👌 Add SavingOptions to save_result API #966

s-weigand · 2022-01-24T02:07:41Z

My take on #874 😝

The main difference is data_filter is applied on the save_result level instead of adding an unused keyword to all save_dataset methods.
I also deprecated the legacy plugin and made folder throw a warning when not used from inside another plugin, thus promoting yml to the goto save_result plugin, which will make the transition to project easier.
The folder plugin now also doesn't save model.yml nor scheme.yml, that way it can easier be reused in different plugins.

Change summary

🚧 Salvage parts of PR 874
🧪 Removed part of a test which fails and should fail
👌 Restored wanted functionality
👌 Homogenized save_result return value to always be a list of strings
👌 Properly reexport functionality from glotaran.deprecation
🗑️ Deprecated save_result legacy plugin and made folder plugin internal use only

Checklist

✔️ Passing the tests (mandatory for all PR's)
🚧 Added changes to changelog (mandatory for all PR's)
👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)
🧪 Adds new tests for the feature (mandatory for ✨ feature and 🩹 bug fix PR's)

Closes issues

closes #874

github-actions · 2022-01-24T02:07:54Z

👈 Launch a binder notebook on branch s-weigand/pyglotaran/improve-saving-options

codecov · 2022-01-24T02:12:38Z

Codecov Report

Merging #966 (c3a7d19) into main (707c227) will increase coverage by 0.2%.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##            main    #966     +/-   ##
=======================================
+ Coverage   85.3%   85.6%   +0.2%     
=======================================
  Files         90      90             
  Lines       4859    4883     +24     
  Branches     913     916      +3     
=======================================
+ Hits        4149    4181     +32     
+ Misses       561     552      -9     
- Partials     149     150      +1

Impacted Files	Coverage Δ
glotaran/builtin/io/folder/folder_plugin.py	`100.0% <100.0%> (+2.3%)`	⬆️
glotaran/builtin/io/yml/yml.py	`90.2% <100.0%> (+1.6%)`	⬆️
glotaran/deprecation/__init__.py	`100.0% <100.0%> (ø)`
glotaran/io/__init__.py	`100.0% <100.0%> (ø)`
glotaran/io/interface.py	`100.0% <100.0%> (ø)`
glotaran/plugin_system/io_plugin_utils.py	`100.0% <100.0%> (ø)`
glotaran/plugin_system/project_io_registration.py	`100.0% <100.0%> (ø)`
glotaran/project/result.py	`88.4% <100.0%> (+7.0%)`	⬆️

Continue to review full report at Codecov.

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github-actions · 2022-01-24T02:13:02Z

Benchmark is done. Checkout the benchmark result page.
Benchmark differences below 5% might be due to CI noise.

Benchmark diff v0.5.1 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)


All benchmarks:

       before           after         ratio
     [96b42630]       [c3a7d195]
     <v0.5.1>                   
       61.5±0.7ms       60.7±0.4ms     0.99  BenchmarkOptimize.time_optimize(False, False, False)
        66.9±10ms         68.5±3ms     1.02  BenchmarkOptimize.time_optimize(False, False, True)
       61.2±0.5ms         62.0±1ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
         66.1±2ms        71.4±20ms     1.08  BenchmarkOptimize.time_optimize(False, True, True)
         75.6±3ms         76.2±2ms     1.01  BenchmarkOptimize.time_optimize(True, False, False)
         82.6±2ms         80.6±1ms     0.98  BenchmarkOptimize.time_optimize(True, False, True)
       74.5±0.5ms       74.8±0.3ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
        87.2±30ms         81.5±6ms     0.93  BenchmarkOptimize.time_optimize(True, True, True)
             202M             199M     0.99  IntegrationTwoDatasets.peakmem_optimize
       2.13±0.02s       2.01±0.03s     0.95  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)


All benchmarks:

       before           after         ratio
     [707c227c]       [c3a7d195]
         61.1±1ms       60.7±0.4ms     0.99  BenchmarkOptimize.time_optimize(False, False, False)
        74.2±30ms         68.5±3ms     0.92  BenchmarkOptimize.time_optimize(False, False, True)
       61.4±0.6ms         62.0±1ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
         68.9±4ms        71.4±20ms     1.04  BenchmarkOptimize.time_optimize(False, True, True)
         76.3±1ms         76.2±2ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
         83.4±5ms         80.6±1ms     0.97  BenchmarkOptimize.time_optimize(True, False, True)
         74.8±1ms       74.8±0.3ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
         81.6±2ms         81.5±6ms     1.00  BenchmarkOptimize.time_optimize(True, True, True)
             207M             199M     0.96  IntegrationTwoDatasets.peakmem_optimize
       2.01±0.08s       2.01±0.03s     1.00  IntegrationTwoDatasets.time_optimize

joernweissenborn

lgtm

glotaran/builtin/io/folder/folder_plugin.py

jsnel

Reviewed ok.

Co-authored-by: Jörn Weißenborn <[email protected]>

Overwriting saved results is only allowed 'if allow_overwrite is True'

…al use only

thanks sonarcloud

sourcery-ai · 2022-01-24T21:15:48Z

Sourcery Code Quality Report

❌ Merging this PR will decrease code quality in the affected files by 1.08%.

