scout-rig 0.1.0 → 0.2.0

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

@@ -2,6 +2,19 @@ scout-rig=/$PWD filter="*" {
  LICENSE.txt
  README.rdoc
  Rakefile
+ chats=chats{
+  documenter.rb
+
+  python_workflow
+
+  python_init
+
+  python_pycall
+
+  python_multi
+
+  docstring
+ }
  lib=lib {
   scout-rig.rb
   scout=scout{
@@ -12,17 +25,29 @@ scout-rig=/$PWD filter="*" {
     script.rb
     util.rb
    }
+   workflow=workflow{
+    python.rb
+    python=python{
+     inputs.rb
+     task.rb
+    }
+   }
   }
  }
  test=test{
   test_helper.rb
  }
  python=python{
+  task=task{
+   hello.py
+  }
   test.py
   scout=scout{
    __init__.py
+   runner.py
    workflow.py
    workflow=workflow{
+    definition.py
     remote.py
    }
   }

data/README.md

@@ -0,0 +1,337 @@
+# scout-rig
+
+scout-rig provides the language interop “rigging” for the Scout ecosystem. It currently focuses on Python: executing Python from Ruby, round‑tripping data (TSV ↔ pandas), and running Scout Workflows from Python code. It builds on the low-level/core packages:
+
+- scout-essentials — low level utilities (Annotation, CMD, ConcurrentStream, IndiferentHash, Log, Open, Path, Persist, TmpFile)
+- scout-gear — data and workflow primitives (TSV, Workflow, KnowledgeBase, Association, Entity, WorkQueue, Semaphore)
+- scout-rig — interop with other languages (currently Python)
+- scout-camp — remote servers, cloud deployments, web interfaces, cross-site operations
+- scout-ai — model training and agentic tools
+
+All packages are available on GitHub under https://github.com/mikisvaz (for example, https://github.com/mikisvaz/scout-gear).
+
+For broader background and many real workflow examples, see Rbbt (the bioinformatics framework from which Scout was refactored) and the Rbbt-Workflows organization:
+- https://github.com/mikisvaz/rbbt
+- https://github.com/Rbbt-Workflows
+
+This README focuses on the Python bridge in scout-rig (ScoutPython). See the docs in doc/ for reference material.
+
+- doc/Python.md — ScoutPython user guide
+
+---
+
+## What you get
+
+ScoutPython (Ruby) and a companion Python package (python/scout) provide:
+
+- Safe, ergonomic execution of Python code from Ruby (PyCall-based), with:
+  - Simple import helpers and localized bindings
+  - Synchronous, direct, or background-thread execution
+  - Logging wrappers that capture Python stdout/stderr
+- Scripting to run ad‑hoc Python text with Ruby variables (including TSV) injected, and results returned
+- Data conversion helpers:
+  - numpy arrays → Ruby Arrays
+  - pandas DataFrame ↔ TSV (key_field, fields, type respected)
+- Python path management (expose package python/ dirs to sys.path)
+- Python‑side helpers to:
+  - Read/write TSVs with headers (pandas)
+  - Run Ruby Workflows from Python
+  - Call remote Workflow services over HTTP
+
+---
+
+## Installation and requirements
+
+Ruby
+- Ruby 2.6+ (or compatible with PyCall)
+- Gems:
+  - pycall (PyCall)
+  - json (standard)
+  - Optional for script result loading:
+    - python/pickle (gem) for loading pickle from Python scripts
+
+Python
+- Python 3
+- Packages:
+  - pandas
+  - numpy
+  - requests (only for remote workflow client)
+- Ensure python3 is in PATH
+
+Add scout-rig to your Ruby project (Gemfile or local checkout), then ensure Python dependencies are installed in your Python environment.
+
+---
+
+## Quick start
+
+Execute Python directly from Ruby:
+
+```ruby
+require 'scout_python'
+
+# Sum with numpy
+arr_sum = ScoutPython.run 'numpy', as: :np do
+  np.array([1,2,3]).sum
+end
+# => PyObject (to_i if needed)
+
+# Background thread execution
+ScoutPython.run_threaded :sys do
+  sys.path.append('/opt/my_py_pkg')
+end
+ScoutPython.stop_thread
+```
+
+Run an ad‑hoc Python script, returning a result value:
+
+```ruby
