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Add deck to papermill plugin task #1111

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CalvinLeather
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@CalvinLeather CalvinLeather commented Jul 28, 2022

TL;DR

This PR modifies the papermill plugin so that, if render_deck=True is passed to init, the rendered output html is inserted as a flyte deck.

Type

  • Bug Fix
  • Feature
  • Plugin

Are all requirements met?

  • Code completed
  • Smoke tested
  • Unit tests added
  • Code documentation added
  • Any pending items have an associated Issue

Complete description

This PR modifies the papermill plugin so that, if a kwarg render_deck is passed, the flyte deck is added automatically, without need for a follow up task. The render_deck kwarg was used to ensure backwards compatibility, by default, the behaviour of the papermill plugin won't be changed (i.e., this deck support is opt-in).

Note that this won't happen for cached execution, there is an open issue out for fixing flyte decks for cached execution.

I tested this change by installing this branch of flytekit into a container and registering one of our company's test notebook tasks, and running it. It gets a deck as intended:
image

image

Not 100% happy with how I tested this plugin. Since the unit tests use local execution, the deck/context functionality I think isn't getting used. Let me know if there is a better way to do test this.

Tracking Issue

n/a (can open an issue if you like, JFDI'd this after discussing with Ketan here)

Follow-up issue

NA

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@CalvinLeather CalvinLeather force-pushed the cleather/papermill-deck branch from 7815b53 to 964fbc7 Compare July 28, 2022 01:06
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Did a quick force push to my branch to --signoff in a rebase.

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codecov bot commented Jul 28, 2022

Codecov Report

Merging #1111 (964fbc7) into master (ef1cda1) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1111   +/-   ##
=======================================
  Coverage   86.97%   86.97%           
=======================================
  Files         276      276           
  Lines       25511    25511           
  Branches     2865     2865           
=======================================
  Hits        22187    22187           
  Misses       2846     2846           
  Partials      478      478           

Continue to review full report at Codecov.

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This is awesome!! Thank you @CalvinLeather. LGTM

@wild-endeavor wild-endeavor merged commit 9e154a0 into flyteorg:master Aug 4, 2022
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Congrats on merging your first pull request! 🎉

eapolinario pushed a commit that referenced this pull request Sep 15, 2022
eapolinario added a commit that referenced this pull request Sep 16, 2022
* Add deck to papermill plugin task (#1111)

Signed-off-by: Calvin Leather <[email protected]>

* Run compilation even in local execution for dynamic tasks to early detect errors (#1121)

Signed-off-by: Yee Hing Tong <[email protected]>

* Set to pyflyte run blob object remote when dealing with remote files (#1128)

Signed-off-by: Yee Hing Tong <[email protected]>
Signed-off-by: Eduardo Apolinario <[email protected]>

* Override voidPromise resource (#1127)

* override void promise resource

Signed-off-by: Kevin Su <[email protected]>

* override void promise resource

Signed-off-by: Kevin Su <[email protected]>

* Fix how ShellTask retrieves the Pod class name (#1132)

* Fix how ShellTask retrieves the Pod class name

Signed-off-by: Matheus Moreno <[email protected]>

* Set Pod class name as a constant

Signed-off-by: Matheus Moreno <[email protected]>

* Revert last commit

Signed-off-by: Matheus Moreno <[email protected]>

* Execute automatic linting

Signed-off-by: Matheus Moreno <[email protected]>

Signed-off-by: Matheus Moreno <[email protected]>

* Add restriction for pandas to be >=1.2 for fsspec plugin (#1136)

Signed-off-by: Yee Hing Tong <[email protected]>

* Use joblib hashing to generate cache key to ensure repeatability (#1126)

* cherry pick 97b454b

Signed-off-by: Yee Hing Tong <[email protected]>

* requirements

Signed-off-by: Yee Hing Tong <[email protected]>

* Fix usage of save in ProtoJoblibHasher

Signed-off-by: Eduardo Apolinario <[email protected]>

* Regenerate requirements using python 3.7

Signed-off-by: Eduardo Apolinario <[email protected]>

* Add test_stable_cache_key

Signed-off-by: Eduardo Apolinario <[email protected]>

Signed-off-by: Yee Hing Tong <[email protected]>
Signed-off-by: Eduardo Apolinario <[email protected]>
Co-authored-by: Eduardo Apolinario <[email protected]>

* Allow None protocol to mean all data persistence supported storage options in Structured Dataset (#1134)

Signed-off-by: Yee Hing Tong <[email protected]>

* handle ImportError and OSError in extras.pytorch (#1141)

* handle ImportError and OSError in extras.pytorch

Signed-off-by: Niels Bantilan <[email protected]>

* isolate exception to torch import

Signed-off-by: Niels Bantilan <[email protected]>

Signed-off-by: Niels Bantilan <[email protected]>

* Register dataframe renderers in structured dataset (#1140)

* Register dataframe renderers in structured dataset

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* fix test

Signed-off-by: Kevin Su <[email protected]>

* more tests

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* pyflyte run imperative workflows (#1131)

Signed-off-by: Kevin Su <[email protected]>

* Using sidecar handler to run Papermill task (#1143)

* remove nb prefix

Signed-off-by: Kevin Su <[email protected]>

* add tests

Signed-off-by: Kevin Su <[email protected]>

* Update requirements.in

Signed-off-by: Kevin Su <[email protected]>

* remove _

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* Properly raise error in NumpyArrayTransformer (#1146)

