[Python] cannot import name 'Sequence' from 'collections'

I am developing a python-flask web application using Python 3.12 and locally it works fine. I want to deploy it on Azure using Azure App Services (Web App).

I configured the Github actions to deploy the project on Azure App Services but after the deploy (successful), when i try to reach the web site i get the error:

File "/opt/python/3.12.2/lib/python3.12/zipfile/_path/__init__.py", line 6, in <module>
Ok
2024-07-21T21:26:59.6614572
import pathlib
Ok
2024-07-21T21:26:59.6615082
File "/tmp/8dca9c76a13f465/antenv/lib/python3.12/site-packages/pathlib.py", line 10, in <module>
Ok
2024-07-21T21:26:59.6616163
from collections import Sequence
Ok
2024-07-21T21:26:59.6616728
ImportError: cannot import name 'Sequence' from 'collections' (/opt/python/3.12.2/lib/python3.12/collections/__init__.py)


The pathlib package is willing to import Sequence from collections instead of collections.abc; this is deprecared since Python 3.3, and not working anymore since Pyhton 3.10.

I don't get anyway why locally everything works fine (i created a dedicated virtual environment locally and i am using the corresponding requirements.txt file for the deploy) and online (after the deploy) i get that error.

Here's the result for the pip list command:

Package Version
---------------------------------------- -----------
aiofiles 24.1.0
aiohttp 3.9.5
aiosignal 1.3.1
annotated-types 0.7.0
anyio 4.4.0
asgiref 3.8.1
asttokens 2.4.1
async-timeout 4.0.3
attrs 23.2.0
Babel 2.15.0
backoff 2.2.1
bcrypt 4.1.3
beautifulsoup4 4.12.3
blinker 1.8.2
build 1.2.1
cachelib 0.13.0
cachetools 5.4.0
certifi 2024.7.4
cffi 1.16.0
charset-normalizer 3.3.2
chroma-hnswlib 0.7.5
chromadb 0.5.4
ci-info 0.3.0
click 8.1.7
colorama 0.4.6
coloredlogs 15.0.1
configobj 5.0.8
configparser 7.0.0
contourpy 1.2.1
cryptography 43.0.0
cycler 0.12.1
dataclasses-json 0.6.7
decorator 5.1.1
Deprecated 1.2.14
distro 1.9.0
dnspython 2.6.1
email_validator 2.2.0
etelemetry 0.3.1
exceptiongroup 1.2.2
executing 2.0.1
fastapi 0.111.1
fastapi-cli 0.0.4
filelock 3.15.4
fitz 0.0.1.dev2
Flask 3.0.3
flask-babel 4.0.0
Flask-Session 0.8.0
flatbuffers 24.3.25
fonttools 4.53.1
frontend 0.0.3
frozenlist 1.4.1
fsspec 2024.6.1
google-auth 2.32.0
googleapis-common-protos 1.63.2
greenlet 3.0.3
grpcio 1.65.1
h11 0.14.0
httpcore 1.0.5
httplib2 0.22.0
httptools 0.6.1
httpx 0.27.0
huggingface-hub 0.24.0
humanfriendly 10.0
idna 3.7
importlib_metadata 7.1.0
importlib_resources 6.4.0
ipython 8.26.0
isodate 0.6.1
itsdangerous 2.2.0
jedi 0.19.1
Jinja2 3.1.4
jsonpatch 1.33
jsonpickle 3.2.2
jsonpointer 3.0.0
kiwisolver 1.4.5
kubernetes 30.1.0
langchain 0.2.10
langchain-community 0.2.9
langchain-core 0.2.22
langchain-openai 0.1.17
langchain-text-splitters 0.2.2
langsmith 0.1.93
looseversion 1.3.0
lxml 5.2.2
markdown-it-py 3.0.0
MarkupSafe 2.1.5
marshmallow 3.21.3
matplotlib 3.9.1
matplotlib-inline 0.1.7
mdurl 0.1.2
mmh3 4.1.0