+tsv = TSV.setup({}, "Key~ValueA,ValueB#:type=:list")
+tsv["k1"] = %w[a1 b1]; tsv["k2"] = %w[a2 b2]
+
+TmpFile.with_file do |target|
+  result = ScoutPython.script <<~PY, df: tsv, target: target
+    import scout
+    # df is a pandas DataFrame (tsv injected)
+    result = df.loc["k2", "ValueB"]
+    scout.save_tsv(target, df)  # save as TSV with header
+  PY
+
+  # result is "b2"; target holds a TSV round-tripped from pandas
+end
+```
+
+Convert between TSV and pandas:
+
+```ruby
+df = ScoutPython.tsv2df(tsv)      # TSV -> pandas DataFrame
+tsv2 = ScoutPython.df2tsv(df)     # pandas DataFrame -> TSV
+```
+
+Run a Workflow from Python:
+
+```python
+import sys
+sys.path.append('python')  # add this repo's python/ on dev checkouts
+
+import scout.workflow as sw
+
+wf = sw.Workflow('Baking')
+print(wf.tasks())
+step = wf.fork('bake_muffin_tray', add_blueberries=True, clean='recursive')
+step.join()
+print(step.load())         # load Ruby job result
+```
+
+---
+
+## Core concepts
+
+### Path management for Python imports
+
+ScoutPython tracks Python directories to add to sys.path:
+
+- ScoutPython.add_path(path) / add_paths(paths)
+- ScoutPython.process_paths  # idempotent; run before/inside sessions
+
+These are applied in Python contexts by run/run_simple/run_direct.
+
+### Running Python from Ruby
+
+Pick the execution model that fits:
+
+- run(mod = nil, imports = nil) { ... }
+  - Initialize PyCall if needed, set up paths, run block; GC after run
+- run_simple(mod = nil, imports = nil) { ... }
+  - Lightweight; process_paths, then run block
+- run_direct(mod = nil, imports = nil) { ... }
+  - Minimal overhead: optional single pyimport/pyfrom, then evaluate
+- run_threaded(mod = nil, imports = nil) { ... }
+  - Queue work into a dedicated Python thread; stop with stop_thread
+
+Logging wrappers capture Python’s stdout/stderr via the Scout Log:
+
+- run_log(mod=nil, imports=nil, severity=Log::LOW, severity_err=nil) { ... }
+- run_log_stderr(mod=nil, imports=nil, severity=Log::LOW) { ... }
+
+Imports
+- Pass 'numpy', as: :np or "module.submodule", import: [:Class, :func]
+
+### Binding scopes and imports
+
+Keep imports local to a binding:
+
+```ruby
+ScoutPython.binding_run do
+  pyimport :torch
+  pyfrom :torch, import: ['nn']
+  # torch and nn available here only
+end
+```
+
+Helpers
+- new_binding, binding_run
+- import_method, call_method
+- get_module, get_class, class_new_obj
+- exec(script) → PyCall.exec
+
+### Scripting
+
+Run arbitrary Python text with Ruby variables injected:
+
+- ScoutPython.script(text, variables = {}) → result
+  - Ruby primitives → Python literals
+  - Arrays/Hashes → recursively converted
+  - TSV variables → materialized to temp file and loaded into pandas via the python/scout helper
+  - result is read back via pickle (default) or JSON (configurable)
+
+Swap result serializer if desired:
+
+```ruby
+class << ScoutPython
+  alias save_script_result save_script_result_json
+  alias load_result        load_json
+end
+```
+
+### Iteration utilities
+
+Traverse Python iterables with optional progress bars:
+
+- iterate(iterator, bar: nil|true|String) { |elem| ... }
+- iterate_index(sequence, bar: ...) { |elem| ... }
+- collect(iterator, bar: ...) { |elem| ... } → Array
+
+### Data conversion and pandas helpers
+
+- numpy2ruby(numpy_array)
+- to_a/py2ruby_a(py_list)
+- obj2hash(py_mapping)
+- tsv2df(tsv) / df2tsv(df, options={type: :list, key_field: ...})
+
+---
+
+## Python-side package (python/scout)
+
+The included Python package is importable as scout and provides:
+
+General utilities
+- scout.libdir(), scout.add_libdir()
+- scout.path(), scout.read()
+- scout.inspect(obj), scout.rich(obj)
+
+TSV IO (pandas-aware)
+- scout.tsv(tsv_path_or_stream, ...) → pandas.DataFrame (Scout headers respected)
+- scout.save_tsv(filename, df, key=None)
