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V0.8.0 #62

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merged 105 commits into from
Oct 16, 2023
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501062d
Check if UnitOperation supports binding model
schmoelder May 26, 2023
e323338
Allow component slicing in plot_purity method
schmoelder May 26, 2023
051bf63
Convert data to np.arrays with correct dimensions
schmoelder May 30, 2023
86f88cd
Fix indexing for components when using total component concentration
schmoelder Jun 1, 2023
c3f43d6
Fix NormLogTransform
schmoelder Jun 13, 2023
2ea0158
Allow specifying Cadet install path for initial conditions.
schmoelder Jun 12, 2023
fa7f8a2
Add cadet.cadet_path check to each CadetAPI call
Jun 20, 2023
f9ee674
Improve autodection and setting of Cadet.install_path
schmoelder Jun 20, 2023
0ad5a6b
Fix particle reaction models
schmoelder Jun 12, 2023
0f01bc5
Use np.rng for creating random numbers
schmoelder Jun 4, 2023
922361e
Improve restoring from checkpoint for pymoo
schmoelder Jun 4, 2023
623de03
Replace inf by large number to avoid pymoo error
schmoelder Jun 4, 2023
7d4d0b9
Use logger.warning
schmoelder Jun 20, 2023
1b0d36c
exclude *.egg-info files from installing the repository as pip -e
flo-schu May 24, 2023
c2c9e67
Add transformed bounds to OptimizationVariable
schmoelder Jun 24, 2023
7174d3a
Add more options to setup_optimization_problem
schmoelder Jun 24, 2023
8e269b9
Formatting
schmoelder Jun 24, 2023
215b3f3
Allow setting metric labels when adding callable
schmoelder Jun 23, 2023
aab9111
Always return list for labels (empty if n_metric==0)
schmoelder Jun 23, 2023
b8454d7
Improve setting descriptor arguments in __init__
schmoelder Jun 15, 2023
aae8708
Rename isIndependent -> is_independent
schmoelder Jun 23, 2023
0cd0853
Check if is_method to auto name callables in OptimizationProblem
schmoelder Jun 23, 2023
28e5e34
Omit corner plot for single individuals
schmoelder Jun 15, 2023
a24a494
Fix plot_objectives when len(population_feasible)==0
schmoelder Jun 23, 2023
6172b88
Make sure ndim==1 for initial values of scipy optimizers
schmoelder Jun 23, 2023
78b6b67
Overwrite x0 when restoring from checkpoint
schmoelder Jun 23, 2023
ca05683
Remove parameters property from OptimizationVariable
schmoelder Jun 23, 2023
546fbda
Provide more unified interface for optimizer options
schmoelder Jun 26, 2023
98f1659
Correct number of evaluations for COBYLA
schmoelder Jun 26, 2023
8b312db
Add note about variable setter
schmoelder Jun 26, 2023
2b2243c
Allow adding additional (kw)args to evaluation functions
schmoelder Jun 26, 2023
cf2e34e
Remove old similarity check
schmoelder Jun 26, 2023
f506f33
Simplify passing G, CV if n_nonlincon==0
schmoelder Jun 26, 2023
c473315
Add current_iteration option to callback args
schmoelder Jun 26, 2023
167de8d
Add optimization test problem fixture module
schmoelder Jun 24, 2023
a54f262
Avoid key collision in pymoo `out` dictionary
schmoelder Jun 30, 2023
2a6d6b8
Separately save pareto and meta fronts
schmoelder Jul 10, 2023
e9e6f35
Formatting
schmoelder Jul 10, 2023
f4d3f1c
Iterate over 2D-Array when transforming
schmoelder Jul 10, 2023
a91c463
Add missing `untransform=True` flag in scipyAdapter
flo-schu Jul 6, 2023
1e88878
Change required scipy version from 1.7 to 1.11
flo-schu Jul 4, 2023
632be93
Add type hints
schmoelder Jul 12, 2023
a2af5ff
Fix: Use transformed linear constraints (A, b) in optimizer
flo-schu Jul 3, 2023
88de7d2
Use numpy arrays and floats for b in linear constraints
flo-schu Jul 4, 2023
338b9bd
Add flag to check if optimizer supports bounds
schmoelder Jul 11, 2023
8ee9d05
Update check functions for Optimizer and OptimizationProblem
flo-schu Jul 2, 2023
890fb6c
Update tests to check transformed and linear constrained problems
flo-schu Jul 4, 2023
bbf9d9a
Add checks for x0
schmoelder Jul 11, 2023
009e3d2
Transform x0 before starting optimization
schmoelder Jul 12, 2023
78271eb
Fix: Use transformed linear equality constraints (Aeq, beq) in optimizer
schmoelder Jul 11, 2023
abd813d
Add missing flag to check if optimizer supports MOO
schmoelder Jul 12, 2023
fd17f85
Increase burn in when creating initial values with equality constraints
schmoelder Jul 12, 2023
9ae54db
Check linear equality constraints in RepairIndividuals
schmoelder Jul 12, 2023
aeb98df
Store untransformed variables in Individual.x, Population.x, and Opti…
schmoelder Jul 13, 2023
3306b3a
Improve setting purity_required
schmoelder Jul 4, 2023
6fd3347
Improve checking ranking
schmoelder Jul 4, 2023
902f1c8
Improve setting custom cycle time for Fractionation/KPI
schmoelder Jul 9, 2023
ac70cc7
Improve docstrings in fractionation module
schmoelder Jul 9, 2023
b9e2f95
Add option to save results of FractionationOptimization
schmoelder Jul 12, 2023
0e271fe
Use linear transform for FractionationOptimization
schmoelder Jul 13, 2023
97c5132
Use np.sum to calculate mass in fraction pool
schmoelder Jul 14, 2023
51665e3
Add option to only plot feasible points
schmoelder Jul 14, 2023
12a25d2
Add option to only plot final Pareto front
schmoelder Jul 14, 2023
0f757e7
Improve docstrings of population module
schmoelder Jul 18, 2023
dec565b
Fix m_avg
schmoelder Jul 18, 2023
36c192a
Add property with feasible individuals indices
schmoelder Jul 18, 2023
e406dce
Update docstrings in stationarity module
schmoelder Jul 17, 2023
1ccbd43
Add flag to raise Exception when n_max_cycles is exceeded
schmoelder Jul 17, 2023
abb403a
Add MassBalanceDifference performance indicator
schmoelder Jul 17, 2023
919d766
Add option to specify custom type for Typed parameter
schmoelder Jul 27, 2023
ebdd23e
Add create_lwe method
schmoelder Jul 27, 2023
081e279
Add selector for parallelization backend
Jul 27, 2023
d59d586
Cleanup after running tests
schmoelder Jul 27, 2023
bc8e421
Add method to access nested attributes
schmoelder Aug 10, 2023
e21e71c
Deprecate @abstractproperty; use @abstractmethod instead
schmoelder Aug 7, 2023
fa69324
Deprecate Source and Sink alias classes
schmoelder Aug 12, 2023
c024f85
Overhaul parameters module
schmoelder Aug 4, 2023
49adb76
Disable default values for NdPolynomials
schmoelder Aug 9, 2023
ac824bb
Fix Solution
schmoelder Aug 10, 2023
6490748
Overhaul Structure as base class
schmoelder Aug 7, 2023
81e3800
Update unit operation parameters
schmoelder Aug 17, 2023
aa32861
Add methods to index inhomogeneous arrays
schmoelder Aug 18, 2023
f952f74
Improve indexing for events and optimization variables
schmoelder Aug 3, 2023
f60eae9
Disable polynomial flow_rate_filter
schmoelder Aug 14, 2023
05d9e7c
Add Parameter Aggregator
schmoelder Aug 17, 2023
2c72c4e
Overhaul reactions module
schmoelder Aug 17, 2023
43d4fc7
Fix default values in ScipyAdapter
schmoelder Aug 17, 2023
a88833d
Formatting
schmoelder Aug 22, 2023
e4305dc
Update pre-commit
schmoelder Aug 22, 2023
8cb2f50
Fix example
schmoelder Aug 23, 2023
f8def06
Use species attr for labelling components
schmoelder Aug 28, 2023
588999c
Use component names for adding concentration profiles
schmoelder Aug 28, 2023
2386f81
Improve cached_properties_when_locked
schmoelder Aug 28, 2023
274e82c
Fix missing prop_cycler error
Sep 26, 2023
5dfd4e8
Demote addict version to fix __freeze issue on addict.copy()
Sep 7, 2023
e54fb5b
Add first fixes to rate_transformed setters
Aug 29, 2023
44be67f
Change reference_concentration interface
Oct 12, 2023
109065e
Fix binding adapter
Oct 12, 2023
703a320
Improve performance by locking the process before checking
Oct 14, 2023
f8ed172
Update optimization documentation
schmoelder Sep 4, 2023
44ffa10
Improve README for building documentation
schmoelder Sep 4, 2023
cd6a3ed
Update dependencies
schmoelder Sep 4, 2023
0056fa4
Test for Python 3.11
schmoelder Oct 11, 2023
29a0bbd
Improve documentation
schmoelder Oct 14, 2023
8c1d9df
v0.8.0
schmoelder Sep 4, 2023
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Use logger.warning
  • Loading branch information
schmoelder committed Sep 9, 2023
commit 7d4d0b93c6429a7752f35723702ed94268e70e1d
4 changes: 2 additions & 2 deletions CADETProcess/optimization/optimizationProblem.py
Original file line number Diff line number Diff line change
@@ -601,7 +601,7 @@ def _evaluate_individual(self, eval_funs, x, force=False):
value = self._evaluate(x, eval_fun, force)
results = np.hstack((results, value))
except CADETProcessError as e:
self.logger.warn(
self.logger.warning(
f'Evaluation of {eval_fun.name} failed at {x} with Error "{e}". '
f'Returning bad metrics.'
)
@@ -1525,7 +1525,7 @@ def evaluate_callbacks(self, ind, current_iteration=1, force=False):
try:
self._evaluate(x, callback, force)
except CADETProcessError:
self.logger.warn(
self.logger.warning(
f'Evaluation of {callback} failed at {x}.'
)