fix ruff

README.md

@@ -2,3 +2,9 @@ refl1d models
 =============
 
 Curated repository of refl1d models.
+
+```
+conda env create -f environment.yml
+source activate refl1d_models
+pip install -e .
+```

environment.yml

@@ -1,4 +1,4 @@
-name: mypythonapp
+name: refl1d_models
 channels:
   - conda-forge
 dependencies:
@@ -14,6 +14,7 @@ dependencies:
   # jupyter: list all jupyter dependencies here, if applicable
   - jupyterlab
   - ipympl
+  - notebook
   # -- Development dependencies
   # utils:
   - pre-commit

pyproject.toml

@@ -57,6 +57,6 @@ norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__", "*dataset*", "*data_set
 
 [tool.ruff]
 line-length = 120
-select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W"]
+lint.select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W"]
 
 # Add additional 3rd party tool configuration here as needed

src/refl1d_models/mixed_model.py

@@ -0,0 +1,87 @@
+"""
+This module provides an example of a mixed model.
+In this example, we incoherently add two cross-sections
+from a non-polarized neutron reflectometry experiment on
+a nickel film.
+"""
+
+from refl1d.names import SLD, FitProblem, MixedExperiment
+
+from .probes import create_qprobe
+
+
+def create_mixed_model(datafile: str = None):
+    """
+    Create a mixed model for the given datafile
+    :param datafile: The datafile to use for the model
+    """
+
+    # Define a probe
+    probe = create_qprobe(datafile)
+
+    # Define the materials for the structure
+    # The SLD class defines the material properties.
+    # The rho parameter is the scattering length density of the material.
+    thf = SLD("THF", rho=6.2)
+    silicon = SLD("Si", rho=2.07)
+    titanium = SLD("Ti", rho=-2.0)
+
+    # In this exammple, we are using the same material for the up and down spins
+    # In this case, nickel has a nominal SLD of 9.4 +- 1.46 for the two spin states
+    nickel_up = SLD("Ni_up", rho=8.3)
+    nickel_down = SLD("Ni_down", rho=10.4)
+
+    # Here we will add an oxide layer on top of the nickel
+    material = SLD(name="material", rho=5.6)
+
+    # Create the sample structure
+    # In this case the incoming beam is coming through the Si substrate
+    sample_up = thf(0, 5) | material(34, 20) | nickel_up(555, 10) | titanium(50, 3) | silicon
+    sample_down = thf(0, 5) | material(34, 20) | nickel_down(555, 10) | titanium(50, 3) | silicon
+
+    # Create a MixedExperiment. We provide the two samples, the probe, the ratio of the contribution
+    # of the two samples, and whether the two samples are coherently added or not.
+    experiment = MixedExperiment(samples=[sample_up, sample_down], probe=probe, ratio=[1, 0.75], coherent=False)
+
+    # Define the range of the parameters
+    sample_down["THF"].material.rho.range(5.5, 7)
+    sample_down["THF"].interface.range(1, 25)
+
+    sample_up["Ni_up"].material.rho.range(5, 12)
+    sample_down["Ni_down"].material.rho.range(5, 12)
+    sample_down["Ni_down"].interface.range(1, 25)
+    sample_down["Ni_down"].thickness.range(400, 600)
+
+    sample_down["Ti"].thickness.range(10.0, 80.0)
+    sample_down["Ti"].material.rho.range(-3.0, 0)
+    sample_down["Ti"].interface.range(1.0, 23.0)
+
+    sample_up["Ti"].thickness = sample_down["Ti"].thickness
+    sample_up["Ti"].interface = sample_down["Ti"].interface
+    sample_up["Ti"].material.rho = sample_down["Ti"].material.rho
+
+    sample_down["material"].thickness.range(10.0, 50.0)
+    sample_down["material"].material.rho.range(1.0, 6)
+    sample_down["material"].interface.range(1.0, 33.0)
+
+    sample_up["material"].thickness = sample_down["material"].thickness
+    sample_up["material"].interface = sample_down["material"].interface
+    sample_up["material"].material.rho = sample_down["material"].material.rho
+
+    probe.intensity.range(0.8, 1.5)
+
+    sample_up["Ni_up"].thickness = sample_down["Ni_down"].thickness
+    sample_up["Ni_up"].interface = sample_down["Ni_down"].interface
+
+    # Choose a range on the ratio of the two samples
+    experiment.ratio[1].range(0, 5)
+
+    # Create a FitProblem
+    problem = FitProblem(experiment)
+
+    return problem, experiment
+
+
+# The following is only necessary so this python file can be
+# used as a model with the refl1d cli.
+problem, _ = create_mixed_model()

src/refl1d_models/probes.py

@@ -0,0 +1,31 @@
+"""
+This module contains example definitions of probes used in refl1d models.
+"""
+
+import numpy as np
+from refl1d.probe import QProbe
+
+
+def create_qprobe(data_file_path: str, fwhm: bool = True) -> QProbe:
+    """
+    Create a QProbe object from a data file.
+
+    :param data_file_path: path to the data file.
+    :type data_file_path: str
+    :return: QProbe object.
+    :rtype: QProbe
+    """
+    if data_file_path is None:
+        q = np.logspace(np.log10(0.005), np.log10(0.2), num=250)
+        dq = 0.025 * q
+        data = errors = None
+    else:
+        q, data, errors, dq = np.loadtxt(data_file_path, unpack=True)
+
+    # If the Q resolution is given as FWHM, convert it to sigma
+    if fwhm:
+        dq /= 2.355
+
+    probe = QProbe(q, dq, data=(data, errors))
+
+    return probe

tests/test_mixed_model.py

@@ -0,0 +1,20 @@
+import os
+from pathlib import Path
+
+from bumps.fitters import fit
+
+from refl1d_models.mixed_model import create_mixed_model
+
+
+def test_mixed_model():
+    """
+    Example use and test of the mixed model
+    """
+    data_dir = str(Path(__file__).parent / "data")
+    data_file = os.path.join(data_dir, "REFL_211832_combined_data_auto.txt")
+
+    problem, experiment = create_mixed_model(data_file)
+    results = fit(problem, method="amoeba", samples=2000, burn=2000, pop=20, verbose=1)
+
+    assert results.success
+    assert results.fun / len(experiment.probe.Q) < 5