✨ Allow import of xarray objects in project API import_data #1235

s-weigand · 2023-02-10T20:22:06Z

This makes data importing with the project API more flexible by allowing direct import from xarray.Dataset or xarray.DataArray.

from glotaran.project import Project

project = Project.open("my_project")

# my_custom_load_function returns a `xarray.Dataset` or `xarray.DataArray`
my_dataset = my_custom_load_function("dataset.foobar")

project.import_data(my_dataset , name="my_dataset ")

Change summary

✨ Allow import of xarray objects in project API import_data

Checklist

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

github-actions · 2023-02-10T20:22:17Z

👈 Launch a binder notebook on branch s-weigand/pyglotaran/project-allow-import-from-xarray

sourcery-ai · 2023-02-10T20:22:17Z

Sourcery Code Quality Report

❌ Merging this PR will decrease code quality in the affected files by 0.77%.

Quality metrics	Before	After	Change
Complexity	0.88 ⭐	1.08 ⭐	0.20 👎
Method Length	68.00 🙂	70.41 🙂	2.41 👎
Working memory	6.71 🙂	6.75 🙂	0.04 👎
Quality	75.25% ⭐	74.48% 🙂	-0.77% 👎

Other metrics	Before	After	Change
Lines	1207	1259	52

Changed files	Quality Before	Quality After	Quality Change
glotaran/project/project.py	83.40% ⭐	83.52% ⭐	0.12% 👍
glotaran/project/project_data_registry.py	74.38% 🙂	61.94% 🙂	-12.44% 👎
glotaran/project/test/test_project.py	72.64% 🙂	72.27% 🙂	-0.37% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/project/test/test_project.py	test_generate_parameters	3 ⭐	213 ⛔	9 🙂	56.54% 🙂	Try splitting into smaller methods
glotaran/project/project_data_registry.py	ProjectDataRegistry.import_data	9 🙂	123 😞	10 😞	57.22% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/project/test/test_project.py	test_missing_file_errors	0 ⭐	276 ⛔	8 🙂	58.36% 🙂	Try splitting into smaller methods
glotaran/project/test/test_project.py	test_generators_allow_overwrite	0 ⭐	151 😞	10 😞	62.82% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/project/test/test_project.py	test_run_optimization	2 ⭐	152 😞	8 🙂	64.98% 🙂	Try splitting into smaller methods

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!

github-actions · 2023-02-10T20:25:01Z

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

Benchmark diff v0.6.0 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)


All benchmarks:

       before           after         ratio
     [6c3c390e]       [18c17306]
     <v0.6.0>                   
!      43.8±0.5ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
!      47.6±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
!      43.7±0.9ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
!      47.6±0.4ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
!        55.6±1ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
!       58.9±40ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
!        57.0±3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
!       59.8±20ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             203M             204M     1.00  IntegrationTwoDatasets.peakmem_optimize
-      1.77±0.04s       1.13±0.03s     0.64  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)


All benchmarks:

       before           after         ratio
     [18c17306]       [73f98af6]
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             204M             207M     1.01  IntegrationTwoDatasets.peakmem_optimize
       1.13±0.03s       1.09±0.04s     0.96  IntegrationTwoDatasets.time_optimize

jsnel

Looks good to me. 😀

codecov · 2023-02-10T20:28:54Z

Codecov Report

Base: 87.9% // Head: 87.9% // Decreases project coverage by -0.1% ⚠️

Coverage data is based on head (73f98af) compared to base (18c1730).
Patch coverage: 88.2% of modified lines in pull request are covered.

Additional details and impacted files

@@           Coverage Diff           @@
##            main   #1235     +/-   ##
=======================================
- Coverage   87.9%   87.9%   -0.1%     
=======================================
  Files        104     104             
  Lines       5010    5019      +9     
  Branches     833     837      +4     
=======================================
+ Hits        4407    4414      +7     
- Misses       487     488      +1     
- Partials     116     117      +1