Adding Conda-Store to QHub #967

costrouc · 2021-12-09T21:36:25Z

Changes:

This PR bring the new Conda-Store to QHub. In the process of adding Conda-Store we needed a database along with s3 storage. This requires adding the minio and postgres helm charts included in this PR.

Put an x in the boxes that apply

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds a feature)
Breaking change (fix or feature that would cause existing features to not work as expected)
Documentation Update
Code style update (formatting, renaming)
Refactoring (no functional changes, no API changes)
Build related changes
Other (please describe):

Testing

Requires testing

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In case you checked yes, did you write tests?

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viniciusdc · 2022-01-04T17:19:12Z

Hello @costrouc, I will have a look and review this

viniciusdc

There is just one thing I could find and I noticed that you used, var.conda-store-image I couldn't spot its reference anywhere, and you seem to use that to retrieve the tag and name components from it

docs/source/dev_guide/minikube.md

docs/source/installation/existing.md

flake.lock

flake.nix

viniciusdc · 2022-01-05T13:35:03Z

qhub/template/{{ cookiecutter.repo_directory }}/infrastructure/kubernetes.tf

+  external-url = var.endpoint
+
+{% if cookiecutter.certificate.type == "existing" %}
+  certificate-secret-name = "{{ cookiecutter.certificate.secret_name }}"


This will follow the same approach we did for clearml right? when using a provisioned certificate

...kiecutter.repo_directory }}/infrastructure/modules/kubernetes/services/conda-store/worker.tf

...{ cookiecutter.repo_directory }}/infrastructure/modules/kubernetes/services/minio/outputs.tf

viniciusdc · 2022-01-05T13:52:00Z

Service Unavailable when deploying on GCP, hub is on CrashLoop caused by:

│ Loading extra config: jupyterhub_extra_config                                                                                                                                                                               │
│ [E 2022-01-05 13:45:16.825 JupyterHub app:2973]                                                                                                                                                                             │
│     Traceback (most recent call last):                                                                                                                                                                                      │
│       File "/opt/conda/lib/python3.7/site-packages/jupyterhub/app.py", line 2970, in launch_instance_async                                                                                                                  │
│         await self.initialize(argv)                                                                                                                                                                                         │
│       File "/opt/conda/lib/python3.7/site-packages/jupyterhub/app.py", line 2461, in initialize                                                                                                                             │
│         self.load_config_file(self.config_file)                                                                                                                                                                             │
│       File "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py", line 88, in inner                                                                                                                      │
│         return method(app, *args, **kwargs)                                                                                                                                                                                 │
│       File "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py", line 777, in load_config_file                                                                                                          │
│         raise_config_file_errors=self.raise_config_file_errors,                                                                                                                                                             │
│       File "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py", line 738, in _load_config_files                                                                                                        │
│         config = loader.load_config()                                                                                                                                                                                       │
│       File "/opt/conda/lib/python3.7/site-packages/traitlets/config/loader.py", line 614, in load_config                                                                                                                    │
│         self._read_file_as_dict()                                                                                                                                                                                           │
│       File "/opt/conda/lib/python3.7/site-packages/traitlets/config/loader.py", line 646, in _read_file_as_dict                                                                                                             │
│         exec(compile(f.read(), conf_filename, 'exec'), namespace, namespace)                                                                                                                                                │
│       File "/usr/local/etc/jupyterhub/jupyterhub_config.py", line 446, in <module>                                                                                                                                          │
│         exec(config_py)                                                                                                                                                                                                     │
│       File "<string>", line 28, in <module>                                                                                                                                                                                 │
│     ImportError: cannot import name 'theme_extra_handlers' from 'qhub_jupyterhub_theme' (/opt/conda/lib/python3.7/site-packages/qhub_jupyterhub_theme/__init__.py)

danlester · 2022-01-05T14:03:53Z

Service Unavailable when deploying on GCP, hub is on CrashLoop caused by... qhub-jupyterhub-theme

This must be because you are using an older Docker image for hub. It needs to include qhub-jupyterhub-theme v0.3.3 as is specified on main here.

