Documentation_improvements: Jupyter Examples #58

RiesBen · 2024-08-13T12:26:27Z

Example JNB Documentation improvements:

Adding text to Example JnB.

Minor Code Changes:

analysis:
- minor modifications on cycle analysis (only check for cylce of size 3 per default)
- make delete more performant, by deleting multiple transformations/components at once if wanted.
- adding graph cost and efficiency
network -planners:
- minor refactors
- display fix, correct number of expected edges.

* analysis: * minor modifications on cycle analysis (only check for cylce of size 3 per default) * make delete more performant, by deleting multiple transformations/components at once if wanted. * adding graph cost and efficiency * jnbs: *Adding text to Example JnB. network -planners: * minor refactors * display fix, correct number of expected edges.

pep8speaks · 2024-08-13T12:26:39Z

Hello @RiesBen! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file src/konnektor/network_analysis/network_analysis.py:

Line 63:80: E501 line too long (82 > 79 characters)
Line 106:80: E501 line too long (82 > 79 characters)
Line 134:80: E501 line too long (88 > 79 characters)
Line 157:80: E501 line too long (84 > 79 characters)
Line 163:80: E501 line too long (84 > 79 characters)
Line 241:80: E501 line too long (87 > 79 characters)

In the file src/konnektor/network_planners/__init__.py:

Line 9:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/network_planners/_networkx_implementations/cyclic_network_algorithm.py:

Line 21:80: E501 line too long (87 > 79 characters)
Line 56:80: E501 line too long (82 > 79 characters)
Line 85:80: E501 line too long (82 > 79 characters)
Line 86:80: E501 line too long (81 > 79 characters)
Line 140:80: E501 line too long (84 > 79 characters)
Line 143:80: E501 line too long (83 > 79 characters)
Line 145:80: E501 line too long (84 > 79 characters)
Line 152:80: E501 line too long (83 > 79 characters)
Line 171:80: E501 line too long (80 > 79 characters)
Line 198:80: E501 line too long (81 > 79 characters)
Line 219:80: E501 line too long (82 > 79 characters)
Line 240:80: E501 line too long (82 > 79 characters)
Line 249:80: E501 line too long (81 > 79 characters)
Line 281:13: E731 do not assign a lambda expression, use a def
Line 281:80: E501 line too long (88 > 79 characters)
Line 291:17: E731 do not assign a lambda expression, use a def
Line 291:80: E501 line too long (82 > 79 characters)
Line 293:31: E713 test for membership should be 'not in'
Line 321:80: E501 line too long (84 > 79 characters)
Line 340:80: E501 line too long (83 > 79 characters)
Line 341:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/network_planners/_networkx_implementations/mst_network_algorithm.py:

Line 13:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/network_planners/_networkx_implementations/n_nodes_edges_network_algorithm.py:

Line 44:80: E501 line too long (82 > 79 characters)

In the file src/konnektor/network_planners/_networkx_implementations/radial_network_algorithm.py:

Line 34:80: E501 line too long (81 > 79 characters)
Line 35:80: E501 line too long (82 > 79 characters)
Line 92:80: E501 line too long (86 > 79 characters)

In the file src/konnektor/network_planners/concatenators/mst_concatenator.py:

Line 112:80: E501 line too long (82 > 79 characters)

In the file src/konnektor/network_planners/generators/_abstract_network_generator.py:

Line 67:80: E501 line too long (88 > 79 characters)

In the file src/konnektor/network_planners/generators/_parallel_mapping_pattern.py:

Line 45:80: E501 line too long (80 > 79 characters)
Line 75:80: E501 line too long (86 > 79 characters)
Line 89:25: E203 whitespace before ':'

In the file src/konnektor/network_planners/generators/clustered_network_generator.py:

Line 38:80: E501 line too long (85 > 79 characters)
Line 41:80: E501 line too long (81 > 79 characters)
Line 48:80: E501 line too long (96 > 79 characters)
Line 52:80: E501 line too long (83 > 79 characters)
Line 53:80: E501 line too long (105 > 79 characters)
Line 59:80: E501 line too long (80 > 79 characters)
Line 65:80: E501 line too long (158 > 79 characters)
Line 67:80: E501 line too long (162 > 79 characters)
Line 94:80: E501 line too long (83 > 79 characters)
Line 109:80: E501 line too long (88 > 79 characters)
Line 133:80: E501 line too long (88 > 79 characters)
Line 180:80: E501 line too long (88 > 79 characters)
Line 202:80: E501 line too long (82 > 79 characters)
Line 208:80: E501 line too long (82 > 79 characters)
Line 214:80: E501 line too long (84 > 79 characters)
Line 215:80: E501 line too long (149 > 79 characters)
Line 217:80: E501 line too long (137 > 79 characters)
Line 218:80: E501 line too long (177 > 79 characters)
Line 219:80: E501 line too long (114 > 79 characters)
Line 224:80: E501 line too long (90 > 79 characters)
Line 226:80: E501 line too long (90 > 79 characters)
Line 228:80: E501 line too long (80 > 79 characters)

In the file src/konnektor/network_planners/generators/cyclic_network_generator.py:

Line 30:80: E501 line too long (92 > 79 characters)
Line 31:80: E501 line too long (167 > 79 characters)
Line 34:80: E501 line too long (143 > 79 characters)
Line 35:80: E501 line too long (131 > 79 characters)
Line 37:80: E501 line too long (133 > 79 characters)
Line 39:80: E501 line too long (293 > 79 characters)
Line 41:80: E501 line too long (249 > 79 characters)
Line 42:80: E501 line too long (150 > 79 characters)
Line 57:80: E501 line too long (96 > 79 characters)
Line 63:80: E501 line too long (99 > 79 characters)
Line 84:80: E501 line too long (88 > 79 characters)
Line 115:80: E501 line too long (82 > 79 characters)
Line 117:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/network_planners/generators/heuristic_maximal_network_generator.py:

Line 29:80: E501 line too long (219 > 79 characters)
Line 30:80: E501 line too long (217 > 79 characters)
Line 32:80: E501 line too long (127 > 79 characters)
Line 35:80: E501 line too long (131 > 79 characters)
Line 36:80: E501 line too long (169 > 79 characters)
Line 65:80: E501 line too long (88 > 79 characters)
Line 90:80: E501 line too long (86 > 79 characters)

In the file src/konnektor/network_planners/generators/maximal_network_generator.py:

Line 18:80: E501 line too long (86 > 79 characters)
Line 21:80: E501 line too long (165 > 79 characters)
Line 22:80: E501 line too long (215 > 79 characters)
Line 24:80: E501 line too long (243 > 79 characters)
Line 28:80: E501 line too long (122 > 79 characters)
Line 29:80: E501 line too long (169 > 79 characters)
Line 52:80: E501 line too long (88 > 79 characters)
Line 96:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/network_planners/generators/minimal_spanning_tree_network_generator.py:

Line 8:80: E501 line too long (84 > 79 characters)
Line 23:80: E501 line too long (167 > 79 characters)
Line 24:80: E501 line too long (88 > 79 characters)
Line 28:80: E501 line too long (115 > 79 characters)
Line 29:80: E501 line too long (169 > 79 characters)
Line 30:80: E501 line too long (93 > 79 characters)
Line 35:80: E501 line too long (87 > 79 characters)
Line 57:80: E501 line too long (88 > 79 characters)
Line 90:36: E741 ambiguous variable name 'l'
Line 90:80: E501 line too long (83 > 79 characters)
Line 92:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/network_planners/generators/n_node_edges_network_generator.py:

Line 26:80: E501 line too long (117 > 79 characters)
Line 29:80: E501 line too long (150 > 79 characters)
Line 43:80: E501 line too long (89 > 79 characters)
Line 44:80: E501 line too long (151 > 79 characters)
Line 79:80: E501 line too long (88 > 79 characters)
Line 106:80: E501 line too long (82 > 79 characters)

In the file src/konnektor/network_planners/generators/redundant_minimal_spanning_tree_network_generator.py:

Line 8:80: E501 line too long (84 > 79 characters)
Line 24:80: E501 line too long (167 > 79 characters)
Line 26:80: E501 line too long (191 > 79 characters)
Line 29:80: E501 line too long (123 > 79 characters)
Line 34:80: E501 line too long (85 > 79 characters)
Line 44:80: E501 line too long (169 > 79 characters)
Line 63:80: E501 line too long (88 > 79 characters)
Line 99:13: E731 do not assign a lambda expression, use a def
Line 115:40: E741 ambiguous variable name 'l'
Line 115:80: E501 line too long (87 > 79 characters)
Line 117:80: E501 line too long (88 > 79 characters)