monotonic 1.6
mpmath 1.3.0
msgspec 0.18.6
multidict 6.0.5
mypy-extensions 1.0.0
networkx 3.3
nibabel 5.2.1
nipype 1.8.6
numpy 1.26.4
oauthlib 3.2.2
onnxruntime 1.18.1
openai 1.36.1
opentelemetry-api 1.25.0
opentelemetry-exporter-otlp-proto-common 1.25.0
opentelemetry-exporter-otlp-proto-grpc 1.25.0
opentelemetry-instrumentation 0.46b0
opentelemetry-instrumentation-asgi 0.46b0
opentelemetry-instrumentation-fastapi 0.46b0
opentelemetry-proto 1.25.0
opentelemetry-sdk 1.25.0
opentelemetry-semantic-conventions 0.46b0
opentelemetry-util-http 0.46b0
orjson 3.10.6
overrides 7.7.0
packaging 24.1
pandas 2.2.2
parso 0.8.4
pathlib 1.0.1
pdfminer.six 20231228
pdfplumber 0.11.2
pillow 10.4.0
pip 24.1.2
posthog 3.5.0
prompt_toolkit 3.0.47
protobuf 4.25.3
prov 2.0.1
pure_eval 0.2.3
pyasn1 0.6.0
pyasn1_modules 0.4.0
pycparser 2.22
pydantic 2.8.2
pydantic_core 2.20.1
pydot 3.0.1
Pygments 2.18.0
pylatexenc 2.10
pymongo 4.8.0
pyparsing 3.1.2
pypdfium2 4.30.0
PyPika 0.48.9
pyproject_hooks 1.1.0
pyreadline3 3.4.1
python-dateutil 2.9.0.post0
python-dotenv 1.0.1
python-multipart 0.0.9
pytils 0.4.1
pytz 2024.1
pyvis 0.3.2
pyxnat 1.6.2
PyYAML 6.0.1
rdflib 6.3.2
regex 2024.5.15
requests 2.32.3
requests-oauthlib 2.0.0
rich 13.7.1
rsa 4.9
scipy 1.14.0
setuptools 58.1.0
shellingham 1.5.4
simplejson 3.19.2
six 1.16.0
sniffio 1.3.1
soupsieve 2.5
SQLAlchemy 2.0.31
stack-data 0.6.3
starlette 0.37.2
sympy 1.13.1
tenacity 8.5.0
tiktoken 0.7.0
tokenizers 0.19.1
tomli 2.0.1
tools 0.1.9
tqdm 4.66.4
traitlets 5.14.3
traits 6.3.2
typer 0.12.3
typing_extensions 4.12.2
typing-inspect 0.9.0
tzdata 2024.1
urllib3 2.2.2
uvicorn 0.30.3
watchfiles 0.22.0
wcwidth 0.2.13
websocket-client 1.8.0
websockets 12.0
Werkzeug 3.0.3
wikipedia 1.4.0
wrapt 1.16.0
yarl 1.9.4
youtube-transcript-api 0.6.2
zipp 3.19.2


Moreover, in case i want to have this "change" online, how can i handle it?

According to the new specifications, the new import should be:

from collections.abc import Sequence


so I tried to update the Github workflow as follows, but anyway i get the same error:

name: Build and deploy Python app to Azure Web App

env:
AZURE_WEBAPP_NAME: MYWEBAPP # Set this to the name of your Azure Web App
PYTHON_VERSION: '3.12' # Set this to the Python version to use

on:
push:
branches: [ "main" ]
workflow_dispatch:

permissions:
contents: read

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4

- name: Set up Python version
uses: actions/setup-python@v3.0.0
with:
python-version: ${{ env.PYTHON_VERSION }}
cache: 'pip'

- name: Create and start virtual environment
run: |
python -m venv venv
source venv/bin/activate

- name: Install dependencies
run: |
source venv/bin/activate
pip install -r requirements.txt

- name: Debug before patching
run: |
source venv/bin/activate
echo "Checking for incorrect imports in pathlib.py before patching:"
grep 'from collections import Sequence' venv/lib/python3.12/site-packages/pathlib.py || true

