbose=verbose,
+            output_lines=output_lines,
+            nf_profile=profile,
+            stub=stub,
+            resume=resume,
+            start=start,
+            target=target,
+        )
+        g = MetaworkflowGraph.from_file(config)
+        run_metapipeline(g, run_options)
+    except (GraphValidationError, ValidationError) as e:
+        click.echo(format_errors_for_cli(e))
+        raise SystemExit(1)
+    except NfMetaRunnerError as e:
+        click.echo(click.style(e.message, fg="red"))
+        raise SystemExit(1)
+    except FileNotFoundError as e:
+        click.echo(click.style(e, fg="red"))
+        raise SystemExit(1)
+
+
+cli.add_command(edit_browser)
+cli.add_command(validate_config)
+cli.add_command(run)
+
+
+if __name__ == "__main__":
+    cli()

nf_meta-0.3.0.dev0/src/nf_meta/core/cache.py

@@ -0,0 +1,39 @@
+import hashlib
+import json
+import logging
+import os
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+_ENV_VAR = "NF_META_CACHE_DIR"
+GLOBAL_CACHE_DIR: Path = Path(
+    os.environ.get(_ENV_VAR) or Path.home() / ".cache" / "nf-meta"
+)
+
+
+def schema_cache_path(url: str, version: str) -> Path:
+    key = hashlib.sha256(f"{url}@{version}".encode()).hexdigest()[:16]
+    return GLOBAL_CACHE_DIR / "schemas" / f"{key}.json"
+
+
+def read_schema_cache(url: str, version: str) -> dict | None:
+    path = schema_cache_path(url, version)
+    if not path.exists():
+        return None
+    try:
+        with open(path) as f:
+            return json.load(f)
+    except Exception as e:
+        logger.warning("Failed to read schema cache at %s: %s", path, e)
+        return None
+
+
+def write_schema_cache(url: str, version: str, schema: dict) -> None:
+    path = schema_cache_path(url, version)
+    try:
+        path.parent.mkdir(parents=True, exist_ok=True)
+        with open(path, "w") as f:
+            json.dump(schema, f)
+    except Exception as e:
+        logger.warning("Failed to write schema cache to %s: %s", path, e)

{nf_meta-0.2.4 → nf_meta-0.3.0.dev0}/src/nf_meta/core/errors.py

@@ -25,7 +25,7 @@ class WorkflowReferenceErrors(GraphValidationError):
 class SessionCommandError(Exception):
     @dataclass
     class FieldError:
-        workflow_id: str
+        workflow_id: Optional[str]
         field: str
         message: str
 

{nf_meta-0.2.4 → nf_meta-0.3.0.dev0}/src/nf_meta/core/events.py

@@ -94,7 +94,7 @@ class Command(Protocol):
 
 @dataclass(frozen=True)
 class Transaction:
-    commands: tuple[Command]
+    commands: tuple[Command, ...]
 
     def apply(self, graph: GraphEventHandler):
         # TODO: Handle errors?

{nf_meta-0.2.4 → nf_meta-0.3.0.dev0}/src/nf_meta/core/graph.py

@@ -7,9 +7,9 @@ import networkx as nx
 
 from .models import (
     MetaworkflowConfig,
-    Workflow,
     GlobalOptions,
     Transition,
+    Workflow,
     load_config,
     dump_config,
     CONFIG_VERSION_MAX,
@@ -167,6 +167,8 @@ class MetaworkflowGraph:
     def validate_param_references(self, wf: Workflow):
         errors = []
         for ref in wf.field_refs:
+            if ref.namespace != "params":
+                continue  # output references not yet validated
             referenced_wf = self.get_workflow_by_id(ref.target_wf_id)
             if not referenced_wf:
                 errors.append(