Signed-off-by: Rahul Mehta <[email protected]>

Signed-off-by: Rahul Mehta <[email protected]>

* Add assert_type in dataclass transformer (#1149)

* Add assert_type in dataclassTransformer

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* more tests

Signed-off-by: Kevin Su <[email protected]>

* fix lint

Signed-off-by: Kevin Su <[email protected]>

* Add one more test

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* Pickle in Union Type (#1147)

* Pickel in Union type

Signed-off-by: Kevin Su <[email protected]>

* Pickel in Union type

Signed-off-by: Kevin Su <[email protected]>

* wip

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* update tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* fix tests

Signed-off-by: Kevin Su <[email protected]>

* Address comment

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* Bump max docker version to 7.0.0 (#1138)

Signed-off-by: Rahul Mehta <[email protected]>

Signed-off-by: Rahul Mehta <[email protected]>

* Set flytekit<2.0 in plugins (#1152)

Signed-off-by: Eduardo Apolinario <[email protected]>

Signed-off-by: Eduardo Apolinario <[email protected]>
Co-authored-by: Eduardo Apolinario <[email protected]>

* Add literal type to union literal (#1144)

* Add literal type to union literal

Signed-off-by: Kevin Su <[email protected]>

* fix test

Signed-off-by: Kevin Su <[email protected]>

* Add tests

Signed-off-by: Kevin Su <[email protected]>

* more tests

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* Fix the type of optional[int] in nested dataclass (#1148)

* Fix the type of optional[int] in nested dataclass

Signed-off-by: Kevin Su <[email protected]>

* update tests

Signed-off-by: Kevin Su <[email protected]>

* update comments

Signed-off-by: Kevin Su <[email protected]>

* nit

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* Added symlink dereferencing in fast packaging and tests (#1151)

* Added symlink dereferencing and tests

Signed-off-by: Vanshika Chowdhary <[email protected]>

* Added flag to register as well

Signed-off-by: Vanshika Chowdhary <[email protected]>

* More flag propagation

Signed-off-by: Vanshika Chowdhary <[email protected]>

Signed-off-by: Vanshika Chowdhary <[email protected]>
Co-authored-by: Vanshika Chowdhary <[email protected]>

* Strip newline from client secret (#1163)

* Strip newline from client secret

* Add logging and rework the secret file comparison to work on windows

Signed-off-by: Eduardo Apolinario <[email protected]>

Signed-off-by: Eduardo Apolinario <[email protected]>
Co-authored-by: Eduardo Apolinario <[email protected]>

* Fix the type of optional[int] in dataclass (#1135)

Signed-off-by: Kevin Su <[email protected]>

* fix: plugins/flytekit-papermill/dev-requirements.txt to reduce vulnerabilities (#1154)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-OAUTHLIB-3021142
- https://snyk.io/vuln/SNYK-PYTHON-PYSPARK-3021131

Signed-off-by: Eduardo Apolinario <[email protected]>

* Using sidecar handler to run Papermill task (#1143)

* remove nb prefix

Signed-off-by: Kevin Su <[email protected]>

* add tests

Signed-off-by: Kevin Su <[email protected]>

* Update requirements.in

Signed-off-by: Kevin Su <[email protected]>

* remove _

Signed-off-by: Kevin Su <[email protected]>

Signed-off-by: Kevin Su <[email protected]>

* fix: plugins/flytekit-papermill/dev-requirements.txt to reduce vulnerabilities (#1145)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-COOKIECUTTER-2414281

* Bump pyspark from 3.2.1 to 3.2.2 in /plugins/flytekit-papermill (#1130)

Bumps [pyspark](https://github.com/apache/spark) from 3.2.1 to 3.2.2.
- [Release notes](https://github.com/apache/spark/releases)
- [Commits](apache/spark@v3.2.1...v3.2.2)

---
updated-dependencies:
- dependency-name: pyspark
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* fix: plugins/flytekit-papermill/dev-requirements.txt to reduce vulnerabilities (#1154)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-OAUTHLIB-3021142
- https://snyk.io/vuln/SNYK-PYTHON-PYSPARK-3021131

Signed-off-by: Calvin Leather <[email protected]>
Signed-off-by: Yee Hing Tong <[email protected]>
Signed-off-by: Eduardo Apolinario <[email protected]>
Signed-off-by: Kevin Su <[email protected]>
Signed-off-by: Matheus Moreno <[email protected]>
Signed-off-by: Niels Bantilan <[email protected]>
Signed-off-by: Rahul Mehta <[email protected]>
Signed-off-by: Vanshika Chowdhary <[email protected]>
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Calvin Leather <[email protected]>
Co-authored-by: Yee Hing Tong <[email protected]>
Co-authored-by: Kevin Su <[email protected]>
Co-authored-by: Matheus Moreno <[email protected]>
Co-authored-by: Eduardo Apolinario <[email protected]>
Co-authored-by: Niels Bantilan <[email protected]>
Co-authored-by: Rahul Mehta <[email protected]>
Co-authored-by: Vanshika Chowdhary <[email protected]>
Co-authored-by: Vanshika Chowdhary <[email protected]>
Co-authored-by: Snyk bot <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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3 participants