ci: Update tooling #1298

eddiebergman · 2024-01-07T14:28:44Z

WIP

Fix the remaining reported bugs (mainly involves typing and converting os.path to Pathlib)
Ensure todos in pyproject are done
Ensure build includes all files correctly
There are a lot of issues in the tests, may be better to disable running certain rules on the tests for now until the tests are upgrade to pytest

What does this PR implement/fix? Explain your changes.

This PR aims to update tooling to ruff. This PR stemmed from cloning the repo and immediately having black format to 88 in my editor due to no file specification.

In general, there's also no import sorting which is probably not problematic for an established repo but good to have.

There should be no breaking changes other than rule FBT which discourages positional boolean arguments. It might be worth disabling this in public user facing functions if it's arleady done to prevent any backwards breaking changes.

Please let me know if I should justify ruff more, there's a lot of good things and very few negatives I could really think of.

How should this PR be tested?

Linting can be run wit make check which runs pre-commit run --all-files

Any other comments?

LennartPurucker · 2024-01-07T16:09:47Z

Some open TODOs for this refactor (I will edit this comment while working on this):

~~Update documentation and contributor guidelines~~
decide on ruff settings (i.e., decide on code style)

codecov-commenter · 2024-01-07T16:41:12Z

Codecov Report

Attention: 140 lines in your changes are missing coverage. Please review.

Comparison is base (56895c2) 84.92% compared to head (52c4d1f) 71.14%.

❗ Current head 52c4d1f differs from pull request most recent head 42b34e7. Consider uploading reports for the commit 42b34e7 to get more accurate results

Files	Patch %	Lines
openml/runs/functions.py	56.86%	22 Missing ⚠️
openml/extensions/sklearn/extension.py	81.69%	13 Missing ⚠️
openml/testing.py	72.91%	13 Missing ⚠️
openml/datasets/dataset.py	70.58%	10 Missing ⚠️
openml/runs/run.py	60.00%	10 Missing ⚠️
openml/utils.py	84.48%	9 Missing ⚠️
openml/config.py	82.60%	8 Missing ⚠️
openml/tasks/split.py	71.42%	8 Missing ⚠️
openml/tasks/functions.py	86.27%	7 Missing ⚠️
openml/datasets/functions.py	83.78%	6 Missing ⚠️
... and 14 more

Additional details and impacted files

@@             Coverage Diff              @@
##           develop    #1298       +/-   ##
============================================
- Coverage    84.92%   71.14%   -13.78%     
============================================
  Files           38       38               
  Lines         5120     5070       -50     
============================================
- Hits          4348     3607      -741     
- Misses         772     1463      +691

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

openml/cli.py

openml/extensions/sklearn/extension.py

openml/runs/functions.py

pyproject.toml

…l-python into refactor/ruff

… into refactor/ruff

eddiebergman · 2024-01-08T08:42:22Z

I reset this branch to an earlier commit as I messed up something fixing lint errors. Perhaps it's better to do that in another PR and have this as a clean state where the tests pass (minus the 3.6 version)

eddiebergman · 2024-01-08T09:18:07Z

One failing test, seems unerlated but not sure

FAILED tests/test_datasets/test_dataset_functions.py::TestOpenMLDataset::test_data_status - openml.exceptions.OpenMLServerException: https://test.openml.org/api/v1/xml/data/status/update returned code 694: Illegal status transition - None

eddiebergman · 2024-01-08T09:39:56Z

Tested the failing test, it was just flaky and due to the test server

* ci: Migrate everything to pyproject.toml * style: Apply ruff fixes * style: Apply (more) ruff fixes * style(ruff): Add some file specific ignores * ci: Fix build with setuptools * ci(ruff): Allow prints in cli.py * fix: Circular import * test: Use raises(..., match=) * fix(cli): re-add missing print statements * fix: Fix some over ruff-ized code * add make check to documentation * ci: Change to `build` for sdist * ci: Add ruff to `"test"` deps --------- Co-authored-by: Lennart Purucker <[email protected]>