Quality metrics	Before	After	Change
Complexity	1.53 ⭐	1.81 ⭐	0.28 👎
Method Length	36.33 ⭐	37.98 ⭐	1.65 👎
Working memory	5.50 ⭐	5.65 ⭐	0.15 👎
Quality	84.95% ⭐	83.87% ⭐	-1.08% 👎

Other metrics	Before	After	Change
Lines	2118	2332	214

Changed files	Quality Before	Quality After	Quality Change
glotaran/builtin/io/folder/folder_plugin.py	59.69% 🙂	60.66% 🙂	0.97% 👍
glotaran/builtin/io/folder/test/test_folder_plugin.py	87.00% ⭐	76.49% ⭐	-10.51% 👎
glotaran/builtin/io/yml/yml.py	77.86% ⭐	76.54% ⭐	-1.32% 👎
glotaran/builtin/io/yml/test/test_save_result.py	87.74% ⭐	86.56% ⭐	-1.18% 👎
glotaran/deprecation/init.py	%	96.84% ⭐	%
glotaran/io/init.py	87.99% ⭐	87.99% ⭐	0.00%
glotaran/io/interface.py	97.71% ⭐	92.39% ⭐	-5.32% 👎
glotaran/plugin_system/io_plugin_utils.py	85.22% ⭐	85.22% ⭐	0.00%
glotaran/plugin_system/project_io_registration.py	83.86% ⭐	84.70% ⭐	0.84% 👍
glotaran/plugin_system/test/test_io_plugin_utils.py	94.79% ⭐	94.79% ⭐	0.00%
glotaran/plugin_system/test/test_project_io_registration.py	90.24% ⭐	90.16% ⭐	-0.08% 👎
glotaran/project/result.py	77.52% ⭐	77.38% ⭐	-0.14% 👎
glotaran/project/test/test_result.py	93.62% ⭐	82.73% ⭐	-10.89% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/builtin/io/yml/yml.py	YmlProjectIo.save_model	15 🙂	106 🙂	13 😞	48.93% 😞	Extract out complex expressions
glotaran/project/result.py	Result.markdown	6 ⭐	173 😞	13 😞	49.52% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/io/folder/folder_plugin.py	FolderProjectIo.save_result	6 ⭐	199 😞	8 🙂	56.82% 🙂	Try splitting into smaller methods
glotaran/plugin_system/project_io_registration.py	save_result	2 ⭐	67 🙂	12 😞	68.19% 🙂	Extract out complex expressions
glotaran/plugin_system/project_io_registration.py	save_model	2 ⭐	58 ⭐	10 😞	73.22% 🙂	Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

⭐ excellent
🙂 good
😞 poor
⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

sonarqubecloud · 2022-01-24T21:16:25Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

No Coverage information
0.9% Duplication

s-weigand requested review from jsnel and a team as code owners January 24, 2022 02:07

joernweissenborn previously approved these changes Jan 24, 2022

View reviewed changes

jsnel reviewed Jan 24, 2022

View reviewed changes

glotaran/builtin/io/folder/folder_plugin.py Outdated Show resolved Hide resolved

jsnel previously approved these changes Jan 24, 2022

View reviewed changes

s-weigand and others added 10 commits January 24, 2022 21:27

🚧 Salvage parts of PR 874

4b8f411

Co-authored-by: Jörn Weißenborn <[email protected]>

🧪 Removed part of a test which fails and should fail

c40a10c

Overwriting saved results is only allowed 'if allow_overwrite is True'

👌 Restored wanted functionality

68d6a6a

👌 Homogenized save_result return value to always be a list of strings

e932d53

👌 Properly reexport functionality from glotaran.deprecation

d292446

🗑️ Deprecated save_result legacy plugin and made folder plugin intern…

7d6d89a

…al use only

🚧 Added change to changelog

dfd10f3

🩹 Fixed missing asserts in tests (thanks sonarcloud)

99f9b81

🩹 Made saving_options keyword only in ProjectIoInterface for consistency

1faa36e

thanks sonarcloud

🚧📚 Added deprecation of legacy plugin to changelog

72ca809

s-weigand dismissed stale reviews from jsnel and joernweissenborn via 72ca809 January 24, 2022 20:27

s-weigand force-pushed the improve-saving-options branch from 3b1ffe8 to 72ca809 Compare January 24, 2022 20:27

🧹 Fix punctuation

c3a7d19

s-weigand merged commit a7f67d4 into glotaran:main Jan 24, 2022

s-weigand deleted the improve-saving-options branch January 24, 2022 22:34

This was referenced Jan 27, 2022

🐛 Deprecate save Result as yml #768

Closed

Refactor code to make SVD properties optional #528

Closed

s-weigand mentioned this pull request Jun 6, 2022

🚧 Decide on pyglotaran and pyglotaran-extras version cupelling glotaran/pyglotaran-extras#84

Closed

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👌 Add SavingOptions to save_result API #966

👌 Add SavingOptions to save_result API #966

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👌 Add SavingOptions to save_result API #966

👌 Add SavingOptions to save_result API #966

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s-weigand commented Jan 24, 2022 • edited Loading

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Closes issues

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