Staging

.copilotignore

@@ -0,0 +1,10 @@
+# Environment & secrets
+.env
+.env*
+*.env
+*.pem
+*.key
+*.cert
+
+# Dependency lockfile
+poetry.lock

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: "🐛 Bug Report"
+about: Report a reproducible error, crash, or incorrect result in Zyra
+title: "[Bug] "
+labels: [bug]
+assignees: ""
+---
+
+## Description
+A clear and concise description of the bug.
+
+## Steps to Reproduce
+Steps to reproduce the behavior:
+1. Run command `...`
+2. Use dataset `...`
+3. Observe error `...`
+
+## Expected Behavior
+What you expected to happen.
+
+## Actual Behavior
+What actually happened, including error messages/logs.
+
+## Environment
+- OS: [e.g. Ubuntu 22.04]
+- Python version: [e.g. 3.10]
+- Zyra version/commit: [e.g. main @ abc123]
+
+## Additional Context
+Add any other context (screenshots, configs, datasets).

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+
+issue_templates:
+  - name: "🐞 Bug Report"
+    description: "Report a reproducible problem in Zyra"
+    file: bug_report.md
+    labels: ["bug"]
+
+  - name: "✨ Feature Request"
+    description: "Propose a new feature or enhancement"
+    file: feature_request.md
+    labels: ["enhancement"]
+
+  - name: "⚡ Workflow Gap / Missing Command"
+    description: "Report missing CLI functionality needed for a workflow"
+    file: workflow_gap.md
+    labels: ["workflow-gap", "enhancement"]
+
+contact_links:
+  - name: "📖 Documentation"
+    url: "https://github.com/NOAA-GSL/zyra/wiki"
+    about: "Check the Zyra documentation for guidance before opening an issue"
+  - name: "💬 Discussions"
+    url: "https://github.com/NOAA-GSL/zyra/discussions"
+    about: "For design, philosophy, and open-ended questions, please use Discussions"

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "✨ Feature Request"
+about: Suggest new functionality to improve Zyra
+title: "[Feature] "
+labels: [enhancement]
+assignees: ""
+---
+
+## Summary
+A clear and concise description of the feature you’d like to see.
+
+## Motivation
+Why is this feature important?  
+(Does it enable a new workflow, improve performance, enhance usability, etc.?)
+
+## Proposed Solution
+If you have ideas about implementation, describe them here.  
+(e.g., new CLI command, pipeline stage, visualization option)
+
+## Alternatives Considered
+Any alternative approaches you’ve tried or considered.
+
+## Additional Context
+Links, diagrams, or references that help explain the feature.

.github/ISSUE_TEMPLATE/workflow_gap.md

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+---
+name: "⚡ Workflow Gap / Missing Command"
+about: "Report missing CLI functionality needed for a workflow"
+title: "[Workflow Gap] <describe missing functionality>"
+labels: ["workflow-gap", "enhancement"]
+assignees: ""
+
+---
+
+## Summary
+A workflow request requires functionality that is not currently implemented in the Zyra CLI.
+
+## Current State
+- **Available commands used:** <list existing commands from manifest>
+- **Missing functionality:** <describe the missing step or CLI command>
+
+## Desired Behavior
+- Add support for: <new command or option>
+- Expected usage example:
+  ```bash
+  zyra <command> --options
+  ```
+
+## Implementation Plan (Proposal)
+- [ ] Implement core functionality in `src/zyra/`
+- [ ] Add tests in `tests/`
+- [ ] Ensure comprehensive docstrings for auto-generated documentation
+- [ ] Include example in sample workflows
+
+## Context
+<Explain why this functionality is needed, who benefits, and any dependencies.>
+
+---
+
+🔗 *Generated by Zyra Helper Bot to ensure workflows map cleanly to implemented commands.*

.github/PULL_REQUEST_TEMPLATE.md

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+# Pull Request Template
+
+## Summary
+
+Provide a short summary of the changes in this PR.
+
+## Related Issue
+
+Closes #<issue-number>  
+(Ensure this PR links to a **Workflow Gap** issue if adding new CLI functionality)
+
+## Changes
+
+- [ ] Implemented functionality in `src/zyra/`
+- [ ] Added/updated tests in `tests/`
+- [ ] Verified comprehensive **docstrings** for auto-generated documentation
+- [ ] Added/updated example in sample workflows
+
+## Checklist
+
+- [ ] Code follows project style guidelines
+- [ ] All tests pass locally
+- [ ] Documentation builds cleanly from docstrings
+- [ ] I have linked this PR to a relevant issue
+
+---
+
+🔗 *Generated by Zyra Helper Bot to ensure contributors align PRs with workflow-gap issues.*

