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Most Configuration via Hydra #532

Merged
merged 78 commits into from
Sep 7, 2024
Merged

Most Configuration via Hydra #532

merged 78 commits into from
Sep 7, 2024

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Pale-Blue-Dot-97
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This PR mostly moves the burden of initiating (or at least locating) user-specified objects in the config via hydra. This helps to standardise how a user specifies an experiment and its constituent parts.

Also included are various bug fixes, including finally addressing a persistent recursion error in PairedGeoDataset and PairedNonGeoDataset.

dependabot bot and others added 30 commits July 15, 2024 22:02
Bumps [setuptools](https://github.com/pypa/setuptools) from 69.1.1 to 70.0.0.
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v69.1.1...v70.0.0)

---
updated-dependencies:
- dependency-name: setuptools
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
…ents/setuptools-70.0.0

Bump setuptools from 69.1.1 to 70.0.0 in /requirements
Bumps [onnx2torch](https://github.com/ENOT-AutoDL/onnx2torch) from 1.5.13 to 1.5.14.
- [Release notes](https://github.com/ENOT-AutoDL/onnx2torch/releases)
- [Commits](ENOT-AutoDL/onnx2torch@v1.5.13...v1.5.14)

---
updated-dependencies:
- dependency-name: onnx2torch
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.6 to 7.4.4.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
- [Commits](sphinx-doc/sphinx@v7.2.6...v7.4.4)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [requests](https://github.com/psf/requests) from 2.32.2 to 2.32.3.
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.32.2...v2.32.3)

---
updated-dependencies:
- dependency-name: requests
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [psutil](https://github.com/giampaolo/psutil) from 5.9.8 to 6.0.0.
- [Changelog](https://github.com/giampaolo/psutil/blob/master/HISTORY.rst)
- [Commits](giampaolo/psutil@release-5.9.8...release-6.0.0)

---
updated-dependencies:
- dependency-name: psutil
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.6.2 to 3.7.1.
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v3.6.2...v3.7.1)

---
updated-dependencies:
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [tox](https://github.com/tox-dev/tox) from 4.14.2 to 4.16.0.
- [Release notes](https://github.com/tox-dev/tox/releases)
- [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst)
- [Commits](tox-dev/tox@4.14.2...4.16.0)

---
updated-dependencies:
- dependency-name: tox
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [ipykernel](https://github.com/ipython/ipykernel) from 6.29.3 to 6.29.5.
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/v6.29.5/CHANGELOG.md)
- [Commits](ipython/ipykernel@v6.29.3...v6.29.5)

---
updated-dependencies:
- dependency-name: ipykernel
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [setuptools](https://github.com/pypa/setuptools) from 70.0.0 to 72.1.0.
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v70.0.0...v72.1.0)

---
updated-dependencies:
- dependency-name: setuptools
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
…ents/setuptools-72.1.0

Bump setuptools from 70.0.0 to 72.1.0 in /requirements
…ents/ipykernel-6.29.5

Bump ipykernel from 6.29.3 to 6.29.5 in /requirements
updates:
- [github.com/psf/black: 24.4.2 → 24.8.0](psf/black@24.4.2...24.8.0)
Bumps [onnx](https://github.com/onnx/onnx) from 1.16.1 to 1.16.2.
- [Release notes](https://github.com/onnx/onnx/releases)
- [Changelog](https://github.com/onnx/onnx/blob/main/docs/Changelog-ml.md)
- [Commits](onnx/onnx@v1.16.1...v1.16.2)

---
updated-dependencies:
- dependency-name: onnx
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.7.1 to 3.8.0.
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v3.7.1...v3.8.0)

---
updated-dependencies:
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
…ents/pre-commit-3.8.0

Bump pre-commit from 3.7.1 to 3.8.0 in /requirements
…ents/onnx-1.16.2

Bump onnx from 1.16.1 to 1.16.2 in /requirements
…nfig

[pre-commit.ci] pre-commit autoupdate
Bumps [mlflow](https://github.com/mlflow/mlflow) from 2.13.2 to 2.15.1.
- [Release notes](https://github.com/mlflow/mlflow/releases)
- [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md)
- [Commits](mlflow/mlflow@v2.13.2...v2.15.1)

---
updated-dependencies:
- dependency-name: mlflow
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [lightly](https://github.com/lightly-ai/lightly) from 1.4.25 to 1.5.11.
- [Release notes](https://github.com/lightly-ai/lightly/releases)
- [Commits](lightly-ai/lightly@v1.4.25...v1.5.11)

---
updated-dependencies:
- dependency-name: lightly
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
…ents/lightly-1.5.11

Bump lightly from 1.4.25 to 1.5.11 in /requirements
…ents/mlflow-2.15.1

Bump mlflow from 2.13.2 to 2.15.1 in /requirements
@Pale-Blue-Dot-97 Pale-Blue-Dot-97 added bug Something isn't working enhancement New feature or request generalise Code needs generalising dependencies Pull requests that update a dependency file python Pull requests that update Python code yaml Updates to yaml files labels Sep 5, 2024
@Pale-Blue-Dot-97 Pale-Blue-Dot-97 added this to the v0.28 milestone Sep 5, 2024
@Pale-Blue-Dot-97 Pale-Blue-Dot-97 self-assigned this Sep 5, 2024
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codecov bot commented Sep 6, 2024

Codecov Report

Attention: Patch coverage is 90.98196% with 45 lines in your changes missing coverage. Please review.

Project coverage is 91.70%. Comparing base (f31982a) to head (2287698).
Report is 693 commits behind head on beta.

Files with missing lines Patch % Lines
minerva/utils/utils.py 78.84% 11 Missing ⚠️
minerva/modelio.py 81.48% 10 Missing ⚠️
minerva/datasets/utils.py 50.00% 7 Missing ⚠️
minerva/datasets/factory.py 93.50% 5 Missing ⚠️
minerva/datasets/paired.py 89.58% 5 Missing ⚠️
minerva/datasets/dfc.py 85.71% 3 Missing ⚠️
minerva/logger/tasklog.py 96.15% 1 Missing ⚠️
minerva/samplers.py 94.73% 1 Missing ⚠️
minerva/trainer.py 97.50% 1 Missing ⚠️
minerva/transforms.py 97.87% 1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (f31982a) and HEAD (2287698). Click for more details.

HEAD has 2 uploads less than BASE
Flag BASE (f31982a) HEAD (2287698)
6 4
Additional details and impacted files
@@            Coverage Diff             @@
##             beta     #532      +/-   ##
==========================================
- Coverage   98.12%   91.70%   -6.42%     
==========================================
  Files          38       42       +4     
  Lines        3889     4992    +1103     
==========================================
+ Hits         3816     4578     +762     
- Misses         73      414     +341     

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

@Pale-Blue-Dot-97 Pale-Blue-Dot-97 merged commit 2d10682 into beta Sep 7, 2024
7 of 13 checks passed
@Pale-Blue-Dot-97 Pale-Blue-Dot-97 deleted the 524-hydra-transforms branch September 11, 2024 15:34
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