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) - [github.com/pycqa/flake8: 6.0.0 → 6.1.0](PyCQA/flake8@6.0.0...6.1.0) * Raise correct TypeError and improve type check * Type check with isinstance instead of type() == * Docker enhancement #1277 (#1278) * Add multiple build platforms * Automatically update Dockerhub description * Launch Python instead of Bash by default * Change `omlp` directory name to less cryptic `openml` * Change directory to `openml` for running purpose of running script For mounted scripts, instructions say to mount them to `/openml`, so we have to `cd` before invoking `python`. * Update readme to reflect updates (python by default, rename dirs) * Add branch/code for doc and test examples as they are required * Ship docker images with readme * Only update readme on release, also try build docker on PR * Update the toc descriptions * fix: carefully replaced minio_url with parquet_url (#1280) * carefully replaced minio with parquet * fix: corrected some mistakes * fix: restored the instances of minio * fix: updated the documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add #1280 I used a `next` header instead of a specific version since we don't know if it will be 0.15.0 or 0.14.2. We can change it before the next release. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pieter Gijsbers <[email protected]> Co-authored-by: Lennart Purucker <[email protected]> * Pytest/utils (#1269) * Extract mocked_perform_api_call because its independent of object * Remove _multiprocess_can_split_ as it is a nose directive and we use pytest * Convert test list all * Add markers and refactor test_list_all_for_tasks for pytest * Add cache marker * Converted remainder of tests to pytest * Documented remaining Attributes of classes and functions (#1283) Add documentation and type hints for the remaining attributes of classes and functions. --------- Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1281) updates: - [github.com/psf/black: 23.7.0 → 23.11.0](psf/black@23.7.0...23.11.0) - [github.com/pre-commit/mirrors-mypy: v1.4.1 → v1.7.0](pre-commit/mirrors-mypy@v1.4.1...v1.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1291) updates: - [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1) - [github.com/pre-commit/mirrors-mypy: v1.7.0 → v1.8.0](pre-commit/mirrors-mypy@v1.7.0...v1.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#1284) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump docker/login-action from 2 to 3 (#1285) Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@v2...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump docker/metadata-action from 4 to 5 (#1286) Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 4 to 5. - [Release notes](https://github.com/docker/metadata-action/releases) - [Upgrade guide](https://github.com/docker/metadata-action/blob/master/UPGRADE.md) - [Commits](docker/metadata-action@v4...v5) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump docker/setup-qemu-action from 2 to 3 (#1287) Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](docker/setup-qemu-action@v2...v3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump docker/build-push-action from 4 to 5 (#1288) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v4...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add more type annotations (#1261) * Add more type annotations * add to progress rst --------- Co-authored-by: Lennart Purucker <[email protected]> * Bump docker/setup-buildx-action from 2 to 3 (#1292) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@v2...v3) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#1293) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Rework Tagging Tests for New Server Specification (#1294) * rework tagging test adjusted for new server specification * update progress.rst * ci: Update tooling (#1298) * ci: Migrate everything to pyproject.toml * style: Apply ruff fixes * style: Apply (more) ruff fixes * style(ruff): Add some file specific ignores * ci: Fix build with setuptools * ci(ruff): Allow prints in cli.py * fix: Circular import * test: Use raises(..., match=) * fix(cli): re-add missing print statements * fix: Fix some over ruff-ized code * add make check to documentation * ci: Change to `build` for sdist * ci: Add ruff to `"test"` deps --------- Co-authored-by: Lennart Purucker <[email protected]> * ci: Disable 3.6 tests (#1302) * fix: Chipping away at ruff lints (#1303) * fix: Chipping away at ruff lints * fix: return lockfile path * Update openml/config.py * Update openml/runs/functions.py * Update openml/tasks/functions.py * Update openml/tasks/split.py * Update openml/utils.py * Update openml/utils.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update openml/config.py * Update openml/testing.py * Update openml/utils.py * Update openml/config.py * Update openml/utils.py * Update openml/utils.py * add concurrency to workflow calls * adjust docstring * adjust docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Lennart Purucker <[email protected]> * Tagging constraints (#1305) * update tagging constraints * openml python tests * small fix * [pre-commit.ci] pre-commit autoupdate (#1306) updates: - https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit - [github.com/astral-sh/ruff-pre-commit: v0.1.5 → v0.1.11](astral-sh/ruff-pre-commit@v0.1.5...v0.1.11) - [github.com/python-jsonschema/check-jsonschema: 0.27.1 → 0.27.3](python-jsonschema/check-jsonschema@0.27.1...0.27.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Linting Everything - Fix All mypy and ruff Errors (#1307) * style: Fix linting split.py * typing: Fix mypy errors split.py * typing: data_feature * typing: trace * more linting fixes * typing: finish up trace * typing: config.py * typing: More fixes on config.py * typing: setup.py * finalize runs linting * typing: evaluation.py * typing: setup * ruff fixes across different files and mypy fixes for run files * typing: _api_calls * adjust setup files' linting and minor ruff changes * typing: utils * late night push * typing: utils.py * typing: tip tap tippity * typing: mypy 78, ruff ~200 * refactor output format name and minor linting stuff * other: midway merge * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * typing: I'm runnign out of good messages * typing: datasets * leinting for flows and some ruff changes * no more mypy errors * ruff runs and setups * typing: Finish off mypy and ruff errors Co-authored-by: Bilgecelik <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * style: File wide ignores of PLR0913 This is because the automated pre-commit.ci bot which made automatic commits and pushes would think the `noqa` on the individualy overloaded functions was not needed. After removing the `noqa`, the linter then raised the issue --------- Co-authored-by: eddiebergman <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bilgecelik <[email protected]> * ci: Remove Python 3.6/7 (#1308) * ci: remove 3.7 patch (#1309) * Make Test Work Again After Ruff and Linter Changes (#1310) * mark production tests * make production test run * fix test bug -1/N * add retry raise again after refactor * fix str dict representation * test: Fix non-writable home mocks * testing: not not a change * testing: trigger CI * typing: Update typing * ci: Update testing matrix * testing: Fixup run flow error check * ci: Manual dispatch, disable double testing * ci: Prevent further ci duplication * ci: Add concurrency checks to all * ci: Remove the max-parallel on test ci There are a lot less now and they cancel previous puhes in the same pr now so it shouldn't be a problem anymore * testing: Fix windows path generation * add pytest for server state * add assert cache state * some formatting * fix with cache fixture * finally remove th finally * doc: Fix link * update test matrix * doc: Update to just point to contributing * add linkcheck ignore for test server --------- Co-authored-by: eddiebergman <[email protected]> * Add Feature Descriptions Rebase Clean (#1316) Co-authored-by: Jan van Rijn <[email protected]> * Make Class Label Retrieval More Lenient (#1315) * mark production tests * make production test run * fix test bug -1/N * add retry raise again after refactor * fix str dict representation * test: Fix non-writable home mocks * testing: not not a change * testing: trigger CI * typing: Update typing * ci: Update testing matrix * testing: Fixup run flow error check * ci: Manual dispatch, disable double testing * ci: Prevent further ci duplication * ci: Add concurrency checks to all * ci: Remove the max-parallel on test ci There are a lot less now and they cancel previous puhes in the same pr now so it shouldn't be a problem anymore * testing: Fix windows path generation * add pytest for server state * add assert cache state * some formatting * fix with cache fixture * finally remove th finally * doc: Fix link * update test matrix * doc: Update to just point to contributing * add linkcheck ignore for test server * add special case for class labels that are dtype string * fix bug and add test * formatting --------- Co-authored-by: eddiebergman <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#1318) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](astral-sh/ruff-pre-commit@v0.1.11...v0.1.13) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix: update fetching a bucket from MinIO (#1314) * Update fetching a bucket from MinIO Previously, each dataset had their own bucket: https://openml1.win.tue.nl/datasets61/dataset_61.pq But we were advised to reduce the amount of buckets and favor hosting many objects in hierarchical structure, so we now have instead some prefixes to divide up the dataset objects into separate subdirectories: https://openml1.win.tue.nl/datasets/0000/0061/dataset_61.pq This commit has bypassed pre-commit. Tests should be updated too. * ci: Trigger ci * ci: Add some files to .gitignore --------- Co-authored-by: PGijsbers <[email protected]> * Update progress.rst for minor release (#1319) * Update progress.rst for minor release * update version number * fix typo * Prepare Develop for Merge with Main (#1321) Co-authored-by: Pieter Gijsbers <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Pieter Gijsbers <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Devansh Varshney (देवांश वार्ष्णेय) <[email protected]> Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: Vishal Parmar <[email protected]> Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Matthias Feurer <[email protected]> Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: janvanrijn <[email protected]> Co-authored-by: Lennart Purucker <[email protected]> Co-authored-by: Bilgecelik <[email protected]>

