Dependency cleanup and Python 3.12 support #2953

bcdurak · 2024-08-27T13:53:51Z

Describe changes

Major changes

Cleaning up the dependencies:
- Removed click-params, httplib2, pyparsing as main dependencies.
- Moved secure to the server extra
- Separated numpy and pandas to implementations to their own integrations.
- Added a limited version of maison to solve a problem with the yamlfix installation.
- Upgraded pydantic to 2.8.*
Upgrading zenml to Python 3.12. The new version is also added to all relevant CI tests.

Minor changes

Minor formatting/linting changes in some of the integrations.
Reworked one of the unit tests to use the PydanticMaterializer instead of the PandasMaterializer.
Limited the pandas version in the deepchecks integration to <2.1.0.
Added placeholder materializers for the PandasMaterializer and the NumpyMaterializer.
mlflow integration slightly reworked. The extra deployment option mlserver and mlserver-mlflow only installed <3.12 now.
Some of our examples use the package: skimage. Previously, we were able to access this package (for instance in mlflow and seldon example tests) because deepchecks was installed in the same environment and deepchecks required it (because we installed all the integration together). However, on 3.12, deepchecks integration is still not supported -> it is not installed -> there is no skimage -> mlflow and seldon example tests fail. The package itself is around 14 MB so I added it to the sklearn integration.

Related PRs

Remaining TODOs

~~Investigate if we should implement a migration script to change the materializer entries to newer paths.~~
~~Investigate Windows testing on 3.12.~~
~~Add warnings/errors for integrations that are not yet supported in 3.12.~~.
~~Ignore the integration tests on 3.12 for integrations that are not yet supported in 3.12.~~.
~~Revert the changes in the CI.~~
~~Create new versions of all templates.~~
~~Investigate httplib2 and pyparsing issue.~~

Pre-requisites

Please ensure you have done the following:

I have read the CONTRIBUTING.md document.
If my change requires a change to docs, I have updated the documentation accordingly.
I have added tests to cover my changes.
I have based my new branch on develop and the open PR is targeting develop. If your branch wasn't based on develop read Contribution guide on rebasing branch to develop.
If my changes require changes to the dashboard, these changes are communicated/requested.

Types of changes

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to change)
Other (add details above)

coderabbitai · 2024-08-27T13:53:58Z

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socket-security · 2024-08-27T13:54:21Z

New and removed dependencies detected. Learn more about Socket for GitHub ↗︎

Package	New capabilities	Transitives	Size	Publisher
pypi/[email protected]	None	`0`	45.6 kB	dbatten4
pypi/[email protected]	environment, eval, filesystem, network, shell, unsafe	`0`	5.32 MB	abravalheri, dstufft, jaraco

🚮 Removed packages: pypi/[email protected]), pypi/[email protected]), pypi/[email protected]), pypi/[email protected]), pypi/[email protected])

View full report↗︎

src/zenml/materializers/__init__.py

src/zenml/integrations/deepchecks/__init__.py

pyproject.toml

bcdurak · 2024-08-28T11:35:36Z

Btw, @schustmi, this PR is still early in development. I was just using it to test things on the CI. Will update you as things move forward.

github-actions · 2024-08-28T15:53:08Z

Classification template updates in examples/mlops_starter have been pushed.

stefannica

Overall looks good, but I had some nits and questions here and there.

src/zenml/integrations/deepchecks/validation_checks.py

tests/integration/integrations/deepchecks/materializers/test_deepchecks_result_materializer.py

stefannica · 2024-09-02T08:06:17Z

scripts/install-zenml-dev.sh

+    # TODO: Remove and add the extra back in
+    uv pip install $PIP_ARGS git+https://github.com/zenml-io/mlstacks.git@feature/upgrade-python-3.12


Please remember to remove this

Thank you for the reminder. I had to add one more of this to the small-checks workflow in the CI, unfortunately. We have to keep them until we can release a new version of mlstacks. I will keep this thread unresolved as a reminder to myself.

@stefannica Just so you know, this is going to be a bit tricky as I can not remove these lines with this PR.

Right now, the changes that I made are not compatible with the latest release of mlstacks(0.9.0). If I remove them now and merge to develop, all the subsequent CI runs on other PRs branching off of develop will fail.

We can potentially release a new version of mlstacks as a solution but if we do that mlstacks will be broken until we release a new version of zenml. (There won't be any zenml versions which can work with this new mlstacks release.)

So, my proposal would be something like this:

I merge this PR while keeping install-zenml-dev and small-checks pointing to my upgrade branch on the mlstacks repo.

I create a follow-up PR which actually reverts them back.

Just before we release a new version of zenml, we do the mlstacks release, merge the PR from point 2 and proceed with the release.

