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towards v1.0 #64

Merged
merged 18 commits into from
Sep 10, 2024
Merged

towards v1.0 #64

merged 18 commits into from
Sep 10, 2024

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RiesBen
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@RiesBen RiesBen commented Aug 21, 2024

This PR lifts Konnektor to v1.0
it contains a lot of improvements and bug fixes on visualizations, network planners and documentation.

additionally it introduces a precommit hook for black

RiesBen and others added 2 commits August 21, 2024 12:46
* Update visualisation of molecules to 2D

* parallelization bug fix

* example: adding charge data

* widget scroll sensitivity improvement.

* bug fix clusteredNetworker understands now own default.

* 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

  * jnbs:
*Adding text to Example JnB.

network -planners:
* minor refactors
* display fix, correct number of expected edges.

* minor text improvments

* Update widget.py

passing variable trough from top to bottom.

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

* applied black to code.

* adding pre-commit and dependencies

* fixing konnektor_networks.ipynb.

* fixing konnektor_networks.ipynb.

* fixing konnektor_example.ipynb.

* Update pyproject.toml

* fix networks.ipynb

* fix widget

---------

Co-authored-by: Julicancode <[email protected]>
* parallelization bug fix

* example: adding charge data

* widget scroll sensitivity improvement.

* bug fix clusteredNetworker understands now own default.

* 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

  * jnbs:
*Adding text to Example JnB.

network -planners:
* minor refactors
* display fix, correct number of expected edges.

* minor text improvments

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

* applied black to code.

* adding pre-commit and dependencies

* make ipycytoscape optional.
@RiesBen RiesBen changed the title [WIP] Refactor black (#62) [WIP] Build v1.0 Aug 21, 2024
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codecov bot commented Aug 21, 2024

Codecov Report

Attention: Patch coverage is 80.74205% with 109 lines in your changes missing coverage. Please review.

Project coverage is 87.06%. Comparing base (193a55d) to head (bd4ab74).

Files with missing lines Patch % Lines
...intermediate_generators/_abstract_intermediator.py 42.42% 19 Missing ⚠️
...ls/intermediate_generators/imerge_intermediator.py 37.93% 18 Missing ⚠️
..._planners/generators/explicit_network_generator.py 68.75% 10 Missing ⚠️
...implementations/n_nodes_edges_network_algorithm.py 58.82% 7 Missing ⚠️
src/konnektor/visualization/widget.py 76.66% 7 Missing ⚠️
...k_planners/generators/_parallel_mapping_pattern.py 80.00% 6 Missing ⚠️
src/konnektor/network_planners/NetworkPlanner.py 73.68% 5 Missing ⚠️
...work_planners/concatenators/cyclic_concatenator.py 0.00% 5 Missing ⚠️
.../generators/heuristic_maximal_network_generator.py 83.87% 5 Missing ⚠️
src/konnektor/network_analysis/network_analysis.py 81.81% 4 Missing ⚠️
... and 11 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #64      +/-   ##
==========================================
- Coverage   91.10%   87.06%   -4.04%     
==========================================
  Files          46       49       +3     
  Lines        1293     1539     +246     
==========================================
+ Hits         1178     1340     +162     
- Misses        115      199      +84     

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

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@IAlibay IAlibay left a comment

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It looks like the aim is for this to be merged and cut a 1.0. In that spirit I'm going to block this PR over user and developer documentation.

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block not approve

@RiesBen
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RiesBen commented Aug 21, 2024

@IAlibay
Docs will be next merges into this PR :)

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RiesBen commented Aug 27, 2024

@IAlibay here are the jupyter notebook changes contained now :)

RiesBen and others added 4 commits September 4, 2024 10:28
* adding intermediate generator to konnektor
* adding abstract class gufe style, making intermediator tokenizable.
---------

Co-authored-by: LindeSchoenmaker <[email protected]>
@RiesBen RiesBen self-assigned this Sep 10, 2024
@RiesBen RiesBen added documentation Improvements or additions to documentation enhancement New feature or request Konnektor labels Sep 10, 2024
@RiesBen RiesBen merged commit 8a625ab into main Sep 10, 2024
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@RiesBen RiesBen changed the title [WIP] Build v1.0 towards v1.0 Sep 10, 2024
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2 participants