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Update to 3.4.0#59

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llegregam merged 117 commits intomasterMetaSys-LISBP/PhysioFit:masterfrom devMetaSys-LISBP/PhysioFit:devCopy head branch name to clipboardJun 13, 2024

Commits

Commits on Apr 29, 2024

• Fixed variable inversion error

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• Bump to 3.3.7

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• removed obelete TODO

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• Added docstring to Configparser

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• Bugfix by coercing experiment name to string

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Commits on Apr 30, 2024

• Sent logs to stream

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• Added test for monod model

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• PEP8 cleanup

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• added logger

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• Added np functions instead of python operators

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• added monod model test

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• Updated lock file

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• Changed python minimum version to 3.8.1 to handle flake8 version

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• Added flake8 testing on the 3.11 python env.

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Commits on May 6, 2024

• Refactoring

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• Refactoring

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Commits on May 7, 2024

• IMPORTANT: Changed names "parameters_to_estimate" to "parameters"

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• IMPORTANT: Changed names "parameters_to_estimate" to "parameters"

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• refactoring

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• changed "params_opti" to "parameters" & "params_not_opti" to "args"

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Commits on May 14, 2024

• changed "model_name" attr to "name"

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• Added data for model tests

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• changed "model_name" to "name"

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• changed "model_name" to "name"

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• Fixed bug where t_lag wasn't actually being used in simulation. Made code clearer. Added clip on values beneath zero.

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• Fixed bug where t_lag wasn't actually being used in simulation. Made code clearer. Added clip on values beneath zero.

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• Added clip on values beneath zero.

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• "model_name" to "name"

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• Updated max version to 4.0.0

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• Modified test data. Put all sds to 0.2 as default for tests.

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• Added unit tests for all models

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Commits on May 15, 2024

• refactoring

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• removed clipping of simulated dataframe.

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• split model tests into different files

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• split model tests into different files

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• Removed fold test_models file

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• Changed some methods to static

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• shifted datasets to test individual test files

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• type-hint

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• finished tests

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• Added more data points to simulated matrixes for plotting

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• Added args (fixed parameters)

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• Added args (fixed parameters)

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• fix model 1

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Commits on May 16, 2024

• Refactoring

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• Made large matrix be created with shape defined by length of the time vector

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• Fixed test data

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• refactored

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• updated gitignore

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• Improved logging and added log file export

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Commits on May 17, 2024

• Improved logging and added log file export

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• Removed logs from __init__

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• Fixed tests

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• Changed "Degradation" to "Degradation constants" & made t-lag default lower bound 1e-6

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• Fixed tests

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• Added check_data_path method

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• Started work on data_path_select from config

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Commits on May 21, 2024

• Added methods to handle wrong data path in config file

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• Spacing

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• PEP8

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• Merge pull request #58 from MetaSys-LISBP/dev_config_data_selector

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Commits on May 22, 2024

• Fixed config parser path input prompting.

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• changed python minimum version to 3.9 for scipy

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• Made function for generating logger

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• Removed actions for 3.8 (not supported anymore)

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• Update to 3.4.0

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• shutdown logger at the end of execution

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• Added khi2 test results to output expanders

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Commits on May 23, 2024

• Updated some logs

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• Added Akaike's information criterion (AIC)

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• Added Akaike's information criterion (AIC) and model selection in FAQ

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• Adding aic_c

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Commits on May 24, 2024

• Added AIC & AICc

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• Added AIC & AICc

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• Added AIC & AICc

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• Updated docs for 3.4.0

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• Temporary fix of data_path_config_context retrieving

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• Added repr ConfigParser

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Commits on May 28, 2024

• update doc

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• update doc

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• update doc

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• update doc

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• update doc

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• update doc

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• update doc

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• update readme

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• update doc typo

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Commits on May 29, 2024

• update tests

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• Added AIC to overview

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• Fixed chi2 test p value explanation

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• Updated image with new name for degradation constants

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• Added "simulate data from parameters" section

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• Clean up FAQ

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• PEP8

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• Rearranged the model testing section

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• Set rtol back to 1e-3

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• minor changes to text for clarity

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Commits on May 30, 2024

• update validation data

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• update validation data

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• Merge branch 'dev' of https://github.com/MetaSys-LISBP/PhysioFit into dev

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• Fixed bug with data paths pointing to config file instead of data

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• update validation doc

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Commits on Jun 4, 2024

• change test name

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Commits on Jun 13, 2024

• Updated CLI

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• removed useless f-string literal

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• Added some debug logs

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• Added flake8 to tox

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• PEP8

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• Merge remote-tracking branch 'origin/dev' into dev

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• Fixed bug when reading config_file in degradation model

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• added check that chosen data path in config parser is tsvv or txt

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• bugfix

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• added import

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• removed CI on python 3.8

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• Changed checkout in CI/CD to v4

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• Removed macos tests

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• flake8 linting

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