Restructure and Reorganize project

.gitignore

@@ -61,3 +61,5 @@ venv.bak/
 .idea
 *.swp
 *.bak
+
+test-files/

.pre-commit-config.yaml

@@ -15,7 +15,6 @@ repos:
         args: [--allow-multiple-documents]
       # - id: end-of-file-fixer
       # - id: trailing-whitespace
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.7.2
     hooks:

Makefile

@@ -61,4 +61,4 @@ format-backend: ## Run ruff formatting on python code
 .PHONY: format-frontend
 format-frontend: ## Run bun formatting on javascript code
 	cd refl1d/webview/client && \
-		$(FE_CMD) run format
+		$(FE_CMD) run format

compareopt/slabs.py

@@ -1,17 +1,19 @@
+import sys
 from random import getrandbits
 
+import numpy as np
 from bumps.parameter import summarize
 from numpy.random import uniform
 
-from refl1d.names import *
+from refl1d.names import SLD, Experiment, FitProblem, NeutronProbe, air, silicon
 
 num_layers = int(sys.argv[1])
 init_file = sys.argv[2] if len(sys.argv) > 2 else "/tmp/problem"
 
 out = open(init_file, "w")
 seed = getrandbits(16)
 print("seed", seed, file=out)
-numpy.random.seed(int(seed))
+np.random.seed(int(seed))
 
 
 # CONSTRAINTS="unknown"
@@ -48,7 +50,7 @@ def genlayer(name):
 
 sample = silicon(0, 5) | layers | air
 
-T = numpy.linspace(0, 5, 100)
+T = np.linspace(0, 5, 100)
 probe = NeutronProbe(T=T, dT=0.01, L=4.75, dL=0.0475)
 
 M = Experiment(probe=probe, sample=sample)

conftest.py

@@ -1,6 +1,6 @@
 collect_ignore = [
     "doc/guide/toffset.py",
-    # "refl1d/wx_gui/",
+    "refl1d/wx_gui/",
     "tests/refl1d/Q_probe_oversample.py",
     # "tests/refl1d/snsdata_test.py",
 ]

doc/conf.py

@@ -37,10 +37,11 @@
 print("== end path ==")
 
 # Register the refl1d model loader
-import refl1d.fitplugin
 import bumps.cli
 
-bumps.cli.install_plugin(refl1d.fitplugin)
+from refl1d.bumps_interface import fitplugin
+
+bumps.cli.install_plugin(fitplugin)
 
 # -- General configuration -----------------------------------------------------
 

doc/examples/distribution/dist-example.py

@@ -1,6 +1,8 @@
 import os
 import sys
 
+import numpy
+
 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
 from refl1d.names import *
 from refl1d.dist import Weights, DistributionExperiment

doc/examples/eiv/model.py

@@ -9,6 +9,8 @@
 an error-in-variables fit.
 """
 
+import numpy as np
+
 from refl1d.names import *
 
 # ********** model setup **********
@@ -26,7 +28,7 @@
 # n = 20
 n = 400
 dT, L, dL = 0.02, 4.75, 0.0475
-T = numpy.linspace(0, 5, n)
+T = np.linspace(0, 5, n)
 
 # Set the motor uncertainty and the measurement uncertainty.
 angle_uncertainty = 0.005
@@ -142,7 +144,7 @@ def residuals(self):
         if self.probe.polarized:
             have_data = not all(x is None or x.R is None for x in self.probe.xs)
         else:
-            have_data = not (self.probe.R is None)
+            have_data = self.probe.R is not None
         if not have_data:
             resid = np.zeros(0)
             self._cache["residuals"] = resid

doc/examples/ex1/gendata.py

@@ -4,14 +4,15 @@
 
 from numpy.random import seed
 from bumps.fitproblem import load_problem
-from refl1d.snsdata import write_file
+
+from refl1d.names import SNS
 
 
 def main():
     seed(1)
     problem = load_problem("nifilm-tof.py")
     for i, p in enumerate(problem.fitness.probe.probes):
-        write_file("nifilm-tof-%d.dat" % (i + 1), p, title="Simulated 100 A Ni film")
+        SNS.write_file("nifilm-tof-%d.dat" % (i + 1), p, title="Simulated 100 A Ni film")
 
 
 if __name__ == "__main__":

doc/examples/ex1/nifilm-back.py

@@ -7,6 +7,8 @@
 #
 # We set up the example as before.
 
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/ex1/nifilm-data.py

@@ -29,7 +29,7 @@
 # The data and sample are combined into an
 # :class:`Experiment <refl1d.experiment.Experiment>`,
 # which again is bundled as a
-# :class:`FitProblem <refl1d.fitter.FitProblem>`
+# :class:`FitProblem <refl1d.bumps_interface.fitproblem.FitProblem>`
 # for the fitting program.
 