In the file src/konnektor/network_planners/generators/star_network_generator.py:

Line 8:80: E501 line too long (87 > 79 characters)
Line 23:80: E501 line too long (141 > 79 characters)
Line 25:80: E501 line too long (80 > 79 characters)
Line 26:80: E501 line too long (136 > 79 characters)
Line 27:80: E501 line too long (95 > 79 characters)
Line 29:80: E501 line too long (177 > 79 characters)
Line 30:80: E501 line too long (121 > 79 characters)
Line 31:80: E501 line too long (114 > 79 characters)
Line 59:80: E501 line too long (82 > 79 characters)
Line 90:80: E501 line too long (83 > 79 characters)
Line 96:80: E501 line too long (86 > 79 characters)

In the file src/konnektor/network_planners/generators/twin_star_network_generator.py:

Line 8:80: E501 line too long (87 > 79 characters)
Line 24:80: E501 line too long (133 > 79 characters)
Line 26:80: E501 line too long (95 > 79 characters)
Line 27:80: E501 line too long (168 > 79 characters)
Line 28:80: E501 line too long (148 > 79 characters)
Line 30:80: E501 line too long (164 > 79 characters)
Line 31:80: E501 line too long (142 > 79 characters)
Line 32:80: E501 line too long (113 > 79 characters)
Line 33:80: E501 line too long (122 > 79 characters)
Line 34:80: E501 line too long (100 > 79 characters)
Line 67:80: E501 line too long (88 > 79 characters)
Line 100:80: E501 line too long (82 > 79 characters)

In the file src/konnektor/network_tools/__init__.py:

Line 3:80: E501 line too long (83 > 79 characters)

In the file src/konnektor/network_tools/clustering/component_diversity_clustering.py:

Line 91:80: E501 line too long (83 > 79 characters)

In the file src/konnektor/network_tools/clustering/scaffold_clustering.py:

Line 45:80: E501 line too long (84 > 79 characters)
Line 148:80: E501 line too long (80 > 79 characters)

In the file src/konnektor/network_tools/network_handling/concatenate.py:

Line 8:80: E501 line too long (85 > 79 characters)
Line 41:80: E501 line too long (83 > 79 characters)
Line 61:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/network_tools/network_handling/delete.py:

Line 18:80: E501 line too long (99 > 79 characters)
Line 26:80: E501 line too long (82 > 79 characters)
Line 30:80: E501 line too long (80 > 79 characters)
Line 32:5: E731 do not assign a lambda expression, use a def
Line 33:80: E501 line too long (80 > 79 characters)
Line 66:5: E731 do not assign a lambda expression, use a def
Line 66:80: E501 line too long (80 > 79 characters)

In the file src/konnektor/network_tools/network_handling/merge.py:

Line 76:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/network_tools/network_handling/misc.py:

Line 8:80: E501 line too long (87 > 79 characters)

In the file src/konnektor/tests/data/conf.py:

Line 93:80: E501 line too long (81 > 79 characters)
Line 95:80: E501 line too long (83 > 79 characters)

In the file src/konnektor/tests/network_planners/_networkx_implemenations/test_cyclic_graph_generator.py:

Line 6:80: E501 line too long (87 > 79 characters)
Line 40:80: E501 line too long (85 > 79 characters)
Line 82:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/tests/network_planners/_networkx_implemenations/test_mst_graph_generator.py:

Line 6:80: E501 line too long (84 > 79 characters)
Line 30:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/tests/network_planners/_networkx_implemenations/test_radial_graph_generator.py:

Line 8:80: E501 line too long (87 > 79 characters)

In the file src/konnektor/tests/network_planners/concatenators/test_bipartite_max_concatenator.py:

Line 6:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/tests/network_planners/conf.py:

Line 41:80: E501 line too long (81 > 79 characters)
Line 82:80: E501 line too long (84 > 79 characters)
Line 96:80: E501 line too long (84 > 79 characters)
Line 98:80: E501 line too long (88 > 79 characters)
Line 103:80: E501 line too long (84 > 79 characters)
Line 105:80: E501 line too long (84 > 79 characters)
Line 110:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_clusterd_network_generator.py:

Line 23:80: E501 line too long (86 > 79 characters)
Line 25:80: E501 line too long (82 > 79 characters)
Line 31:80: E501 line too long (84 > 79 characters)
Line 41:80: E501 line too long (83 > 79 characters)
Line 45:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_explicit_network_planner.py:

Line 17:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_heuristic_maximal_network_planner.py:

Line 16:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_maximal_network_planner.py:

Line 28:80: E501 line too long (83 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_mst_netwok_planner.py:

Line 29:80: E501 line too long (82 > 79 characters)
Line 42:80: E501 line too long (82 > 79 characters)
Line 52:80: E501 line too long (85 > 79 characters)
Line 96:80: E501 line too long (86 > 79 characters)
Line 97:80: E501 line too long (87 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_rmst_netwok_planner.py:

Line 11:80: E501 line too long (83 > 79 characters)
Line 60:80: E501 line too long (85 > 79 characters)
Line 63:80: E501 line too long (86 > 79 characters)
Line 75:80: E501 line too long (83 > 79 characters)
Line 114:80: E501 line too long (88 > 79 characters)

In the file src/konnektor/tests/network_planners/generators/test_star_network_planner.py:

Line 20:80: E501 line too long (81 > 79 characters)
Line 43:80: E501 line too long (83 > 79 characters)
Line 63:80: E501 line too long (86 > 79 characters)
Line 65:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/tests/network_tools/test_clustering.py:

Line 3:80: E501 line too long (86 > 79 characters)

In the file src/konnektor/tests/network_tools/test_concatenate.py:

Line 24:80: E501 line too long (85 > 79 characters)
Line 47:80: E501 line too long (81 > 79 characters)
Line 55:80: E501 line too long (84 > 79 characters)

In the file src/konnektor/tests/network_tools/test_merge.py:

Line 22:80: E501 line too long (87 > 79 characters)

In the file src/konnektor/tests/network_tools/test_misc.py:

Line 39:80: E501 line too long (81 > 79 characters)
Line 51:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/tests/test_network_analysis.py:

Line 49:80: E501 line too long (84 > 79 characters)
Line 57:80: E501 line too long (84 > 79 characters)
Line 106:80: E501 line too long (86 > 79 characters)
Line 149:80: E501 line too long (86 > 79 characters)
Line 154:80: E501 line too long (85 > 79 characters)

In the file src/konnektor/tests/test_network_visualization.py:

Line 18:80: E501 line too long (83 > 79 characters)

In the file src/konnektor/tests/test_toy_data.py:

Line 90:80: E501 line too long (81 > 79 characters)
Line 109:80: E501 line too long (86 > 79 characters)
Line 111:80: E501 line too long (80 > 79 characters)

In the file src/konnektor/utils/toy_data.py:

Line 15:80: E501 line too long (94 > 79 characters)
Line 105:80: E501 line too long (88 > 79 characters)
Line 111:80: E501 line too long (80 > 79 characters)
Line 146:80: E501 line too long (85 > 79 characters)
Line 185:80: E501 line too long (85 > 79 characters)
Line 191:58: E203 whitespace before ':'
Line 193:58: E203 whitespace before ':'
Line 195:48: E203 whitespace before ':'

In the file src/konnektor/visualization/color_schemes.py:

Line 6:1: E731 do not assign a lambda expression, use a def
Line 6:80: E501 line too long (86 > 79 characters)

In the file src/konnektor/visualization/visualization.py:

Line 48:80: E501 line too long (81 > 79 characters)

In the file src/konnektor/visualization/widget.py:

Line 34:80: E501 line too long (85 > 79 characters)
Line 35:80: E501 line too long (85 > 79 characters)
Line 70:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-08-18 10:54:56 UTC

- Notebook improvements, more documentation, black formatting - improving network generator documentation - vscode -> gitignore

RiesBen · 2024-08-16T11:43:54Z

@hannahbaumann hi, I improved both notebooks :)
could you have a look, when you have time? :)
The additional files in this PR, are improvements of the networkgenerator docs. (this was easy to do in one go with the konnektor_networks.ipynb)

If you think: konnektor_networks.ipynb is too redundant, we can remove it. (I would not lose work, as it is also in the docs ;) )

codecov · 2024-08-21T10:18:37Z

Codecov Report

Attention: Patch coverage is 90.37801% with 28 lines in your changes missing coverage. Please review.