.github/copilot-instructions.md

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+# Copilot Repository Instructions for Zyra
+
+## Project Summary
+Zyra is an open-source **Python framework for scientific data visualization**.  
+It provides a **modular pipeline** for:
+- Data acquisition
+- Data processing
+- Rendering
+- Dissemination (export, publishing)
+
+The project supports **educators, researchers, and developers** who need reproducible, extensible workflows.
+
+- **Language:** Python 3.10+  
+- **Package Manager:** [Poetry](https://python-poetry.org/)  
+- **Containerization:** Docker / Docker Compose  
+- **Linting/Formatting:** Ruff + Pre-commit hooks  
+- **Tests:** Pytest  
+
+---
+
+## Environment & Build Instructions
+
+### Bootstrap
+- Always use **Poetry** for dependency management.
+- Run:
+  ```bash
+  poetry install
+  ```
+- This creates the virtual environment and installs dependencies from `pyproject.toml` + `poetry.lock`.
+
+### Build & Run
+- Build is managed via Poetry:
+  ```bash
+  poetry build
+  ```
+- Run Zyra inside Poetry shell:
+  ```bash
+  poetry shell
+  python -m zyra
+  ```
+
+### Tests
+- Tests are located in `tests/`.
+- Always run via Poetry:
+  ```bash
+  poetry run pytest
+  ```
+
+### Lint & Formatting
+- Ruff is configured in `ruff.toml`.
+- Run:
+  ```bash
+  poetry run ruff check .
+  poetry run ruff format .
+  ```
+- Pre-commit is configured in `.pre-commit-config.yaml`:
+  ```bash
+  pre-commit install
+  pre-commit run --all-files
+  ```
+
+### Docker/Docker Compose
+- To build the Docker image:
+  ```bash
+  docker build -t zyra .
+  ```
+- To run with Compose:
+  ```bash
+  docker-compose up
+  ```
+
+---
+
+## Validation & CI
+- GitHub Actions run on **push/PR**:
+  - Install & lint (`ruff`, `pre-commit`)
+  - Run tests (`pytest`)
+  - Build validation (`poetry build`)
+- To replicate locally, run the same Poetry + lint/test steps listed above.
+
+---
+
+## Project Layout
+- `src/zyra/` → Core source code modules  
+- `tests/` → Unit and integration tests  
+- `docs/` → Documentation and wiki sources  
+- `scripts/` → Utility scripts for workflows  
+- `samples/` → Example data and workflows  
+- `data/` → Supporting datasets  
+
+### Key Configuration Files
+- `pyproject.toml` → Poetry, build, lint/test configs  
+- `poetry.lock` → Locked dependencies  
+- `ruff.toml` → Ruff lint/format rules  
+- `.pre-commit-config.yaml` → Git hooks  
+- `Dockerfile` / `docker-compose.yml` → Containerization setup  
+
+### Repo Root Files
+- `README.md` – Overview, usage, examples  
+- `CONTRIBUTING.md` – Contribution guidelines  
+- `SECURITY.md` – Security practices  
+- `CITATION.cff` – Citation metadata  
+- `LICENSE` – Open source license  
+
+---
+
+## Explicit Guidance for Copilot
+- Always use **Poetry commands** (`poetry install`, `poetry run pytest`, `poetry run ruff check`) instead of raw `pip` or `pytest`.  
+- Trust these instructions for build, test, and validation steps.  
+- Only perform additional searching if these instructions are incomplete or produce errors.  
+- Keep contributions modular and ensure **tests + linting pass locally** before suggesting PRs.  
+
+---

CONTRIBUTING.md

@@ -53,6 +53,40 @@ To keep development organized, we use a two-branch model:
 