This needs to be communicated to the product team as well, I will take over that.

src/zenml/integrations/deepchecks/__init__.py

avishniakov

I agree with the concerns raised by @stefannica. On top, I added a few minor comments.

pyproject.toml

src/zenml/zen_stores/sql_zen_store.py

Co-authored-by: Andrei Vishniakov <[email protected]>

avishniakov · 2024-09-03T12:46:46Z

src/zenml/zen_server/zen_server_api.py

+from zenml.zen_server.secure_headers import (
+    initialize_secure_headers,
+    secure_headers,
+)


Nice move 👍🏼

github-actions · 2024-09-03T14:21:18Z

LLM Finetuning template updates in examples/llm_finetuning have been pushed.

github-actions · 2024-09-03T14:27:24Z

E2E template updates in examples/e2e have been pushed.

github-actions · 2024-09-03T14:32:01Z

NLP template updates in examples/e2e_nlp have been pushed.

github-actions · 2024-09-03T15:02:33Z

Classification template updates in examples/mlops_starter have been pushed.

bcdurak added 2 commits August 27, 2024 15:46

dependency cleanup

3f8c142

adding 3.12 to tests

b24a0ec

github-actions bot added internal To filter out internal PRs and issues enhancement New feature or request labels Aug 27, 2024

bcdurak added 7 commits August 27, 2024 17:32

integration changes

91d4446

removed pandas and numpy from the main package

7428594

formatting

7ea24e0

init files fixed

651c78f

removing pd from base abstraction

999f41f

ignoring mlflow huggingface and tensorflow for now

b393d76

moving the materializer tests to integration tests

c5ef3aa

schustmi requested changes Aug 28, 2024

View reviewed changes

src/zenml/materializers/__init__.py Show resolved Hide resolved

src/zenml/integrations/deepchecks/__init__.py Outdated Show resolved Hide resolved

pyproject.toml Show resolved Hide resolved

bcdurak and others added 14 commits August 28, 2024 13:37

missing licenses

87f81b7

formatting

c36b4b2

relaxed maison to <2.0

20a0558

proper formatting

4fe85b0

integration changes

b7142a1

integration fixes again

786db93

resolving huggingface conflicts

d43f47e

switch the pandas test to pydantic

e93f0ea

first test

645022f

added mocked libs

6e78cc4

change the template

745c133

migration testing

a86b46b

fixing the templates and setuptools

a740017

Auto-update of Starter template

5b4d254

bcdurak added 5 commits September 1, 2024 23:36

using discord instead of kubeflow

fd356de

try upgrading pydantic

5631c04

lets try this first

d0fc578

bumping pydantic

1ca2bf1

typo

9d95530

stefannica requested changes Sep 2, 2024

View reviewed changes

avishniakov reviewed Sep 2, 2024

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pyproject.toml Outdated Show resolved Hide resolved

src/zenml/zen_stores/sql_zen_store.py Show resolved Hide resolved

bcdurak and others added 3 commits September 2, 2024 11:14

Update pyproject.toml

3d4a328

Co-authored-by: Andrei Vishniakov <[email protected]>

for mlstacks

5102cbd

improved explanation

b2ec5be

bcdurak requested review from stefannica and avishniakov September 2, 2024 09:48

stefannica approved these changes Sep 2, 2024

View reviewed changes

bcdurak and others added 4 commits September 2, 2024 18:49

Merge branch 'develop' into feature/PRD-566-dependency-cleanup

ce96a0f

removed secure headers to a different file

a573668

Merge branch 'develop' into feature/PRD-566-dependency-cleanup

61ec239

Merge branch 'develop' into feature/PRD-566-dependency-cleanup

b486e67

avishniakov approved these changes Sep 3, 2024

View reviewed changes

schustmi approved these changes Sep 3, 2024

View reviewed changes

bcdurak and others added 2 commits September 3, 2024 16:08

adding main back

cb6623f

Auto-update of LLM Finetuning template

4c6a5d7

Auto-update of E2E template

81d5c40

Auto-update of NLP template

f9e951c

Auto-update of Starter template

d3dad36

bcdurak merged commit 142f7f1 into develop Sep 3, 2024
4 checks passed

bcdurak deleted the feature/PRD-566-dependency-cleanup branch September 3, 2024 22:08

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Dependency cleanup and Python 3.12 support #2953

Dependency cleanup and Python 3.12 support #2953

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		# TODO: Remove and add the extra back in
		uv pip install $PIP_ARGS git+https://github.com/zenml-io/mlstacks.git@feature/upgrade-python-3.12

Dependency cleanup and Python 3.12 support #2953

Dependency cleanup and Python 3.12 support #2953

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bcdurak commented Aug 27, 2024 • edited Loading

Describe changes

Major changes

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Related PRs

Remaining TODOs

Pre-requisites

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