📚 Update quickstart guide to use Project API

[s-weigand]

This PR updates the quickstart guide to using the project API with a single import.
Note that this is just a translation of the current quickstart guide to the Project API and not how the quickstart should look like for the 0.7.0 release.
For a proper quickstart we should incorporate the plotting functionality of the pyglotaran_extras so users can get an idea about the actual day to day workflow they would use.

Change summary

• 📚👌 Rewirte quickstart with project API
• 🔧 Updated remove_notebook_written_data script to clean project data

Documentation changes

• quickstart

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 documentation of the feature

Closes issues

closes #1075

[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/quickstart-project-api

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 1.87%.

Quality metrics	Before	After	Change
Complexity	0.83 ⭐	0.89 ⭐	0.06 👎
Method Length	16.67 ⭐	27.33 ⭐	10.66 👎
Working memory	3.33 ⭐	2.89 ⭐	-0.44 👍
Quality	96.12% ⭐	94.25% ⭐	-1.87% 👎

Other metrics	Before	After	Change
Lines	27	31	4

Changed files	Quality Before	Quality After	Quality Change
docs/remove_notebook_written_data.py	96.12% ⭐	94.25% ⭐	-1.87% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation

Legend and Explanation

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[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]       [2bc0818e]
     <v0.6.0>                   
!      42.6±0.4ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
!      46.4±0.8ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
!      43.4±0.4ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
!      47.2±0.6ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
!      53.8±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
!        149±50ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
!      53.9±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
!       57.3±30ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             206M             210M     1.02  IntegrationTwoDatasets.peakmem_optimize
-      1.65±0.05s       1.08±0.02s     0.65  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [2bc0818e]       [b3e15018]
           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)
             210M             210M     1.00  IntegrationTwoDatasets.peakmem_optimize
       1.08±0.02s       1.07±0.02s     0.99  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Base: 88.1% // Head: 88.1% // No change to project coverage 👍

Coverage data is based on head (b3e1501) compared to base (2bc0818).
Patch has no changes to coverable lines.

Additional details and impacted files

@@          Coverage Diff          @@
##            main   #1241   +/-   ##
=====================================
  Coverage   88.1%   88.1%           
=====================================
  Files        104     104           
  Lines       5064    5064           
  Branches     842     842           
=====================================
  Hits        4462    4462           
  Misses       484     484           
  Partials     118     118           

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[s-weigand]

For now, this PR is a draft since it needs to be rebased after merging #1240, which it also doubles as a preview for.

[s-weigand]

Now waiting for #1244, so it properly renders 😅

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[jsnel]

Approve to merge, taking into account this important note:

"Note that this is just a translation of the current quickstart guide to the Project API and not how the quickstart should look like for the 0.7.0 release.
For a proper quickstart we should incorporate the plotting functionality of the pyglotaran_extras so users can get an idea about the actual day to day workflow they would use."
Agreed 💯