Update:

有朋友提示用 uiaotumator，多线程，一边安装一边检测是否有弹窗，亲测可行，完美解决。

# encoding:UTF8
import pexpect, sys, os.path, subprocess
from uiautomator import Device
from time import sleep
import threading

def install_apk(device, path_to_apk):
    print 'Installing apk: {0} to device: {1}'.format(path_to_apk, device)
    P = subprocess.Popen("adb -s {0} install {1}".format(device, path_to_apk),stdout=subprocess.PIPE, shell=True)
    data = P.stdout.read()
    if "Success" in str(data):
        print 'Installing apk: {0} for device: {1} Success'.format(path_to_apk, device)
        exit(1)
    if "Failure" in str(data):
        print 'Installing apk: {0} for device: {1} Failure'.format(path_to_apk, device)
        exit(0)

def uninstall_apk(device, package):
    print 'Uninstalling apk: {0} for device: {1}'.format(package, device)

    result = str(pexpect.run('adb -s {0} uninstall {1}'.format(device, package))).strip().lower()

    if 'failure' == result:
        print 'WARN: Uninstall apk: {0} for device: {1} has error, maybe not exists.'.format(package, device);
        exit(0)

    if 'success' != result:
        print 'Uninstall apk: {0} for device: {1} failed, msg: {2}'.format(package, device, result)
        exit(1)

def protect(nub,device):
    sleep(2)
    for i in range(nub):
        d = Device(device)
        el1 = d(text="安装")
        el2 = d(text="确定")
        if el1.exists:
            el1.click() 
        if el2.exists:
            el2.click()  
        sleep(2)

if __name__ == '__main__':
    if len(sys.argv) < 4:
        print 'Arguments error, usage: python install_app <install | uninstall> <device> <apk | package>'
        exit(1)

    op = sys.argv[1]
    device = sys.argv[2]
    apk = sys.argv[3]

    if op == 'install':
        threads = []
        install = threading.Thread(target=install_apk, args=(device,apk))
        protect = threading.Thread(target=protect, args=(30,device))
        threads.append(install)
        threads.append(protect)
        for t in threads:
            t.setDaemon(True)
            t.start()
        t.join()        
    else :
        package = sys.argv[3]
        uninstall_apk(device, package)

原文:

最近在 moto x 上（5.0 的，不确定是不是所有 5.0 都这样）跑 case 遇到一个问题：每次在 appium 安装应用的时候系统会弹窗提示是否确认安装。需要手动点击确认才能继续，否则就只能卡在这里。

翻看源码发现 appium 使用的是adb install来安装应用的，手动执行adb install确实会弹窗
度娘那里得来还有一种安装方法pm install
手动尝试先把包 push 到手机上，再pm install，没有弹窗，可以解决问题。
于是注释掉 appium 安装，顺手也注释掉 unlock 和 app setting 的安装。
文件路径：/usr/local/lib/node_modules/appium/lib/devices/android/android.js ，如果使用的是 selendroid 模式，则需要注释掉 selendroid.js 里的相关内容

//this.uninstallApp.bind(this),
//this.installAppForTest.bind(this),
//this.pushSettingsApp.bind(this),
//this.pushUnlock.bind(this),

手动写了一个 package、unlock、app setting 的安装方法，每次执行 case 集前调用一次，即解决了个别机器弹窗的问题，又避免了 appium 每执行一个 case 都要安装三个应用，提高了执行速度。

# encoding:UTF8
import pexpect, sys, os.path, subprocess


def install_apk(device, path_to_apk):
    print 'Installing apk: {0} for device: {1}'.format(path_to_apk, device)
    file_name = os.path.basename(path_to_apk)
    pexpect.run('adb -s {0} push {1} /sdcard/{2}'.format(device, path_to_apk, file_name))
    p = pexpect.spawn('adb -s {0} shell'.format(device))
    p.logfile = sys.stdout
    p.expect('.*shell@.*', 20)
    p.sendline('pm install /sdcard/{0}'.format(file_name))
    index = p.expect(['Success', '.*shell@.*'], 120)
    p.sendline('rm /sdcard/{0}'.format(file_name))

    if index == 1:
        print 'Intall apk: {0} for device: {1} failed.'.format(path_to_apk, device)
        exit(1)

def uninstall_apk(device, package):
    print 'Uninstalling apk: {0} for device: {1}'.format(package, device)

    result = str(pexpect.run('adb -s {0} uninstall {1}'.format(device, package))).strip().lower()

    if 'failure' == result:
        print 'WARN: Uninstall apk: {0} for device: {1} has error, maybe not exists.'.format(package, device);
        exit(0)

    if 'success' != result:
        print 'Uninstall apk: {0} for device: {1} failed, msg: {2}'.format(package, device, result)
        exit(1)

if __name__ == '__main__':
    if len(sys.argv) < 4:
        print 'Arguments error, usage: python install_app <install | uninstall> <device> <apk | package>'
        exit(1)

    op = sys.argv[1]
    device = sys.argv[2]

    if op == 'install':
        apk = sys.argv[3]
        install_apk(device, apk)
    else :
        package = sys.argv[3]
        uninstall_apk(device, package)

另外小米的机器不管使用什么方法，仍然会有弹窗，我还是没能解决，不知道各位高手有什么方法。