eddiebergman added 4 commits January 7, 2024 14:44

ci: Migrate everything to pyproject.toml

3399c60

style: Apply ruff fixes

d6e140f

style: Apply (more) ruff fixes

c167a4a

style(ruff): Add some file specific ignores

a56961c

LennartPurucker mentioned this pull request Jan 7, 2024

Doc/type def #1255

Closed

eddiebergman added 3 commits January 7, 2024 17:10

ci: Fix build with setuptools

2b30a89

ci(ruff): Allow prints in cli.py

514d4af

fix: Circular import

ce58b56

LennartPurucker requested changes Jan 7, 2024

View reviewed changes

eddiebergman and others added 9 commits January 7, 2024 17:49

test: Use raises(..., match=)

f296148

fix(cli): re-add missing print statements

50fd988

fix: Fix some over ruff-ized code

910acd6

add make check to documentation

837be03

Merge branch 'refactor/ruff' of https://github.com/eddiebergman/openm…

c6ae153

…l-python into refactor/ruff

ci: Change to build for sdist

0a65f67

Merge remote-tracking branch 'eddie/refactor/ruff' into refactor/ruff

876f8e4

ci: Add ruff to "test" deps

8d80aa4

Merge branch 'refactor/ruff' of github.com:eddiebergman/openml-python…

42b34e7

… into refactor/ruff

eddiebergman force-pushed the refactor/ruff branch from 52c4d1f to 42b34e7 Compare January 8, 2024 08:39

eddiebergman marked this pull request as ready for review January 8, 2024 08:45

LennartPurucker approved these changes Jan 8, 2024

View reviewed changes

LennartPurucker merged commit 783f7cd into openml:develop Jan 8, 2024
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ci: Update tooling #1298

ci: Update tooling #1298

eddiebergman commented Jan 7, 2024

LennartPurucker commented Jan 7, 2024 •

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eddiebergman commented Jan 8, 2024

ci: Update tooling #1298

ci: Update tooling #1298

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eddiebergman commented Jan 7, 2024

WIP

What does this PR implement/fix? Explain your changes.

How should this PR be tested?

Any other comments?

LennartPurucker commented Jan 7, 2024 • edited Loading

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Codecov Report

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