 ---
 
+## Workflow Gap Issues & PRs
+
+Zyra now uses structured **Workflow Gap** issue and PR templates to ensure new CLI functionality is properly tracked.
+
+### Filing Bug Reports
+- Use the `🐞 Bug Report` template (`.github/ISSUE_TEMPLATE/bug_report.md`).
+- Provide clear steps to reproduce, expected vs. actual behavior, and environment details.
+
+### Filing Feature Requests
+- Use the `✨ Feature Request` template (`.github/ISSUE_TEMPLATE/feature_request.md`).
+- Describe the feature, motivation, proposed solution, and alternatives.
+- Use this template only for enhancements that do **not** map directly to CLI commands.
+
+
+### Filing Workflow Gap Issues
+- Use the `⚡ Workflow Gap / Missing Command` template (`.github/ISSUE_TEMPLATE/workflow_gap.md`).
+- Clearly describe:
+  - Which CLI commands exist today
+  - What is missing
+  - Why the feature is needed
+- The template will guide you to include an implementation plan and examples.
+
+### Submitting PRs for Workflow Gaps
+- All PRs that add CLI functionality should link to the related Workflow Gap issue.
+- The PR template (`.github/PULL_REQUEST_TEMPLATE.md`) includes a checklist:
+  - Add tests
+  - Write comprehensive **docstrings** (for auto-generated docs)
+  - Include examples in workflows
+- Ensure all boxes are checked before requesting review.
+
+By following these templates, contributors help keep Zyra’s CLI aligned with real workflows and ensure documentation stays accurate and reproducible.
+
+---
+
 ## Code Style
 
 - Python 3.10+ required.  

llm/README.md

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+LLM Content (Repo-only)
+
+Purpose
+- Repository-local content for LLM tooling that does not need to be packaged
+  with the Python distribution. Suitable for ChatGPT Actions, Open WebUI tools,
+  experiments, and deployment artifacts.
+
+Layout
+- `prompts/`: System and task prompts for human or tool use.
+- `actions/`: ChatGPT Action definitions (`ai-plugin.json`, `openapi.yaml`).
+- `open-webui/`: Local Python tools and examples (not imported by `zyra`).
+- `examples/`: Snippets (curl payloads, screenshots, config examples).
+
+Open WebUI Tool Settings (Valves)
+- Tools in `llm/open-webui/tools/` (e.g., `zyra_cli_manifest.py`) expose configurable Valves in the Open WebUI UI
+  under Workspace → Tools → <tool> → Settings.
+- Common valves for `zyra_cli_manifest`:
+  - `zyra_api_base`: Base URL for Zyra API (default `http://localhost:8000`). The tool calls `GET /commands` with
+    query params.
+  - `zyra_api_key`: Optional API key; may be left blank.
+  - `api_key_header`: Header to send the API key (default `X-API-Key`).
+  - `api_timeout` / `net_timeout`: Short timeouts (seconds) for API and other HTTP fetches.
+  - `caps_url`: Optional direct URL to `zyra_capabilities.json`; used if the API is unreachable. May be blank.
+  - `offline`: If true, skip all network fetches.
+- If Settings doesn’t reflect new fields or optional status after a code update, re‑save (or remove/re‑add) the tool
+  and refresh the page — some builds cache the previous schema.
+
+See also
+- `llm/open-webui/README.md` for usage notes and paste‑ready tool workflow.
+
+Configuration
+- Set `ZYRA_LLM_DIR` to override the default external LLM directory.
+- Default lookup path can be `llm/` when no env var is provided.
+
+Conventions
+- No secrets; prefer env vars and documented config.
+- Keep prompts small, composable, and versioned via filenames.
+- Use relative paths; avoid absolute paths.

llm/actions/cli_manifest/README.md

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+Zyra CLI Manifest API (ChatGPT-friendly OpenAPI)
+
+Purpose
+- Minimal OpenAPI spec that exposes the Zyra CLI manifest (`zyra_capabilities.json`) directly from GitHub.
+- Quick to import into ChatGPT Actions or similar tools to let an LLM inspect available CLI commands.
+
+Usage (ChatGPT Actions)
+- In ChatGPT → Actions → Create, supply a URL to this `openapi.yaml` (host from a raw URL in your fork or static hosting).
+- Only the `/zyra_capabilities.json` endpoint is active (served by GitHub raw). The `/execute` endpoint is a placeholder and not hosted.
+
+Notes
+- Anonymous access works; GitHub raw applies rate limits. For higher limits or non-public use, host a copy of the manifest yourself.
+- Source of truth for this Action lives here (`llm/actions/cli_manifest/`).
+