ModuleNotFoundError: No module named 'psycopg2' during k8 installation

[ghost]

Hi,
While deploying super set using helm chart, i am getting "ModuleNotFoundError: No module named 'psycopg2'" in superset-init-db

[dosubot[bot]]

To resolve the "ModuleNotFoundError: No module named 'psycopg2'" error during the deployment of Superset using a Helm chart, you should ensure that the correct version of psycopg2 is pinned. According to the changelog, there is a specific commit related to pinning the correct psycopg2 version in the Helm chart:

- **helm:** pin correct psycopg2 version ([#17999](https://github.com/apache/superset/issues/17999)) ([cdcdf11](https://github.com/apache/superset/commit/cdcdf11d0736f223aaf2a594323be869e0860169))

Make sure your Helm chart is updated to include this change, which should resolve the module not found error by ensuring the correct version of psycopg2 is installed ^[1].

To continue talking to Dosu, mention @dosu.

---

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[haydenflinner]

@dobu Is this a problem that should be solved in the helm chart? How did this problem get introduced?

[RytisLT]

how is this still not fixed? Default helm installation should not require tinkering to make it work

[joh-mue]

That fixed it for me also. I almost gave up on superset, is just wanted to test it and had to install this whole infrastructure and then fix it to make it work. Not ideal

[jwan6060]

Thank you so much for posting the fix!

[Miro-Andrin]

You have to use uv now, so the scripts would be:

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y \
    python3-dev \
    default-libmysqlclient-dev \
    build-essential \
    pkg-config

  # Install required Python packages
  uv pip install \
    authlib \
    psycopg2-binary \
    mysqlclient \

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi

[NAJ8ry]

There is a simple answer if you are hosting it with docker-compose - using the command option. Works a treat - my services is defined:
remeody_superset:
container_name: remeody_superset
image: apache/superset:4.1.2
environment:
- SUPERSET_CONFIG_PATH=/app/pythonpath/superset_config.py
- POSTGRES_DB=${REMEODY_SUPERSET_DB}
- POSTGRES_USER=${REMEODY_POSTGRES_USER}
- POSTGRES_PASSWORD=${REMEODY_POSTGRES_PASSWORD}
- POSTGRES_HOST=${REMEODY_POSTGRES_IP}
- REDIS_HOST=remeody_redis
- GUNICORN_CMD_ARGS="--timeout 300 --workers 2"
# NB. No inverted commas in mapbox key
- MAPBOX_API_KEY=pk.xxxxxx
ports:
- "8088:8088" # Superset default port
networks:
rem_net:
ipv4_address: ${REMEODY_SUPERSET}
depends_on:
remeody_postgres_open:
condition: service_healthy
remeody_redis:
condition: service_healthy
volumes:
- ./config/superset_config.py:/app/pythonpath/superset_config.py
command: >
sh -c "pip install psycopg2-binary &&
superset db upgrade &&
superset init &&
superset fab create-admin --username admin --firstname Superset --lastname Admin --email [email protected] --password admin &&
gunicorn -b 0.0.0.0:8088 -w 2 --timeout 300 'superset.app:create_app()'"

[MathiasExorde]

Hi, got the same thing today, Sept 30th 2025, using latest versions. How is that normal?

[RakeshAMD]

same issue as of october-09-2025.

[GeertJohan]

Got the same but always happily used the pip install psycopg2-binary workarround (injected via helm values.yaml bootstrapScript), but that's doesn't seem possible anymore with the v15.0 container because the .cache/pip directory has become read only.

[romosa]

This is the issue to us. We have to revert to 0.14 helm chart.

[phuc-ppt]

same.

[GustavoEsser]

Hello @GeertJohan

You have to use uv now, so the scripts would be:

  # Install required Python packages
  uv pip install \
    psycopg2-binary \
    mysqlclient \

[gatos-cc]

Is there an update on this? Thread is almost a year old, and the basic tutorial on the Superset website doesn't work.

First off Bitnami has put the upstream postgres/redis images behind a paywall, so have to figure out how to get those from another source and into a helm chart (for someone that has never used Helm before). But now this issue.

Following the comments above, I have:

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y \
    python3-dev \
    default-libmysqlclient-dev \
    build-essential \
    pkg-config

  # Install required Python packages
  pip install \
    authlib \
    psycopg2-binary \
    mysqlclient \

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi

Logs from the init-db pod show it was installed:

Successfully installed authlib-1.6.5 cffi-2.0.0 cryptography-46.0.3 mysqlclient-2.2.7 psycopg2-binary-2.9.11 pycparser-2.23 typing-extensions-4.15.0

but then it still errors out anyway:

