Fix/cli0.5

[joernweissenborn]

This PR fixes up the CLI.

Change summary

• Adapt CLI to API changes
• Add CLI tests

Checklist

• ✔️ Passing the tests (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)
• 📚 Adds documentation of the feature

Closes issues

closes #719

[github-actions]

👈 Launch a binder notebook on branch joernweissenborn/pyglotaran/fix/cli0.5

[codecov]

Codecov Report

Merging #765 (f4e607c) into staging (cee1834) will increase coverage by 2.3%.
The diff coverage is 77.5%.

@@            Coverage Diff            @@
##           staging    #765     +/-   ##
=========================================
+ Coverage     80.8%   83.2%   +2.3%     
=========================================
  Files           71      72      +1     
  Lines         4061    4081     +20     
  Branches       730     736      +6     
=========================================
+ Hits          3285    3397    +112     
+ Misses         645     550     -95     
- Partials       131     134      +3     

Impacted Files	Coverage Δ
glotaran/cli/commands/optimize.py	25.3% <50.0%> (+25.3%)	⬆️
glotaran/cli/commands/util.py	35.6% <71.4%> (+35.6%)	⬆️
glotaran/cli/__init__.py	100.0% <100.0%> (ø)
glotaran/cli/commands/pluginlist.py	100.0% <100.0%> (+100.0%)	⬆️
glotaran/cli/main.py	100.0% <100.0%> (+100.0%)	⬆️
glotaran/project/scheme.py	90.0% <100.0%> (ø)
glotaran/cli/commands/print.py	21.0% <0.0%> (+21.0%)	⬆️
... and 3 more

---

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[s-weigand]

The CLI also should have some tests, so if it breaks again we actually see it.
click already has a framework for that, dummy example below.

from glotaran import cli
from click.testing import CliRunner

def test_command_line_interface():
    """Test the CLI."""
    runner = CliRunner()
    result = runner.invoke(cli.main)
    assert result.exit_code == 0
    assert "glotaran.cli.main" in result.output
    help_result = runner.invoke(cli.main, ["--help"])
    assert help_result.exit_code == 0
    assert "--help  Show this message and exit." in help_result.output

[s-weigand]

There is still room for more fixes 😛

[jsnel]

Left some comments suggestion to avoid importing glotaran as gta and to call the entrypoint of the CLI main.

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.09%.

Quality metrics	Before	After	Change
Complexity	8.96 🙂	8.79 🙂	-0.17 👍
Method Length	45.15 ⭐	46.06 ⭐	0.91 👎
Working memory	10.99 😞	11.67 😞	0.68 👎
Quality	65.03% 🙂	64.94% 🙂	-0.09% 👎

Other metrics	Before	After	Change
Lines	419	461	42

Changed files	Quality Before	Quality After	Quality Change
glotaran/cli/init.py	%	%	%
glotaran/cli/main.py	89.95% ⭐	89.63% ⭐	-0.32% 👎
glotaran/cli/commands/optimize.py	12.59% ⛔	11.73% ⛔	-0.86% 👎
glotaran/cli/commands/pluginlist.py	87.13% ⭐	86.81% ⭐	-0.32% 👎
glotaran/cli/commands/util.py	73.09% 🙂	73.47% 🙂	0.38% 👍
glotaran/project/scheme.py	90.75% ⭐	90.75% ⭐	0.00%

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/cli/commands/optimize.py	optimize_cmd	29 😞	457 ⛔	29 ⛔	11.73% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/cli/commands/util.py	select_data	9 🙂	131 😞	9 🙂	58.32% 🙂	Try splitting into smaller methods
glotaran/cli/commands/util.py	ValOrRangeOrList.convert	6 ⭐	88 🙂	11 😞	62.86% 🙂	Extract out complex expressions
glotaran/cli/commands/util.py	write_data	1 ⭐	42 ⭐	10 😞	76.78% ⭐	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.

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Help us improve this quality report!

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[s-weigand]

I resolved the issues I found, so @joernweissenborn and @jsnel release review my changes.

[github-actions]

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

Benchmark diff

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [dc00e6da]       [f4e607c3]
     <v0.4.0>                   
-        61.5±1ms         42.5±2ms     0.69  BenchmarkOptimize.time_optimize(False, False, False)
-         341±3ms        68.5±20ms     0.20  BenchmarkOptimize.time_optimize(False, False, True)
-      88.5±0.9ms         73.8±2ms     0.83  BenchmarkOptimize.time_optimize(False, True, False)
       89.1±0.8ms         84.9±1ms     0.95  BenchmarkOptimize.time_optimize(False, True, True)
         61.3±1ms       56.9±0.6ms     0.93  BenchmarkOptimize.time_optimize(True, False, False)
-         337±4ms         68.9±1ms     0.20  BenchmarkOptimize.time_optimize(True, False, True)
         87.5±1ms         92.1±2ms     1.05  BenchmarkOptimize.time_optimize(True, True, False)
         91.6±1ms         137±10ms    ~1.49  BenchmarkOptimize.time_optimize(True, True, True)
             181M             180M     1.00  IntegrationTwoDatasets.peakmem_create_result
             198M             198M     1.00  IntegrationTwoDatasets.peakmem_optimize
-         287±3ms          223±4ms     0.78  IntegrationTwoDatasets.time_create_result
-      5.78±0.01s       1.70±0.05s     0.29  IntegrationTwoDatasets.time_optimize

[jsnel]

Still needs a bit better test coverage but otherwise ok for merge now.