♻️ Move optimization to new module glotaran.optimization

benchmark/benchmarks/integration/ex_two_datasets/benchmark.py

@@ -1,6 +1,10 @@
 from pathlib import Path
 
-from glotaran.analysis.optimize import optimize
+try:
+    from glotaran.analysis.optimize import optimize
+except ImportError:
+    from glotaran.optimization.optimize import optimize
+
 from glotaran.io import load_dataset
 from glotaran.io import load_model
 from glotaran.io import load_parameters

benchmark/benchmarks/unit/analysis/bench_optimize.py

@@ -1,19 +1,20 @@
 import numpy as np
 import xarray as xr
 
-from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
-from glotaran.analysis.test.models import MultichannelMulticomponentDecay
+try:
+    from glotaran.analysis.optimize import optimize
+    from glotaran.analysis.simulation import simulate
+    from glotaran.analysis.test.models import MultichannelMulticomponentDecay
+except ImportError:
+    from glotaran.optimization.optimize import optimize
+    from glotaran.simulation import simulate
+    from glotaran.optimization.test.models import MultichannelMulticomponentDecay
+
 from glotaran.project import Scheme
 
 
 class BenchmarkOptimize:
-    """
-    Integration test for a two dataset analysis.
-
-    Ref:
-    https://github.com/glotaran/pyglotaran-examples/tree/main/pyglotaran_examples/ex_two_datasets
-    """
+    """Optimization benchmark based on unitests."""
 
     timeout = 300
     params = (

benchmark/pytest/analysis/test_optimization_group.py

@@ -6,10 +6,10 @@
 import pytest
 import xarray as xr
 
-from glotaran.analysis.optimization_group import OptimizationGroup
 from glotaran.model import Megacomplex
 from glotaran.model import Model
 from glotaran.model import megacomplex
+from glotaran.optimization.optimization_group import OptimizationGroup
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.testing.plugin_system import monkeypatch_plugin_registry

changelog.md

@@ -20,6 +20,7 @@
 - 👌 Improve Result, Parameter and ParameterGroup markdown (#1012)
 - 👌🧹 Add suffix to rate and lifetime and guard for missing datasets (#1022)
 - ♻️ Move simulation to own module (#1041)
+- ♻️ Move optimization to new module glotaran.optimization (#1047)
 
 ### 🩹 Bug fixes
 
@@ -32,6 +33,7 @@
 
 - `glotaran.io.save_result(result, result_path, format_name='legacy')` -> `glotaran.io.save_result(result, Path(result_path) / 'result.yml')`
 - `glotaran.analysis.simulation` -> `glotaran.simulation.simulation`
+- `glotaran.analysis.optimize` -> `glotaran.optimization.optimize`
 
 ### 🚧 Maintenance
 

docs/source/notebooks/quickstart/quickstart.ipynb

@@ -33,11 +33,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from glotaran.analysis.optimize import optimize\n",
     "from glotaran.io import load_model\n",
     "from glotaran.io import load_parameters\n",
     "from glotaran.io import save_dataset\n",
     "from glotaran.io.prepare_dataset import prepare_time_trace_dataset\n",
+    "from glotaran.optimization.optimize import optimize\n",
     "from glotaran.project.scheme import Scheme"
    ]
   },

glotaran/analysis/__init__.py

@@ -18,3 +18,9 @@
     new_module_name="glotaran.simulation.simulation",
     to_be_removed_in_version="0.8.0",
 )
+
+optimize = deprecate_submodule(
+    deprecated_module_name="glotaran.analysis.optimize",
+    new_module_name="glotaran.optimization.optimize",
+    to_be_removed_in_version="0.8.0",
+)

glotaran/builtin/io/folder/test/test_folder_plugin.py

@@ -5,9 +5,9 @@
 
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.deprecation import GlotaranApiDeprecationWarning
 from glotaran.io import save_result
+from glotaran.optimization.optimize import optimize
 from glotaran.project.result import Result
 from glotaran.testing.simulated_data.sequential_spectral_decay import SCHEME
 

glotaran/builtin/io/yml/test/test_save_result.py

@@ -7,8 +7,8 @@
 import pytest
 
 from glotaran import __version__
-from glotaran.analysis.optimize import optimize
 from glotaran.io import save_result
+from glotaran.optimization.optimize import optimize
 from glotaran.project.result import Result
 from glotaran.testing.simulated_data.sequential_spectral_decay import SCHEME
 

glotaran/builtin/megacomplexes/baseline/test/test_baseline_megacomplex.py

@@ -1,9 +1,9 @@
 import numpy as np
 
-from glotaran.analysis.util import calculate_matrix
 from glotaran.builtin.megacomplexes.baseline import BaselineMegacomplex
 from glotaran.builtin.megacomplexes.decay import DecayMegacomplex
 from glotaran.model import Model
+from glotaran.optimization.util import calculate_matrix
 from glotaran.parameter import ParameterGroup
 
 

glotaran/builtin/megacomplexes/clp_guide/test/test_clp_guide_megacomplex.py

@@ -1,13 +1,13 @@
 import numpy as np
 
-from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.builtin.megacomplexes.clp_guide import ClpGuideMegacomplex
 from glotaran.builtin.megacomplexes.decay import DecaySequentialMegacomplex
 from glotaran.builtin.megacomplexes.decay.test.test_decay_megacomplex import create_gaussian_clp
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation.simulation import simulate
 
 
 def test_clp_guide():

glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py

@@ -2,11 +2,11 @@
 import pytest
 import xarray as xr
 
-from glotaran.analysis.optimize import optimize
-from glotaran.analysis.util import calculate_matrix
 from glotaran.builtin.megacomplexes.coherent_artifact import CoherentArtifactMegacomplex
 from glotaran.builtin.megacomplexes.decay import DecayMegacomplex
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
+from glotaran.optimization.util import calculate_matrix
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.simulation import simulate

glotaran/builtin/megacomplexes/damped_oscillation/test/test_doas_model.py

@@ -3,12 +3,12 @@
 import numpy as np
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.builtin.megacomplexes.damped_oscillation import DampedOscillationMegacomplex
 from glotaran.builtin.megacomplexes.decay import DecayMegacomplex
 from glotaran.builtin.megacomplexes.spectral import SpectralMegacomplex
 from glotaran.model import Megacomplex
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.simulation import simulate

glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py

@@ -4,8 +4,8 @@
 import pytest
 import xarray as xr
 
-from glotaran.analysis.optimize import optimize
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.simulation import simulate

glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py

@@ -5,9 +5,9 @@
 import numpy as np
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.io import load_model
 from glotaran.io import load_parameters
+from glotaran.optimization.optimize import optimize
 from glotaran.project import Scheme
 from glotaran.simulation import simulate
 

glotaran/builtin/megacomplexes/spectral/test/test_spectral_model.py

@@ -4,12 +4,12 @@
 import pytest
 import xarray as xr
 
-from glotaran.analysis.optimize import optimize
-from glotaran.analysis.util import calculate_matrix
 from glotaran.builtin.megacomplexes.decay.test.test_decay_megacomplex import DecayModel
 from glotaran.builtin.megacomplexes.spectral import SpectralMegacomplex
 from glotaran.model import Megacomplex
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
+from glotaran.optimization.util import calculate_matrix
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.simulation import simulate

glotaran/builtin/megacomplexes/test/test_spectral_decay.py

@@ -1,9 +1,9 @@
 import numpy as np
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.io import load_model
 from glotaran.io import load_parameters
+from glotaran.optimization.optimize import optimize
 from glotaran.project import Scheme
 from glotaran.simulation import simulate
 

glotaran/builtin/megacomplexes/test/test_spectral_decay_full_model.py

@@ -1,9 +1,9 @@
 import numpy as np
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.io import load_model
 from glotaran.io import load_parameters
+from glotaran.optimization.optimize import optimize
 from glotaran.project import Scheme
 from glotaran.simulation import simulate
 

glotaran/builtin/megacomplexes/test/test_spectral_penalties.py

@@ -6,12 +6,12 @@
 
 import numpy as np
 
-from glotaran.analysis.optimize import optimize
 from glotaran.builtin.megacomplexes.decay import DecayMegacomplex
 from glotaran.builtin.megacomplexes.spectral import SpectralMegacomplex
 from glotaran.io import prepare_time_trace_dataset
 from glotaran.model import Megacomplex
 from glotaran.model import Model
+from glotaran.optimization.optimize import optimize
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
 from glotaran.simulation import simulate

glotaran/cli/commands/optimize.py

@@ -3,8 +3,8 @@
 
 import click
 
-from glotaran.analysis.optimize import optimize
 from glotaran.cli.commands import util
+from glotaran.optimization.optimize import optimize
 from glotaran.plugin_system.data_io_registration import known_data_formats
 from glotaran.plugin_system.project_io_registration import save_result
 from glotaran.project.scheme import Scheme

glotaran/deprecation/modules/test/test_changed_imports.py

@@ -9,6 +9,7 @@
 from glotaran.deprecation.deprecation_utils import GlotaranApiDeprecationWarning
 from glotaran.deprecation.deprecation_utils import module_attribute
 from glotaran.io import load_dataset
+from glotaran.optimization import optimize as optimize_module
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Result
 from glotaran.project import Scheme
@@ -105,6 +106,23 @@ def test_analysis_result_from_import(recwarn: WarningsRecorder):
     assert analysis_result == Result
 
 
+def test_analysis_optimization(recwarn: WarningsRecorder):
+    """Usage of glotaran.analysis.optimization"""
+    warnings.simplefilter("always")
+
+    from glotaran.analysis import optimize as analysis_optimize
+
+    assert len(recwarn) == 0
+    assert analysis_optimize.optimize == optimize_module.optimize  # type: ignore[attr-defined]
+
+    check_recwarn(recwarn)
+
+
+def test_analysis_optimization_from_import(recwarn: WarningsRecorder):
+    """Same as 'from glotaran.analysis.optimize import optimizations analysis_scheme'"""
+    changed_import_test_warn(recwarn, "glotaran.analysis.optimize", attribute_name="optimize")
+
+
 def test_analysis_simulation(recwarn: WarningsRecorder):
     """Usage of glotaran.analysis.simulation"""
     warnings.simplefilter("always")

glotaran/deprecation/modules/test/test_project_result.py

@@ -3,8 +3,8 @@
 
 import pytest
 
-from glotaran.analysis.optimize import optimize
 from glotaran.deprecation.modules.test import deprecation_warning_on_call_test_helper
+from glotaran.optimization.optimize import optimize
 from glotaran.project.result import Result
 from glotaran.testing.simulated_data.sequential_spectral_decay import SCHEME
 

glotaran/optimization/__init__.py

@@ -0,0 +1 @@
+"""This package contains functions for optimization."""