 M = Experiment(probe=probe, sample=sample)

doc/examples/ex1/nifilm-tof.py

@@ -39,7 +39,7 @@
 # so much for a time-of-flight measurement, the central points will be
 # measured with much better precision, and the end points will be measured
 # with lower precision.  See
-# :meth:`Pulsed.simulate <refl1d.instrument.Pulsed.simulate>` for details
+# :meth:`Pulsed.simulate <refl1d.probe.instrument.Pulsed.simulate>` for details
 # on all simulation parameters.
 
 # Finally, we bundle the simulated measurement as a fit problem which

doc/examples/ex1/nifilm.py

@@ -26,9 +26,15 @@
 #
 # The first step in any model is to load the names of the functions and
 # data that we are going to use.  These are defined in a module named
-# refl1d.names, and we import them all as follows:
+# refl1d.names, and we can import them as follows:
 
+import numpy  # This is the numpy library, which is used for numerical operations
+from refl1d.names import Material, Experiment, NeutronProbe, FitProblem, silicon, air
+
+# Alternatively, you can import them all, using:
 from refl1d.names import *
+# but this is not recommended for anything but simple scripts,
+# and may cause linting issues in your IDE.
 
 # This statement imports functions like SLD and Material for defining
 # materials, Parameter, Slab and Stack for defining materials,

doc/examples/four_column/model.py

@@ -43,7 +43,7 @@
 # Here's the new loader.  Much simplified since the reduction computes the
 # appropriate $\Delta Q$ for the data points, and we don't need to specify
 # the slit openings and distances for the data set.  The options to the
-# :func:`refl1d.probe.load4` function allow you to override things during
+# :func:`refl1d.probe.data_loaders.load4.load4` function allow you to override things during
 # load, such as the sample broadening of the resolution.
 
 probe = load4("refl.txt")

doc/examples/freemag/pmf.py

@@ -1,5 +1,5 @@
+import numpy
 from refl1d.names import *
-from copy import copy
 
 # FIT USING REFL1D 0.6.12
 # === Data files ===

doc/examples/ill_posed/anticor.py

@@ -15,6 +15,7 @@
 # Since silicon and air are defined, the only material we need to
 # define is nickel.
 
+import numpy
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/ill_posed/tethered.py

@@ -1,7 +1,10 @@
-from refl1d.names import *
-import periodictable
 from copy import copy
 
+import numpy
+import periodictable
+
+from refl1d.names import *
+
 numpy.random.seed(1)
 
 # Start with an SiOx layer of pure silicon so there is no contrast match.

doc/examples/interface/model.py

@@ -1,3 +1,5 @@
+import numpy
+
 from refl1d.names import *
 
 

doc/examples/magrough/model.py

@@ -1,3 +1,5 @@
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/mixed/mixed.py

@@ -16,6 +16,8 @@
 # Since silicon and air are defined, the only material we need to
 # define is nickel.
 
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/mixed/mixed_magnetic.py

@@ -1,3 +1,5 @@
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/polymer/tethered.py

@@ -17,15 +17,15 @@
 
 # In this case we are using the neutron scattering length density as is
 # standard practice in reflectivity experiments rather than the chemical
-# formula and mass density.  The :class:`SLD <refl1d.material.SLD>` class
+# formula and mass density.  The :class:`SLD <refl1d.sample.material.SLD>` class
 # allows us to name the material and define the real and imaginary components
 # of scattering length density $\rho$.  Note that we are using the imaginary
 # $\rho_i$ rather than the absorption coefficient $\mu = 2\lambda\rho_i$
 # since it removes the dependence on wavelength from the calculation of
 # the reflectivity.
 #
 # For the tethered polymer we don't use a simple slab model, but instead
-# define a :class:`PolymerBrush <refl1d.polymer.PolymerBrush>`
+# define a :class:`PolymerBrush <refl1d.sample.polymer.PolymerBrush>`
 # layer, which understands that the system is compose of polymer plus
 # solvent, and that the polymer chains tail off like:
 #

doc/examples/profile/model.py

@@ -12,10 +12,10 @@
 from refl1d.names import *
 
 # FunctionalProfile and FunctionalMagnetism are already available from
-# refl1d.names, but a couple of aliases make them a little easier to access.
+# refl1d.sample.flayer, but a couple of aliases make them a little easier to access.
 
-from refl1d.flayer import FunctionalProfile as FP
-from refl1d.flayer import FunctionalMagnetism as FM
+from refl1d.names import FunctionalProfile as FP
+from refl1d.names import FunctionalMagnetism as FM
 
 # Define the nuclear profile function.
 #

doc/examples/random/model.py

@@ -32,19 +32,22 @@
 # Still, it is a good enough starting point, and does lead to some
 # models with low contrast in neighbouring layers.
 
