Refactor/logging #519

schroedk · 2024-08-09T14:09:15Z

The proposed logging is described here.

This refactoring introduces the following abstractions:

LogOptions (implementation SQLiteLogOptions), configuration
LogStore(implementation _SQLiteLogStore, not exposed), write access
LogReader (implementation SQLiteLogReader), read access

The old class OptimizationLogReader redirects to SQLiteLogReader in a backward-compatible way.

review-notebook-app · 2024-08-09T14:09:21Z

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…toring iteration, step and problem information

* move base data classes for dict and tuple like access to optimagic.typing * make all dataclasses frozen

* implement SQLiteLogger * expose primary_key property in AbstractKeyValueStore * add optimization type enum * improve type hints

for more information, see https://pre-commit.ci

codecov · 2024-08-09T14:22:46Z

Codecov Report

Attention: Patch coverage is 94.16283% with 38 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/optimagic/logging/base.py	85.71%	11 Missing ⚠️
src/optimagic/logging/logger.py	95.34%	10 Missing ⚠️
src/optimagic/logging/sqlalchemy.py	95.56%	7 Missing ⚠️
src/optimagic/typing.py	84.09%	7 Missing ⚠️
src/optimagic/optimization/multistart.py	71.42%	2 Missing ⚠️
...imagic/optimization/create_optimization_problem.py	90.90%	1 Missing ⚠️

Files with missing lines	Coverage Δ
src/estimagic/estimate_ml.py	`82.47% <ø> (ø)`
src/estimagic/estimate_msm.py	`89.68% <ø> (ø)`
src/optimagic/__init__.py	`100.00% <100.00%> (+8.33%)`	⬆️
src/optimagic/deprecations.py	`100.00% <100.00%> (ø)`
src/optimagic/logging/__init__.py	`100.00% <100.00%> (ø)`
src/optimagic/logging/read_log.py	`100.00% <100.00%> (+4.27%)`	⬆️
src/optimagic/logging/types.py	`100.00% <100.00%> (ø)`
src/optimagic/optimization/get_algorithm.py	`93.04% <100.00%> (-0.06%)`	⬇️
...imagic/optimization/internal_criterion_template.py	`82.60% <100.00%> (ø)`
src/optimagic/optimization/optimization_logging.py	`100.00% <100.00%> (ø)`
... and 10 more

... and 2 files with indirect coverage changes

… argument to None

* improve existence handling * move RobustPickler * remove obsolete code * fix usage in depending subpackages

* add NonUpdatableKeyValueStore, raises exception when try to call update * split hierarchy into updatable and nonupdatable stores * make IterationStore nonupdatable

…move obsolete submodule

* move store implementation to logging.sqlalchemy, remove dependency to SQLiteConfig * move SQLiteConfig to logging.logger * remove obsolete file logging.sqlite * rename test files to mirror subpackage structure

…sionError

janosg

I am through now. Thanks a lot for this PR!

One thing that is left to do is adding a logger field to the OptimizeResult.

src/optimagic/logging/__init__.py

src/optimagic/logging/types.py

src/optimagic/logging/logger.py

…rations from reader

…ions

…ing db file at init.

* split Logger into LogStore for writing and LogReader for reading * add new abstraction LogOptions

schroedk · 2024-08-19T06:58:54Z

I am through now. Thanks a lot for this PR!

One thing that is left to do is adding a logger field to the OptimizeResult.

Done

…om LogStore

tests/optimagic/test_deprecations.py

src/optimagic/typing.py

src/optimagic/logging/types.py

…ze, estimate_ml, estimate_msm

janosg

Thanks a lot! From my side this is ready to merge!

schroedk changed the base branch from main to 0.5.0 August 9, 2024 14:09

schroedk added 12 commits August 9, 2024 16:12

Add simple wrapper abstractions for logging tables

9a95f92

Add abstraction of a key value store, which serves as interface for s…

1fc3eb9

…toring iteration, step and problem information

Add type definitions to describe iteration, step and problem information

ccb46f2

Implement a sqlalchemy table acting as a KeyValueStore

4f59893

Add sqlite implementations for iteration, step and problem store

12c03fb

Add tests for sqlite implementations

d8075de

Remove obsolete file

3a8493f

Refactor logging types:

a38243c

* move base data classes for dict and tuple like access to optimagic.typing * make all dataclasses frozen

Add bound to TyepVar, remove type:ignore

eb1cfc8

Add Logger class:

56364e2

* implement SQLiteLogger * expose primary_key property in AbstractKeyValueStore * add optimization type enum * improve type hints

Deprecate OptimieLogReader and redirect to SQLiteLogger

07ba628

Adapt read tests for logging to new SQLiteLogger

8c88dfa

schroedk force-pushed the refactor/logging branch from 25546c5 to 8c88dfa Compare August 9, 2024 14:13

[pre-commit.ci] auto fixes from pre-commit.com hooks

dee344c

for more information, see https://pre-commit.ci

schroedk added 13 commits August 9, 2024 16:28

Remove obsolete type cast

afd0795

Update environment files to include sqlalchemy-stubs

3d7f89a

Merge remote-tracking branch 'origin/0.5.0' into refactor/logging

aadea23

Move OptimizationStrategy type from logging.types to typing

0474e63

Deprecate log_options in estimate_ml and estimate_msm, change default…

79e213c

… argument to None

Add functionality to handle deprecated parameter log_options

f034d2e

Delet obsolete files

ba67eaa

Refactor logging subpackage:

3c2b24d

* improve existence handling * move RobustPickler * remove obsolete code * fix usage in depending subpackages

Rename AbstractKeyValueStore to KeyValueStore

c57edf0

Refactor logging:

64082f6

* add NonUpdatableKeyValueStore, raises exception when try to call update * split hierarchy into updatable and nonupdatable stores * make IterationStore nonupdatable

Merge remote-tracking branch 'origin/0.5.0' into refactor/logging

a912d3e

Move util functions from logging submodule to optimagic.utilities, re…

164d35a

…move obsolete submodule

Fix issue in handling existing database file

911dbcc

schroedk added 7 commits August 13, 2024 21:50

Improve ValueError message for logging types

0930bd5

Fix issue in create_engine method, due to not overriding correctly

1449d30

Raise warning in case table exists and if_table_exists="replace"

365ed94

Increase test coverage

ba3a9df

Refactor logging package:

3c332ce

* move store implementation to logging.sqlalchemy, remove dependency to SQLiteConfig * move SQLiteConfig to logging.logger * remove obsolete file logging.sqlite * rename test files to mirror subpackage structure

Fix an issue in replacing the database file on windows, due to Permis…

3dc7a05

…sionError

Switch order of file removal and warning in try block

1b4110d

janosg reviewed Aug 14, 2024

View reviewed changes

schroedk added 7 commits August 14, 2024 17:58

Move history return types to optimagic.typing

ce504c1

Do not store flattened pytrees in logger stores, remove unflatten ope…

d98c240

…rations from reader

Raise ValueError instead of warning in handling og deprecated log_opt…

462e7a3

…ions

Move metadate creation from init to cached property, due to not creat…

a67035f

…ing db file at init.

Refactor logging subpackage:

5634837

* split Logger into LogStore for writing and LogReader for reading * add new abstraction LogOptions

Improve docstrings and type annotations

142060b

Fix test to catch a warning

6366692

schroedk added 5 commits August 19, 2024 09:08

Adapt documentation for logging

dade965

Add reader creation from path to documentation

bfb2dcc

Remove method 'from_path' from SQLiteLogReader, remove 'as_reader' fr…

d6f2c62

…om LogStore

Improve future warning for log options handling

620a62e

Extend CHANGES.md

a612912

janosg reviewed Aug 19, 2024

View reviewed changes

tests/optimagic/test_deprecations.py Show resolved Hide resolved

src/optimagic/typing.py Show resolved Hide resolved

src/optimagic/logging/types.py Outdated Show resolved Hide resolved

schroedk added 5 commits August 19, 2024 12:30

Rename CriterionEvaluationResult -> IterationState

3668e58

Raise FileNotFoundError for SQLiteLogReader in case no db file found

4eb9032

Add tests for covering deprecation of log_options in minimize, maximi…

a7d3eaa

…ze, estimate_ml, estimate_msm

Add test for dprecated OptimizationLogReader

cf6f0b9

Fix broken test

3d815fc

janosg approved these changes Aug 19, 2024

View reviewed changes

schroedk merged commit 24e44a7 into 0.5.0 Aug 19, 2024
16 checks passed

schroedk deleted the refactor/logging branch August 19, 2024 14:07

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Refactor/logging #519

Refactor/logging #519

schroedk commented Aug 9, 2024 •

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Refactor/logging #519

Refactor/logging #519

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schroedk commented Aug 9, 2024 •

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