Project coverage is 90.96%. Comparing base (193a55d) to head (9c00002).

Files	Patch %	Lines
...work_planners/concatenators/cyclic_concatenator.py	0.00%	5 Missing ⚠️
src/konnektor/network_analysis/network_analysis.py	80.95%	4 Missing ⚠️
src/konnektor/visualization/widget.py	78.94%	4 Missing ⚠️
...planners/generators/clustered_network_generator.py	82.35%	3 Missing ⚠️
...tworkx_implementations/radial_network_algorithm.py	80.00%	2 Missing ⚠️
...k_planners/generators/_parallel_mapping_pattern.py	66.66%	2 Missing ⚠️
...erators/minimal_spanning_tree_network_generator.py	75.00%	2 Missing ⚠️
...dundant_minimal_spanning_tree_network_generator.py	80.00%	2 Missing ⚠️
src/konnektor/data/__init__.py	85.71%	1 Missing ⚠️
...tworkx_implementations/cyclic_network_algorithm.py	97.50%	1 Missing ⚠️
... and 2 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #58      +/-   ##
==========================================
- Coverage   91.10%   90.96%   -0.15%     
==========================================
  Files          46       46              
  Lines        1293     1306      +13     
==========================================
+ Hits         1178     1188      +10     
- Misses        115      118       +3

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

RiesBen · 2024-08-27T11:57:09Z

will be further discussed in build_v1

RiesBen added 5 commits August 5, 2024 10:18

parallelization bug fix

f556245

example: adding charge data

7e6250e

widget scroll sensitivity improvement.

96ad12a

bug fix clusteredNetworker understands now own default.

1ca8b02

RiesBen self-assigned this Aug 13, 2024

RiesBen added the documentation Improvements or additions to documentation label Aug 13, 2024

RiesBen added 2 commits August 13, 2024 14:34

minor text improvments

2d22256

Changes:

c087039

- Notebook improvements, more documentation, black formatting - improving network generator documentation - vscode -> gitignore

RiesBen requested review from hannahbaumann and IAlibay August 16, 2024 11:42

RiesBen added 2 commits August 18, 2024 12:22

applied black to code.

e18c6ab

adding pre-commit and dependencies

5408678

RiesBen mentioned this pull request Aug 18, 2024

Refactor black #62

Merged

RiesBen added 5 commits August 18, 2024 12:54

fixing konnektor_networks.ipynb.

486c2ba

fixing konnektor_networks.ipynb.

5dabffc

fixing konnektor_example.ipynb.

dbb68e6

Update pyproject.toml

61e8853

fix networks.ipynb

9c00002

RiesBen changed the base branch from main to build_v1 August 21, 2024 10:39

RiesBen added 2 commits August 21, 2024 13:30

Merge branch 'build_v1' into documentation_improvements

af3e91f

Merge branch 'build_v1' into documentation_improvements

1bf7103

RiesBen merged commit f1b82d1 into build_v1 Aug 27, 2024

RiesBen deleted the documentation_improvements branch October 16, 2024 12:57

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Documentation_improvements: Jupyter Examples #58

Documentation_improvements: Jupyter Examples #58

RiesBen commented Aug 13, 2024 •

edited

Loading

pep8speaks commented Aug 13, 2024 •

edited

Loading

RiesBen commented Aug 16, 2024

codecov bot commented Aug 21, 2024

RiesBen commented Aug 27, 2024

Documentation_improvements: Jupyter Examples #58

Documentation_improvements: Jupyter Examples #58

Conversation

RiesBen commented Aug 13, 2024 • edited Loading

pep8speaks commented Aug 13, 2024 • edited Loading

Comment last updated at 2024-08-18 10:54:56 UTC

RiesBen commented Aug 16, 2024

codecov bot commented Aug 21, 2024

Codecov Report

RiesBen commented Aug 27, 2024

RiesBen commented Aug 13, 2024 •

edited

Loading

pep8speaks commented Aug 13, 2024 •

edited

Loading