♻️ Move simulation to own module (#1041)

* Moved simulation to glotaran.simulation module * Change simulation imports to new simulation module. * Updated simulation docstrings. * Fixed mypy issues. * 🩹🧪 Fixed deperecation test for simulation module * 🚧📚 Added change to changelog * 📚 Minor improvements to docstrings Co-authored-by: s-weigand <s.weigand.phy@gmail.com> Co-authored-by: Joris Snellenburg <jsnel@users.noreply.github.com>
glotaran · Apr 2, 2022 · 712170f · 712170f
1 parent d1a9637
commit 712170f
Show file tree

Hide file tree

Showing 24 changed files with 128 additions and 66 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -101,15 +101,15 @@ repos:
         args:
           - "--select=D,DAR"
         name: "flake8 lint docstrings"
-        files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project|model/property.py|builtin/io/pandas)"
+        files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project|simulation|model/property.py|builtin/io/pandas)"
         exclude: "docs|tests?/"
         additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.942
     hooks:
       - id: mypy
-        files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project|model/property.py|builtin/io/pandas)"
+        files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project|simulation|model/property.py|builtin/io/pandas)"
         exclude: "docs"
         additional_dependencies: [types-all]
 

diff --git a/changelog.md b/changelog.md
@@ -18,6 +18,7 @@
 - 👌 Added IRF shift to result dataset (#994)
 - 👌 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)
 
 ### 🩹 Bug fixes
 
@@ -29,6 +30,7 @@
 ### 🗑️ Deprecations (due in 0.8.0)
 
 - `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`
 
 ### 🚧 Maintenance
 

diff --git a/glotaran/analysis/__init__.py b/glotaran/analysis/__init__.py
@@ -12,3 +12,9 @@
     new_module_name="glotaran.project.scheme",
     to_be_removed_in_version="0.6.0",
 )
+
+simulation = deprecate_submodule(
+    deprecated_module_name="glotaran.analysis.simulation",
+    new_module_name="glotaran.simulation.simulation",
+    to_be_removed_in_version="0.8.0",
+)
diff --git a/glotaran/analysis/test/test_constraints.py b/glotaran/analysis/test/test_constraints.py
@@ -3,10 +3,10 @@
 import pytest
 
 from glotaran.analysis.optimization_group import OptimizationGroup
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import TwoCompartmentDecay as suite
 from glotaran.model import ZeroConstraint
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.mark.parametrize("index_dependent", [True, False])

diff --git a/glotaran/analysis/test/test_multiple_goups.py b/glotaran/analysis/test/test_multiple_goups.py
@@ -1,10 +1,10 @@
 import numpy as np
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import DecayModel
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 def test_multiple_groups():

diff --git a/glotaran/analysis/test/test_optimization.py b/glotaran/analysis/test/test_optimization.py
@@ -3,13 +3,13 @@
 import xarray as xr
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import FullModel
 from glotaran.analysis.test.models import MultichannelMulticomponentDecay
 from glotaran.analysis.test.models import OneCompartmentDecay
 from glotaran.analysis.test.models import ThreeDatasetDecay
 from glotaran.analysis.test.models import TwoCompartmentDecay
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.mark.parametrize("is_index_dependent", [True, False])

diff --git a/glotaran/analysis/test/test_optimization_group.py b/glotaran/analysis/test/test_optimization_group.py
@@ -8,13 +8,13 @@
 from glotaran.analysis.optimization_group_calculator_linked import (
     OptimizationGroupCalculatorLinked,
 )
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import FullModel
 from glotaran.analysis.test.models import MultichannelMulticomponentDecay as suite
 from glotaran.analysis.test.models import SimpleTestModel
 from glotaran.analysis.util import CalculatedMatrix
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.fixture(

diff --git a/glotaran/analysis/test/test_penalties.py b/glotaran/analysis/test/test_penalties.py
@@ -4,11 +4,11 @@
 import pytest
 
 from glotaran.analysis.optimization_group import OptimizationGroup
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import TwoCompartmentDecay as suite
 from glotaran.model import EqualAreaPenalty
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.mark.parametrize("index_dependent", [True, False])

diff --git a/glotaran/analysis/test/test_relations.py b/glotaran/analysis/test/test_relations.py
@@ -3,11 +3,11 @@
 import pytest
 
 from glotaran.analysis.optimization_group import OptimizationGroup
-from glotaran.analysis.simulation import simulate
 from glotaran.analysis.test.models import TwoCompartmentDecay as suite
 from glotaran.model import Relation
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.mark.parametrize("index_dependent", [True, False])

diff --git a/glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py b/glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py
@@ -3,13 +3,13 @@
 import xarray as xr
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 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.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 @pytest.mark.parametrize(

diff --git a/glotaran/builtin/megacomplexes/damped_oscillation/test/test_doas_model.py b/glotaran/builtin/megacomplexes/damped_oscillation/test/test_doas_model.py
@@ -4,14 +4,14 @@
 import pytest
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 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.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 class DampedOscillationsModel(Model):

diff --git a/glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py b/glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py
@@ -5,10 +5,10 @@
 import xarray as xr
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.model import Model
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 def create_gaussian_clp(labels, amplitudes, centers, widths, axis):

diff --git a/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py b/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py
@@ -6,10 +6,10 @@
 import pytest
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.io import load_model
 from glotaran.io import load_parameters
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 MODEL_BASE = """\
 default_megacomplex: decay

diff --git a/glotaran/builtin/megacomplexes/spectral/test/test_spectral_model.py b/glotaran/builtin/megacomplexes/spectral/test/test_spectral_model.py
@@ -5,14 +5,14 @@
 import xarray as xr
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 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.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 
 class SpectralModel(Model):

diff --git a/glotaran/builtin/megacomplexes/test/test_spectral_decay.py b/glotaran/builtin/megacomplexes/test/test_spectral_decay.py
@@ -2,10 +2,10 @@
 import pytest
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.io import load_model
 from glotaran.io import load_parameters
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 MODEL_3C_NO_IRF = """\
 dataset:

diff --git a/glotaran/builtin/megacomplexes/test/test_spectral_decay_full_model.py b/glotaran/builtin/megacomplexes/test/test_spectral_decay_full_model.py
@@ -2,10 +2,10 @@
 import pytest
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 from glotaran.io import load_model
 from glotaran.io import load_parameters
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 MODEL_3C_BASE = """\
 dataset:

diff --git a/glotaran/builtin/megacomplexes/test/test_spectral_penalties.py b/glotaran/builtin/megacomplexes/test/test_spectral_penalties.py
@@ -7,14 +7,14 @@
 import numpy as np
 
 from glotaran.analysis.optimize import optimize
-from glotaran.analysis.simulation import simulate
 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.parameter import ParameterGroup
 from glotaran.project import Scheme
+from glotaran.simulation import simulate
 
 ParameterSpec = namedtuple("ParameterSpec", "base equal_area shapes")
 NoiseSpec = namedtuple("NoiseSpec", "active seed std_dev")

diff --git a/glotaran/deprecation/modules/test/test_changed_imports.py b/glotaran/deprecation/modules/test/test_changed_imports.py
@@ -14,6 +14,7 @@
 from glotaran.project import Scheme
 from glotaran.project import result as project_result
 from glotaran.project import scheme as project_scheme
+from glotaran.simulation import simulation as simulation_module
 
 if TYPE_CHECKING:
     from _pytest.recwarn import WarningsRecorder
@@ -104,6 +105,23 @@ def test_analysis_result_from_import(recwarn: WarningsRecorder):
     assert analysis_result == Result
 
 
+def test_analysis_simulation(recwarn: WarningsRecorder):
+    """Usage of glotaran.analysis.simulation"""
+    warnings.simplefilter("always")
+
+    from glotaran.analysis import simulation as analysis_simulation
+
+    assert len(recwarn) == 0
+    assert analysis_simulation.simulate == simulation_module.simulate  # type: ignore[attr-defined]
+
+    check_recwarn(recwarn)
+
+
+def test_analysis_simulation_from_import(recwarn: WarningsRecorder):
+    """Same as 'from glotaran.analysis.simulation import simulate as analysis_scheme'"""
+    changed_import_test_warn(recwarn, "glotaran.analysis.simulation", attribute_name="simulate")
+
+
 def test_analysis_scheme(recwarn: WarningsRecorder):
     """Usage of glotaran.analysis.scheme"""
     warnings.simplefilter("always")

diff --git a/glotaran/simulation/__init__.py b/glotaran/simulation/__init__.py
@@ -0,0 +1,4 @@
+"""Package containing code for simulation of dataset models."""
+from glotaran.simulation.simulation import simulate
+
+__all__ = ["simulate"]