From e95b44b8a6cfd5f69931d109c6dee42d1e6f0c4f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 31 Aug 2026 21:46:07 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pycqa/isort: 6.0.1 → 9.0.1](https://github.com/pycqa/isort/compare/6.0.1...9.0.1) - https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror - [github.com/psf/black-pre-commit-mirror: 25.1.0 → 26.5.1](https://github.com/psf/black-pre-commit-mirror/compare/25.1.0...26.5.1) --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 771488b1..84ca7f88 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,12 +1,12 @@ repos: - repo: https://github.com/pycqa/isort - rev: 6.0.1 + rev: 9.0.1 hooks: - id: isort additional_dependencies: [toml] - - repo: https://github.com/psf/black - rev: 25.1.0 + - repo: https://github.com/psf/black-pre-commit-mirror + rev: 26.5.1 hooks: - id: black additional_dependencies: [toml] From 30a0e8e848fb4179b912e97b64853665000924c2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 31 Aug 2026 21:46:20 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- biomass/construction/julia_template.py | 32 +++++--------------- biomass/construction/template/problem.py | 4 +-- biomass/model_object.py | 2 +- biomass/models/Nakakuki_Cell_2010/problem.py | 4 +-- biomass/models/circadian_clock/problem.py | 4 +-- biomass/models/g1s_transition/problem.py | 4 +-- biomass/models/insulin_signaling/problem.py | 4 +-- biomass/models/jak_stat_pathway/problem.py | 4 +-- biomass/models/mapk_cascade/problem.py | 4 +-- biomass/models/nfkb_pathway/problem.py | 4 +-- biomass/models/pan_rtk/problem.py | 4 +-- biomass/models/prolif_quies/problem.py | 4 +-- biomass/models/tgfb_smad/problem.py | 4 +-- 13 files changed, 31 insertions(+), 47 deletions(-) diff --git a/biomass/construction/julia_template.py b/biomass/construction/julia_template.py index 2bc5e52f..8456ea03 100644 --- a/biomass/construction/julia_template.py +++ b/biomass/construction/julia_template.py @@ -7,9 +7,7 @@ from typing import Final -PARAMETERS: Final[ - str -] = """\ +PARAMETERS: Final[str] = """\ module C const NAMES = [] @@ -24,9 +22,7 @@ """ -SPECIES: Final[ - str -] = """\ +SPECIES: Final[str] = """\ module V const NAMES = [] @@ -41,9 +37,7 @@ """ -ODE: Final[ - str -] = """\ +ODE: Final[str] = """\ function diffeq!(du, u, p, t) v = Dict{Int64,Float64}() @@ -69,9 +63,7 @@ """ -OBSERVABLE: Final[ - str -] = """\ +OBSERVABLE: Final[str] = """\ const observables = [] function observables_index(observable_name::String)::Int @@ -83,9 +75,7 @@ """ -SIMULATION: Final[ - str -] = """\ +SIMULATION: Final[str] = """\ module Sim include("./name2idx/parameters.jl") include("./name2idx/species.jl") @@ -187,9 +177,7 @@ """ -EXPERIMENTAL_DATA: Final[ - str -] = """\ +EXPERIMENTAL_DATA: Final[str] = """\ module Exp include("./observable.jl") @@ -204,9 +192,7 @@ """ -SEARCH_PARAM: Final[ - str -] = """\ +SEARCH_PARAM: Final[str] = """\ # Specify model parameters and/or initial values to optimize function get_search_index()::Tuple{Array{Int64,1},Array{Int64,1}} # parameters @@ -437,9 +423,7 @@ end """ -PROBLEM: Final[ - str -] = """\ +PROBLEM: Final[str] = """\ # Residual Sum of Squares function compute_objval_rss( sim_data::Vector{Float64}, diff --git a/biomass/construction/template/problem.py b/biomass/construction/template/problem.py index cf1472b7..9a696e1d 100644 --- a/biomass/construction/template/problem.py +++ b/biomass/construction/template/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized.""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/model_object.py b/biomass/model_object.py index 449de373..51440801 100644 --- a/biomass/model_object.py +++ b/biomass/model_object.py @@ -109,7 +109,7 @@ def load_param(self, paramset: int) -> OptimizedValues: Optimized parameter/initial values. """ best_individual = self.get_individual(paramset) - (x, y0) = self.problem.update(best_individual) + x, y0 = self.problem.update(best_individual) optimized_values = OptimizedValues(x, y0) return optimized_values diff --git a/biomass/models/Nakakuki_Cell_2010/problem.py b/biomass/models/Nakakuki_Cell_2010/problem.py index c6ce97e5..30023de7 100644 --- a/biomass/models/Nakakuki_Cell_2010/problem.py +++ b/biomass/models/Nakakuki_Cell_2010/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/circadian_clock/problem.py b/biomass/models/circadian_clock/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/circadian_clock/problem.py +++ b/biomass/models/circadian_clock/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/g1s_transition/problem.py b/biomass/models/g1s_transition/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/g1s_transition/problem.py +++ b/biomass/models/g1s_transition/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/insulin_signaling/problem.py b/biomass/models/insulin_signaling/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/insulin_signaling/problem.py +++ b/biomass/models/insulin_signaling/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/jak_stat_pathway/problem.py b/biomass/models/jak_stat_pathway/problem.py index cf1472b7..9a696e1d 100644 --- a/biomass/models/jak_stat_pathway/problem.py +++ b/biomass/models/jak_stat_pathway/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized.""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/mapk_cascade/problem.py b/biomass/models/mapk_cascade/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/mapk_cascade/problem.py +++ b/biomass/models/mapk_cascade/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/nfkb_pathway/problem.py b/biomass/models/nfkb_pathway/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/nfkb_pathway/problem.py +++ b/biomass/models/nfkb_pathway/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/pan_rtk/problem.py b/biomass/models/pan_rtk/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/pan_rtk/problem.py +++ b/biomass/models/pan_rtk/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/prolif_quies/problem.py b/biomass/models/prolif_quies/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/prolif_quies/problem.py +++ b/biomass/models/prolif_quies/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)") diff --git a/biomass/models/tgfb_smad/problem.py b/biomass/models/tgfb_smad/problem.py index d7675901..4777c8cb 100644 --- a/biomass/models/tgfb_smad/problem.py +++ b/biomass/models/tgfb_smad/problem.py @@ -44,11 +44,11 @@ def _diff_sim_and_exp(sim_matrix, exp_dict, exp_timepoint, conditions, sim_norm_ def objective(self, indiv, *args): """Define an objective function to be minimized""" if len(args) == 0: - (x, y0) = self.update(indiv) + x, y0 = self.update(indiv) elif len(args) == 1: raise ValueError("not enough values to unpack (expected 2, got 1)") elif len(args) == 2: - (x, y0) = args + x, y0 = args else: raise ValueError("too many values to unpack (expected 2)")