Update documentation for Python-only CLI

- Rewrite README.md to focus on Python installation
- Rename PYTHON_DEVELOPMENT.md to DEVELOPMENT.md
- Update DEVELOPMENT.md to remove Java references
- Mark PYTHON_REWRITE_PROGRESS.md as historical archive
- Remove PHASE_6_PLAN.md (complete)

The CLI is now fully Python-based with:
- 479 passing tests
- All major commands implemented
- Modern Python tooling (ruff, mypy, pytest)

Author: claude

DEVELOPMENT.md

@@ -0,0 +1,276 @@
+# Development Guide
+
+Guide for developing the Seqera Platform CLI.
+
+## Quick Start
+
+### Installation
+
+```bash
+# Install in development mode with all dependencies
+pip install -e ".[dev]"
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run specific test file
+pytest tests/credentials/test_credentials_cmd.py
+
+# Run with verbose output
+pytest -v
+
+# Run with coverage
+pytest --cov=seqera --cov-report=html
+```
+
+### Running the CLI
+
+```bash
+# Run the CLI directly
+python -m seqera.main --help
+
+# Or if installed
+seqera --help
+
+# Example: List credentials
+seqera credentials list
+
+# Example with custom server
+seqera --url http://localhost:8080 --access-token your_token credentials list
+```
+
+## Project Structure
+
+```text
+tower-cli/
+├── src/seqera/              # Python source code
+│   ├── main.py              # CLI entry point
+│   ├── api/                 # API client
+│   │   └── client.py        # SeqeraClient class
+│   ├── commands/            # CLI commands
+│   │   ├── actions/         # Actions commands
+│   │   ├── computeenvs/     # Compute environment commands
+│   │   ├── credentials/     # Credentials commands
+│   │   ├── datalinks/       # Data links commands
+│   │   ├── datasets/        # Datasets commands
+│   │   ├── labels/          # Labels commands
+│   │   ├── members/         # Members commands
+│   │   ├── organizations/   # Organizations commands
+│   │   ├── participants/    # Participants commands
+│   │   ├── pipelines/       # Pipeline commands
+│   │   ├── runs/            # Runs commands
+│   │   ├── secrets/         # Secrets commands
+│   │   ├── studios/         # Data studios commands
+│   │   ├── teams/           # Teams commands
+│   │   ├── workspaces/      # Workspaces commands
+│   │   ├── info.py          # Info command
+│   │   └── launch.py        # Launch command
+│   ├── exceptions/          # Custom exceptions
+│   ├── responses/           # Response models
+│   └── utils/               # Utilities (output formatting, etc.)
+└── tests/                   # Tests
+    ├── conftest.py          # Pytest fixtures
+    └── ...                  # Command-specific tests
+```
+
+## Code Quality
+
+### Linting
+
+```bash
+# Check code style
+ruff check src/ tests/
+
+# Fix auto-fixable issues
+ruff check --fix src/ tests/
+```
+
+### Formatting
+
+```bash
+# Format code
+ruff format src/ tests/
+```
+
+### Type Checking
+
+```bash
+# Run mypy
+mypy src/seqera
+```
+
+### Pre-commit Hooks
+
+Install pre-commit hooks to run checks automatically:
+
+```bash
+pre-commit install
+```
+
+## Testing
+
+### Test Structure
+
+Tests are organized by command:
+
+```text
+tests/
+├── conftest.py              # Common fixtures
+├── test_info_cmd.py         # Info command tests
+├── test_launch_cmd.py       # Launch command tests
+├── actions/                 # Actions tests
+├── credentials/             # Credentials tests
+└── ...
+```
+
+### Writing Tests
+
+Tests use pytest and pytest-httpserver for mocking API responses:
+
+```python
+import pytest
+from pytest_httpserver import HTTPServer
+from tests.conftest import exec_command
+
+
+def test_list_credentials(
+    httpserver: HTTPServer,
+    cli_runner,
+    base_args,
+) -> None:
+    """Test credentials list command."""
+    # Mock API response
+    httpserver.expect_request(
+        "/credentials",
+        method="GET",
+    ).respond_with_json({
+        "credentials": [
+            {"id": "1", "name": "test-cred"}
+        ]
+    })
+
+    # Run command
+    out = exec_command(
+        cli_runner,
+        base_args,
+        ["credentials", "list"],
+        output_format="json"
+    )
+
+    # Assert
+    assert out.exit_code == 0
+    assert "test-cred" in out.stdout
+```
+
+### Test Fixtures
+
+Common fixtures in `conftest.py`:
+
+- `cli_runner` - Typer CLI test runner
+- `base_args` - Base CLI arguments (--url, --access-token, --insecure)
+- `api_url` - Mock server URL
+- `auth_token` - Test authentication token
+- `user_workspace_name` - Test user workspace name
+
+### Running Specific Tests
+
+```bash
+# Run tests for a specific command
+pytest tests/credentials/ -v
+
+# Run tests matching a pattern
+pytest -k "test_list" -v
+
+# Run with output capture disabled (for debugging)
+pytest -s tests/test_info_cmd.py
+```
+
+## Adding New Commands
+
+### 1. Create Command Module
+
+```python
+# src/seqera/commands/mycommand/__init__.py
+import typer
+
+app = typer.Typer(name="mycommand", help="My command description")
+
+
+@app.command("list")
+def list_items(
+    workspace: str | None = typer.Option(None, "-w", "--workspace"),
+) -> None:
+    """List items."""
+    # Implementation
+    pass
+```
+
+### 2. Register Command
+
+```python
+# src/seqera/main.py
+from seqera.commands import mycommand
+
+app.add_typer(mycommand.app, name="mycommand")
+```
+
+### 3. Add Tests
+
+```python
+# tests/mycommand/test_mycommand_cmd.py
+def test_list(httpserver, cli_runner, base_args):
+    httpserver.expect_request("/my-endpoint").respond_with_json({...})
+    out = exec_command(cli_runner, base_args, ["mycommand", "list"])
+    assert out.exit_code == 0
+```
+
+## Dependencies
+
+### Runtime Dependencies
+
+- `typer` - CLI framework
+- `httpx` - HTTP client
+- `rich` - Terminal formatting
+- `pydantic` - Data validation
+- `pyyaml` - YAML support
+
+### Development Dependencies
+
+- `pytest` - Testing framework
+- `pytest-httpserver` - HTTP mocking
+- `ruff` - Linter and formatter
+- `mypy` - Type checker
+- `pre-commit` - Git hooks
+
+## Release Process
+
+1. Update version in `pyproject.toml`
+2. Run tests: `pytest`
+3. Run quality checks: `ruff check && mypy src/seqera`
+4. Create release commit and tag
+5. Push to trigger CI/CD
+
+## Troubleshooting
+
+### Import Errors
+
+If you get import errors, ensure the package is installed in development mode:
+
+```bash
+pip install -e .
+```
+
+### Test Discovery Issues
+
+Ensure test files and functions follow naming conventions:
+- Files: `test_*.py`
+- Functions: `test_*`
+- Classes: `Test*`
+
+### HTTP Mock Issues
+
+If tests fail with unexpected requests, check the mock server logs for the actual requests being made vs. what was expected.