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fix: fixed enzyme optimization with Kcat fitness function #237

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fix: fixed enzyme optimization with Kcat fitness function #237

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yvesnana
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Resolved inconsistencies in core.py and updated the example file to ensure accurate execution of optimization with the KCAT fitness model.

fix: fixed enzyme optmization with Kcat fitness function
510123b 
Signed-off-by: Cloud User <cloud-user@vm-rxn.rxnaamapper.zc2.ibm.com>
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cla-bot bot commented Apr 24, 2024

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@yvesnana yvesnana assigned yvesnana and unassigned yvesnana Apr 24, 2024
drugilsberg
drugilsberg requested changes Apr 24, 2024
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Fix the build and address comments and then it's good to go.

examples/enzeptional/example_enzeptional.py Outdated
@@ -5,12 +5,16 @@
from gt4sd.configuration import GT4SDConfiguration, sync_algorithm_with_s3


def initialize_environment():
def initialize_environment(model = "feasibility"):
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typing and docstring missing, please add

src/gt4sd/frameworks/enzeptional/core.py Outdated
top_k: int = 2,
selection_ratio: float = 0.5,
perform_crossover: bool = False,
crossover_type: str = "uniform",
minimum_interval_length: int = 8,
pad_intervals: bool = False,
concat_order=["sequence", "substrate", "product"],
scaler_filepath: Optional[str] = None,
fitness_kcat: Optional[bool] = False,
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rename the parameter to something more generic

@yvesnana
fix: fixed enzyme optmization with Kcat fitness function
e73bac8 
Signed-off-by: yvesnana <yves.g.nana@gmail.com>
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cla-bot bot commented Apr 24, 2024

Thank you for your pull request and welcome to our community. We could not parse the GitHub identity of the following contributors: Cloud User.
This is most likely caused by a git client misconfiguration; please make sure to:

  1. check if your git client is configured with an email to sign commits git config --list | grep email
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@yvesnana
fix: fixed enzyme optmization with Kcat fitness function
4d4c6fc 
Signed-off-by: yvesnana <yves.g.nana@gmail.com>
@cla-bot cla-bot
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cla-bot bot commented Apr 24, 2024

Thank you for your pull request and welcome to our community. We could not parse the GitHub identity of the following contributors: Cloud User.
This is most likely caused by a git client misconfiguration; please make sure to:

  1. check if your git client is configured with an email to sign commits git config --list | grep email
  2. If not, set it up using git config --global user.email email@example.com
  3. Make sure that the git commit email is configured in your GitHub account settings, see https://github.com/settings/emails

@yvesnana yvesnana closed this Apr 24, 2024
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@yvesnana @drugilsberg