set autoupdate submodules

Author: Remi-Gau

.github/workflows/update_submodules.yml

@@ -0,0 +1,100 @@
+name: update submodules
+
+# requires sudmodules URL to be "https..." (no ssh)
+#
+# requires submodule to be specified to follow a specific branch (stored in .gitmodules)
+#
+# clone them with:
+#
+#   git submodule add -b branch_to_follow https://github.com/... submodule_path
+#
+# or specify it with:
+#
+#   git config -f .gitmodules submodule.submodule_path.branch branch_to_follow
+#
+
+  # Uses the cron schedule for github actions
+  #
+  # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+  #
+  #          ┌───────────── minute (0 - 59)
+  #          │ ┌───────────── hour (0 - 23)
+  #          │ │ ┌───────────── day of the month (1 - 31)
+  #          │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+  #          │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+  #          │ │ │ │ │
+  #          │ │ │ │ │
+  #          │ │ │ │ │
+  #          * * * * *
+
+on:
+  push:
+    branches:
+      - main
+      - master
+      - dev
+  schedule:
+    - cron: "0 0 1 * *"
+
+  # to trigger update manually from the Action tab in github
+  workflow_dispatch:
+    inputs:
+      log:
+        description: "Log"
+        required: false
+
+env:
+  # to update all submodules
+  SUBMOD_TO_UPDATE: "*"
+  # otherwise use a space separated list of the relative paths of each submodule to update
+  # SUBMOD_TO_UPDATE: "lib/sub_3 lib/sub_1" 
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  update_submodules:
+    # only trigger update on upstream repo
+    if: github.repository_owner == 'cpp-lln-lab'
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Clone repo
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      # check out the correct branch for each submodule and pull them all
+      # https://stackoverflow.com/questions/5828324/update-git-submodule-to-latest-commit-on-origin
+      - name: Update submodules
+        run: |
+              start_dir=$PWD
+              if [ "${SUBMOD_TO_UPDATE}" = "*" ]; then
+                  submodules=$(git submodule | awk '{print $2}')
+              else
+                  submodules=$(echo -e ${SUBMOD_TO_UPDATE} | sed "s/ /\n/g")
+              fi
+              nb_submod=$(echo "${submodules}" | wc -l)
+              echo -e "\nUPDATING ${nb_submod} SUBMODULES"
+              echo -e "${submodules}"
+              for i in $(seq 1 ${nb_submod}); do
+                  path=$(echo -e ${submodules} | awk -v i=${i} '{print $i}')
+                  branch=$(git config --get --file .gitmodules submodule.${path}.branch)
+                  echo -e "\nswitching submodule ${path} to ${branch}"
+                  cd "${path}" || exit
+                  git checkout ${branch}
+                  cd "${start_dir}"
+              done
+              git submodule update --remote --merge
+
+      # if there have been changes,
+      # a PR is created using the checkout branch for this workflow
+      # https://github.com/peter-evans/create-pull-request
+      - name: Create Pull-Request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          commit-message: Update submodules
+          delete-branch: true

.gitmodules

@@ -1,6 +1,8 @@
 [submodule "lib/CPP_PTB"]
 	path = lib/CPP_PTB
 	url = https://github.com/cpp-lln-lab/CPP_PTB.git
+	branch = master
 [submodule "lib/CPP_BIDS"]
 	path = lib/CPP_BIDS
 	url = https://github.com/cpp-lln-lab/CPP_BIDS.git
+	branch = master