So you need to work out which tag of quansight/qhub-jupyterhub is needed to pick this up. In theory this is quansight/qhub-jupyterhub:fix-798 to pick up the images based on the PR. But it is possible that the PR needs to be rebased - the strange thing is that it has picked up the commit to jupyterhub_config.py.j2 that attempts import theme_extra_handlers from qhub_jupyterhub_theme but does not have the correct version built into the image. Or it's possible you just have an older tag left in your qhub-config.yaml that picks up an older Docker image.

viniciusdc · 2022-01-05T15:06:24Z

Service Unavailable when deploying on GCP, hub is on CrashLoop caused by... qhub-jupyterhub-theme

This must be because you are using an older Docker image for hub. It needs to include qhub-jupyterhub-theme v0.3.3 as is specified on main here.

So you need to work out which tag of quansight/qhub-jupyterhub is needed to pick this up. In theory this is quansight/qhub-jupyterhub:fix-798 to pick up the images based on the PR. But it is possible that the PR needs to be rebased - the strange thing is that it has picked up the commit to jupyterhub_config.py.j2 that attempts import theme_extra_handlers from qhub_jupyterhub_theme but does not have the correct version built into the image. Or it's possible you just have an older tag left in your qhub-config.yaml that picks up an older Docker image.

That might be the case Dan, thanks for the pointer

viniciusdc · 2022-01-13T17:24:18Z

Hi @costrouc , I just tested the deployment for this PR it seems that there might be some changes with the Jupyterhub docker image as the following error showed up during deployment:

│ Loading /usr/local/etc/jupyterhub/secret/values.yaml
│ No config at /usr/local/etc/jupyterhub/existing-secret/values.yaml
│ Loading extra config: jupyterhub_extra_config 
│ [C 2022-01-13 17:15:39.728 JupyterHub application:90] Bad config encountered during initialization: 
The 'spawner_class' trait of <jupyterhub.app.JupyterHub object at 0x7fd9af233110> instance must be a type, but 
cdsdashboards.hubextension.spawners.variablekube.VariableKubeSpawner' could not be imported

Using the main one instead resulted in any issues.

viniciusdc · 2022-01-14T20:57:10Z

Hi @costrouc, by some reason the icons for some buttons are not showing up correctly

viniciusdc · 2022-01-14T21:05:06Z

Just finished testing, all seems fine with conda-store. I will proceed to test the minio port changes, then will test on GCP as well to confirm. My only concern is within the issue with the main jupyterhub image..

ps. Also, not sure about this one, but there might be a duplicate constraint somewhere in the postsql config:
ERROR: duplicate key value violates unique constraint "_conda_package_uc"

* FEAT: Add additional port to handle Minio object storage * Add missing vars * Update minio entrypoint and disable tls * Exclude traitlets config from pre-commit * Update conda-store minio service eternal endpoint Co-authored-by: viniciusdc <[email protected]>

dharhas · 2022-01-19T18:00:15Z

Per #987

minio is AGPLv3 which means might we can't include it.

costrouc changed the title ~~Adding Conda-Store to QHub~~ [WIP] Adding Conda-Store to QHub Dec 9, 2021

costrouc added 5 commits December 20, 2021 20:36

Adding support for nix flakes

7c71420

Adding dependencies

7ac8b60

Adding .direnv

586aa4f

Adding conda-store terraform charts along with postgres/minio charts

3e8db12

Adding changes to ensure postgresql and minio deployment

4171d25

costrouc force-pushed the fix-798 branch from f5ffa91 to 4171d25 Compare December 21, 2021 06:19

costrouc added 4 commits December 21, 2021 11:30

Make easy connection to s3 and database storage

c52f628

Adding url for conda-store in qhub

d73689e

Adding documentation on Conda-Store environment management

bd3b041

Fixing all refrences to old conda-store image

faf2ea5

costrouc changed the title ~~[WIP] Adding Conda-Store to QHub~~ Adding Conda-Store to QHub Dec 22, 2021

Remove use of fstring flake8 formatting

1aaf695

viniciusdc approved these changes Jan 5, 2022

View reviewed changes

danlester mentioned this pull request Jan 11, 2022

v0.4.0 testing tracker #976

Closed

92 tasks

costrouc merged commit b27a14f into main Jan 18, 2022

costrouc deleted the fix-798 branch January 18, 2022 19:00

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Adding Conda-Store to QHub #967

Adding Conda-Store to QHub #967

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Adding Conda-Store to QHub #967

Adding Conda-Store to QHub #967

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