Viper doesn't dump CLI overrides for sub vipers

main.go

package main

import (
	"encoding/json"
	"fmt"
	"os"

	"github.com/spf13/cobra"
	"github.com/spf13/viper"
)

var RootCmd = &cobra.Command{
	Use: "vipertest",
}

var SubCmd = &cobra.Command{
	Use: "subcmd",
	Run: subRun,
}

func init() {
	RootCmd.AddCommand(SubCmd)
	RootCmd.PersistentFlags().StringP("log-level", "l", "warn", "log level")

	SubCmd.PersistentFlags().String("value1", "y", "")
	SubCmd.PersistentFlags().String("value2", "", "")
	SubCmd.PersistentFlags().StringSlice("value3", []string{}, "")

	viper.BindPFlag("log_level", RootCmd.PersistentFlags().Lookup("log-level"))

	viper.BindPFlag("subcmd.value1", SubCmd.PersistentFlags().Lookup("value1"))
	viper.BindPFlag("subcmd.value2", SubCmd.PersistentFlags().Lookup("value2"))

	cobra.OnInitialize(cfgInit)
}

func cfgInit() {
	viper.SetConfigFile("./test.yaml")
	err := viper.ReadInConfig()
	if err != nil {
		panic(err)
	}

	fmt.Printf("ALL SETTINGS JSON\n")
	b, err := json.MarshalIndent(viper.AllSettings(), "", "  ")
	if err != nil {
		fmt.Println(err)
		os.Exit(0)
	}
	fmt.Println(string(b))

	fmt.Printf("SUB SETTINGS JSON\n")
	b, err = json.MarshalIndent(viper.Sub("subcmd").AllSettings(), "", "  ")
	if err != nil {
		fmt.Println(err)
		os.Exit(0)
	}
	fmt.Println(string(b))

}

func subRun(cmd *cobra.Command, args []string) {
	os.Exit(0)
}

func main() {
	if err := RootCmd.Execute(); err != nil {
		fmt.Println(err)
		os.Exit(-1)
	}
}

here is test.yaml that needs to be in the same directory

log_level: info
subcmd:
  value1: a