Commit d0a0208a authored Mar 20, 2026 by Jan Reimes

feat(config): add configuration files for tasks and tools

* Add default tasks for running, upgrading tools, and syncing environment.
* Implement formatting tasks for source code and Markdown files.
* Introduce linting tasks with options for fixing issues.
* Add MCP server management tasks and quality check tasks.

parent 1e247742

.config/mise/conf.d/default.toml

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		[tasks.default]
		run = "mise tasks"

		[tasks.upgrade-tools]
		description = "Upgrade all development tools to their latest versions"
		run = ["mise install", "mise up", "mise prune"]

		[tasks.env-sync]
		description = "Sync the virtual environment with pyproject.toml dependencies"
		run = "uv sync -U --dev --all-extras --all-groups"

.config/mise/conf.d/format.toml

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		[tasks.format]
		description = "Format source code and tests"
		run = [
		"uv run undersort corr_plot/ tests/ --exclude .config/",
		"ruff check --select I --fix", # isort-equivalent sorting of imports
		"ruff format corr_plot/ tests/ --exclude .config",
		]

		[tasks.format-md]
		description = "Format Markdown files"
		run = "uvx mdformat . --exclude .agents/"

.config/mise/conf.d/lint.toml

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		[tasks.lint]
		description = "Lint source code and tests (no fixes)"
		run = "ruff check corr_plot/ tests/ packages/"

		[tasks.lint-fix]
		description = "Lint source code and tests and fix safe issues"
		run = "ruff check --fix corr_plot/ tests/ packages/"

		[tasks.lint-fix-unsafe]
		description = "Lint source code and tests and fix safe and unsafe issues"
		run = "ruff check --fix --unsafe-fixes corr_plot/ tests/ packages/"

.config/mise/conf.d/mcp.toml

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		[tasks.add-mcp-servers]

		depends = ["upgrade-tools", "env-sync"]

		usage = '''
		arg "<ai_agent>" help="AI assistant to use: claude, gemini, copilot, opencode, ... see: https://github.com/neondatabase/add-mcp"
		'''
		shell = "pwsh -NoProfile -Command"
		run = [
		'cls',
		#'bun x add-mcp -y -a {{usage.ai_agent}} "grepai mcp-serve"',
		'bun x add-mcp -y -a {{usage.ai_agent}} -n cytoscnpy-mcp "cytoscnpy mcp-server"',

		]

.config/mise/conf.d/quality.toml

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		[tasks.analyze]
		# see: https://github.com/djinn-soul/CytoScnPy/blob/main/docs/usage.md
		description = "Run quality checks on source code and tests"
		run = "cytoscnpy . --secrets --danger --quality --include-tests"