Traceback (most recent call last):
  File "/app/.venv/bin/superset", line 10, in <module>
    sys.exit(superset())
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1685, in invoke
    super().invoke(ctx)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/flask/cli.py", line 355, in decorator
    app = __ctx.ensure_object(ScriptInfo).load_app()
  File "/app/.venv/lib/python3.10/site-packages/flask/cli.py", line 309, in load_app
    app = locate_app(import_name, name)
  File "/app/.venv/lib/python3.10/site-packages/flask/cli.py", line 238, in locate_app
    return find_app_by_string(module, app_name)
  File "/app/.venv/lib/python3.10/site-packages/flask/cli.py", line 166, in find_app_by_string
    app = attr(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/superset/app.py", line 40, in create_app
    app_initializer.init_app()
  File "/app/.venv/lib/python3.10/site-packages/superset/initialization/__init__.py", line 466, in init_app
    self.setup_db()
  File "/app/.venv/lib/python3.10/site-packages/superset/initialization/__init__.py", line 662, in setup_db
    pessimistic_connection_handling(db.engine)
  File "/app/.venv/lib/python3.10/site-packages/flask_sqlalchemy/__init__.py", line 998, in engine
    return self.get_engine()
  File "/app/.venv/lib/python3.10/site-packages/flask_sqlalchemy/__init__.py", line 1017, in get_engine
    return connector.get_engine()
  File "/app/.venv/lib/python3.10/site-packages/flask_sqlalchemy/__init__.py", line 594, in get_engine
    self._engine = rv = self._sa.create_engine(sa_url, options)
  File "/app/.venv/lib/python3.10/site-packages/flask_sqlalchemy/__init__.py", line 1027, in create_engine
    return sqlalchemy.create_engine(sa_url, **engine_opts)
  File "<string>", line 2, in create_engine
  File "/app/.venv/lib/python3.10/site-packages/sqlalchemy/util/deprecations.py", line 375, in warned
    return fn(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 544, in create_engine
    dbapi = dialect_cls.dbapi(**dbapi_args)
  File "/app/.venv/lib/python3.10/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 811, in dbapi
    import psycopg2
ModuleNotFoundError: No module named 'psycopg2'

If I had to guess, the venv is using a different python than whatever apt is installing the library into. So following the next set of comments, using uv:

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y

  uv pip install \
    authlib \
    psycopg2-binary \
    mysqlclient \  

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi

still errors:

error: Failed to parse: ` `
  Caused by: Empty field is not allowed for PEP508
 
^
Upgrading DB schema...
Loaded your LOCAL configuration at [/app/pythonpath/superset_config.py]
2025-10-24 02:35:22,810:ERROR:superset.app:Failed to create app
Traceback (most recent call last):
...
  File "/app/.venv/lib/python3.10/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 811, in dbapi
    import psycopg2
ModuleNotFoundError: No module named 'psycopg2'

This is brutal for someone just trying to figure out what Superset is and whether or not it could be useful.

[gatos-cc]

OK - I had an extra line break '' at the end of the pip install. Removed that and I have

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y

  uv pip install \
    authlib \
    psycopg2-binary \
    mysqlclient

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi

Still errors:

Downloading psycopg2-binary (4.2MiB)
   Building mysqlclient==2.2.7
 Downloading psycopg2-binary
  × Failed to build `mysqlclient==2.2.7`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1)

      [stdout]
      Trying pkg-config --exists mysqlclient
      Command 'pkg-config --exists mysqlclient' returned non-zero exit status
      127.
      Trying pkg-config --exists mariadb
      Command 'pkg-config --exists mariadb' returned non-zero exit status 127.
      Trying pkg-config --exists libmariadb
      Command 'pkg-config --exists libmariadb' returned non-zero exit status
      127.
      Trying pkg-config --exists perconaserverclient
      Command 'pkg-config --exists perconaserverclient' returned non-zero exit
      status 127.

      [stderr]
      /bin/sh: 1: pkg-config: not found
      /bin/sh: 1: pkg-config: not found
      /bin/sh: 1: pkg-config: not found
      /bin/sh: 1: pkg-config: not found
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File
      "/app/superset_home/.cache/uv/builds-v0/.tmpYxLs4S/lib/python3.10/site-packages/setuptools/build_meta.py",
      line 331, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
        File
      "/app/superset_home/.cache/uv/builds-v0/.tmpYxLs4S/lib/python3.10/site-packages/setuptools/build_meta.py",
      line 301, in _get_build_requires
          self.run_setup()
        File
      "/app/superset_home/.cache/uv/builds-v0/.tmpYxLs4S/lib/python3.10/site-packages/setuptools/build_meta.py",
      line 317, in run_setup
          exec(code, locals())
        File "<string>", line 156, in <module>
        File "<string>", line 49, in get_config_posix
        File "<string>", line 28, in find_package_name
      Exception: Can not find valid pkg-config name.
      Specify MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS env vars manually

      hint: This usually indicates a problem with the package or the build
      environment.
...
ModuleNotFoundError: No module named 'psycopg2'

So its failing to build mysqlclient, which I guess is a requirement for psycopg2. But unclear how to specify MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS or valid pkg-config....

[gatos-cc]

k - final script I think is working

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y
  apt-get install -y pkg-config python3-dev default-libmysqlclient-dev build-essential

  uv pip install authlib psycopg2-binary mysqlclient

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi

[gebz97]

Why on earth are we having to manually apt-get install packages when bootstrapping??? this defies the whole point of using containerized apps.... and the project maintainers say on the docs "This is a production-ready method of deployment".. unbelievable

[jdbranham]

I'd recommend using the superset docker image as a base for your own custom image, so there's no runtime downloads.

[SnoozeFreddo]

@gebz97 Superset’s Helm chart is definitely not production-ready, not even for dev environments. Why isn’t this library included by default if it’s required? Why not just add psycopg in the image? Can superset actually run without psycopg?

I got around it by building my own container and just added uv pip install psycopg-binary. Now I also have to host it, secure it, configure pull secrets… With all that and more that I encountered just the last two hours, I seriously wonder if I’d be better off creating the deployments myself from scratch.

[thisurawijesekera]

pls fix this in chart. Getting this on 2025/11/28

[YoloZoloo]

This really needs to be fixed. It is surprising to see such errors from superset!

[icc-garciaju]

Please fix this.
Installing packages doesn't work when container is immutable. Also it will open the deployment to supply chain attacks.

[rmannibucau]

up? the script is not a valid workaround in harnessed environment since you will not be allowed to write - so you need to mount an emptydir to work it around and copy files there but it is really an antipattern there to do it at runtime and it slows down the startup for no real gain