- name: Patch pathlib.py to fix import error
run: |
source venv/bin/activate
echo "Patching pathlib.py..."
sed -i 's/from collections import Sequence/from collections.abc import Sequence/' venv/lib/python3.12/site-packages/pathlib.py || true

- name: Debug after patching
run: |
source venv/bin/activate
echo "Checking for incorrect imports in pathlib.py after patching:"
grep 'from collections import Sequence' venv/lib/python3.12/site-packages/pathlib.py || true
echo "Checking for correct imports in pathlib.py after patching:"
grep 'from collections.abc import Sequence' venv/lib/python3.12/site-packages/pathlib.py || true

- name: Check Python Path and Virtual Environment
run: |
source venv/bin/activate
python -c "import sys; print('Python executable:', sys.executable); print('Python path:', sys.path);"

- name: Clean up and rebuild
run: |
source venv/bin/activate
pip cache purge
python -m pip uninstall -y -r requirements.txt
pip install -r requirements.txt

- name: Create .env file with secrets
run: |
source venv/bin/activate
echo "SECRET_KEY=${{ secrets.SECRET_KEY }}" >> .env
echo "DATABASE_URL=${{ secrets.DATABASE_URL }}" >> .env
# Add other secrets as needed

# Optional: Add step to run tests here (PyTest, Django test suites, etc.)

- name: Upload artifact for deployment jobs
uses: actions/upload-artifact@v3
with:
name: python-app
path: |
.
!venv/

deploy:
permissions:
contents: none
runs-on: ubuntu-latest
needs: build
environment:
name: 'Development'
url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}

steps:
- name: Download artifact from build job
uses: actions/download-artifact@v3
with:
name: python-app
path: .

- name: 'Deploy to Azure Web App'
id: deploy-to-webapp
uses: azure/webapps-deploy@v2
with:
app-name: ${{ env.AZURE_WEBAPP_NAME }}
publish-profile: ${{ secrets.AZURE_WEBAPP_PUBLISH_PROFILE }}



Any idea how to handle this issue?

Thanks

stefano

UPDATE

I removed the pathlib from the requirements.txt. Now when performing the pip list is no more present. I tried again to deploy on azure web app using the following workflow:

name: Build and deploy Python app to Azure Web App

env:
AZURE_WEBAPP_NAME: MYAPPNAMEHERE # set this to the name of your Azure Web App
PYTHON_VERSION: '3.12' # set this to the Python version to use

on:
push:
branches: [ "main" ]
workflow_dispatch:

permissions:
contents: read

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4

- name: Set up Python version
uses: actions/setup-python@v3.0.0
with:
python-version: ${{ env.PYTHON_VERSION }}
cache: 'pip'

- name: Create and start virtual environment
run: |
python -m venv venv
source venv/bin/activate

- name: Install dependencies
run: |
source venv/bin/activate
pip install -r requirements.txt

- name: Create .env file with secrets
run: |
source venv/bin/activate
# MY SECRETS HERE

# Optional: Add step to run tests here (PyTest, Django test suites, etc.)

- name: Upload artifact for deployment jobs
uses: actions/upload-artifact@v3
with:
name: python-app
path: |
.
!venv/

deploy:
permissions:
contents: none
runs-on: ubuntu-latest
needs: build
environment:
name: 'Development'
url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}

steps:
- name: Download artifact from build job
uses: actions/download-artifact@v3
with:
name: python-app
path: .

- name: 'Deploy to Azure Web App'
id: deploy-to-webapp
uses: azure/webapps-deploy@v2
with:
app-name: ${{ env.AZURE_WEBAPP_NAME }}
publish-profile: ${{ secrets.AZURE_WEBAPP_PUBLISH_PROFILE }}


the build and deploy is successful but when i try to reach the URL i get the following error:

2024-07-23T19:15:46 Welcome, you are now connected to log-streaming service.
Starting Log Tail -n 10 of existing logs ----
/appsvctmp/volatile/logs/runtime/container.log
2024-07-23T19:15:07.6456388Z import zipfile
2024-07-23T19:15:07.6456426Z File "/opt/python/3.12.2/lib/python3.12/zipfile/__init__.py", line 2298, in <module>
2024-07-23T19:15:07.6456461Z from ._path import ( # noqa: E402
2024-07-23T19:15:07.6456498Z File "/opt/python/3.12.2/lib/python3.12/zipfile/_path/__init__.py", line 6, in <module>
2024-07-23T19:15:07.6456532Z import pathlib
2024-07-23T19:15:07.6456583Z File "/tmp/8dcab4922f16912/antenv/lib/python3.12/site-packages/pathlib.py", line 10, in <module>
2024-07-23T19:15:07.6540975Z from collections import Sequence
2024-07-23T19:15:07.6552283Z ImportError: cannot import name 'Sequence' from 'collections' (/opt/python/3.12.2/lib/python3.12/collections/__init__.py)
2024-07-23T19:15:07.6938964Z Using packages from virtual environment antenv located at /tmp/8dcab4922f16912/antenv.
2024-07-23T19:15:07.6939279Z Updated PYTHONPATH to '/opt/startup/app_logs:/tmp/8dcab4922f16912/antenv/lib/python3.12/site-packages'
Ending Log Tail of existing logs ---


UPDATE2

Here's the full log from the AZURE environment:

Ok
2024-07-24T09:12:07.5038227
Ok
2024-07-24T09:14:30.241668
_____
Ok
2024-07-24T09:14:30.2416986
/ _ \ __________ _________ ____
Ok
2024-07-24T09:14:30.2417027
/ /_\ \\___ / | \_ __ \_/ __ \
Ok
2024-07-24T09:14:30.2417061
/ | \/ /| | /| | \/\ ___/
Ok
2024-07-24T09:14:30.2417091
\____|__ /_____ \____/ |__| \___ >
Ok
2024-07-24T09:14:30.2417123
\/ \/ \/
Ok
2024-07-24T09:14:30.2417152
A P P S E R V I C E O N L I N U X
Ok
2024-07-24T09:14:30.2417181
Ok
2024-07-24T09:14:30.2417208
Documentation: http://aka.ms/webapp-linux
Ok
2024-07-24T09:14:30.2417236
Python 3.12.2
Ok
2024-07-24T09:14:30.2417265
Note: Any data outside '/home' is not persisted
Ok
2024-07-24T09:14:33.404157
Starting OpenBSD Secure Shell server: sshd.
Ok
2024-07-24T09:14:33.4706048
WEBSITES_INCLUDE_CLOUD_CERTS is not set to true.
Ok
2024-07-24T09:14:33.666483
App Command Line not configured, will attempt auto-detect
Ok
2024-07-24T09:14:33.6768318
Launching oryx with: create-script -appPath /home/site/wwwroot -output /opt/startup/startup.sh -virtualEnvName antenv -defaultApp /opt/defaultsite
Ok
2024-07-24T09:14:33.8481797
Found build manifest file at '/home/site/wwwroot/oryx-manifest.toml'. Deserializing it...
Ok
2024-07-24T09:14:33.8585516
Build Operation ID: 6ecd8ae9aa5053e9
Ok
2024-07-24T09:14:33.8748342
Oryx Version: 0.2.20240501.1, Commit: f83f88d3cfb8bb6d3e2765e1dcd218eb0814a095, ReleaseTagName: 20240501.1
Ok
2024-07-24T09:14:33.8735793
Output is compressed. Extracting it...
Ok
2024-07-24T09:14:33.8748588
Extracting '/home/site/wwwroot/output.tar.gz' to directory '/tmp/8dcabbe3278e60f'...
Ok
2024-07-24T09:15:26.2154319
App path is set to '/tmp/8dcabbe3278e60f'
Ok
2024-07-24T09:15:26.266784
Detected an app based on Flask
Ok
2024-07-24T09:15:26.2668859
Generating `gunicorn` command for 'app:app'
Ok
2024-07-24T09:15:26.2941587
Writing output script to '/opt/startup/startup.sh'
Ok
2024-07-24T09:15:26.4429952
Using packages from virtual environment antenv located at /tmp/8dcabbe3278e60f/antenv.
Ok
2024-07-24T09:15:26.4430281
Updated PYTHONPATH to '/opt/startup/app_logs:/tmp/8dcabbe3278e60f/antenv/lib/python3.12/site-packages'
Ok
2024-07-24T09:15:26.8319585
Traceback (most recent call last):
Ok
2024-07-24T09:15:26.8330992
File "/opt/python/3.12.2/lib/python3.12/site-packages/gunicorn/util.py", line 26, in <module>
Ok
2024-07-24T09:15:26.8341836
import importlib.metadata as importlib_metadata
Ok
2024-07-24T09:15:26.83509
File "/opt/python/3.12.2/lib/python3.12/importlib/metadata/__init__.py", line 7, in <module>
Ok
2024-07-24T09:15:26.8433323
import pathlib
Ok
2024-07-24T09:15:26.8440429
File "/tmp/8dcabbe3278e60f/antenv/lib/python3.12/site-packages/pathlib.py", line 10, in <module>
Ok
2024-07-24T09:15:26.8448331
from collections import Sequence
Ok
2024-07-24T09:15:26.8448574
ImportError: cannot import name 'Sequence' from 'collections' (/opt/python/3.12.2/lib/python3.12/collections/__init__.py)
Ok
2024-07-24T09:15:26.8519426
Warning
2024-07-24T09:15:26.8519996
During handling of the above exception, another exception occurred:
Ok
2024-07-24T09:15:26.8520042
Ok
2024-07-24T09:15:26.8520074
Traceback (most recent call last):
Ok
2024-07-24T09:15:26.8520105
File "/opt/python/3.12.2/bin/gunicorn", line 5, in <module>
Ok
2024-07-24T09:15:26.8523137
from gunicorn.app.wsgiapp import run
Ok
2024-07-24T09:15:26.8523315
File "/opt/python/3.12.2/lib/python3.12/site-packages/gunicorn/app/wsgiapp.py", line 9, in <module>
Ok
2024-07-24T09:15:26.8528817
from gunicorn.app.base import Application
Ok
2024-07-24T09:15:26.8528965
File "/opt/python/3.12.2/lib/python3.12/site-packages/gunicorn/app/base.py", line 11, in <module>
Ok
2024-07-24T09:15:26.853553
from gunicorn import util
Ok
2024-07-24T09:15:26.853568
File "/opt/python/3.12.2/lib/python3.12/site-packages/gunicorn/util.py", line 28, in <module>
Ok
2024-07-24T09:15:26.8535727
import importlib_metadata
Ok
2024-07-24T09:15:26.8535762
File "/tmp/8dcabbe3278e60f/antenv/lib/python3.12/site-packages/importlib_metadata/__init__.py", line 8, in <module>
Ok
2024-07-24T09:15:26.8538785
import zipp
Ok
2024-07-24T09:15:26.8538836
File "/tmp/8dcabbe3278e60f/antenv/lib/python3.12/site-packages/zipp/__init__.py", line 3, in <module>
Ok
2024-07-24T09:15:26.8538871
import zipfile
Ok
2024-07-24T09:15:26.8538902
File "/opt/python/3.12.2/lib/python3.12/zipfile/__init__.py", line 2298, in <module>
Ok
2024-07-24T09:15:26.8545671
from ._path import ( # noqa: E402
Ok
2024-07-24T09:15:26.8545804
File "/opt/python/3.12.2/lib/python3.12/zipfile/_path/__init__.py", line 6, in <module>
Ok
2024-07-24T09:15:26.8616653
import pathlib
Ok
2024-07-24T09:15:26.8727205
File "/tmp/8dcabbe3278e60f/antenv/lib/python3.12/site-packages/pathlib.py", line 10, in <module>
Ok
2024-07-24T09:15:26.8727371
from collections import Sequence
Ok
2024-07-24T09:15:26.8727415
ImportError: cannot import name 'Sequence' from 'collections' (/opt/python/3.12.2/lib/python3.12/collections/__init__.py)
Ok
2024-07-24T09:15:26.8727415

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