+
+Workflow wrappers
+- scout.run_job(workflow, task, name='Default', fork=False, clean=False, **inputs)
+  - Shells out to the Ruby CLI to execute/fork jobs
+- scout.workflow.Workflow(name).run/fork/tasks/task_info
+- scout.workflow.Step(path).info/status/join/load
+
+Remote workflows (HTTP)
+- scout.workflow.remote.RemoteWorkflow(url).job/task_info
+- scout.workflow.remote.RemoteStep(url).status/wait/raw/json
+
+---
+
+## Error handling and threading
+
+- Python process errors from script are surfaced as ConcurrentStreamProcessFailed (non‑zero exit), with stderr logged via Log if a logging wrapper is used
+- Background thread execution must be stopped explicitly:
+  - ScoutPython.stop_thread — sends a sentinel, tries to join/kill, GCs, and finalizes PyCall if available
+
+---
+
+## Command line usage and discovery
+
+Scout commands are discovered under scout_commands across installed packages using the Path subsystem. The dispatcher resolves nested commands by adding terms until a file is found to execute; if you stop on a directory, it lists available subcommands.
+
+- General pattern:
+  - scout <top-level> [<subcommand> ...] [options] [args...]
+- Examples relevant to Python integration (executed from Ruby CLI but callable from Python via scout.run_job):
+  - scout workflow task <Workflow> <task> [task-input-options...]
+  - scout workflow prov <step_path>
+  - scout workflow info <step_path>
+
+Notes
+- The bin/scout launcher walks scout_commands/… across packages; Workflows and other packages can add their own commands and they will be discovered
+- See the Workflow, TSV, and KnowledgeBase docs for their CLI suites:
+  - TSV: scout tsv …
+  - Workflow: scout workflow …
+  - KnowledgeBase: scout kb …
+
+scout-rig itself does not register standalone CLI commands; instead, its Python wrapper invokes the existing Ruby CLI to run jobs from Python.
+
+---
+
+## Reference
+
+Read the full module guide in doc/Python.md. For core building blocks referenced above, see these docs in scout-essentials and scout-gear:
+
+- Annotation.md, CMD.md, ConcurrentStream.md, IndiferentHash.md, Log.md, Open.md, Path.md, Persist.md, TmpFile.md
+- TSV.md, Workflow.md, KnowledgeBase.md, Association.md, Entity.md, WorkQueue.md, Semaphore.md
+
+---
+
+## Examples
+
+Direct PyCall with imports:
+
+```ruby
+ScoutPython.run 'numpy', as: :np do
+  a = np.array([1,2,3])
+  a.sum            # PyObject; convert with to_i if needed
+end
+```
+
+Script with a returned value and TSV round‑trip:
+
+```ruby
+tsv = TSV.setup({}, "Key~ValueA,ValueB#:type=:list")
+tsv["k1"] = ["a1", "b1"]; tsv["k2"] = ["a2", "b2"]
+
+TmpFile.with_file do |target|
+  result = ScoutPython.script <<~PY, df: tsv, target: target
+    import scout
+    result = df.loc["k2", "ValueB"]
+    scout.save_tsv(target, df)
+  PY
+  # result == "b2"; target contains the saved TSV
+end
+```
+
+numpy conversion:
+
+```ruby
+ra = ScoutPython.run :numpy, as: :np do
+  na = np.array([[[1,2,3], [4,5,6]]])
+  ScoutPython.numpy2ruby(na)
+end
+ra[0][1][2] # => 6
+```
+
+Run workflows from Python:
+
+```python
+import scout.workflow as sw
+
+wf = sw.Workflow('Baking')
+step = wf.fork('bake_muffin_tray', add_blueberries=True, clean='recursive')
+step.join()
+print(step.load())
+```
+
+---
+
+## Project links
+
+- scout-essentials — https://github.com/mikisvaz/scout-essentials
+- scout-gear — https://github.com/mikisvaz/scout-gear
+- scout-rig — https://github.com/mikisvaz/scout-rig
+- scout-camp — https://github.com/mikisvaz/scout-camp
+- scout-ai — https://github.com/mikisvaz/scout-ai
+- Rbbt — https://github.com/mikisvaz/rbbt
+- Rbbt-Workflows — https://github.com/Rbbt-Workflows
+
+Contributions and issues are welcome in their respective GitHub repositories.

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0