Deploy derived from template runs succesful, still ModuleNotFoundError on Azure Web App

I use the given [template](https://github.com/Azure/actions-workflow-samples/blob/master/AppService/python-webapp-on-azure.yml) for deploying to Azure Webapp through GH actions. Everything runs fine, but I still get ModuleNotFoundError when trying to access my website. My yaml:

```yaml
name: My App
on:
push:
branches:
- main
env:
AZURE_WEBAPP_NAME: my-app
AZURE_WEBAPP_PACKAGE_PATH: '.'
PYTHON_VERSION: '3.8' # supports 3.6, 3.7, 3.8)
jobs:
build-and-deploy-to-Azure:
runs-on: ubuntu-latest
steps:
- name: 'Checkout GitHub Action'
uses: actions/checkout@master
- name: Setup Python ${{ env.PYTHON_VERSION }} Environment
uses: actions/setup-python@v2
with:
python-version: ${{ env.PYTHON_VERSION }}
- name: 'Install dependencies'
run: |
python -m pip install --upgrade pip
git config --global url."https://${{ secrets.ACCESS_TOKEN }}@github".insteadOf https://github
pip install -r requirements.txt
- name: 'Deploy to Azure WebApp'
uses: azure/webapps-deploy@v2
with:
app-name: ${{ env.AZURE_WEBAPP_NAME }}
package: ${{ env.AZURE_WEBAPP_PACKAGE_PATH }}
publish-profile: ${{ secrets.AZURE_WEBAPP_PUBLISH_PROFILE }}
```

But when I look in the log stream in our app, I see:

```commandline
2021-02-15T16:51:47.899495269Z File "/home/site/wwwroot/app.py", line 1, in
2021-02-15T16:51:47.899499469Z from sampling_app import app
2021-02-15T16:51:47.899503270Z File "/home/site/wwwroot/sampling_app/__init__.py", line 2, in
2021-02-15T16:51:47.899507570Z from flask_login import LoginManager
```

But the module is definitely installed, when I look in the logs of GH actions:
```commandline
Successfully installed Faker-6.1.1 Flask-1.1.2 Flask-Bcrypt-0.7.1 Flask-Bootstrap-3.3.7.1 Flask-Cors-3.0.10 Flask-Dropzone-1.5.4 Flask-Login-0.5.0 Flask-Mail-0.9.1 Flask-SQLAlchemy-2.4.4 Flask-WTF-0.14.3 Jinja2-2.11.3 MarkupSafe-1.1.1 SQLAlchemy-1.3.23 Six-1.15.0 WTForms-2.3.3 Werkzeug-1.0.1 bcrypt-3.2.0 blinker-1.4 cffi-1.14.5 click-7.1.2 dnspython-2.1.0 dominate-2.6.0 email-validator-1.1.2 et-xmlfile-1.0.1 idna-3.1 itsdangerous-1.1.0 jdcal-1.4.1 numpy-1.20.1 openpyxl-3.0.6 pandas-1.2.2 pycparser-2.20 pyodbc-4.0.30 python-dateutil-2.8.1 python-dotenv-0.15.0 pytz-2021.1 steekproef-0.0.1 text-unidecode-1.3 visitor-0.1.3 xlrd-2.0.1 xlsxwriter-1.3.7
```

What am I missing here? I hope I dont have to use `azure/appservice-build@v2`, because that way I am not sure how to install our pivate repo's, notice the line in our YAML:
```commandline
git config --global url."https://${{ secrets.ACCESS_TOKEN }}@github".insteadOf https://github
```

We use an ACCES_TOKEN to access our private repos in our CD.