+import numpy
+import sys
+
 from refl1d.names import *
 
 # Process command line arguments to the model
 
 n = int(sys.argv[1]) if len(sys.argv) > 1 else 2
 noise = float(sys.argv[2]) if len(sys.argv) > 2 else 3.0
-seed = int(sys.argv[3]) if len(sys.argv) > 3 else np.random.randint(1, 9999)
+seed = int(sys.argv[3]) if len(sys.argv) > 3 else numpy.random.randint(1, 9999)
 
 # Set the seed for the random number generator.  Later we will print the
 # seed, even if it was not set explicitly, so that interesting profiles
 # can be regenerated.
 
-np.random.seed(seed)
+numpy.random.seed(seed)
 
 # Set up a model with the desired number of layers.  We will set the layer
 # thickness and interfaces later.
@@ -78,17 +81,19 @@
 # can work.  Exponential distribution isn't suitable for single layer systems
 
 for L in layers:
-    L.thickness.value = min(np.random.exponential(400.0 / np.sqrt(n)), 950) if n > 1 else np.random.uniform(5, 950)
+    L.thickness.value = (
+        min(numpy.random.exponential(400.0 / numpy.sqrt(n)), 950) if n > 1 else numpy.random.uniform(5, 950)
+    )
 
 # Set interface limits based on neighbouring layer thickness, with substrate
 # and surface having infinite thickness.  Choose an interface of at least 1 A
 
 interfaces = [
-    min(sample[i].thickness.value if i > 0 else np.inf, sample[i + 1].thickness.value if i < n else np.inf)
+    min(sample[i].thickness.value if i > 0 else numpy.inf, sample[i + 1].thickness.value if i < n else numpy.inf)
     for i in range(n + 1)
 ]
 for L, w in zip(sample[: n + 1], interfaces):
-    L.interface.value = 1 + np.random.exponential(w / 7)
+    L.interface.value = 1 + numpy.random.exponential(w / 7)
     # Update the fit range if interface is excessively broad
     if L.interface.value > 200:
         L.interface.range(0, 2 * L.interface.value)

doc/examples/spinvalve/n101G.py

@@ -19,7 +19,7 @@
 
 # The materials are stacked as usual, but the layers with magnetism have
 # an additional magnetism property specified.  This example use
-# :class:`refl1d.magnetism.Magnetism` to define a flat magnetic layer with
+# :class:`refl1d.sample.magnetism.Magnetism` to define a flat magnetic layer with
 # the given magnetic scattering length density *rhoM* and angle *thetaM*.
 #
 # The magnetism is anchored to the corresponding nuclear layer, and by
@@ -33,7 +33,7 @@
 # indicates the interface above.  Using *extent=2*, the single magnetism
 # definition can extend over two consecutive layers.
 #
-# The :class:`refl1d.magnetism.MagnetismTwist` allows you to define a magnetic
+# The :class:`refl1d.sample.magnetism.MagnetismTwist` allows you to define a magnetic
 # layer whose values of theta and rho change linearly throughout the layer.
 # There are additional magnetism types defined in :mod:`reflid.magnetism`.
 # Note that the current definition of interface only transitions smoothly

doc/examples/staj/De2_VATR.py

@@ -1,5 +1,4 @@
 from refl1d.names import *
-from refl1d.stajconvert import load_mlayer
 
 # Load neutron model and data from staj file
 # Layer names are ordered from substrate to surface, and defaults to

doc/examples/step/tethered.py

@@ -1,6 +1,9 @@
-from refl1d.names import *
 from copy import copy
 
+import numpy
+
+from refl1d.names import *
+
 # === Materials ===
 SiOx = SLD(name="SiOx", rho=3.47)
 D_polystyrene = SLD(name="D-PS", rho=6.2)

doc/examples/superlattice/NiTi.py

@@ -21,6 +21,8 @@
 
 # First define the materials we will use
 
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")

doc/examples/superlattice/PEMU.py

@@ -27,6 +27,8 @@
 # Bring in all of the functions from refl1d.names so that we can use them
 # in the remainder of the script.
 
+import numpy
+
 from refl1d.names import *
 
 # The polymer system is deposited on a gold film with chromium as an

doc/examples/superlattice/freeform.py

@@ -18,6 +18,8 @@
 
 # The materials are straight forward:
 
+import numpy
+
 from refl1d.names import *
 
 chrome = Material("Cr")

doc/examples/superlattice/readme.rst

@@ -4,7 +4,7 @@ Superlattice Models
 
 .. contents:: :local:
 
-Any structure can be turned into a superlattice using a :class:`refl1d.model.Repeat`.
+Any structure can be turned into a superlattice using a :class:`refl1d.sample.layer.Repeat`.
 
 Simply form a stack as usual, then use that stack within another stack, with a
 repeat modifier.

doc/examples/thick/nifilm.py

@@ -1,7 +1,8 @@
+import numpy
+
 from refl1d.names import *
 
 nickel = Material("Ni")
-
 # nickel = SLD(rho=9.4)
 
 sample = silicon(0, 5) | nickel(10000, 5) | air