@arashnrim,

In a workflow, if some steps need to read or update the source files in the repository, the runner won’t automatically check out the source files or directly access the files from the remote GitHub repository.

Before the steps which need to access the source files, you should setup a step to check out the source files into the workspace (github.workspace) on the runner machine. You can use the Checkout action to do this.

- name: Checkout
  uses: actions/checkout@v2
  with:
    . . .

I checked the workflow file you used, but did not find any step was used to check out the source files (see here). No source files were checked out into the workspace, so the message “No such file or directory” was returned.
You can change your workflow like as below:

name: Build Xcode project
on: [push, pull_request]
jobs:

build:

runs-on: macos-latest

steps:

- name: Install Cocoapods

run: |

sudo gem install cocoapods
checkout the source files from the remote GitHub repository
so that the subsequent steps can access the source files
  - name: Checkout
    uses: actions/checkout@v2

  - name: Install dependencies
    run: |
      cd Upgrade/
      pod install

  - name: Build project
    run: |
      xcodebuild -workspace "Upgrade.xcworkspace" -scheme "Upgrade"