scout-rig 0.2.2 → 0.2.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.vimproject

@@ -38,9 +38,7 @@ scout-rig=/$PWD filter="*" {
  test=test{
   test_helper.rb
  }
- python=python{
-  task=task{
-  }
+ python=python filter="*.py"{
   test.py
   scout=scout{
    __init__.py

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.5

data/lib/scout/workflow/python.rb

@@ -22,7 +22,10 @@ module PythonWorkflow
                    m
                  end
 
-    path = Scout.python.task
+    Kernel.const_set workflow_name, workflow
+
+    path = Scout.python.task if path.nil?
+
     workflow.python_task_dir = path
     path.glob_names("*.py").each do |name|
       name = name.sub '.py', ''

data/python/.gitignore

@@ -0,0 +1,8 @@
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+*.egg-info/
+build/
+dist/
+.pytest_cache/

data/python/README.md

@@ -0,0 +1,105 @@
+# scout-rig Python package
+
+This directory contains the Python companion package for scout-rig.
+
+It provides the `scout` Python module used to:
+
+- read and write Scout-style TSV files with pandas
+- run Scout workflows from Python through the standard Scout CLI
+- inspect workflow metadata
+- define Python functions as Scout-compatible tasks with `scout.task(...)`
+- call remote workflow servers over HTTP
+
+The Python package is meant to work together with the Ruby Scout stack.
+It does not replace the Ruby runtime. Instead, it offers a convenient Python interface on top of Scout command-line workflows and PythonWorkflow integration.
+
+## Requirements
+
+The package expects the Scout and Rbbt command-line tools used by the library to be available in your environment.
+
+In particular, local workflow execution helpers use commands such as:
+
+- `rbbt_exec.rb`
+- `rbbt workflow task ...`
+
+So, in practice, you should already have the Ruby scout-rig and related Scout packages installed and configured.
+
+Base Python dependencies:
+
+- `numpy`
+- `pandas`
+
+Optional dependencies:
+
+- `requests` for the remote workflow client
+- `rich` for `scout.rich(...)`
+
+## Install from GitHub with pip
+
+Because this repository is primarily a Ruby project and the Python package lives under `python/`, install it with the `subdirectory` fragment:
+
+    pip install "scout-rig @ git+https://github.com/mikisvaz/scout-rig.git@main#subdirectory=python"
+
+You can also omit the explicit package name:
+
+    pip install "git+https://github.com/mikisvaz/scout-rig.git@main#subdirectory=python"
+
+For editable local development from a clone of the repository:
+
+    pip install -e python
+
+## Optional extras
+
+For remote workflow support:
+
+    pip install "scout-rig[remote] @ git+https://github.com/mikisvaz/scout-rig.git@main#subdirectory=python"
+
+For rich object inspection:
+
+    pip install "scout-rig[inspect] @ git+https://github.com/mikisvaz/scout-rig.git@main#subdirectory=python"
+
+## Quick example
+
+    import scout
+    import scout.workflow as sw
+
+    wf = sw.Workflow('Baking')
+    print(wf.tasks())
+    print(wf.run('bake_muffin_tray', add_blueberries=True))
+
+## PythonWorkflow example
+
+    import scout
+
+    def hello(name: str, excited: bool = False) -> str:
+        """Generate a greeting."""
+        return f"Hello, {name}{'!' if excited else ''}"
+
+    scout.task(hello)
+
+Then inspect metadata with:
+
+    python hello.py --scout-metadata
+
+## What pip installs
+
+The pip package installs only the Python module contained in this directory.
+It does not install the Ruby scout-rig gem or the rest of the Scout stack.
+
+That separation is intentional:
+
+- Ruby remains responsible for workflow execution and PythonWorkflow integration
+- Python provides helper functions and a convenient development interface
+
+## Package layout
+
+- `scout.__init__` - TSV helpers, path helpers, workflow execution helpers
+- `scout.runner` - `scout.task(...)` and metadata extraction for PythonWorkflow
+- `scout.workflow` - local workflow wrapper
+- `scout.workflow.remote` - remote workflow client
+
+## Running a simple import test
+
+From the repository root:
+
+    PYTHONPATH=python python -c "import scout; print(scout.__file__)"

data/python/pyproject.toml

@@ -0,0 +1,49 @@
+[build-system]
+requires = ["setuptools>=69", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scout-rig"
+version = "0.2.4"
+description = "Python helpers for Scout workflows, TSV files, and PythonWorkflow task metadata"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [
+  { name = "Miki S. Vazquez" }
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Software Development :: Libraries :: Python Modules",
+  "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+dependencies = [
+  "numpy",
+  "pandas"
+]
+
+[project.optional-dependencies]
+remote = [
+  "requests"
+]
+inspect = [
+  "rich"
+]
+
+[project.urls]
+Homepage = "https://github.com/mikisvaz/scout-rig"
+Repository = "https://github.com/mikisvaz/scout-rig"
+Issues = "https://github.com/mikisvaz/scout-rig/issues"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["scout*"]
+
+[tool.setuptools]
+include-package-data = true

data/python/scout/__init__.py

@@ -188,7 +188,7 @@ def save_job_inputs(data):
     return temp_dir
 
 
-def run_job(workflow, task, jobname='Default', fork=False, clean=False, **kwargs):
+def run_job(workflow, task, jobname='Default', fork=False, clean=False, exec=False, **kwargs):
     inputs_dir = save_job_inputs(kwargs)
     cmd = ['rbbt', 'workflow', 'task', workflow, task, '--jobname', jobname, '--load_inputs', inputs_dir, '--nocolor']
 
@@ -196,6 +196,9 @@ def run_job(workflow, task, jobname='Default', fork=False, clean=False, **kwargs
         cmd.append('--fork')
         cmd.append('--detach')
 
+    if exec:
+        cmd.append('--exec')
+
     if clean:
         if clean == 'recursive':
             cmd.append('--recursive_clean')

data/scout-rig.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: scout-rig 0.2.2 ruby lib
+# stub: scout-rig 0.2.5 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-rig".freeze
-  s.version = "0.2.2".freeze
+  s.version = "0.2.5".freeze
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
@@ -36,6 +36,9 @@ Gem::Specification.new do |s|
     "lib/scout/workflow/python.rb",
     "lib/scout/workflow/python/inputs.rb",
     "lib/scout/workflow/python/task.rb",
+    "python/.gitignore",
+    "python/README.md",
+    "python/pyproject.toml",
     "python/scout/__init__.py",
     "python/scout/runner.py",
     "python/scout/workflow.py",

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: scout-rig
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.5
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -62,6 +62,9 @@ files:
 - lib/scout/workflow/python.rb
 - lib/scout/workflow/python/inputs.rb
 - lib/scout/workflow/python/task.rb
+- python/.gitignore
+- python/README.md
+- python/pyproject.toml
 - python/scout/__init__.py
 - python/scout/runner.py
 - python/scout/workflow.py