Visualization refactoring

[plakrisenko]

Major visualization refactoring. Visualization functionality is rewritten using object oriented approach.

It was decided to get rid of grouping by number options (sim_cond_num_list, observable_num_list parameters in plot_data_and_simulation) as it doesn't seem to be clear that the numbering is based on the order in the measurement_df.

Additionally, it is now possible to set axes limits for all subplots (Figure.set_axes_limits).

Fixed issues:

• noise visualization issues, plotting replicates: #31, #33, #24
• barplot labeling issues: #23
• plotting only simulation: #13
• plotting bug for the case when measurements order is different in measurements_df and simulations_df: #30 and #36
• vis spec expansion issue: #28, #34
• yValues order: #38

[codecov-io]

Codecov Report

Merging #58 (5b253d1) into develop (d481eda) will increase coverage by 0.38%. The diff coverage is 78.93%.

@@             Coverage Diff             @@
##           develop      #58      +/-   ##
===========================================
+ Coverage    78.79%   79.17%   +0.38%     
===========================================
  Files           24       26       +2     
  Lines         2334     2857     +523     
  Branches       552      681     +129     
===========================================
+ Hits          1839     2262     +423     
- Misses         361      426      +65     
- Partials       134      169      +35     

Impacted Files	Coverage Δ
petab/visualize/__init__.py	100.00% <ø> (ø)
petab/visualize/plotting_config.py	57.29% <66.66%> (+0.30%)	:arrow_up:
petab/visualize/plotter.py	67.05% <67.05%> (ø)
petab/visualize/plot_data_and_simulation.py	84.46% <70.96%> (+9.12%)	:arrow_up:
petab/visualize/helper_functions.py	82.87% <80.00%> (-0.58%)	:arrow_down:
petab/visualize/plotting.py	86.69% <86.69%> (ø)
petab/C.py	100.00% <100.00%> (ø)

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[codecov-commenter]

Codecov Report

Merging #58 (321c577) into develop (74838ec) will increase coverage by 0.17%. The diff coverage is 78.01%.

@@             Coverage Diff             @@
##           develop      #58      +/-   ##
===========================================
+ Coverage    78.85%   79.02%   +0.17%     
===========================================
  Files           24       26       +2     
  Lines         2331     2880     +549     
  Branches       552      688     +136     
===========================================
+ Hits          1838     2276     +438     
- Misses         359      430      +71     
- Partials       134      174      +40     

Impacted Files	Coverage Δ
petab/visualize/__init__.py	100.00% <ø> (ø)
petab/visualize/plotter.py	65.51% <65.51%> (ø)
petab/visualize/plotting_config.py	57.29% <66.66%> (+0.30%)	:arrow_up:
petab/visualize/plot_data_and_simulation.py	84.46% <70.96%> (+9.12%)	:arrow_up:
petab/visualize/helper_functions.py	82.87% <80.00%> (-0.58%)	:arrow_down:
petab/visualize/plotting.py	85.33% <85.33%> (ø)
petab/C.py	100.00% <100.00%> (ø)
petab/yaml.py	90.66% <100.00%> (ø)
... and 1 more

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Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 74838ec...321c577. Read the comment docs.