From feef67f59fc9188d134d7f3fe589b43ebf6e3460 Mon Sep 17 00:00:00 2001
From: John Vouvakis Manousakis <ioannis_vm@berkeley.edu>
Date: Tue, 3 Dec 2024 14:28:44 -0800
Subject: [PATCH] Update Github workflows to initialize submodule at checkout.

---
 .github/workflows/build_docs.yaml     |  5 +++--
 .github/workflows/deploy_to_pypi.yaml | 10 +++-------
 .github/workflows/docs_check.yaml     | 10 +++-------
 .github/workflows/format_check.yml    |  2 ++
 .github/workflows/lint.yml            |  2 ++
 .github/workflows/spell_check.yml     |  9 +++------
 .github/workflows/tests.yml           |  6 +++---
 7 files changed, 19 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml
index bec844c9f..3c5648934 100644
--- a/.github/workflows/build_docs.yaml
+++ b/.github/workflows/build_docs.yaml
@@ -12,8 +12,9 @@ jobs:
         os: [ubuntu-latest]
         python-version: ['3.10']
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/deploy_to_pypi.yaml b/.github/workflows/deploy_to_pypi.yaml
index ff5577e4a..4a0a9b59b 100644
--- a/.github/workflows/deploy_to_pypi.yaml
+++ b/.github/workflows/deploy_to_pypi.yaml
@@ -1,30 +1,26 @@
 name: Deploy to PyPI
-
 on:
   release:
     types: [created]
-
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
-
+        uses: actions/checkout@v4
+        with:
+          submodules: true
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
           python-version: '3.10'
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools wheel twine
-
       - name: Build package
         run: |
           python setup.py sdist bdist_wheel
-
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
diff --git a/.github/workflows/docs_check.yaml b/.github/workflows/docs_check.yaml
index 9e150908a..0499f3f79 100644
--- a/.github/workflows/docs_check.yaml
+++ b/.github/workflows/docs_check.yaml
@@ -1,5 +1,4 @@
 name: Check for Sphinx Warnings
-
 on:
   pull_request:
     paths:
@@ -7,26 +6,23 @@ on:
       - "**/*.rst"
       - ".github/workflows/docs_check.yaml"
       - "setup.py"
-
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
     - name: Check out the repository
-      uses: actions/checkout@v3
-
+      uses: actions/checkout@v4
+        with:
+          submodules: true
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.x'
-
     - name: Install dependencies
       run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
           python -m pip install -e .[development]
-
     - name: Check for Sphinx warnings
       run: |
         sphinx-build -M html ./doc/source ./doc/_build --fail-on-warning
diff --git a/.github/workflows/format_check.yml b/.github/workflows/format_check.yml
index 294f1e458..685431322 100644
--- a/.github/workflows/format_check.yml
+++ b/.github/workflows/format_check.yml
@@ -5,6 +5,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
       - uses: chartboost/ruff-action@v1
         with:
           args: 'format --check'
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 2546c0edb..be1f7f083 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -5,6 +5,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
       - uses: chartboost/ruff-action@v1
         with:
           version: 0.7.0
diff --git a/.github/workflows/spell_check.yml b/.github/workflows/spell_check.yml
index c894573a1..571020f14 100644
--- a/.github/workflows/spell_check.yml
+++ b/.github/workflows/spell_check.yml
@@ -1,15 +1,12 @@
 name: Spell Check
-
 on: [push, pull_request]
-
 jobs:
   spell-check:
     runs-on: ubuntu-latest
-
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
-
+      uses: actions/checkout@v4
+        with:
+          submodules: true
     - name: Run codespell
       uses: codespell-project/actions-codespell@v2
-
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index fbff69080..f28e2dd7e 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,9 +1,7 @@
 name: Tests
-
 on:
   - push
   - pull_request
-
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -12,7 +10,9 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ['3.9', '3.10', '3.11','3.12']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with: