「cobra」の検索結果

Golang CLI command tree library using spf13/cobra — cobra.Command, RunE vs Run, PersistentPreRunE hook chain, Args validators (NoArgs, ExactArgs, MatchAll, custom), persistent vs local flags, command groups, ValidArgsFunction, RegisterFlagCompletionFunc, ShellCompDirective, usage/help template customization, man-page and markdown doc generation, and testing with SetArgs/SetOut/SetErr. Apply when using or adopting spf13/cobra, or when the codebase imports `github.com/spf13/cobra`. For configuration layering alongside cobra, see the `samber/cc-skills-golang@golang-spf13-viper` skill. For general CLI architecture (project layout, exit codes, signal handling, I/O patterns), see `samber/cc-skills-golang@golang-cli`.

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Golang CLI application development. Use when building, modifying, or reviewing a Go CLI tool — especially for command structure, flag handling, configuration layering, version embedding, exit codes, I/O patterns, signal handling, shell completion, argument validation, and CLI unit testing. Also triggers when code uses cobra, viper, or urfave/cli. For cobra-specific APIs → See `samber/cc-skills-golang@golang-spf13-cobra` skill; for viper configuration layering → See `samber/cc-skills-golang@golang-spf13-viper` skill.

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Expert skill for building CLI applications with Cobra and Viper, authored by spf13 — the original creator of both libraries. Covers command-first architecture, decoupled business logic, configuration management, environment variable binding, context-aware commands, and in-memory CLI testing. Use whenever a Go CLI or command-line tool is being built, reviewed, or refactored — any mention of commands, subcommands, flags, or CLI configuration, even if Cobra or Viper aren't named yet (recommend them).

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Building production-quality CLI tools with Cobra command framework and Viper configuration management

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Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and metabolic engineering.

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Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.

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Generate Cobra/Viper-based Go CLI applications with persistent flags, subcommands, and configuration management. Creates production-ready Go CLI with modern patterns.

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Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

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Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.

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Builds command-line tools in Go with Cobra, the library behind kubectl, Hugo and the GitHub CLI: subcommands, flags, argument validation, generated help and shell completions. Use when a user asks to create a Go CLI, add subcommands or flags, validate arguments, bind flags to config files and environment variables with Viper, or generate bash, zsh, fish or PowerShell completions.

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Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

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Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus SED-ML COMBINE archives. Use for reaction-network time courses, kinetic parameters, concentration dynamics and reproducible simulation experiments; steady-state constraint-based metabolic flux analysis belongs to cobrapy.

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Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags experiments requiring nonstationary MFA.

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Use when building CLI tools, implementing argument parsing, or adding interactive prompts. Invoke for parsing flags and subcommands, displaying progress bars and spinners, generating bash/zsh/fish completion scripts, CLI design, shell completions, and cross-platform terminal applications using commander, click, typer, or cobra.

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Golang configuration library using spf13/viper — layered precedence (flag > env > file > KV > default), BindPFlag/BindPFlags, SetEnvPrefix + SetEnvKeyReplacer + AutomaticEnv, ReadInConfig + ConfigFileNotFoundError, Unmarshal + mapstructure struct tags, Sub for sub-trees, WatchConfig + OnConfigChange for hot reload, viper.New() for test isolation, and remote KV integration. Apply when using or adopting spf13/viper, or when the codebase imports `github.com/spf13/viper`. For CLI command structure alongside viper, see the `samber/cc-skills-golang@golang-spf13-cobra` skill. For general CLI architecture, see `samber/cc-skills-golang@golang-cli`.

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Constraint-based metabolic modeling and flux balance analysis

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Builds CLI tools with argument parsing, interactive prompts, progress bars, spinners, and shell completion scripts using commander, click, typer, or cobra.

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CLI best practices for LlamaFarm. Covers Cobra, Bubbletea, Lipgloss patterns for Go CLI development.

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Build professional command-line interfaces in Python, Go, and Rust using modern frameworks like Typer, Cobra, and clap. Use when creating developer tools, automation scripts, or infrastructure management CLIs with robust argument parsing, interactive features, and multi-platform distribution.

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Build, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/kinetic laws, species, rules, FBC extension for flux balance, conversion. Interoperates with COBRApy, Tellurium/RoadRunner, COPASI. Use when programmatically constructing ODE or constraint-based metabolic/signaling models in SBML.

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BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data. 80K+ enzymes, 7M+ values. Free academic registration. For metabolic modeling use cobrapy-metabolic-modeling; metabolites use hmdb-database.

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Review a Go design spec before implementation begins - dispatch a subagent that checks a design doc for completeness, consistency, and idiomatic Go (simplicity, small consumer-defined interfaces, explicit wrapped errors, context propagation) plus Cobra/Viper conventions where applicable. Use when a user has a Go spec to review, asks "is this spec ready?", or is about to implement from a written design. Distilled from spf13/go-skills and adapted to this repo's conventions.

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Think and work like an expert Fermentation Scientist. Use when a task calls for Fermentation Scientist judgment. Reasons from Monod–Luedeking–Piret kinetics, overflow μcrit, OTR/RQ/RAMOS analytics, DoE media optimization, and 13C-MFA/COBRApy flux bounds while treating stuck-ferment ethanol×T synergy, SSF heat/moisture gradients, and OD-as-biomass red herrings as first-class failure modes.

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Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.

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