Dev/genome reorder #239

HenrikMettler · 2020-08-25T12:11:34Z

Implements a first solution to #225
Reorders the nodes in the parents genome(s) before creating offspring, without violating any node dependencies, as suggested in Goldman 2015. Works only with levels_back = n_columns and n_rows = 1 since possible issue with limitations in levels_back and more than 1 row are not accounted for.
Currently I did not add a new example for this functionality but changed levels_back = n_columns in example_minimal.py and set the boolean for doing reorder to true.
Testing currently only covers repeated application of reorder on two examples genomes, while asserting no changes in the resulting sympy expression.

jakobj

awesome, thanks for working on this! 🚀

i've added a few inline comments that should be addressed

cgp/genome.py

cgp/hl_api.py

test/test_genome.py

examples/example_minimal.py

cgp/population.py

jakobj · 2020-09-01T15:16:54Z

also: mypy reports issues, please fix them :)

HenrikMettler · 2020-09-02T14:36:35Z

Should I add more tests for the auxiliary functions used in reorder_genome or is the general empirical test sufficient?

jakobj

awesome, this is already much easier to understand, isn't it? 👌

i've added a few more inline comment

cgp/genome.py

cgp/hl_api.py

jakobj

nice, we're getting there :) some more inline suggestions

cgp/genome.py

mschmidt87 · 2020-09-14T12:11:55Z

Are you still working on this, @HenrikMettler ?

HenrikMettler · 2020-09-14T12:51:38Z

Yes, was on holiday last week and this week I have some other priorities. Will probably wrap this up next week.

jakobj

awesome work! 🥇

i've added some inline comments that should be addressed before merging

cgp/genome.py

test/test_genome.py

jakobj

nice work! 🚀

i've left a few more inline comments, i'd say one more round and we're ready to merge.

test/test_genome.py

cgp/genome.py

cgp/hl_api.py

cgp/ea/mu_plus_lambda.py

jakobj · 2020-10-28T12:52:13Z

cgp/ea/mu_plus_lambda.py

@@ -25,6 +25,7 @@ def __init__(
        n_processes: int = 1,
        local_search: Callable[[IndividualBase], None] = lambda combined: None,
        k_local_search: Union[int, None] = None,
+        reorder_genome: bool = True,


@mschmidt87 any strong feelings about changing this default behaviour? for 1.0 i'd anyway like to use this as the default, so we might as well change it now, right?

Should I set this default behavior to False for now? Otherwise, the tests and examples would require adaptation.

ok, do it :) we can still change it at a later point in time.

jakobj

thanks for the update!

a bit more nitpicking and please implement the test that raise exceptions as my inline comment indicates. otherwise this looks awesome!

cgp/ea/mu_plus_lambda.py

cgp/genome.py

examples/example_reorder.py

test/test_genome.py

jakobj

awesome stuff! 👍

just one more question and I'd like to hear @mschmidt87's thoughts on changing the default behavior. if the default is changed, i guess we should adopt all tests and examples accordingly.

also, before merging it would be good to rewrite commit history such that each commit applies a logical change.

cgp/genome.py

jakobj

awesome, great work! 👍

before merging, the history still needs some cleaning up imho. i would suggest organizing this PR in three commits:

implementation of reorder
addition of tests
addition of example

HenrikMettler · 2020-11-04T14:02:04Z

Is it ok, if I squash everything in one commit? Due to the previous squashing it is difficult to separate implementation, examples and test development (but I will try to keep this better seperated in future PR's)

HenrikMettler · 2020-11-05T08:48:32Z

@jakobj travis found a logic mistake in the example. I fixed it and while doing also adapted some docstrings to make more sense. Could you quickly look at them before merging?

jakobj · 2020-11-05T12:06:30Z

looks great, thanks! 👍 travis is also happy! please squash the new commit, then it's ready to be merged. 🎉

HenrikMettler marked this pull request as draft August 25, 2020 12:12

HenrikMettler requested a review from jakobj August 25, 2020 12:22

jakobj added this to the 0.3.0 milestone Aug 27, 2020

jakobj linked an issue Aug 27, 2020 that may be closed by this pull request

Reorder genome to reduce limitations of gene connections #225

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jakobj marked this pull request as ready for review September 4, 2020 15:58

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Implementation of genome reorder function

13ae8b4

HenrikMettler force-pushed the dev/genome_reorder branch from 5fff500 to 13ae8b4 Compare November 5, 2020 12:28

HenrikMettler merged commit c2bd94d into Happy-Algorithms-League:master Nov 5, 2020

HenrikMettler deleted the dev/genome_reorder branch November 5, 2020 12:45

jakobj modified the milestones: 0.3.0, 0.2.0 Nov 5, 2020

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Dev/genome reorder #239

Dev/genome reorder #239

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Dev/genome reorder #239

Dev/genome reorder #239

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