glotaran/analysis/optimization_group.py → glotaran/optimization/optimization_group.py

@@ -7,20 +7,20 @@
 import numpy as np
 import xarray as xr
 
-from glotaran.analysis.nnls import residual_nnls
-from glotaran.analysis.optimization_group_calculator import OptimizationGroupCalculator
-from glotaran.analysis.optimization_group_calculator_linked import (
-    OptimizationGroupCalculatorLinked,
-)
-from glotaran.analysis.optimization_group_calculator_unlinked import (
-    OptimizationGroupCalculatorUnlinked,
-)
-from glotaran.analysis.util import get_min_max_from_interval
-from glotaran.analysis.variable_projection import residual_variable_projection
 from glotaran.io.prepare_dataset import add_svd_to_dataset
 from glotaran.model import DatasetGroup
 from glotaran.model import DatasetModel
 from glotaran.model import Model
+from glotaran.optimization.nnls import residual_nnls
+from glotaran.optimization.optimization_group_calculator import OptimizationGroupCalculator
+from glotaran.optimization.optimization_group_calculator_linked import (
+    OptimizationGroupCalculatorLinked,
+)
+from glotaran.optimization.optimization_group_calculator_unlinked import (
+    OptimizationGroupCalculatorUnlinked,
+)
+from glotaran.optimization.util import get_min_max_from_interval
+from glotaran.optimization.variable_projection import residual_variable_projection
 from glotaran.parameter import ParameterGroup
 from glotaran.parameter import ParameterHistory
 from glotaran.project import Scheme
@@ -53,10 +53,10 @@ def __init__(
         scheme: Scheme,
         dataset_group: DatasetGroup,
     ):
-        """Create OptimizationGroup instance  from a scheme (:class:`glotaran.analysis.scheme.Scheme`)
+        """Create OptimizationGroup instance  from a scheme (:class:`.Scheme`)
 
         Args:
-            scheme (Scheme): An instance of :class:`glotaran.analysis.scheme.Scheme`
+            scheme (Scheme): An instance of :class:`.Scheme`
                 which defines your model, parameters, and data
         """
 
@@ -69,11 +69,11 @@ def __init__(
 
         try:
             self._residual_function = residual_functions[dataset_group.model.residual_function]
-        except KeyError:
+        except KeyError as e:
             raise ValueError(
                 f"Unknown residual function '{dataset_group.model.residual_function}', "
                 f"allowed functions are: {list(residual_functions.keys())}."
-            )
+            ) from e
         self._dataset_models = dataset_group.dataset_models
 
         self._overwrite_index_dependent = self.model.need_index_dependent()

glotaran/analysis/optimization_group_calculator.py → glotaran/optimization/optimization_group_calculator.py

@@ -6,7 +6,7 @@
 import xarray as xr
 
 if TYPE_CHECKING:
-    from glotaran.analysis.optimization_group import OptimizationGroup
+    from glotaran.optimization.optimization_group import OptimizationGroup
 
 
 class OptimizationGroupCalculator:

glotaran/analysis/optimization_group_calculator_linked.py → glotaran/optimization/optimization_group_calculator_linked.py

@@ -10,19 +10,19 @@
 import numpy as np
 import xarray as xr
 
-from glotaran.analysis.optimization_group_calculator import OptimizationGroupCalculator
-from glotaran.analysis.util import CalculatedMatrix
-from glotaran.analysis.util import apply_weight
-from glotaran.analysis.util import calculate_clp_penalties
-from glotaran.analysis.util import calculate_matrix
-from glotaran.analysis.util import find_closest_index
-from glotaran.analysis.util import find_overlap
-from glotaran.analysis.util import reduce_matrix
-from glotaran.analysis.util import retrieve_clps
 from glotaran.model import DatasetModel
+from glotaran.optimization.optimization_group_calculator import OptimizationGroupCalculator
+from glotaran.optimization.util import CalculatedMatrix
+from glotaran.optimization.util import apply_weight
+from glotaran.optimization.util import calculate_clp_penalties
+from glotaran.optimization.util import calculate_matrix
+from glotaran.optimization.util import find_closest_index
+from glotaran.optimization.util import find_overlap
+from glotaran.optimization.util import reduce_matrix
+from glotaran.optimization.util import retrieve_clps
 
 if TYPE_CHECKING:
-    from glotaran.analysis.optimization_group import OptimizationGroup
+    from glotaran.optimization.optimization_group import OptimizationGroup
 
 
 class DatasetIndexModel(NamedTuple):