✨ Allow usage of subfolders in project API for parameters, models and data

[s-weigand]

This change allows using of files in subfolders for (parameters, models and data) with the project API.
It handles the ambiguity of files (same file name different extensions next to each other) gracefully by creating unique names and warning the user.

Change summary

• ♻️ Factor out item name to be an init parameter
• ✨ Allow usage of subfolders in project parameters, models and data
• 👌 Gracefully handle and warn the user about ambiguity due to files with the same name but different extensions next to each other
• ♻️ Sort file paths when globbing to make errors deterministic

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)

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 1.35%.

Quality metrics	Before	After	Change
Complexity	1.15 ⭐	1.27 ⭐	0.12 👎
Method Length	58.95 ⭐	62.86 🙂	3.91 👎
Working memory	6.67 🙂	6.87 🙂	0.20 👎
Quality	76.84% ⭐	75.49% ⭐	-1.35% 👎

Other metrics	Before	After	Change
Lines	1507	1661	154

Changed files	Quality Before	Quality After	Quality Change
glotaran/project/project.py	82.79% ⭐	83.40% ⭐	0.61% 👍
glotaran/project/project_data_registry.py	74.46% 🙂	74.38% 🙂	-0.08% 👎
glotaran/project/project_model_registry.py	76.47% ⭐	76.37% ⭐	-0.10% 👎
glotaran/project/project_parameter_registry.py	65.83% 🙂	65.74% 🙂	-0.09% 👎
glotaran/project/project_registry.py	89.44% ⭐	76.65% ⭐	-12.79% 👎
glotaran/project/project_result_registry.py	81.61% ⭐	81.58% ⭐	-0.03% 👎
glotaran/project/test/test_project.py	73.18% 🙂	72.64% 🙂	-0.54% 👎

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_registry.py	AmbiguousNameWarning.__init__	0 ⭐	91 🙂	18 ⛔	59.40% 🙂	Extract out complex expressions
glotaran/project/project_parameter_registry.py	ProjectParameterRegistry.generate_parameters	8 ⭐	113 🙂	10 😞	59.42% 🙂	Extract out complex expressions
glotaran/project/project_registry.py	ProjectRegistry.items	7 ⭐	115 🙂	10 😞	60.12% 🙂	Extract out complex expressions
glotaran/project/test/test_project.py	test_missing_file_errors	0 ⭐	220 ⛔	8 🙂	61.27% 🙂	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]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/project-allow-nested-dir

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[github-actions]

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]       [bb4ef933]
     <v0.6.0>                   
!      42.0±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
!      44.8±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
!      42.0±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
!        45.1±1ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
!      52.3±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
!       68.5±30ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
!      52.2±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
!        60.2±2ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             201M             206M     1.02  IntegrationTwoDatasets.peakmem_optimize
-      1.90±0.06s       1.03±0.04s     0.54  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [bb4ef933]       [9cc3c343]
           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)
             206M             208M     1.01  IntegrationTwoDatasets.peakmem_optimize
       1.03±0.04s       1.02±0.03s     0.99  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Base: 87.9% // Head: 87.9% // Increases project coverage by +0.0% 🎉

Coverage data is based on head (9cc3c34) compared to base (bb4ef93).
Patch coverage: 100.0% of modified lines in pull request are covered.

Additional details and impacted files

@@          Coverage Diff          @@
##            main   #1232   +/-   ##
=====================================
  Coverage   87.9%   87.9%           
=====================================
  Files        104     104           
  Lines       5004    5010    +6     
  Branches     830     833    +3     
=====================================
+ Hits        4401    4407    +6     
  Misses       487     487           
  Partials     116     116           

Impacted Files	Coverage Δ
glotaran/project/project_data_registry.py	100.0% <ø> (ø)
glotaran/project/project_model_registry.py	100.0% <ø> (ø)
glotaran/project/project_parameter_registry.py	95.8% <ø> (ø)
glotaran/project/project_result_registry.py	100.0% <ø> (ø)
glotaran/project/project.py	100.0% <100.0%> (ø)
glotaran/project/project_registry.py	96.0% <100.0%> (+1.6%)	⬆️

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[jsnel]

Good quality of life improvement.