streamflow-documentation

name	StreamFlow Documentation
description	This skill should be used when the user asks to "write documentation", "add a doc page", "update RST files", "add a tutorial", or when writing or editing Sphinx RST documentation for StreamFlow.
version	0.1.0

StreamFlow Documentation Skill

Guidelines for writing Sphinx RST documentation for StreamFlow. Docs live under docs/source/. The Sphinx build uses sphinx.ext.autosectionlabel, so every section title is automatically a valid :ref: target.

Writing Style

• Use American English throughout.
• Use double backticks for all code entities: file names, environment variables, class names, function names, CLI commands, YAML keys, CWL fields.
• Never reference a file without first telling the user how to create it.
• Keep source files shown via literalinclude within 80 characters per line.

RST Conventions

All documentation files use .rst format.

Section title underlines

Every title underline (and overline) must be exactly as long as the title text — no shorter, no longer. Count Unicode characters, not bytes.

MPI Application
===============    ← 15 chars, underline is 15 chars  ✓

Run with Kubernetes
-------------------  ← 19 chars, underline is 19 chars  ✓

After editing headings, verify with:

python3 -c "
with open('docs/source/.../file.rst') as f:
    lines = f.readlines()
ul = set('=-~^\"\\'\`#*+')
for i,l in enumerate(lines):
    s = l.rstrip()
    if i+1 < len(lines):
        n = lines[i+1].rstrip()
        if n and len(set(n))==1 and n[0] in ul and len(s)!=len(n):
            print(f'Line {i+1}: title={len(s)}, underline={len(n)}: {s!r}')
"

Highlighting changed lines

Use :emphasize-lines: with both code-block and literalinclude directives. Prefer literalinclude whenever the file exists on disk.

When a tutorial shows multiple versions of the same file for different environments (e.g. Docker Compose → Kubernetes → Helm variants of streamflow.yml), use :emphasize-lines: to highlight the lines that differ from the base version, so the reader can spot the changes at a glance:

.. literalinclude:: streamflow-k8s.yml
   :language: yaml
   :emphasize-lines: 12, 16, 20-25

Cross-references

Use :ref: to link to other sections. Targets are section titles verbatim:

:ref:`DockerComposeConnector`
:ref:`Put it all together`

Common targets: Install, Write your workflow, Put it all together, Binding steps and deployments, Import your environment, CWL Runner, DockerComposeConnector, KubernetesConnector, Helm4Connector.

Subskills

Task	Subskill
Add a new worked example tutorial	StreamFlow Documentation — Adding Examples

See Also

• StreamFlow Code Style skill — Python code style and docstring conventions
• StreamFlow Git Workflow skill — commit message format